diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/README.md b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/README.md new file mode 100644 index 0000000000000000000000000000000000000000..2bf06ed5f8c8cc47a390dc6df177f780c3c0af7e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/README.md @@ -0,0 +1,105 @@ +# Example for water (LDA to PBE) : using ABACUS in scf iteration + +This is an example on how to use `deepks` library to train a **LDA-to-PBE** model for water molecules, with SCF calculation done by **[ABACUS](https://github.com/deepmodeling/abacus-develop)**. + +The sub-folders are grouped as following: + +- `systems` contains atom data with PBE energy and force. +- `iter` contains input files used to train a self consistent model iteratively (DeePKS). + +## Running this example locally + +To train a self-consistant model with ABACUS, you can `cd iter` and run: + +`python -u -m deepks iterate machines.yaml params.yaml systems.yaml scf_abacus.yaml >> log.iter 2> err.iter` + +or directly + +`cd iter && bash run.sh` + +## Running this example with DPDispatcher + +If you want the jobs submitted to supercomputer platforms by **[DPDispatcher](https://github.com/deepmodeling/dpdispatcher)** , you need to set `dispatcher` as `"dpdispatcher"`and set `dpdispatcher_machine` and `dpdispatcher_resources` according to [DPDispatcher docs](https://dpdispatcher.readthedocs.io/) (see `machines_bohrium.yaml`). Remember to set the remote `abacus_path` (see `scf_abacus_bohrium.yaml`). Taking **[Bohrium](https://bohrium.dp.tech/)** as an example, `cd iter` and run: + +`python -u -m deepks iterate machines_bohrium.yaml params.yaml systems.yaml scf_abacus_bohrium.yaml >> log.iter 2> err.iter` + +or directly + +`cd iter && bash run.sh` + +## Prameters for ABACUS +ABACUS parameters are specified in `scf_abacus.yaml`. These parameters can be divided into 3 categories: + +- Paras for running ABACUS: + - `abacus_path`: the path of ABACUS binary executable file (ABACUS) + - `run_cmd`: command to run ABACUS, usually `mpirun` + +- Paras for `INPUT` file: + - `ntype`: number of atom types + - `nbands`: total number of bands to calculate + - `ecutwfc`: energy cutoff for plane wave functions + - `scf_thr`: the charge density error threshold between two sequential density from electronic iterations to judge convergence + - `scf_nmax`: max scf steps + - `dft_functional`: Exchange-Correlation functional, which can be 'lda', 'gga', 'pbe', etc + - `gamma_only`: 1 for gamma-point, 0 for multi-kpoints + - `cal_force`: set 1 to calculate force, default 0 + - `cal_stress`: set 1 to calculate stress, default 0 + +- Paras for `STRU` file: + - `orb_files`: paths of atom orbitals, a list of str with the order same as the order of atom types in `atoms.npy` + - `pp_files`: paths of pseudo potential files, a list of str with the order same as the order of atom types in `atoms.npy` + - `proj_file`: path of orbital file for descripor basis + - `lattice_constant`: spacial period, in Bohr + - `lattice_vector`: spacial period of x,y and z, in Bohr +tips: you can set different STRU parasmeters for each data group, by adding a `stru_abacus.yaml`in systems/group.xx. + +There are some other important parameters for using ABACUS in `params.yaml ` and `machines.yaml`: +- `use_abacus`: set `true` to calculate SCF by ABACUS, `false` for using PySCF +- `cpus_per_task`: how many cpu cores are used for calculating each frame in using ABACUS +- `sub_size`: how many frames are calculated simultaneously + +**Caution**: The meanings of `cpus_per_task` and `sub_size` when using ABACUS are kind of different to using PySCF, because ABACUS supports parallel calculation in **each single frame (configuration)** while PySCF not. Each frame's calculation is an "ABACUS task" with a unique workdir. + + +## Data units +`deepks` accept `.npy` data in following units: +Property | Unit +--- | :---: +Length | Bohr (Å if from xyz) +Energy | $E_h$ (Hartree) +Force | $E_h$/Bohr ($E_h$/Å if from xyz) + +In this example, each grouped folder contain an `atom.npy` that has shape `n_frames x n_atoms x 4` and the four elements correspond to the nuclear charge of the atom and its three spacial coordinates. +Other properties can be provided as separate files like `energy.npy` and `force.npy`. + + +## Train a model: DeePHF or DeePKS + +Set `n_iter = 0` to train a perturbative energy model, which is a pure machine learning task. Please see [DeePHF paper](https://arxiv.org/pdf/2005.00169.pdf) for a detailed explanation of the construction of the descriptors. + +After SCF calculation, the following result files will be saved in `iter.init/00.scf/data_train(test)` prepared to training: + +- descriptor (`dm_eig`) +- energy labels (`l_e_delta`) +- force labels (`l_f_delta`) , only when `cal_force = 1 ` + +Set `n_iter` to a positive integer to train a self consistent model, following the iterative approach described in [DeePKS paper](https://arxiv.org/pdf/2008.00167.pdf). In scf calculation , a trained model file `model.pth` will be loaded into ABACUS. And beside above result files, a `grad_vx` file will appear in `iter.xx/00.scf/data_train(test)` when force label is used in training. + + +## Explaination for output files + +### RECORD file + +For each iteration, each sub-step would correspond to a row in `RECORD` file, used to indicate which steps have finished. It would have three numbers. The first one correspond to the iteration number. The second one correspond to the sub-folder in the iteration and the third correspond to step in that folder. + +- (`X 0 0`): pre process of SCF, generate ABACUS work direcotry and input files in each group of `systems` +- (`X 0 1`): run SCF calculation with given model by ABACUS +- (`X 0 2`): concatenate and check the SCF result and print convergence and accuracy +- (`X 1 0`): train a new model using the old one as starting point +- (`X 1 1`): test the model on all data to see the pure fitting error + +### log file + +One can check `iter.*/00.scf/log.data` for stats of SCF results, `iter*/01.train/log.train` for training curve and `iter*/01.train/log.test` for model prediction of $E_\delta$ (e_delta). + + \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/H_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/H_ONCV_PBE-1.0.upf new file mode 100644 index 0000000000000000000000000000000000000000..f8b1ebb63c87d413e9291f7c0b9fd8707f9c8256 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/H_ONCV_PBE-1.0.upf @@ -0,0 +1,897 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + H 1.00 0 1 4 upf +# +# n l f energy (Ha) + 1 0 1.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 0 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.13748 -0.23860 5 8 9.72141 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 0.49352 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 1.27464 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 0.0800 0.0900 0.1000 0.1100 0.1200 0.1300 0.1400 0.1500 + 0.1600 0.1700 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0000000000000000000000000000000000000000..7e7db6d66f69ceb7e960ade73fd5d8885fb5ffb8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/O_ONCV_PBE-1.0.upf @@ -0,0 +1,1224 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + O 8.00 1 2 4 upf +# +# n l f energy (Ha) + 1 0 2.00 + 2 0 2.00 + 2 1 4.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 1 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.29195 -0.88057 5 8 8.98916 + 1 1.47310 -0.33187 5 8 9.14990 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 0.90330 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 1.51851 + 1 2 1.53631 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 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-1.490716328841e-02 -9.903722304457e-03 -4.931701771028e-03 +4.773444701199e-14 4.882628890872e-03 9.707589564902e-03 1.446645969794e-02 +1.915100382853e-02 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/log.iter b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/log.iter new file mode 100644 index 0000000000000000000000000000000000000000..c259afef2af9134a38cfbfb85a1af2c97da8e6e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/log.iter @@ -0,0 +1,103 @@ +# starting step: (0,) +# starting step: (0, 0) +# starting step: (0, 0, 0) +# starting step: (0, 0, 1) +2022-09-27 16:39:10,965 - INFO : info:check_all_finished: False +2022-09-27 16:39:10,965 - INFO : checking all job has been uploaded +2022-09-27 16:39:17,124 - INFO : job: f4d5d2d1d302c71dc704d97cc01d08e9814fb272 submit; job_id is 2165403:job_group_id:316477 +2022-09-27 16:39:17,568 - INFO : job: 54f05969e57daeab82eae6840e270e5fd82387b8 submit; job_id is 2165404:job_group_id:316477 +2022-09-27 16:39:18,006 - INFO : job: 7fd62a561025a8840e7c2a9eac071836dfc3cc8d submit; job_id is 2165406:job_group_id:316477 +2022-09-27 16:39:18,466 - INFO : job: 82d83d61c790f8391d494d274bf4e979b33e5b78 submit; job_id is 2165408:job_group_id:316477 +# starting step: (0, 0, 2) +# starting step: (0, 1) +# starting step: (0, 1, 0) +2022-09-27 16:52:58,469 - INFO : info:check_all_finished: False +2022-09-27 16:52:58,469 - INFO : checking all job has been uploaded +2022-09-27 16:52:59,934 - INFO : job: 1cef05b334bf149b3c7f377465a44c2359c41dd3 submit; job_id is 2165595:job_group_id:316584 +# starting step: (0, 1, 1) +# starting step: (1,) +# starting step: (1, 0) +# starting step: (1, 0, 0) +# starting step: (1, 0, 1) +2022-09-27 17:00:33,064 - INFO : info:check_all_finished: False +2022-09-27 17:00:33,064 - INFO : checking all job has been uploaded +2022-09-27 17:00:39,701 - INFO : job: f4d5d2d1d302c71dc704d97cc01d08e9814fb272 submit; job_id is 2165663:job_group_id:316652 +2022-09-27 17:00:40,168 - INFO : job: 54f05969e57daeab82eae6840e270e5fd82387b8 submit; job_id is 2165664:job_group_id:316652 +2022-09-27 17:00:40,617 - INFO : job: 7fd62a561025a8840e7c2a9eac071836dfc3cc8d submit; job_id is 2165665:job_group_id:316652 +2022-09-27 17:00:41,106 - INFO : job: 82d83d61c790f8391d494d274bf4e979b33e5b78 submit; job_id is 2165666:job_group_id:316652 +# starting step: (1, 0, 2) +# starting step: (1, 1) +# starting step: (1, 1, 0) +2022-09-27 17:17:23,066 - INFO : info:check_all_finished: False +2022-09-27 17:17:23,066 - INFO : checking all job has been uploaded +2022-09-27 17:17:24,632 - INFO : job: 70d284f8fa0bc3706a6210ccd696bc51d9985ffb submit; job_id is 2165740:job_group_id:316722 +# starting step: (1, 1, 1) +# starting step: (2,) +# starting step: (2, 0) +# starting step: (2, 0, 0) +# starting step: (2, 0, 1) +2022-09-27 17:26:28,195 - INFO : info:check_all_finished: False +2022-09-27 17:26:28,195 - INFO : checking all job has been uploaded +2022-09-27 17:26:34,979 - INFO : job: f4d5d2d1d302c71dc704d97cc01d08e9814fb272 submit; job_id is 2165761:job_group_id:316739 +2022-09-27 17:26:35,435 - INFO : job: 54f05969e57daeab82eae6840e270e5fd82387b8 submit; job_id is 2165762:job_group_id:316739 +2022-09-27 17:26:35,882 - INFO : job: 7fd62a561025a8840e7c2a9eac071836dfc3cc8d submit; job_id is 2165763:job_group_id:316739 +2022-09-27 17:26:36,327 - INFO : job: 82d83d61c790f8391d494d274bf4e979b33e5b78 submit; job_id is 2165764:job_group_id:316739 +# starting step: (2, 0, 2) +# starting step: (2, 1) +# starting step: (2, 1, 0) +2022-09-27 17:43:18,869 - INFO : info:check_all_finished: False +2022-09-27 17:43:18,869 - INFO : checking all job has been uploaded +2022-09-27 17:43:20,367 - INFO : job: 70d284f8fa0bc3706a6210ccd696bc51d9985ffb submit; job_id is 2165943:job_group_id:316780 +# starting step: (2, 1, 1) +# starting step: (3,) +# starting step: (3, 0) +# starting step: (3, 0, 0) +# starting step: (3, 0, 1) +2022-09-27 17:52:53,899 - INFO : info:check_all_finished: False +2022-09-27 17:52:53,899 - INFO : checking all job has been uploaded +2022-09-27 17:53:00,725 - INFO : job: f4d5d2d1d302c71dc704d97cc01d08e9814fb272 submit; job_id is 2165966:job_group_id:316803 +2022-09-27 17:53:01,182 - INFO : job: 54f05969e57daeab82eae6840e270e5fd82387b8 submit; job_id is 2165967:job_group_id:316803 +2022-09-27 17:53:01,644 - INFO : job: 7fd62a561025a8840e7c2a9eac071836dfc3cc8d submit; job_id is 2165968:job_group_id:316803 +2022-09-27 17:53:02,100 - INFO : job: 82d83d61c790f8391d494d274bf4e979b33e5b78 submit; job_id is 2165969:job_group_id:316803 +# starting step: (3, 0, 2) +# starting step: (3, 1) +# starting step: (3, 1, 0) +2022-09-27 18:10:14,075 - INFO : info:check_all_finished: False +2022-09-27 18:10:14,076 - INFO : checking all job has been uploaded +2022-09-27 18:10:15,692 - INFO : job: 70d284f8fa0bc3706a6210ccd696bc51d9985ffb submit; job_id is 2166044:job_group_id:316878 +# starting step: (3, 1, 1) +# restarting after step (3,) +# starting step: (4,) +# starting step: (4, 0) +# starting step: (4, 0, 0) +# starting step: (4, 0, 1) +2022-09-28 10:31:38,372 - INFO : info:check_all_finished: False +2022-09-28 10:31:38,372 - INFO : checking all job has been uploaded +2022-09-28 10:31:45,958 - INFO : job: f4d5d2d1d302c71dc704d97cc01d08e9814fb272 submit; job_id is 2167873:job_group_id:317438 +2022-09-28 10:31:46,430 - INFO : job: 54f05969e57daeab82eae6840e270e5fd82387b8 submit; job_id is 2167874:job_group_id:317438 +2022-09-28 10:31:46,881 - INFO : job: 7fd62a561025a8840e7c2a9eac071836dfc3cc8d submit; job_id is 2167875:job_group_id:317438 +2022-09-28 10:31:47,336 - INFO : job: 82d83d61c790f8391d494d274bf4e979b33e5b78 submit; job_id is 2167876:job_group_id:317438 +# starting step: (4, 0, 2) +# starting step: (4, 1) +# starting step: (4, 1, 0) +2022-09-28 10:49:29,848 - INFO : info:check_all_finished: False +2022-09-28 10:49:29,848 - INFO : checking all job has been uploaded +2022-09-28 10:49:31,452 - INFO : job: 70d284f8fa0bc3706a6210ccd696bc51d9985ffb submit; job_id is 2167901:job_group_id:317459 +# starting step: (4, 1, 1) +# starting step: (5,) +# starting step: (5, 0) +# starting step: (5, 0, 0) +# starting step: (5, 0, 1) +2022-09-28 10:59:04,936 - INFO : info:check_all_finished: False +2022-09-28 10:59:04,936 - INFO : checking all job has been uploaded +2022-09-28 10:59:12,204 - INFO : job: f4d5d2d1d302c71dc704d97cc01d08e9814fb272 submit; job_id is 2167937:job_group_id:317473 +2022-09-28 10:59:12,656 - INFO : job: 54f05969e57daeab82eae6840e270e5fd82387b8 submit; job_id is 2167938:job_group_id:317473 +2022-09-28 10:59:13,167 - INFO : job: 7fd62a561025a8840e7c2a9eac071836dfc3cc8d submit; job_id is 2167939:job_group_id:317473 +2022-09-28 10:59:13,612 - INFO : job: 82d83d61c790f8391d494d274bf4e979b33e5b78 submit; job_id is 2167940:job_group_id:317473 +# starting step: (5, 0, 2) +# starting step: (5, 1) +# starting step: (5, 1, 0) +2022-09-28 11:15:55,874 - INFO : info:check_all_finished: False +2022-09-28 11:15:55,874 - INFO : checking all job has been uploaded +2022-09-28 11:15:57,444 - INFO : job: 70d284f8fa0bc3706a6210ccd696bc51d9985ffb submit; job_id is 2167986:job_group_id:317487 +# starting step: (5, 1, 1) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/machines.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/machines.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f2addccf99a34cbabd85d4fd4fa6740cae53811b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/machines.yaml @@ -0,0 +1,25 @@ +# this is only part of input settings. +# should be used together with systems.yaml and params.yaml +scf_machine: + group_size: 100 + resources: + cpus_per_task: 4 + sub_size: 1 + dispatcher: + context: local + batch: shell # set to shell to run on local machine, you can also use `slurm` + +train_machine: + dispatcher: + context: local + batch: shell # same as above, use shell to run on local machine + remote_profile: null # use lazy local + python: "python" # use python in path + # resources are no longer needed, and the task will use gpu automatically if there is one + +# other settings (these are default, can be omitted) +cleanup: false # whether to delete slurm and err files +strict: true # do not allow undefined machine parameters + +#paras for abacus +use_abacus: true # use abacus in scf calculation diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/machines_bohrium.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/machines_bohrium.yaml new file mode 100644 index 0000000000000000000000000000000000000000..0466a32a6157d11a1a1dc66674e39585d07b32c3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/machines_bohrium.yaml @@ -0,0 +1,66 @@ +# this is only part of input settings. +# should be used together with systems.yaml and params.yaml +scf_machine: + resources: + task_per_node: 4 + dispatcher: dpdispatcher + dpdispatcher_resources: + number_node: 1 + cpu_per_node: 8 + group_size: 100 + source_list: [/opt/intel/oneapi/setvars.sh] + sub_size: 1 + dpdispatcher_machine: + context_type: lebesguecontext + batch_type: lebesgue + local_root: ./ + remote_profile: + email: ou_qi@163.com + password: Quio_7401 + program_id: 717 + input_data: + log_file: log.scf + err_file: err.scf + job_type: indicate + grouped: true + job_name: deepks-scf + disk_size: 100 + scass_type: c8_m8_cpu + platform: ali + image_name: abacus-workshop1 + on_demand: 0 +train_machine: + dispatcher: dpdispatcher + dpdispatcher_machine: + context_type: lebesguecontext + batch_type: lebesgue + local_root: ./ + remote_profile: + email: ou_qi@163.com + password: Quio_7401 + program_id: 717 + input_data: + log_file: log.train + err_file: err.train + job_type: indicate + grouped: true + job_name: deepks-train + disk_size: 100 + scass_type: c8_m8_cpu + platform: ali + image_name: abacus-workshop1 + on_demand: 0 + dpdispatcher_resources: + number_node: 1 + cpu_per_node: 8 + group_size: 1 + source_list: [~/.bashrc] + python: "/usr/bin/python3" # use python in path + # resources are no longer needed, and the task will use gpu automatically if there is one + +# other settings (these are default, can be omitted) +cleanup: false # whether to delete slurm and err files +strict: true # do not allow undefined machine parameters + +#paras for abacus +use_abacus: true # use abacus in scf calculation diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/params.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/params.yaml new file mode 100644 index 0000000000000000000000000000000000000000..e04ab2c4042b424d9dd765588e1ee87ff41f2c92 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/params.yaml @@ -0,0 +1,62 @@ +# this is only part of input settings. +# should be used together with systems.yaml and machines.yaml + +# number of iterations to do, can be set to zero for DeePHF training +n_iter: 5 + +# directory setting (these are default choices, can be omitted) +workdir: "." +share_folder: "share" # folder that stores all other settings + +# scf settings, set to false when n_iter = 0 to skip checking +scf_input: false + + +# train settings, set to false when n_iter = 0 to skip checking +train_input: + # model_args is ignored, since this is used as restart + data_args: + batch_size: 16 + group_batch: 1 + extra_label: true + conv_filter: true + conv_name: conv + preprocess_args: + preshift: false # restarting model already shifted. Will not recompute shift value + prescale: false # same as above + prefit_ridge: 1e1 + prefit_trainable: false + train_args: + decay_rate: 0.5 + decay_steps: 1000 + display_epoch: 100 + force_factor: 1 + n_epoch: 5000 + start_lr: 0.0001 + +# init settings, these are for DeePHF task +init_model: false # do not use existing model to restart from + +init_scf: True + +init_train: # parameters for nn training + model_args: + hidden_sizes: [100, 100, 100] # neurons in hidden layers + output_scale: 100 # the output will be divided by 100 before compare with label + use_resnet: true # skip connection + actv_fn: mygelu # same as gelu, support force calculation + data_args: + batch_size: 16 + group_batch: 1 # can collect multiple system in one batch + preprocess_args: + preshift: true # shift the descriptor by its mean + prescale: false # scale the descriptor by its variance (can cause convergence problem) + prefit_ridge: 1e1 # do a ridge regression as prefitting + prefit_trainable: false + train_args: + decay_rate: 0.96 # learning rate decay factor + decay_steps: 500 # decay the learning rate every this steps + display_epoch: 100 + n_epoch: 5000 + start_lr: 0.0003 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/run.sh b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/run.sh new file mode 100644 index 0000000000000000000000000000000000000000..96bcd43fedc7f25918517cd53af402fea13b07fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/run.sh @@ -0,0 +1 @@ +nohup python -u -m deepks iterate machines.yaml params.yaml systems.yaml scf_abacus.yaml >> log.iter 2> err.iter & diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/run_bohrium.sh b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/run_bohrium.sh new file mode 100755 index 0000000000000000000000000000000000000000..937c6321ac55a981a0ea76910846dbf417c45cf3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/run_bohrium.sh @@ -0,0 +1,2 @@ +nohup python -u -m deepks iterate machines_bohrium.yaml params.yaml systems.yaml scf_abacus.yaml >> log.iter 2> err.iter & +echo $! > PID diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/scf_abacus.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/scf_abacus.yaml new file mode 100644 index 0000000000000000000000000000000000000000..e046ea74ac88f0ac988bfb02181394445c654618 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/scf_abacus.yaml @@ -0,0 +1,38 @@ +scf_abacus: + #INPUT args + ntype: 2 + nbands: 8 + ecutwfc: 50 + scf_thr: 1e-7 + scf_nmax: 50 + dft_functional: "lda" + gamma_only: 1 + cal_force: 1 + #STRU args ( Here are default STRU args, you can set for each group in ../systems/group.xx/stru_abacus.yaml ) + orb_files: ["O_gga_6au_60Ry_2s2p1d.orb", "H_gga_6au_60Ry_2s1p.orb"] + pp_files: ["O_ONCV_PBE-1.0.upf", "H_ONCV_PBE-1.0.upf"] + proj_file: ["jle.orb"] + lattice_constant: 1 + lattice_vector: [[28, 0, 0], [0, 28, 0], [0, 0, 28]] + coord_type: "Cartesian" + #cmd args + run_cmd : "mpirun" + abacus_path: "/root/abacus-develop/build/abacus" +init_scf_abacus: + orb_files: ["O_gga_6au_60Ry_2s2p1d.orb", "H_gga_6au_60Ry_2s1p.orb"] + pp_files: ["O_ONCV_PBE-1.0.upf", "H_ONCV_PBE-1.0.upf"] + proj_file: ["jle.orb"] + ntype: 2 + nbands: 8 + ecutwfc: 50 + scf_thr: 1e-7 + scf_nmax: 50 + dft_functional: "lda" + gamma_only: 1 + cal_force: 0 + lattice_constant: 1 + lattice_vector: [[28, 0, 0], [0, 28, 0], [0, 0, 28]] + coord_type: "Cartesian" + #cmd args + run_cmd : "mpirun" + abacus_path: "/root/abacus-develop/build/abacus" diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/scf_abacus_bohrium.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/scf_abacus_bohrium.yaml new file mode 100644 index 0000000000000000000000000000000000000000..aa261193fa3337c791d1e984dce7bec08625b8ff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/scf_abacus_bohrium.yaml @@ -0,0 +1,38 @@ +scf_abacus: + #INPUT args + ntype: 2 + nbands: 8 + ecutwfc: 50 + scf_thr: 1e-7 + scf_nmax: 50 + dft_functional: "lda" + gamma_only: 1 + cal_force: 1 + #STRU args ( Here are default STRU args, you can set for each group in ../systems/group.xx/stru_abacus.yaml ) + orb_files: ["O_gga_6au_60Ry_2s2p1d.orb", "H_gga_6au_60Ry_2s1p.orb"] + pp_files: ["O_ONCV_PBE-1.0.upf", "H_ONCV_PBE-1.0.upf"] + proj_file: ["jle.orb"] + deepks_descriptor_lmax: 2 + lattice_constant: 1 + lattice_vector: [[28, 0, 0], [0, 28, 0], [0, 0, 28]] + #cmd args + run_cmd : "mpirun" + abacus_path: "/root/abacus-develop/build/abacus" +init_scf_abacus: + orb_files: ["O_gga_6au_60Ry_2s2p1d.orb", "H_gga_6au_60Ry_2s1p.orb"] + pp_files: ["O_ONCV_PBE-1.0.upf", "H_ONCV_PBE-1.0.upf"] + proj_file: ["jle.orb"] + ntype: 2 + nbands: 8 + ecutwfc: 50 + scf_thr: 1e-7 + scf_nmax: 50 + dft_functional: "lda" + gamma_only: 1 + cal_force: 0 + deepks_descriptor_lmax: 2 + lattice_constant: 1 + lattice_vector: [[28, 0, 0], [0, 28, 0], [0, 0, 28]] + #cmd args + run_cmd : "mpirun" + abacus_path: "/root/abacus-develop/build/abacus" diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/H_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/H_ONCV_PBE-1.0.upf new file mode 100644 index 0000000000000000000000000000000000000000..f8b1ebb63c87d413e9291f7c0b9fd8707f9c8256 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/H_ONCV_PBE-1.0.upf @@ -0,0 +1,897 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + H 1.00 0 1 4 upf +# +# n l f energy (Ha) + 1 0 1.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 0 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.13748 -0.23860 5 8 9.72141 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 0.49352 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 1.27464 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 0.0800 0.0900 0.1000 0.1100 0.1200 0.1300 0.1400 0.1500 + 0.1600 0.1700 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0000000000000000000000000000000000000000..7e7db6d66f69ceb7e960ade73fd5d8885fb5ffb8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/O_ONCV_PBE-1.0.upf @@ -0,0 +1,1224 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + O 8.00 1 2 4 upf +# +# n l f energy (Ha) + 1 0 2.00 + 2 0 2.00 + 2 1 4.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 1 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.29195 -0.88057 5 8 8.98916 + 1 1.47310 -0.33187 5 8 9.14990 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 0.90330 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 1.51851 + 1 2 1.53631 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 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+coord_type: Cartesian +dft_functional: lda +ecutwfc: 50 +gamma_only: 1 +lattice_constant: 1 +lattice_vector: +- [28, 0, 0] +- [0, 28, 0] +- [0, 0, 28] +nbands: 8 +ntype: 2 +orb_files: [O_gga_6au_60Ry_2s2p1d.orb, H_gga_6au_60Ry_2s1p.orb] +pp_files: [O_ONCV_PBE-1.0.upf, H_ONCV_PBE-1.0.upf] +proj_file: [jle.orb] +run_cmd: mpirun +scf_nmax: 50 +scf_thr: 1e-07 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/init_train.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/init_train.yaml new file mode 100644 index 0000000000000000000000000000000000000000..0bbd2f080d9164ea1165f5750c343f21ef3a64f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/init_train.yaml @@ -0,0 +1,9 @@ +data_args: {batch_size: 16, group_batch: 1} +model_args: + actv_fn: mygelu + hidden_sizes: [100, 100, 100] + output_scale: 100 + use_resnet: true +preprocess_args: {prefit_ridge: 10.0, prefit_trainable: false, prescale: false, preshift: true} +train_args: {decay_rate: 0.96, decay_steps: 500, display_epoch: 100, n_epoch: 5000, + start_lr: 0.0003} diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/jle.orb b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/jle.orb new file mode 100644 index 0000000000000000000000000000000000000000..6fecaa8b6846050e2ef2109adccd3748f1f1c3ed --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/jle.orb @@ -0,0 +1,336 @@ +--------------------------------------------------------------------------- +Energy Cutoff(Ry) 20 +Radius Cutoff(a.u.) 2 +Lmax 2 +Number of Sorbitals--> 2 +Number of Porbitals--> 2 +Number of Dorbitals--> 2 +--------------------------------------------------------------------------- +SUMMARY END + +Mesh 205 +dr 0.01 + Type L N + 0 0 0 +1.000000000000e+00 9.999588771557e-01 9.998355147105e-01 9.996299309272e-01 +9.993421562398e-01 9.989722332485e-01 9.985202167122e-01 9.979861735385e-01 +9.973701827725e-01 9.966723355824e-01 9.958927352436e-01 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/scf_abacus.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7f21493f30617341ab4c561aac3405c376b96ce2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/scf_abacus.yaml @@ -0,0 +1,19 @@ +abacus_path: /root/abacus-develop/build/abacus +cal_force: 1 +coord_type: Cartesian +dft_functional: lda +ecutwfc: 50 +gamma_only: 1 +lattice_constant: 1 +lattice_vector: +- [28, 0, 0] +- [0, 28, 0] +- [0, 0, 28] +nbands: 8 +ntype: 2 +orb_files: [O_gga_6au_60Ry_2s2p1d.orb, H_gga_6au_60Ry_2s1p.orb] +pp_files: [O_ONCV_PBE-1.0.upf, H_ONCV_PBE-1.0.upf] +proj_file: [jle.orb] +run_cmd: mpirun +scf_nmax: 50 +scf_thr: 1e-07 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/systems_test/group.03 b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/systems_test/group.03 new file mode 120000 index 0000000000000000000000000000000000000000..dbeff21d9d8cc95a9b2858aaa573f3cee8106231 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/systems_test/group.03 @@ -0,0 +1 @@ +/root/deepks_test/water_single_lda2pbe_abacus/systems/group.03 \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/systems_train/group.00 b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/systems_train/group.00 new file mode 120000 index 0000000000000000000000000000000000000000..1de47a3d12ebd307b65268650835a72d8e9af3eb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/systems_train/group.00 @@ -0,0 +1 @@ +/root/deepks_test/water_single_lda2pbe_abacus/systems/group.00 \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/train_input.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/train_input.yaml new file mode 100644 index 0000000000000000000000000000000000000000..8fa228ce8d9b90c6439320f5707b1035ffa335bd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/share/train_input.yaml @@ -0,0 +1,5 @@ +data_args: {batch_size: 16, conv_filter: true, conv_name: conv, extra_label: true, + group_batch: 1} +preprocess_args: {prefit_ridge: 10.0, prefit_trainable: false, prescale: false, preshift: false} +train_args: {decay_rate: 0.5, decay_steps: 1000, display_epoch: 100, force_factor: 1, + n_epoch: 5000, start_lr: 0.0001} diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/systems.yaml b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/systems.yaml new file mode 100644 index 0000000000000000000000000000000000000000..068710dc231bb801032353f77f4d3ab83db8c10e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/iter/systems.yaml @@ -0,0 +1,9 @@ +# this is only part of input settings. +# should be used together with params.yaml and machines.yaml + +# training and testing systems +systems_train: # can also be files that containing system paths + - ../systems/group.00 # support glob + +systems_test: # if empty, use the last system of training set + - ../systems/group.03 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/H_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/H_ONCV_PBE-1.0.upf new file mode 120000 index 0000000000000000000000000000000000000000..9880d5f3474a67f84e7a20ef438603329c983a07 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/H_ONCV_PBE-1.0.upf @@ -0,0 +1 @@ +../../../../iter/H_ONCV_PBE-1.0.upf \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/H_gga_6au_60Ry_2s1p.orb b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/H_gga_6au_60Ry_2s1p.orb new file mode 120000 index 0000000000000000000000000000000000000000..c79b62f8b6dcf731268379ef0ddf2f3217ed86e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/H_gga_6au_60Ry_2s1p.orb @@ -0,0 +1 @@ +../../../../iter/H_gga_6au_60Ry_2s1p.orb \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fec4395ee7d7dee5f840e56d8986a953a6a4af38 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.68499 0.0198613 0.206681 +H 0.737263 0.0609936 0.208978 +H 0.703007 0.991759 0.151281 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2c04abf3d6e2bb6b9225fffdefc91c09775c5208 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4789 2 + 2 -12.5322 2 + 3 -9.6146 2 + 4 -6.78786 2 + 5 1.20393 0 + 6 4.36064 0 + 7 11.0634 0 + 8 11.3648 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f43dfa297e9065a4086a56c017377d6968e344f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:52 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.179723531 0.556117645516 5.78706081801 0 0 0 0 + tauc_H1 20.6433699266 1.70781947776 5.85137512725 0 0 0 0 + tauc_H2 19.6841906027 27.7692630016 4.23586843828 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871445763334 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0916626423333 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11059704342 (SEC) + + DONE : INIT CHARGE Time : 0.1587892274 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438627 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000971 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00081 + + Density error is 0.212784659265 + + Energy Rydberg eV + E_KohnSham -34.1865498166 -465.131872467 + E_Harris -34.3753796385 -467.701033997 + E_Fermi -0.406514914998 -5.53091916596 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00126986611912 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103753717907 + + Density error is 0.0974658426336 + + Energy Rydberg eV + E_KohnSham -34.2756870381 -466.344646583 + E_Harris -34.2826357477 -466.439188627 + E_Fermi -0.216928311859 -2.9514610988 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120144310228 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000990477700521 + + Density error is 0.0625393814082 + + Energy Rydberg eV + E_KohnSham -34.2760329937 -466.34935355 + E_Harris -34.2805327547 -466.41057594 + E_Fermi -0.206780025728 -2.81338658249 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110436836362 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000937947278285 + + Density error is 0.00192530195823 + + Energy Rydberg eV + E_KohnSham -34.2759957997 -466.3488475 + E_Harris -34.2759962926 -466.348854206 + E_Fermi -0.170765137362 -2.32337888787 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011083173383 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000941993850019 + + Density error is 0.000932387234086 + + Energy Rydberg eV + E_KohnSham -34.2759390735 -466.348075701 + E_Harris -34.2759406225 -466.348096776 + E_Fermi -0.170412612564 -2.31858254194 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110627796612 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000940620220586 + + Density error is 0.000105006271404 + + Energy Rydberg eV + E_KohnSham -34.2759758218 -466.348575686 + E_Harris -34.2759758378 -466.348575905 + E_Fermi -0.170265784719 -2.31658484661 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110597339659 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000940470740675 + + Density error is 3.52533264638e-05 + + Energy Rydberg eV + E_KohnSham -34.2759648012 -466.348425744 + E_Harris -34.2759648067 -466.348425818 + E_Fermi -0.170173345237 -2.31532714294 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110591964204 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000940419769832 + + Density error is 1.89888688808e-05 + + Energy Rydberg eV + E_KohnSham -34.2759666319 -466.348450652 + E_Harris -34.2759666334 -466.348450672 + E_Fermi -0.170210573513 -2.31583365962 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110591377268 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000940427566838 + + Density error is 1.86370454506e-06 + + Energy Rydberg eV + E_KohnSham -34.2759652168 -466.348431398 + E_Harris -34.2759652168 -466.348431398 + E_Fermi -0.17018957958 -2.31554802252 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110591605791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000940429311084 + + Density error is 3.39746810837e-07 + + Energy Rydberg eV + E_KohnSham -34.2759655003 -466.348435256 + E_Harris -34.2759655003 -466.348435256 + E_Fermi -0.17018854035 -2.31553388306 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110591690155 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000940430132491 + + Density error is 1.04789628318e-07 + + Energy Rydberg eV + E_KohnSham -34.2759655294 -466.348435651 + E_Harris -34.2759655294 -466.348435652 + E_Fermi -0.170188401159 -2.31553198927 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110591697766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000940430272065 + + Density error is 1.13993224141e-08 + + Energy Rydberg eV + E_KohnSham -34.2759655331 -466.348435701 + E_Harris -34.2759655331 -466.348435701 + E_band -7.99864905364 -108.827203432 + E_one_elec -69.3027307344 -942.912024947 + E_Hartree +36.0283385418 +490.190693641 + E_xc -8.20743033693 -111.66781852 + E_Ewald +7.33009838949 +99.7311049977 + E_demet -2.52648216107e-75 -3.43745532859e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194870537828 -2.65134968678 + E_Fermi -0.170188290934 -2.31553048959 + + charge density convergence is achieved + final etot is -466.348435701 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4789 2.00000 + 2 -12.5322 2.00000 + 3 -9.61460 2.00000 + 4 -6.78786 2.00000 + 5 1.20393 0.00000 + 6 4.36064 0.00000 + 7 11.0634 0.00000 + 8 11.3648 0.00000 + + EFERMI = -2.315530489589801 eV + OUT.ABACUS/ final etot is -466.3484357013835 eV + correction force for each atom along direction 1 is 0.000168709 + correction force for each atom along direction 2 is 4.46777e-05 + correction force for each atom along direction 3 is -0.000115235 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.78845657 +0.82983267 +0.31293449 + H1 -0.44903500 +0.17509695 +0.68262604 + H2 -0.33942156 -1.0049296 -0.99556052 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3484357013835 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0351 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0246 1 7.0 1.e+02% + Potential init_pot 0.28445 2 0.14 4.0% + PW_Basis recip2real 0.28292 17 0.017 4.0% + PW_Basis gathers_scatterp 0.12039 17 0.0071 1.7% + Potential v_of_rho 0.94200 14 0.067 13.% + XC_Functional v_xc 0.26372 15 0.018 3.7% + H_Hartree_pw v_hartree 0.63869 14 0.046 9.1% + PW_Basis real2recip 0.59981 41 0.015 8.5% + PW_Basis gatherp_scatters 0.23393 41 0.0057 3.3% + ORB_control set_orb_tables 1.1004 1 1.1 16.% + ORB_gen_tables gen_tables 1.1004 1 1.1 16.% + ORB_table_phi init_Table 0.48314 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47826 126 0.0038 6.8% + ORB_table_beta init_Table_Beta 0.18653 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18509 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.25323 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.25140 66 0.0038 3.6% + LOOP_ions opt_ions 5.4093 1 5.4 77.% + ESolver_KS_LCAO Run 4.8485 1 4.8 69.% + HSolverLCAO solve 2.7071 12 0.23 38.% + HamiltLCAO updateHk 1.3821 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3406 12 0.11 19.% + Gint_interface cal_gint 2.5809 25 0.10 37.% + Gint_Gamma distri_vl 2.5127 6 0.42 36.% + LCAO_Deepks cal_projected_DM 5.2315 14 0.37 74.% + LCAO_gen_fixedH add_v_delta 2.3815 6 0.40 34.% + LCAO_DESCRIPTOR add_v_delta 2.3815 6 0.40 34.% + ElecStateLCAO psiToRho 1.3101 12 0.11 19.% + Charge mix_rho 0.71337 11 0.065 10.% + LOOP_ions force_stress 0.56066 1 0.56 8.0% + Force_Stress_LCAO getForceStress 0.56063 1 0.56 8.0% + Force_LCAO_gamma ftable_gamma 0.34779 1 0.35 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.34108 1 0.34 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:52 2022 + Finish Time : Wed Sep 28 11:05:59 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..80b9945d744cf6589422c4eaec528c36b0ebce19 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124136 ima = 3.7072e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122368385293 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111065325406 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111721995438 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111990882372 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111936093925 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111965447446 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111963796712 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111966485378 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111965660333 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111965578119 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011196556379 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111965558504 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/O_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/O_ONCV_PBE-1.0.upf new file mode 120000 index 0000000000000000000000000000000000000000..ff914a6806b2192868a9bc36694ff03c0dc9e450 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/O_ONCV_PBE-1.0.upf @@ -0,0 +1 @@ +../../../../iter/O_ONCV_PBE-1.0.upf \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/O_gga_6au_60Ry_2s2p1d.orb b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/O_gga_6au_60Ry_2s2p1d.orb new file mode 120000 index 0000000000000000000000000000000000000000..5d2ff63b151809f86337680c77401e9918d3ca92 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/O_gga_6au_60Ry_2s2p1d.orb @@ -0,0 +1 @@ +../../../../iter/O_gga_6au_60Ry_2s2p1d.orb \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/STRU new file mode 100644 index 0000000000000000000000000000000000000000..82d7bc79b5fef29e34693133c974edbda6f1a857 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.820276468984 0.556117645521 5.787060818012 0 0 0 +H +0.0 +2 +-7.356630073377 1.707819477768 5.851375127279 0 0 0 +-8.315809397290 -0.230736998458 4.235868438293 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/conv new file mode 100644 index 0000000000000000000000000000000000000000..ad4f2b2bd146eb43e6bc53593e024b152bdd6377 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/conv @@ -0,0 +1 @@ +0 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..042f708f01bedbe4d6f5758d231f3e39fb3aa0b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.756720462 0.01285616598 1.268428508 1.347301155 1.469919555 0.01009272587 0.01575023072 0.03923983483 +1.875978095e-18 0.0008091804643 0.002984226941 0.01405738496 0.04735706276 -5.237707639e-20 3.231274493e-06 8.384488719e-06 +0.001599365919 0.006193355942 + +H atom_index 1 n_descriptor 18 +1.227553814 0.03602078292 0.1061675241 0.1394755664 0.3112533731 0.02282111323 0.02690614017 0.03915384246 +-4.596489349e-17 4.761677442e-05 0.09917900793 0.1142854091 0.1193838759 8.727813729e-18 3.250923402e-06 0.01383891912 +0.02669705232 0.02967223982 + +H atom_index 2 n_descriptor 18 +1.268591947 0.03467691495 0.121072759 0.158598688 0.3251363123 0.02493835222 0.02932220942 0.03785432717 +5.368415094e-18 5.120653333e-05 0.1070390885 0.1185435725 0.1358750662 -5.863879064e-19 1.198143099e-06 0.01345997395 +0.02822178005 0.03158068015 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d7bfa193ad865ca366caf3e9b71b1a0d762750e5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/e_base.npy 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/dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..67b1206ae0b0f71735dd479b7832fcc223c22bd1 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/jle.orb b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/jle.orb new file mode 120000 index 0000000000000000000000000000000000000000..ec013d36e71b0af8561def26fd6025ab0b7550d0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/jle.orb @@ -0,0 +1 @@ +../../../../iter/jle.orb \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..555d110b9127e05d9c11224569ff1ebb44c9e694 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:52 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871682 SEC) : SETUP UNITCELL + DONE(0.0916797 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11062 SEC) : INIT PLANEWAVE + DONE(0.15892 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438702 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651319e+02 0.000000e+00 2.128e-01 5.205e-01 + GE2 -4.663446e+02 -1.212774e+00 9.747e-02 4.425e-01 + GE3 -4.663494e+02 -4.706967e-03 6.254e-02 5.010e-01 + GE4 -4.663488e+02 5.060499e-04 1.925e-03 3.956e-01 + GE5 -4.663481e+02 7.717992e-04 9.324e-04 3.878e-01 + GE6 -4.663486e+02 -4.999855e-04 1.050e-04 3.858e-01 + GE7 -4.663484e+02 1.499420e-04 3.525e-05 3.822e-01 + GE8 -4.663485e+02 -2.490778e-05 1.899e-05 3.668e-01 + GE9 -4.663484e+02 1.925364e-05 1.864e-06 3.682e-01 + GE10 -4.663484e+02 -3.857833e-06 3.397e-07 3.644e-01 + GE11 -4.663484e+02 -3.954001e-07 1.048e-07 3.631e-01 + GE12 -4.663484e+02 -4.990182e-08 1.140e-08 3.090e-01 +E_delta_band = -7.06291448e-02 Ry = -9.60958814e-01 eV +E_delta_NN= -1.94870538e-01 Ry = -2.65134969e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0351 11 0.64 1e+02 % + Run_lcao lcao_line 7.0246 1 7 1e+02 % + Potential init_pot 0.28445 2 0.14 4 % + PW_Basis recip2real 0.28292 17 0.017 4 % + PW_Basis gathers_scatterp 0.12039 17 0.0071 1.7 % + Potential v_of_rho 0.942 14 0.067 13 % + XC_Functional v_xc 0.26372 15 0.018 3.7 % + H_Hartree_pw v_hartree 0.63869 14 0.046 9.1 % + PW_Basis real2recip 0.59981 41 0.015 8.5 % + PW_Basis gatherp_scatters 0.23393 41 0.0057 3.3 % + ORB_control set_orb_tables 1.1004 1 1.1 16 % + ORB_gen_tables gen_tables 1.1004 1 1.1 16 % + ORB_table_phi init_Table 0.48314 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47826 126 0.0038 6.8 % + ORB_table_beta init_Table_Beta 0.18653 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18509 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.25323 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.2514 66 0.0038 3.6 % + LOOP_ions opt_ions 5.4093 1 5.4 77 % + ESolver_KS_LCAO Run 4.8485 1 4.8 69 % + HSolverLCAO solve 2.7071 12 0.23 38 % + HamiltLCAO updateHk 1.3821 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3406 12 0.11 19 % + Gint_interface cal_gint 2.5809 25 0.1 37 % + Gint_Gamma distri_vl 2.5127 6 0.42 36 % + LCAO_Deepks cal_projected_DM 5.2315 14 0.37 74 % + LCAO_gen_fixedH add_v_delta 2.3815 6 0.4 34 % + LCAO_DESCRIPTOR add_v_delta 2.3815 6 0.4 34 % + ElecStateLCAO psiToRho 1.3101 12 0.11 19 % + Charge mix_rho 0.71337 11 0.065 10 % + LOOP_ions force_stress 0.56066 1 0.56 8 % + Force_Stress_LCAO getForceStress 0.56063 1 0.56 8 % + Force_LCAO_gamma ftable_gamma 0.34779 1 0.35 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.34108 1 0.34 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:52 2022 + FINISH Time : Wed Sep 28 11:05:59 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/0/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..dbdf4b2199eff8ff2cccd2b85983f5e9decb6758 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.674223 0.0229675 0.229861 +H 0.641394 0.0796784 0.23149 +H 0.711721 0.0191473 0.174881 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1ed508064e863469e8217e3c475feed57b8deed5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.06 2 + 2 -13.2542 2 + 3 -8.77184 2 + 4 -6.68779 2 + 5 1.21806 0 + 6 4.32055 0 + 7 11.1129 0 + 8 11.3336 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..47cd8f48be059177c9d6cd7ec2c7502b9131cc13 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:43 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.8782362619 0.643088993209 6.43611065068 0 0 0 0 + tauc_H1 17.9590282772 2.2309946542 6.48172683957 0 0 0 0 + tauc_H2 19.9281878179 0.536124436454 4.89665739344 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0858127159618 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0960170232377 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11419428145 (SEC) + + DONE : INIT CHARGE Time : 0.162408571414 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441218 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000535 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115 + + Density error is 0.214874054976 + + Energy Rydberg eV + E_KohnSham -34.1899378269 -465.177968711 + E_Harris -34.3809159405 -467.776359249 + E_Fermi -0.397218947537 -5.40444104006 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000821946044653 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123979239207 + + Density error is 0.0985235669507 + + Energy Rydberg eV + E_KohnSham -34.278986439 -466.389537235 + E_Harris -34.2857404625 -466.481430439 + E_Fermi -0.206200282496 -2.80549877115 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000796509872206 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117579413436 + + Density error is 0.0632956246765 + + Energy Rydberg eV + E_KohnSham -34.2792495728 -466.393117355 + E_Harris -34.2835836382 -466.45208534 + E_Fermi -0.196016181752 -2.66693697203 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000768283409233 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107312239662 + + Density error is 0.00212338989405 + + Energy Rydberg eV + E_KohnSham -34.2792211573 -466.392730742 + E_Harris -34.2792257488 -466.392793212 + E_Fermi -0.160974358816 -2.19016851179 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000767877335499 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107152000211 + + Density error is 0.000855592501403 + + Energy Rydberg eV + E_KohnSham -34.279177563 -466.39213761 + E_Harris -34.2791779859 -466.392143364 + E_Fermi -0.160317244138 -2.18122800793 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000767471558677 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107020954744 + + Density error is 0.000200764326292 + + Energy Rydberg eV + E_KohnSham -34.2792035646 -466.39249138 + E_Harris -34.2792036119 -466.392492023 + E_Fermi -0.160177449392 -2.17932600283 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000767700946998 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107032817022 + + Density error is 3.50382068072e-05 + + Energy Rydberg eV + E_KohnSham -34.2791937238 -466.392357489 + E_Harris -34.2791937298 -466.392357571 + E_Fermi -0.160060063548 -2.1777288865 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00076763894323 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107026454736 + + Density error is 1.61483338172e-05 + + Energy Rydberg eV + E_KohnSham -34.2791982492 -466.392419061 + E_Harris -34.2791982503 -466.392419076 + E_Fermi -0.160094678913 -2.1781998527 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000767642257646 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107025305864 + + Density error is 1.65178199759e-06 + + Energy Rydberg eV + E_KohnSham -34.2791969243 -466.392401034 + E_Harris -34.2791969243 -466.392401034 + E_Fermi -0.160077717697 -2.17796908351 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000767643209919 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107025183817 + + Density error is 2.54323637524e-07 + + Energy Rydberg eV + E_KohnSham -34.279197169 -466.392404364 + E_Harris -34.279197169 -466.392404364 + E_Fermi -0.160076230836 -2.17794885374 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000767643761998 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107025248343 + + Density error is 6.63573841749e-08 + + Energy Rydberg eV + E_KohnSham -34.2791971879 -466.392404621 + E_Harris -34.2791971879 -466.392404621 + E_band -7.90460201359 -107.547627807 + E_one_elec -69.0496594113 -939.468812953 + E_Hartree +35.9392701495 +488.978855995 + E_xc -8.19291590348 -111.470339522 + E_Ewald +7.14899714978 +97.2670962227 + E_demet -2.57071476748e-70 -3.49763687705e-69 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194184291046 -2.64201282032 + E_Fermi -0.160076128116 -2.17794745616 + + charge density convergence is achieved + final etot is -466.392404621 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0600 2.00000 + 2 -13.2542 2.00000 + 3 -8.77184 2.00000 + 4 -6.68779 2.00000 + 5 1.21806 0.00000 + 6 4.32055 0.00000 + 7 11.1129 0.00000 + 8 11.3336 0.00000 + + EFERMI = -2.177947456160562 eV + OUT.ABACUS/ final etot is -466.3924046205584 eV + correction force for each atom along direction 1 is -8.19360e-05 + correction force for each atom along direction 2 is 7.91376e-05 + correction force for each atom along direction 3 is -0.000141160 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.40343989 -0.65216558 -0.068747740 + H1 +0.16469154 +0.18564346 -0.41302467 + H2 -0.56813143 +0.46652212 +0.48177241 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3924046205584 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4160 11 0.58 1.0e+02% + Run_lcao lcao_line 6.4070 1 6.4 1.e+02% + Potential init_pot 0.28361 2 0.14 4.4% + PW_Basis recip2real 0.26060 16 0.016 4.1% + PW_Basis gathers_scatterp 0.10926 16 0.0068 1.7% + Potential v_of_rho 0.87379 13 0.067 14.% + XC_Functional v_xc 0.25143 14 0.018 3.9% + H_Hartree_pw v_hartree 0.58551 13 0.045 9.1% + PW_Basis real2recip 0.55147 38 0.015 8.6% + PW_Basis gatherp_scatters 0.21520 38 0.0057 3.4% + ORB_control set_orb_tables 1.1022 1 1.1 17.% + ORB_gen_tables gen_tables 1.1022 1 1.1 17.% + ORB_table_phi init_Table 0.48230 1 0.48 7.5% + ORB_table_phi cal_ST_Phi12_R 0.47734 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18862 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18712 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25351 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25168 66 0.0038 3.9% + LOOP_ions opt_ions 4.7863 1 4.8 75.% + ESolver_KS_LCAO Run 4.2380 1 4.2 66.% + HSolverLCAO solve 2.2696 11 0.21 35.% + HamiltLCAO updateHk 1.1774 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1391 11 0.10 18.% + Gint_interface cal_gint 2.1397 23 0.093 33.% + Gint_Gamma distri_vl 2.0438 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.6214 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9105 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9105 6 0.32 30.% + ElecStateLCAO psiToRho 1.0785 11 0.098 17.% + Charge mix_rho 0.65762 10 0.066 10.% + LOOP_ions force_stress 0.54813 1 0.55 8.5% + Force_Stress_LCAO getForceStress 0.54810 1 0.55 8.5% + Force_LCAO_gamma ftable_gamma 0.33457 1 0.33 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.32777 1 0.33 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:43 2022 + Finish Time : Wed Sep 28 11:08:50 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6a267be9d100d7063fe10eb64c9b79d9b146c33c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123505 ima = 3.68984e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123819070396 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112866464711 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113415502077 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113615493783 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113583738836 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113604025245 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113595985306 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113598639386 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113597938593 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113597883 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113597870758 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b8b584baad51b1231e0ce084d31c5fe7ff4caa20 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.121763738102 0.643088993210 6.436110650681 0 0 0 +H +0.0 +2 +-10.040971722804 2.230994654225 6.481726839553 0 0 0 +-8.071812182112 0.536124436475 4.896657393456 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/conv new file mode 100644 index 0000000000000000000000000000000000000000..15ea1183b42238a250bf9f8923d355029c78e1da --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/conv @@ -0,0 +1 @@ +1 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..98093ba0c4e9640ce22eca754df32c0c81ee4d2a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74347251 0.01249739035 1.267535752 1.364134182 1.46829205 0.007519587575 0.02028747332 0.03885422821 +8.826898471e-19 0.001086989228 0.002268927149 0.01195315733 0.04098542995 2.66424122e-19 1.337305614e-06 4.362118333e-06 +0.001791898853 0.005573451668 + +H atom_index 1 n_descriptor 18 +1.237868503 0.03404619826 0.1042591021 0.1462454458 0.3199297473 0.02117600187 0.02785127457 0.03725403168 +-4.311270944e-17 3.476184116e-05 0.09803224546 0.1145680749 0.1254312704 -2.609788068e-19 4.506343814e-06 0.01294633015 +0.02536722039 0.03035255847 + +H atom_index 2 n_descriptor 18 +1.21295152 0.03492245718 0.09626738361 0.1353805882 0.3116016671 0.02008830279 0.02640780945 0.0381863281 +-2.648746711e-17 3.288552214e-05 0.09136968308 0.1139959955 0.1159597873 6.108976978e-18 5.397151509e-06 0.01338807372 +0.0243908027 0.0291514296 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..439e03ce31b2d339b29c540f90c59ddd69efeab1 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/dm_eig.npy differ diff --git 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@@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:43 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0858332 SEC) : SETUP UNITCELL + DONE(0.0960344 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.114213 SEC) : INIT PLANEWAVE + DONE(0.162539 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.441306 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651780e+02 0.000000e+00 2.149e-01 4.999e-01 + GE2 -4.663895e+02 -1.211569e+00 9.852e-02 4.209e-01 + GE3 -4.663931e+02 -3.580120e-03 6.330e-02 4.844e-01 + GE4 -4.663927e+02 3.866132e-04 2.123e-03 3.694e-01 + GE5 -4.663921e+02 5.931312e-04 8.556e-04 3.704e-01 + GE6 -4.663925e+02 -3.537694e-04 2.008e-04 3.623e-01 + GE7 -4.663924e+02 1.338907e-04 3.504e-05 3.511e-01 + GE8 -4.663924e+02 -6.157153e-05 1.615e-05 3.464e-01 + GE9 -4.663924e+02 1.802652e-05 1.652e-06 3.441e-01 + GE10 -4.663924e+02 -3.329575e-06 2.543e-07 3.428e-01 + GE11 -4.663924e+02 -2.568012e-07 6.636e-08 2.856e-01 +E_delta_band = -6.92951186e-02 Ry = -9.42808457e-01 eV +E_delta_NN= -1.94184291e-01 Ry = -2.64201282e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.416 11 0.58 1e+02 % + Run_lcao lcao_line 6.407 1 6.4 1e+02 % + Potential init_pot 0.28361 2 0.14 4.4 % + PW_Basis recip2real 0.2606 16 0.016 4.1 % + PW_Basis gathers_scatterp 0.10926 16 0.0068 1.7 % + Potential v_of_rho 0.87379 13 0.067 14 % + XC_Functional v_xc 0.25143 14 0.018 3.9 % + H_Hartree_pw v_hartree 0.58551 13 0.045 9.1 % + PW_Basis real2recip 0.55147 38 0.015 8.6 % + PW_Basis gatherp_scatters 0.2152 38 0.0057 3.4 % + ORB_control set_orb_tables 1.1022 1 1.1 17 % + ORB_gen_tables gen_tables 1.1022 1 1.1 17 % + ORB_table_phi init_Table 0.4823 1 0.48 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.47734 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18862 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18712 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.25351 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.25168 66 0.0038 3.9 % + LOOP_ions opt_ions 4.7863 1 4.8 75 % + ESolver_KS_LCAO Run 4.238 1 4.2 66 % + HSolverLCAO solve 2.2696 11 0.21 35 % + HamiltLCAO updateHk 1.1774 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1391 11 0.1 18 % + Gint_interface cal_gint 2.1397 23 0.093 33 % + Gint_Gamma distri_vl 2.0438 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.6214 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9105 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9105 6 0.32 30 % + ElecStateLCAO psiToRho 1.0785 11 0.098 17 % + Charge mix_rho 0.65762 10 0.066 10 % + LOOP_ions force_stress 0.54813 1 0.55 8.5 % + Force_Stress_LCAO getForceStress 0.5481 1 0.55 8.5 % + Force_LCAO_gamma ftable_gamma 0.33457 1 0.33 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.32777 1 0.33 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:43 2022 + FINISH Time : Wed Sep 28 11:08:50 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/1/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fedb05c8aaba6f69df045f5327ddf1c167b885b1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.574626 0.187908 0.36561 +H 0.54997 0.186497 0.303005 +H 0.595225 0.247598 0.369203 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8f583c5529d5f243bcae6e874dfed5b1d3ea9c96 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4097 2 + 2 -12.9243 2 + 3 -9.28001 2 + 4 -6.7692 2 + 5 1.27126 0 + 6 4.49538 0 + 7 11.057 0 + 8 11.3128 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fcd04e6a3bd64cdfca9f3f42a5d55b4620fbf1c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:11 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.0895174066 5.261424607 10.2370888262 0 0 0 0 + tauc_H1 15.3991662954 5.22190764528 8.4841346106 0 0 0 0 + tauc_H2 16.6662879621 6.93273899896 10.3376921855 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.087109707337 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0990372731169 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117237144483 (SEC) + + DONE : INIT CHARGE Time : 0.166831953781 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446916 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00167 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108 + + Density error is 0.214700685092 + + Energy Rydberg eV + E_KohnSham -34.187560012 -465.14561688 + E_Harris -34.3794728036 -467.756724365 + E_Fermi -0.408979939153 -5.56445754018 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00151014921744 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013482543193 + + Density error is 0.0977631965301 + + Energy Rydberg eV + E_KohnSham -34.2769702836 -466.362106034 + E_Harris -34.2837445533 -466.454274701 + E_Fermi -0.219062251436 -2.98049483624 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00138373995103 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128521692287 + + Density error is 0.0625894800586 + + Energy Rydberg eV + E_KohnSham -34.2772097722 -466.365364443 + E_Harris -34.2815873665 -466.424924669 + E_Fermi -0.207283045884 -2.82023052281 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011627009463 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119738064807 + + Density error is 0.00197149629811 + + Energy Rydberg eV + E_KohnSham -34.2772039008 -466.365284559 + E_Harris -34.2772045809 -466.365293813 + E_Fermi -0.171456079322 -2.33277963552 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116136246797 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120002822031 + + Density error is 0.00085242105695 + + Energy Rydberg eV + E_KohnSham -34.2771467944 -466.364507586 + E_Harris -34.2771478369 -466.364521771 + E_Fermi -0.170778020779 -2.32355417576 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115900519511 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119866634673 + + Density error is 0.000110786650166 + + Energy Rydberg eV + E_KohnSham -34.2771826841 -466.364995891 + E_Harris -34.2771826982 -466.364996082 + E_Fermi -0.170751477904 -2.32319304142 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115877828013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119867049805 + + Density error is 4.22112329718e-05 + + Energy Rydberg eV + E_KohnSham -34.2771712174 -466.364839879 + E_Harris -34.2771712275 -466.364840015 + E_Fermi -0.17064081153 -2.32168734815 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115878692142 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119859886815 + + Density error is 1.24622545801e-05 + + Energy Rydberg eV + E_KohnSham -34.2771743167 -466.364882047 + E_Harris -34.2771743173 -466.364882055 + E_Fermi -0.170684019898 -2.32227522816 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115875891132 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119859678184 + + Density error is 2.04155239606e-06 + + Energy Rydberg eV + E_KohnSham -34.2771729377 -466.364863285 + E_Harris -34.2771729378 -466.364863285 + E_Fermi -0.170671088533 -2.32209928791 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115875424603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119859651792 + + Density error is 1.73034142155e-07 + + Energy Rydberg eV + E_KohnSham -34.2771730791 -466.364865208 + E_Harris -34.2771730791 -466.364865208 + E_Fermi -0.170669311571 -2.32207511111 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115875448472 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011985970686 + + Density error is 7.72462431951e-08 + + Energy Rydberg eV + E_KohnSham -34.2771731204 -466.36486577 + E_Harris -34.2771731204 -466.36486577 + E_band -7.99417943051 -108.766391089 + E_one_elec -69.396610559 -944.189325489 + E_Hartree +36.0838650182 +490.94617011 + E_xc -8.21704280007 -111.798602791 + E_Ewald +7.37672188016 +100.365450131 + E_demet -2.09253583461e-78 -2.84704106199e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195094918091 -2.65440253688 + E_Fermi -0.17066930447 -2.32207501449 + + charge density convergence is achieved + final etot is -466.36486577 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4097 2.00000 + 2 -12.9243 2.00000 + 3 -9.28001 2.00000 + 4 -6.76920 2.00000 + 5 1.27126 0.00000 + 6 4.49538 0.00000 + 7 11.0570 0.00000 + 8 11.3128 0.00000 + + EFERMI = -2.322075014493299 eV + OUT.ABACUS/ final etot is -466.3648657695888 eV + correction force for each atom along direction 1 is 3.72248e-05 + correction force for each atom along direction 2 is 4.16381e-05 + correction force for each atom along direction 3 is -1.97407e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.1006819 -1.8798741 -1.2863322 + H1 +0.27126541 -0.23082680 +0.89652080 + H2 +0.82941647 +2.1107009 +0.38981137 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3648657695888 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9870 11 0.64 1.0e+02% + Run_lcao lcao_line 6.9775 1 7.0 1.e+02% + Potential init_pot 0.28347 2 0.14 4.1% + PW_Basis recip2real 0.26579 16 0.017 3.8% + PW_Basis gathers_scatterp 0.12257 16 0.0077 1.8% + Potential v_of_rho 0.98648 13 0.076 14.% + XC_Functional v_xc 0.31108 14 0.022 4.5% + H_Hartree_pw v_hartree 0.63722 13 0.049 9.1% + PW_Basis real2recip 0.64867 38 0.017 9.3% + PW_Basis gatherp_scatters 0.28685 38 0.0075 4.1% + ORB_control set_orb_tables 1.0884 1 1.1 16.% + ORB_gen_tables gen_tables 1.0884 1 1.1 16.% + ORB_table_phi init_Table 0.47370 1 0.47 6.8% + ORB_table_phi cal_ST_Phi12_R 0.46849 126 0.0037 6.7% + ORB_table_beta init_Table_Beta 0.18316 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18161 56 0.0032 2.6% + ORB_table_alpha init_Table_Alpha 0.24492 1 0.24 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24298 66 0.0037 3.5% + LOOP_ions opt_ions 5.3623 1 5.4 77.% + ESolver_KS_LCAO Run 4.7588 1 4.8 68.% + HSolverLCAO solve 2.4745 11 0.22 35.% + HamiltLCAO updateHk 1.2846 11 0.12 18.% + LCAO_Hamilt cal_Hgamma 1.2574 11 0.11 18.% + Gint_interface cal_gint 0.67157 23 0.029 9.6% + Gint_Gamma distri_vl_value 0.59603 11 0.054 8.5% + Gint_Gamma distri_vl 2.2981 6 0.38 33.% + LCAO_Deepks cal_projected_DM 4.9825 13 0.38 71.% + LCAO_gen_fixedH add_v_delta 2.1536 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1536 6 0.36 31.% + ElecStateLCAO psiToRho 1.1647 11 0.11 17.% + Charge mix_rho 0.76524 10 0.077 11.% + LOOP_ions force_stress 0.60332 1 0.60 8.6% + Force_Stress_LCAO getForceStress 0.60330 1 0.60 8.6% + Force_LCAO_gamma ftable_gamma 0.38585 1 0.39 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.15703 1 0.16 2.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:11 2022 + Finish Time : Wed Sep 28 11:11:18 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ff300f356b5e637999b0f2a37aa17bde94cbe4c6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123976 ima = 3.66725e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122807650025 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111776561235 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318080645 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112573824683 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112522924628 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112550721006 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112545940974 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112548950208 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112548474642 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112548371168 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112548365648 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/STRU new file mode 100644 index 0000000000000000000000000000000000000000..34fac0510be0d7f5c61423fe7e972f67ebf98d7b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.910482593425 5.261424607004 10.237088826221 0 0 0 +H +0.0 +2 +-12.600833704662 5.221907645259 8.484134610586 0 0 0 +-11.333712037926 6.932738998949 10.337692185552 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/conv new file mode 100644 index 0000000000000000000000000000000000000000..a8dba8b346c7b52f2e8c36223554071080c472f4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/conv @@ -0,0 +1 @@ +10 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..3cc5a43f0d472482d99e1f4e833c10eda976ab7c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751924771 0.01271763154 1.269574434 1.366371124 1.469841009 0.009065322043 0.0178145054 0.03911824067 +6.726257144e-19 0.001002565423 0.002760516724 0.0127860751 0.04668957193 2.637515014e-19 2.401490388e-06 6.694110498e-06 +0.001595836697 0.006020462019 + +H atom_index 1 n_descriptor 18 +1.207475888 0.0359662872 0.09530599251 0.1309645678 0.3053904614 0.02063005686 0.02576834593 0.03924461129 +-1.243115157e-17 4.497865676e-05 0.09152767383 0.1121666855 0.1134109473 1.403916156e-18 5.933689239e-06 0.01407004462 +0.02498162558 0.02865929495 + +H atom_index 2 n_descriptor 18 +1.296849496 0.03304221385 0.1269425436 0.1729490895 0.3343461666 0.02490004241 0.03096374939 0.03675405071 +4.140643395e-18 5.345129196e-05 0.1080199384 0.1229192562 0.1482938655 -4.434707966e-19 1.237099584e-06 0.01366670862 +0.02823725869 0.03265051268 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..cb6014d6904e90ad0ffd661669335291144ab31c Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..3da5e0d3a8989e85c9102a59b26d06c52c8fae84 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..6d2527ea381f65c4e0a4e0a725273266dde04a5a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..edd8138d442dccd000581680053d302bb84a4716 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..f3a792701573b38bc344013ad367c4db3b07d3f5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:11 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871331 SEC) : SETUP UNITCELL + DONE(0.0990568 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.117257 SEC) : INIT PLANEWAVE + DONE(0.166973 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446978 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651456e+02 0.000000e+00 2.147e-01 5.395e-01 + GE2 -4.663621e+02 -1.216489e+00 9.776e-02 4.826e-01 + GE3 -4.663654e+02 -3.258409e-03 6.259e-02 5.526e-01 + GE4 -4.663653e+02 7.988436e-05 1.971e-03 4.125e-01 + GE5 -4.663645e+02 7.769726e-04 8.524e-04 4.131e-01 + GE6 -4.663650e+02 -4.883049e-04 1.108e-04 4.038e-01 + GE7 -4.663648e+02 1.560123e-04 4.221e-05 3.953e-01 + GE8 -4.663649e+02 -4.216807e-05 1.246e-05 3.898e-01 + GE9 -4.663649e+02 1.876210e-05 2.042e-06 3.912e-01 + GE10 -4.663649e+02 -1.922828e-06 1.730e-07 3.917e-01 + GE11 -4.663649e+02 -5.620121e-07 7.725e-08 3.250e-01 +E_delta_band = -7.09882584e-02 Ry = -9.65844805e-01 eV +E_delta_NN= -1.95094918e-01 Ry = -2.65440254e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.987 11 0.64 1e+02 % + Run_lcao lcao_line 6.9775 1 7 1e+02 % + Potential init_pot 0.28347 2 0.14 4.1 % + PW_Basis recip2real 0.26579 16 0.017 3.8 % + PW_Basis gathers_scatterp 0.12257 16 0.0077 1.8 % + Potential v_of_rho 0.98648 13 0.076 14 % + XC_Functional v_xc 0.31108 14 0.022 4.5 % + H_Hartree_pw v_hartree 0.63722 13 0.049 9.1 % + PW_Basis real2recip 0.64867 38 0.017 9.3 % + PW_Basis gatherp_scatters 0.28685 38 0.0075 4.1 % + ORB_control set_orb_tables 1.0884 1 1.1 16 % + ORB_gen_tables gen_tables 1.0884 1 1.1 16 % + ORB_table_phi init_Table 0.4737 1 0.47 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.46849 126 0.0037 6.7 % + ORB_table_beta init_Table_Beta 0.18316 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18161 56 0.0032 2.6 % + ORB_table_alpha init_Table_Alpha 0.24492 1 0.24 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24298 66 0.0037 3.5 % + LOOP_ions opt_ions 5.3623 1 5.4 77 % + ESolver_KS_LCAO Run 4.7588 1 4.8 68 % + HSolverLCAO solve 2.4745 11 0.22 35 % + HamiltLCAO updateHk 1.2846 11 0.12 18 % + LCAO_Hamilt cal_Hgamma 1.2574 11 0.11 18 % + Gint_interface cal_gint 0.67157 23 0.029 9.6 % + Gint_Gamma distri_vl_value 0.59603 11 0.054 8.5 % + Gint_Gamma distri_vl 2.2981 6 0.38 33 % + LCAO_Deepks cal_projected_DM 4.9825 13 0.38 71 % + LCAO_gen_fixedH add_v_delta 2.1536 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1536 6 0.36 31 % + ElecStateLCAO psiToRho 1.1647 11 0.11 17 % + Charge mix_rho 0.76524 10 0.077 11 % + LOOP_ions force_stress 0.60332 1 0.6 8.6 % + Force_Stress_LCAO getForceStress 0.6033 1 0.6 8.6 % + Force_LCAO_gamma ftable_gamma 0.38585 1 0.39 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.15703 1 0.16 2.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:11 2022 + FINISH Time : Wed Sep 28 11:11:18 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/10/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ea50e5568adc8f2c2ee1db55c93f0d6db1becd58 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.195869 0.448098 0.30789 +H 0.171561 0.461882 0.244659 +H 0.142617 0.423243 0.333031 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..88813fbfc9ef2aa173a6a47f809f893f198b4be5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2656 2 + 2 -12.613 2 + 3 -9.39246 2 + 4 -6.73861 2 + 5 1.04355 0 + 6 4.20119 0 + 7 11.0997 0 + 8 11.3607 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c9c53df5e105e4e3e6c49fc10e7ba7448c67acab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:32 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.48433032351 12.5467548464 8.62090903435 0 0 0 0 + tauc_H1 4.80370969025 12.9326939393 6.85045789331 0 0 0 0 + tauc_H2 3.99328851141 11.8508116402 9.32487664882 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0895157344459 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0897972939352 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105508633613 (SEC) + + DONE : INIT CHARGE Time : 0.147892727516 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.415424 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 100 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00105 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00155 + + Density error is 0.212976216498 + + Energy Rydberg eV + E_KohnSham -34.1838414123 -465.095022736 + E_Harris -34.3730191496 -467.668917898 + E_Fermi -0.399122204848 -5.43033618426 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00138907874753 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132710482138 + + Density error is 0.0984791383014 + + Energy Rydberg eV + E_KohnSham -34.2742222335 -466.324716895 + E_Harris -34.2813635468 -466.421879446 + E_Fermi -0.208677351107 -2.8392010186 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00131825484627 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012296373052 + + Density error is 0.0634132531149 + + Energy Rydberg eV + E_KohnSham -34.2747081191 -466.331327707 + E_Harris -34.2792924621 -466.393700893 + E_Fermi -0.200878648844 -2.73309423082 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122001698431 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010579060101 + + Density error is 0.0019144919603 + + Energy Rydberg eV + E_KohnSham -34.2746304971 -466.330271605 + E_Harris -34.2746306662 -466.330273907 + E_Fermi -0.164996254679 -2.24488921229 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122396478449 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105974334935 + + Density error is 0.00100851435493 + + Energy Rydberg eV + E_KohnSham -34.2745792468 -466.329574309 + E_Harris -34.2745802202 -466.329587553 + E_Fermi -0.164897583968 -2.2435467284 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0012220960421 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105694163196 + + Density error is 0.00012679871898 + + Energy Rydberg eV + E_KohnSham -34.274604157 -466.32991323 + E_Harris -34.2746041699 -466.329913405 + E_Fermi -0.164543341063 -2.23872700641 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0012220885058 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010568931669 + + Density error is 3.52932111186e-05 + + Energy Rydberg eV + E_KohnSham -34.2745964566 -466.32980846 + E_Harris -34.2745964606 -466.329808515 + E_Fermi -0.164490203658 -2.23800403492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122201553524 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105686648928 + + Density error is 1.51720486368e-05 + + Energy Rydberg eV + E_KohnSham -34.2745990494 -466.329843738 + E_Harris -34.2745990504 -466.329843751 + E_Fermi -0.164511935233 -2.23829970818 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122201780237 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105685181495 + + Density error is 2.97109105267e-06 + + Energy Rydberg eV + E_KohnSham -34.274597819 -466.329826997 + E_Harris -34.274597819 -466.329826997 + E_Fermi -0.164498230461 -2.23811324519 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122201590876 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010568450713 + + Density error is 1.81229744733e-07 + + Energy Rydberg eV + E_KohnSham -34.2745980037 -466.32982951 + E_Harris -34.2745980037 -466.32982951 + E_Fermi -0.164495161123 -2.2380714847 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122201659079 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105684540519 + + Density error is 6.59324517366e-08 + + Energy Rydberg eV + E_KohnSham -34.2745980617 -466.329830299 + E_Harris -34.2745980617 -466.329830299 + E_band -7.93926623689 -108.019258761 + E_one_elec -68.9888372747 -938.641285331 + E_Hartree +35.8866217743 +488.262538101 + E_xc -8.1854941461 -111.369361333 + E_Ewald +7.13800823439 +97.1175843586 + E_demet -7.75834213925e-66 -1.05557660127e-64 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194418373107 -2.64519767014 + E_Fermi -0.164495119306 -2.23807091575 + + charge density convergence is achieved + final etot is -466.329830299 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2656 2.00000 + 2 -12.6130 2.00000 + 3 -9.39246 2.00000 + 4 -6.73861 2.00000 + 5 1.04355 0.00000 + 6 4.20119 0.00000 + 7 11.0997 0.00000 + 8 11.3607 0.00000 + + EFERMI = -2.238070915747025 eV + OUT.ABACUS/ final etot is -466.3298302994429 eV + correction force for each atom along direction 1 is -0.000105049 + correction force for each atom along direction 2 is -0.000131543 + correction force for each atom along direction 3 is -8.41583e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.21199843 +0.96662194 -2.6981280 + H1 +1.0328354 -0.22514363 +1.6245951 + H2 -1.2448339 -0.74147831 +1.0735329 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3298302994429 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0536 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0439 1 7.0 1.e+02% + Potential init_pot 0.24010 2 0.12 3.4% + PW_Basis recip2real 0.22510 16 0.014 3.2% + PW_Basis gathers_scatterp 0.10438 16 0.0065 1.5% + Potential v_of_rho 0.87510 13 0.067 12.% + XC_Functional v_xc 0.28306 14 0.020 4.0% + H_Hartree_pw v_hartree 0.55857 13 0.043 7.9% + PW_Basis real2recip 0.59566 38 0.016 8.4% + PW_Basis gatherp_scatters 0.23992 38 0.0063 3.4% + ORB_control set_orb_tables 0.89589 1 0.90 13.% + ORB_gen_tables gen_tables 0.89589 1 0.90 13.% + ORB_table_phi init_Table 0.37531 1 0.38 5.3% + ORB_table_phi cal_ST_Phi12_R 0.37114 126 0.0029 5.3% + ORB_table_beta init_Table_Beta 0.15428 1 0.15 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15299 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20773 1 0.21 2.9% + ORB_table_alpha S_PhiAlpha_R 0.20611 66 0.0031 2.9% + LOOP_ions opt_ions 5.6276 1 5.6 80.% + ESolver_KS_LCAO Run 5.0877 1 5.1 72.% + HSolverLCAO solve 2.9358 11 0.27 42.% + HamiltLCAO updateHk 1.4822 11 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.4588 11 0.13 21.% + Gint_interface cal_gint 1.6141 23 0.070 23.% + Gint_Gamma distri_vl_value 0.42785 11 0.039 6.1% + Gint_Gamma distri_vl 2.4973 6 0.42 35.% + LCAO_Deepks cal_projected_DM 5.3836 13 0.41 76.% + LCAO_gen_fixedH add_v_delta 2.3098 6 0.38 33.% + LCAO_DESCRIPTOR add_v_delta 2.3098 6 0.38 33.% + ElecStateLCAO psiToRho 1.3977 11 0.13 20.% + Charge mix_rho 0.76017 10 0.076 11.% + LOOP_ions force_stress 0.53980 1 0.54 7.7% + Force_Stress_LCAO getForceStress 0.53975 1 0.54 7.7% + Force_LCAO_gamma ftable_gamma 0.34475 1 0.34 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.25785 1 0.26 3.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:32 2022 + Finish Time : Wed Sep 28 11:01:39 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..96f2fa27c6ebee1299b42cb16dcc1e42ba3d6f56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012388 ima = 3.65721e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123089611512 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111551250082 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318215514 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112575140633 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112539483197 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112559437282 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112555434051 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112557866817 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112557219803 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112557072832 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112557064183 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/STRU new file mode 100644 index 0000000000000000000000000000000000000000..bf0d329e37f3593163cb142b9150bea643c039a5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.515669676488 12.546754846372 8.620909034364 0 0 0 +H +0.0 +2 +-23.196290309742 12.932693939336 6.850457893297 0 0 0 +-24.006711488603 11.850811640201 9.324876648828 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/conv new file mode 100644 index 0000000000000000000000000000000000000000..c91c3d02dec518a9a3fc8dedae96c57a745e4a7e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/conv @@ -0,0 +1 @@ +100 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..65c91779132a14b1c696074d2c01756461304510 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754406041 0.012599163 1.248286857 1.351241484 1.469254108 0.009439120687 0.01669774127 0.03922690307 +6.201218258e-19 0.0008479675946 0.002732111138 0.0125451784 0.04517583065 8.822749773e-20 2.353735118e-06 6.723346706e-06 +0.00155612464 0.006015280492 + +H atom_index 1 n_descriptor 18 +1.169634447 0.03729811478 0.08480819113 0.1158863545 0.2901363578 0.01901650041 0.02352095834 0.04106717707 +1.303933461e-17 3.941094961e-05 0.08082250971 0.09864718326 0.1115276255 6.404473714e-18 6.582559385e-06 0.01537635162 +0.02318304741 0.02654162312 + +H atom_index 2 n_descriptor 18 +1.283830844 0.03372601251 0.1227895143 0.1661758323 0.3306759263 0.02457975598 0.03021279441 0.03717904277 +1.869820613e-17 4.964663417e-05 0.1066700152 0.1196316621 0.1423743916 -2.469419338e-18 1.422496837e-06 0.01344895491 +0.02765656311 0.03216125627 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fce869a36f03a33396cc2b5f61401af7fb21465d Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..9fbd2901b7947738feece39b3794b5b23136b333 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:32 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0895315 SEC) : SETUP UNITCELL + DONE(0.0898062 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105521 SEC) : INIT PLANEWAVE + DONE(0.148016 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.415464 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650950e+02 0.000000e+00 2.130e-01 6.502e-01 + GE2 -4.663247e+02 -1.229694e+00 9.848e-02 5.015e-01 + GE3 -4.663313e+02 -6.610812e-03 6.341e-02 5.611e-01 + GE4 -4.663303e+02 1.056102e-03 1.914e-03 4.341e-01 + GE5 -4.663296e+02 6.972961e-04 1.009e-03 4.351e-01 + GE6 -4.663299e+02 -3.389210e-04 1.268e-04 4.299e-01 + GE7 -4.663298e+02 1.047698e-04 3.529e-05 4.160e-01 + GE8 -4.663298e+02 -3.527793e-05 1.517e-05 4.186e-01 + GE9 -4.663298e+02 1.674099e-05 2.971e-06 4.223e-01 + GE10 -4.663298e+02 -2.513341e-06 1.812e-07 4.155e-01 + GE11 -4.663298e+02 -7.891907e-07 6.593e-08 3.500e-01 +E_delta_band = -6.95217235e-02 Ry = -9.45891574e-01 eV +E_delta_NN= -1.94418373e-01 Ry = -2.64519767e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0536 11 0.64 1e+02 % + Run_lcao lcao_line 7.0439 1 7 1e+02 % + Potential init_pot 0.2401 2 0.12 3.4 % + PW_Basis recip2real 0.2251 16 0.014 3.2 % + PW_Basis gathers_scatterp 0.10438 16 0.0065 1.5 % + Potential v_of_rho 0.8751 13 0.067 12 % + XC_Functional v_xc 0.28306 14 0.02 4 % + H_Hartree_pw v_hartree 0.55857 13 0.043 7.9 % + PW_Basis real2recip 0.59566 38 0.016 8.4 % + PW_Basis gatherp_scatters 0.23992 38 0.0063 3.4 % + ORB_control set_orb_tables 0.89589 1 0.9 13 % + ORB_gen_tables gen_tables 0.89589 1 0.9 13 % + ORB_table_phi init_Table 0.37531 1 0.38 5.3 % + ORB_table_phi cal_ST_Phi12_R 0.37114 126 0.0029 5.3 % + ORB_table_beta init_Table_Beta 0.15428 1 0.15 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15299 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20773 1 0.21 2.9 % + ORB_table_alpha S_PhiAlpha_R 0.20611 66 0.0031 2.9 % + LOOP_ions opt_ions 5.6276 1 5.6 80 % + ESolver_KS_LCAO Run 5.0877 1 5.1 72 % + HSolverLCAO solve 2.9358 11 0.27 42 % + HamiltLCAO updateHk 1.4822 11 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.4588 11 0.13 21 % + Gint_interface cal_gint 1.6141 23 0.07 23 % + Gint_Gamma distri_vl_value 0.42785 11 0.039 6.1 % + Gint_Gamma distri_vl 2.4973 6 0.42 35 % + LCAO_Deepks cal_projected_DM 5.3836 13 0.41 76 % + LCAO_gen_fixedH add_v_delta 2.3098 6 0.38 33 % + LCAO_DESCRIPTOR add_v_delta 2.3098 6 0.38 33 % + ElecStateLCAO psiToRho 1.3977 11 0.13 20 % + Charge mix_rho 0.76017 10 0.076 11 % + LOOP_ions force_stress 0.5398 1 0.54 7.7 % + Force_Stress_LCAO getForceStress 0.53975 1 0.54 7.7 % + Force_LCAO_gamma ftable_gamma 0.34475 1 0.34 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.25785 1 0.26 3.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:32 2022 + FINISH Time : Wed Sep 28 11:01:39 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/100/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ae8be87aaf46d8395aa12048c98da54a321f3b25 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.205428 0.451404 0.295753 +H 0.197206 0.416937 0.245542 +H 0.146257 0.448479 0.330989 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..88f6c54fb6f9df13bad6c3f9615b7f2571991159 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3648 2 + 2 -13.1852 2 + 3 -9.01714 2 + 4 -6.74954 2 + 5 1.19392 0 + 6 4.61464 0 + 7 11.0534 0 + 8 11.2635 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..6cffc6e239df279bcdb6571087b7ca412f15fc75 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:38 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.75198405346 12.639311742 8.28107340616 0 0 0 0 + tauc_H1 5.52176401563 11.6742455609 6.87517881404 0 0 0 0 + tauc_H2 4.09520995642 12.5574170961 9.26769101126 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.102620653107 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.104944642654 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123074343468 (SEC) + + DONE : INIT CHARGE Time : 0.166471774363 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448916 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 100 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000581 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0014 + + Density error is 0.217893877385 + + Energy Rydberg eV + E_KohnSham -34.1752822982 -464.978570013 + E_Harris -34.3747565682 -467.69255669 + E_Fermi -0.413427895113 -5.62497508568 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000976949641675 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120591229802 + + Density error is 0.0984798685899 + + Energy Rydberg eV + E_KohnSham -34.268470985 -466.246467143 + E_Harris -34.2752904635 -466.339250909 + E_Fermi -0.219644785939 -2.98842062477 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000947605025596 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111965862219 + + Density error is 0.0631656625738 + + Energy Rydberg eV + E_KohnSham -34.2688271899 -466.25131356 + E_Harris -34.2732077194 -466.310913722 + E_Fermi -0.208454987782 -2.83617561035 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000920408678353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000971874661176 + + Density error is 0.00207656521667 + + Energy Rydberg eV + E_KohnSham -34.2688184624 -466.251194817 + E_Harris -34.2688209135 -466.251228166 + E_Fermi -0.17255986966 -2.34779747351 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000920772079663 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000969987778705 + + Density error is 0.000949662562972 + + Energy Rydberg eV + E_KohnSham -34.268756489 -466.250351624 + E_Harris -34.2687573656 -466.250363552 + E_Fermi -0.171913875375 -2.33900827037 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00092018330208 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968137017582 + + Density error is 0.000175331695772 + + Energy Rydberg eV + E_KohnSham -34.2687880583 -466.250781147 + E_Harris -34.2687881215 -466.250782007 + E_Fermi -0.171801746023 -2.33748267226 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000920564593064 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968222450965 + + Density error is 4.73975906033e-05 + + Energy Rydberg eV + E_KohnSham -34.2687765925 -466.250625147 + E_Harris -34.2687766038 -466.250625301 + E_Fermi -0.171676210335 -2.3357746716 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000920420132736 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968168724923 + + Density error is 1.91056296832e-05 + + Energy Rydberg eV + E_KohnSham -34.2687815546 -466.250692659 + E_Harris -34.268781556 -466.250692679 + E_Fermi -0.171720321572 -2.33637483578 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000920431989387 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968146376445 + + Density error is 3.10113774692e-06 + + Energy Rydberg eV + E_KohnSham -34.2687798991 -466.250670136 + E_Harris -34.2687798992 -466.250670136 + E_Fermi -0.171701469822 -2.33611834455 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000920436729173 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00096814401372 + + Density error is 4.18161823482e-07 + + Energy Rydberg eV + E_KohnSham -34.2687801215 -466.250673161 + E_Harris -34.2687801215 -466.250673161 + E_Fermi -0.1716984638 -2.33607744553 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000920437423234 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968143984935 + + Density error is 1.78810126283e-07 + + Energy Rydberg eV + E_KohnSham -34.2687801708 -466.250673832 + E_Harris -34.2687801708 -466.250673832 + E_Fermi -0.171698355428 -2.33607597104 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000920437749366 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968143795898 + + Density error is 1.2684716161e-08 + + Energy Rydberg eV + E_KohnSham -34.2687801716 -466.250673844 + E_Harris -34.2687801716 -466.250673844 + E_band -7.984401082 -108.633349833 + E_one_elec -69.4323302456 -944.675316757 + E_Hartree +36.1099733107 +491.301391654 + E_xc -8.22211019422 -111.867548225 + E_Ewald +7.39976563663 +100.678976523 + E_demet -9.27253551328e-76 -1.26159317888e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195224931618 -2.65617146167 + E_Fermi -0.171698186936 -2.3360736786 + + charge density convergence is achieved + final etot is -466.250673844 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3648 2.00000 + 2 -13.1852 2.00000 + 3 -9.01714 2.00000 + 4 -6.74954 2.00000 + 5 1.19392 0.00000 + 6 4.61464 0.00000 + 7 11.0534 0.00000 + 8 11.2635 0.00000 + + EFERMI = -2.336073678597727 eV + OUT.ABACUS/ final etot is -466.2506738435357 eV + correction force for each atom along direction 1 is -0.000170297 + correction force for each atom along direction 2 is 7.25948e-05 + correction force for each atom along direction 3 is 2.63105e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0375724 +2.3028057 +4.4161497 + H1 -0.67576194 -2.3100863 -3.2754847 + H2 +1.7133344 +0.0072805619 -1.1406650 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2506738435357 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8109 11 0.71 1.0e+02% + Run_lcao lcao_line 7.8018 1 7.8 1.e+02% + Potential init_pot 0.28309 2 0.14 3.6% + PW_Basis recip2real 0.27282 17 0.016 3.5% + PW_Basis gathers_scatterp 0.12019 17 0.0071 1.5% + Potential v_of_rho 0.90982 14 0.065 12.% + XC_Functional v_xc 0.25011 15 0.017 3.2% + H_Hartree_pw v_hartree 0.61521 14 0.044 7.9% + PW_Basis real2recip 0.70345 41 0.017 9.0% + PW_Basis gatherp_scatters 0.28738 41 0.0070 3.7% + ORB_control set_orb_tables 1.0926 1 1.1 14.% + ORB_gen_tables gen_tables 1.0926 1 1.1 14.% + ORB_table_phi init_Table 0.47293 1 0.47 6.1% + ORB_table_phi cal_ST_Phi12_R 0.46773 126 0.0037 6.0% + ORB_table_beta init_Table_Beta 0.18201 1 0.18 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18048 56 0.0032 2.3% + ORB_table_alpha init_Table_Alpha 0.24626 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24429 66 0.0037 3.1% + LOOP_ions opt_ions 6.1834 1 6.2 79.% + ESolver_KS_LCAO Run 5.5488 1 5.5 71.% + HSolverLCAO solve 3.0496 12 0.25 39.% + HamiltLCAO updateHk 1.5492 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.5197 12 0.13 19.% + Gint_interface cal_gint 1.7122 25 0.068 22.% + Gint_Gamma distri_vl_value 0.44266 12 0.037 5.7% + Gint_Gamma distri_vl 2.8849 6 0.48 37.% + LCAO_Deepks cal_projected_DM 5.8621 14 0.42 75.% + LCAO_gen_fixedH add_v_delta 2.7372 6 0.46 35.% + LCAO_DESCRIPTOR add_v_delta 2.7372 6 0.46 35.% + ElecStateLCAO psiToRho 1.4763 12 0.12 19.% + Charge mix_rho 0.97535 11 0.089 12.% + LOOP_ions force_stress 0.63449 1 0.63 8.1% + Force_Stress_LCAO getForceStress 0.63446 1 0.63 8.1% + Force_LCAO_gamma ftable_gamma 0.43521 1 0.44 5.6% + Force_LCAO_gamma cal_fvl_dphi 0.27473 1 0.27 3.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:38 2022 + Finish Time : Wed Sep 28 11:11:45 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2bbec80ed88807626ce963ebde1f473a508530e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123884 ima = 3.68e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123704873102 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112462374413 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113031999161 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113301595384 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113256229229 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113281603304 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113273048635 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113276472487 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113275750426 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113275620724 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113275609527 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113275600697 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/STRU new file mode 100644 index 0000000000000000000000000000000000000000..83e0ac5a998d5d50df6d31fa2e69c96eaa829921 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.248015946552 12.639311742038 8.281073406168 0 0 0 +H +0.0 +2 +-22.478235984350 11.674245560877 6.875178814059 0 0 0 +-23.904790043599 12.557417096150 9.267691011247 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/conv new file mode 100644 index 0000000000000000000000000000000000000000..ed430902179171ccfa2a38d2c499f51a054bd814 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/conv @@ -0,0 +1 @@ +101 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b2615a6a4d401e2b9ec62520bc7d04656bc29b6b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748144075 0.01251081365 1.262693177 1.385938516 1.469907399 0.008480011996 0.01956182604 0.03906230505 +9.75352252e-19 0.001113333834 0.002582238262 0.01207158702 0.04535403938 -2.729561923e-19 1.7150452e-06 5.480061892e-06 +0.001637583294 0.005660070623 + +H atom_index 1 n_descriptor 18 +1.332475343 0.03161361105 0.1401106502 0.193597015 0.3441259681 0.02558530063 0.03300190989 0.03679328908 +-3.213034031e-18 5.105932905e-05 0.1062570539 0.1333553853 0.1654966081 -1.480927282e-17 4.419248517e-07 0.01504830864 +0.02870060261 0.03369418677 + +H atom_index 2 n_descriptor 18 +1.166981066 0.03667666079 0.08240180518 0.1158604844 0.2920844851 0.01823260446 0.02354929757 0.04041481087 +-5.377246553e-18 3.661769199e-05 0.08004009565 0.09886037309 0.111648555 -4.201053651e-18 7.316074941e-06 0.01506395572 +0.02277651051 0.02657498361 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0e50425f291a4dc5f0c7e8f92213ad377ed53014 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:38 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.102654 SEC) : SETUP UNITCELL + DONE(0.104959 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123097 SEC) : INIT PLANEWAVE + DONE(0.166611 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448985 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.649786e+02 0.000000e+00 2.179e-01 5.568e-01 + GE2 -4.662465e+02 -1.267897e+00 9.848e-02 5.168e-01 + GE3 -4.662513e+02 -4.846417e-03 6.317e-02 5.861e-01 + GE4 -4.662512e+02 1.187437e-04 2.077e-03 4.422e-01 + GE5 -4.662504e+02 8.431923e-04 9.497e-04 4.427e-01 + GE6 -4.662508e+02 -4.295229e-04 1.753e-04 4.409e-01 + GE7 -4.662506e+02 1.560006e-04 4.740e-05 4.326e-01 + GE8 -4.662507e+02 -6.751272e-05 1.911e-05 4.253e-01 + GE9 -4.662507e+02 2.252340e-05 3.101e-06 4.256e-01 + GE10 -4.662507e+02 -3.025051e-06 4.182e-07 4.266e-01 + GE11 -4.662507e+02 -6.715114e-07 1.788e-07 4.260e-01 + GE12 -4.662507e+02 -1.106814e-08 1.268e-08 3.641e-01 +E_delta_band = -7.11462524e-02 Ry = -9.67994424e-01 eV +E_delta_NN= -1.95224932e-01 Ry = -2.65617146e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8109 11 0.71 1e+02 % + Run_lcao lcao_line 7.8018 1 7.8 1e+02 % + Potential init_pot 0.28309 2 0.14 3.6 % + PW_Basis recip2real 0.27282 17 0.016 3.5 % + PW_Basis gathers_scatterp 0.12019 17 0.0071 1.5 % + Potential v_of_rho 0.90982 14 0.065 12 % + XC_Functional v_xc 0.25011 15 0.017 3.2 % + H_Hartree_pw v_hartree 0.61521 14 0.044 7.9 % + PW_Basis real2recip 0.70345 41 0.017 9 % + PW_Basis gatherp_scatters 0.28738 41 0.007 3.7 % + ORB_control set_orb_tables 1.0926 1 1.1 14 % + ORB_gen_tables gen_tables 1.0926 1 1.1 14 % + ORB_table_phi init_Table 0.47293 1 0.47 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.46773 126 0.0037 6 % + ORB_table_beta init_Table_Beta 0.18201 1 0.18 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.18048 56 0.0032 2.3 % + ORB_table_alpha init_Table_Alpha 0.24626 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24429 66 0.0037 3.1 % + LOOP_ions opt_ions 6.1834 1 6.2 79 % + ESolver_KS_LCAO Run 5.5488 1 5.5 71 % + HSolverLCAO solve 3.0496 12 0.25 39 % + HamiltLCAO updateHk 1.5492 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.5197 12 0.13 19 % + Gint_interface cal_gint 1.7122 25 0.068 22 % + Gint_Gamma distri_vl_value 0.44266 12 0.037 5.7 % + Gint_Gamma distri_vl 2.8849 6 0.48 37 % + LCAO_Deepks cal_projected_DM 5.8621 14 0.42 75 % + LCAO_gen_fixedH add_v_delta 2.7372 6 0.46 35 % + LCAO_DESCRIPTOR add_v_delta 2.7372 6 0.46 35 % + ElecStateLCAO psiToRho 1.4763 12 0.12 19 % + Charge mix_rho 0.97535 11 0.089 12 % + LOOP_ions force_stress 0.63449 1 0.63 8.1 % + Force_Stress_LCAO getForceStress 0.63446 1 0.63 8.1 % + Force_LCAO_gamma ftable_gamma 0.43521 1 0.44 5.6 % + Force_LCAO_gamma cal_fvl_dphi 0.27473 1 0.27 3.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:38 2022 + FINISH Time : Wed Sep 28 11:11:45 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/101/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9c8a0ff4a514b37d3787c2d78d9e9f95dd45d339 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.217357 0.449282 0.287409 +H 0.236996 0.381888 0.284666 +H 0.192908 0.446121 0.344257 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b76935b9df402431ae4500ccf852d060583af135 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.445 2 + 2 -12.5255 2 + 3 -9.54279 2 + 4 -6.77046 2 + 5 0.955955 0 + 6 4.38995 0 + 7 11.0691 0 + 8 11.31 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..34e0a284599affc7038857291b3861a3d450cc1c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:01 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.08598772058 12.5798958077 8.04745254544 0 0 0 0 + tauc_H1 6.63589099304 10.6928711491 7.9706428566 0 0 0 0 + tauc_H2 5.40142913827 12.4913977798 9.63919509354 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0725439817443 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.072821974902 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0889818665535 (SEC) + + DONE : INIT CHARGE Time : 0.130077984227 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.376214 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000688 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124 + + Density error is 0.213293876535 + + Energy Rydberg eV + E_KohnSham -34.1743672839 -464.966120605 + E_Harris -34.3652852479 -467.563692766 + E_Fermi -0.406532498202 -5.53115839773 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100746544024 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00146762637683 + + Density error is 0.0979698136223 + + Energy Rydberg eV + E_KohnSham -34.2640915498 -466.186881871 + E_Harris -34.2711705175 -466.283196168 + E_Fermi -0.218578655509 -2.9739151761 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000960660915587 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138519355992 + + Density error is 0.0628894503525 + + Energy Rydberg eV + E_KohnSham -34.264391149 -466.190958127 + E_Harris -34.268943884 -466.252901264 + E_Fermi -0.208701760971 -2.83953313185 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000906875709846 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126875243565 + + Density error is 0.00195521665991 + + Energy Rydberg eV + E_KohnSham -34.2643371394 -466.190223289 + E_Harris -34.2643383511 -466.190239775 + E_Fermi -0.17228844001 -2.34410448367 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000911769708634 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127455171299 + + Density error is 0.000816032861159 + + Energy Rydberg eV + E_KohnSham -34.2643012806 -466.189735405 + E_Harris -34.2643018832 -466.189743604 + E_Fermi -0.172149747288 -2.34221747238 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000910744511076 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127247375036 + + Density error is 0.000146712890069 + + Energy Rydberg eV + E_KohnSham -34.2643188235 -466.189974088 + E_Harris -34.264318835 -466.189974245 + E_Fermi -0.171805685833 -2.33753627613 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000910751187052 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127240827735 + + Density error is 3.09568177468e-05 + + Energy Rydberg eV + E_KohnSham -34.2643137962 -466.189905689 + E_Harris -34.2643137975 -466.189905705 + E_Fermi -0.171773188299 -2.33709412449 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000910691202931 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127230152289 + + Density error is 1.3477494074e-05 + + Energy Rydberg eV + E_KohnSham -34.2643159457 -466.189934934 + E_Harris -34.2643159466 -466.189934946 + E_Fermi -0.171781208937 -2.33720325087 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000910701118064 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127230825771 + + Density error is 2.08582637137e-06 + + Energy Rydberg eV + E_KohnSham -34.2643149138 -466.189920893 + E_Harris -34.2643149138 -466.189920894 + E_Fermi -0.171769842066 -2.33704859665 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000910703967903 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127231052599 + + Density error is 8.13805427109e-07 + + Energy Rydberg eV + E_KohnSham -34.2643151616 -466.189924265 + E_Harris -34.2643151616 -466.189924265 + E_Fermi -0.17176917871 -2.33703957124 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000910704788356 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127231107856 + + Density error is 1.72436691959e-07 + + Energy Rydberg eV + E_KohnSham -34.2643151669 -466.189924338 + E_Harris -34.2643151669 -466.189924338 + E_Fermi -0.171768561551 -2.33703117436 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000910704903585 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127231106501 + + Density error is 1.2381447641e-08 + + Energy Rydberg eV + E_KohnSham -34.2643151787 -466.189924498 + E_Harris -34.2643151787 -466.189924498 + E_band -7.97956206068 -108.56751157 + E_one_elec -69.1817679675 -941.266242072 + E_Hartree +35.9726017715 +489.432355977 + E_xc -8.20013130242 -111.568510061 + E_Ewald +7.26948972044 +98.9064817504 + E_demet -2.82991237487e-66 -3.85029331389e-65 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194914578427 -2.65194888988 + E_Fermi -0.171768378431 -2.33702868288 + + charge density convergence is achieved + final etot is -466.189924498 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4450 2.00000 + 2 -12.5255 2.00000 + 3 -9.54279 2.00000 + 4 -6.77046 2.00000 + 5 0.955955 0.00000 + 6 4.38995 0.00000 + 7 11.0691 0.00000 + 8 11.3100 0.00000 + + EFERMI = -2.337028682882153 eV + OUT.ABACUS/ final etot is -466.1899244975909 eV + correction force for each atom along direction 1 is 0.000108248 + correction force for each atom along direction 2 is -0.000114528 + correction force for each atom along direction 3 is 0.000140025 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +2.0946796 -2.8683584 -2.9279750 + H1 -0.42923730 +2.3614034 -0.49330805 + H2 -1.6654423 +0.50695505 +3.4212831 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.1899244975909 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6238 11 0.69 1.0e+02% + Run_lcao lcao_line 7.6166 1 7.6 1.e+02% + Potential init_pot 0.24619 2 0.12 3.2% + PW_Basis recip2real 0.24623 17 0.014 3.2% + PW_Basis gathers_scatterp 0.11855 17 0.0070 1.6% + Potential v_of_rho 0.96052 14 0.069 13.% + XC_Functional v_xc 0.30674 15 0.020 4.0% + H_Hartree_pw v_hartree 0.61804 14 0.044 8.1% + PW_Basis real2recip 0.66200 41 0.016 8.7% + PW_Basis gatherp_scatters 0.30134 41 0.0073 4.0% + ORB_control set_orb_tables 0.90451 1 0.90 12.% + ORB_gen_tables gen_tables 0.90451 1 0.90 12.% + ORB_table_phi init_Table 0.37846 1 0.38 5.0% + ORB_table_phi cal_ST_Phi12_R 0.37430 126 0.0030 4.9% + ORB_table_beta init_Table_Beta 0.15704 1 0.16 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15569 56 0.0028 2.0% + ORB_table_alpha init_Table_Alpha 0.21078 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20914 66 0.0032 2.7% + LOOP_ions opt_ions 6.2658 1 6.3 82.% + ESolver_KS_LCAO Run 5.7096 1 5.7 75.% + HSolverLCAO solve 3.3273 12 0.28 44.% + HamiltLCAO updateHk 1.6608 12 0.14 22.% + LCAO_Hamilt cal_Hgamma 1.6357 12 0.14 21.% + Gint_interface cal_gint 1.6414 25 0.066 22.% + Gint_Gamma distri_vl_value 0.62477 12 0.052 8.2% + Gint_Gamma distri_vl 2.9536 6 0.49 39.% + LCAO_Deepks cal_projected_DM 6.0006 14 0.43 79.% + LCAO_gen_fixedH add_v_delta 2.8243 6 0.47 37.% + LCAO_DESCRIPTOR add_v_delta 2.8243 6 0.47 37.% + ElecStateLCAO psiToRho 1.6491 12 0.14 22.% + Charge mix_rho 0.82324 11 0.075 11.% + LOOP_ions force_stress 0.55602 1 0.56 7.3% + Force_Stress_LCAO getForceStress 0.55600 1 0.56 7.3% + Force_LCAO_gamma ftable_gamma 0.35969 1 0.36 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.25490 1 0.25 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:01 2022 + Finish Time : Wed Sep 28 11:13:09 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4fbc7c153632bcfcb47d28dc52ab1e4e292be3da --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124136 ima = 3.69141e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122739750061 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111433228399 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112131926326 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112389290882 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011236299255 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112376735686 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112373713149 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112375577945 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112374873677 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112374823595 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112374785113 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112374775544 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/STRU new file mode 100644 index 0000000000000000000000000000000000000000..90dbb380fd6d0bfeb61db6eec43592076502e480 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.914012279439 12.579895807732 8.047452545427 0 0 0 +H +0.0 +2 +-21.364109006971 10.692871149085 7.970642856609 0 0 0 +-22.598570861752 12.491397779787 9.639195093515 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/conv new file mode 100644 index 0000000000000000000000000000000000000000..30b02cc5b36845eef3d2677e515508afc5b5cc53 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/conv @@ -0,0 +1 @@ +102 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ea46194c85bff8323191f48391156186ee9d8806 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.756862163 0.01257799941 1.240508053 1.366928013 1.470126695 0.01009837821 0.01630913443 0.0393397436 +-7.824568567e-19 0.0008041035415 0.002925163985 0.01312426723 0.04696890367 -3.319078751e-19 2.658808177e-06 7.569416064e-06 +0.001527364413 0.005934828494 + +H atom_index 1 n_descriptor 18 +1.146831472 0.03804348722 0.08005383499 0.1074923295 0.2797482106 0.0183893447 0.02217485751 0.04214030278 +-1.409102524e-17 3.888964979e-05 0.07698799918 0.09115952758 0.1094162211 -6.130851736e-18 6.669169442e-06 0.01633199606 +0.02265530539 0.02523207695 + +H atom_index 2 n_descriptor 18 +1.327275951 0.03292543161 0.143500646 0.1900255556 0.3419740543 0.02738999344 0.03265287142 0.03749813664 +2.526047659e-17 5.426398304e-05 0.1065815265 0.1334572829 0.1622152787 -2.884286024e-18 1.387670746e-09 0.01499064595 +0.02937115281 0.03361008249 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f7de25fe8a6da42584cd2dea68fda758d97b51b7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:01 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0725585 SEC) : SETUP UNITCELL + DONE(0.0728306 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0889939 SEC) : INIT PLANEWAVE + DONE(0.130204 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.376258 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.649661e+02 0.000000e+00 2.133e-01 5.535e-01 + GE2 -4.661869e+02 -1.220761e+00 9.797e-02 5.280e-01 + GE3 -4.661910e+02 -4.076256e-03 6.289e-02 5.881e-01 + GE4 -4.661902e+02 7.348378e-04 1.955e-03 4.644e-01 + GE5 -4.661897e+02 4.878842e-04 8.160e-04 4.644e-01 + GE6 -4.661900e+02 -2.386832e-04 1.467e-04 4.646e-01 + GE7 -4.661899e+02 6.839937e-05 3.096e-05 4.428e-01 + GE8 -4.661899e+02 -2.924545e-05 1.348e-05 4.443e-01 + GE9 -4.661899e+02 1.404062e-05 2.086e-06 4.415e-01 + GE10 -4.661899e+02 -3.371757e-06 8.138e-07 4.465e-01 + GE11 -4.661899e+02 -7.287202e-08 1.724e-07 4.417e-01 + GE12 -4.661899e+02 -1.594790e-07 1.238e-08 3.764e-01 +E_delta_band = -7.04071778e-02 Ry = -9.57938798e-01 eV +E_delta_NN= -1.94914578e-01 Ry = -2.65194889e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6238 11 0.69 1e+02 % + Run_lcao lcao_line 7.6166 1 7.6 1e+02 % + Potential init_pot 0.24619 2 0.12 3.2 % + PW_Basis recip2real 0.24623 17 0.014 3.2 % + PW_Basis gathers_scatterp 0.11855 17 0.007 1.6 % + Potential v_of_rho 0.96052 14 0.069 13 % + XC_Functional v_xc 0.30674 15 0.02 4 % + H_Hartree_pw v_hartree 0.61804 14 0.044 8.1 % + PW_Basis real2recip 0.662 41 0.016 8.7 % + PW_Basis gatherp_scatters 0.30134 41 0.0073 4 % + ORB_control set_orb_tables 0.90451 1 0.9 12 % + ORB_gen_tables gen_tables 0.90451 1 0.9 12 % + ORB_table_phi init_Table 0.37846 1 0.38 5 % + ORB_table_phi cal_ST_Phi12_R 0.3743 126 0.003 4.9 % + ORB_table_beta init_Table_Beta 0.15704 1 0.16 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15569 56 0.0028 2 % + ORB_table_alpha init_Table_Alpha 0.21078 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20914 66 0.0032 2.7 % + LOOP_ions opt_ions 6.2658 1 6.3 82 % + ESolver_KS_LCAO Run 5.7096 1 5.7 75 % + HSolverLCAO solve 3.3273 12 0.28 44 % + HamiltLCAO updateHk 1.6608 12 0.14 22 % + LCAO_Hamilt cal_Hgamma 1.6357 12 0.14 21 % + Gint_interface cal_gint 1.6414 25 0.066 22 % + Gint_Gamma distri_vl_value 0.62477 12 0.052 8.2 % + Gint_Gamma distri_vl 2.9536 6 0.49 39 % + LCAO_Deepks cal_projected_DM 6.0006 14 0.43 79 % + LCAO_gen_fixedH add_v_delta 2.8243 6 0.47 37 % + LCAO_DESCRIPTOR add_v_delta 2.8243 6 0.47 37 % + ElecStateLCAO psiToRho 1.6491 12 0.14 22 % + Charge mix_rho 0.82324 11 0.075 11 % + LOOP_ions force_stress 0.55602 1 0.56 7.3 % + Force_Stress_LCAO getForceStress 0.556 1 0.56 7.3 % + Force_LCAO_gamma ftable_gamma 0.35969 1 0.36 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.2549 1 0.25 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:01 2022 + FINISH Time : Wed Sep 28 11:13:09 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/102/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..92e2af7f10d80f6bd089271eed7fb78008a066ac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.232769 0.429585 0.288929 +H 0.265912 0.376964 0.285402 +H 0.201831 0.431361 0.348979 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..fb57da17866442bd276b9e4da4da676fc7012bf6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3305 2 + 2 -13.3301 2 + 3 -8.9125 2 + 4 -6.74639 2 + 5 1.31545 0 + 6 4.63492 0 + 7 11.0533 0 + 8 11.2679 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f38a0cd31433a99d30f52b49377157bb4fceb4bc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:40 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.51753868627 12.0283914663 8.08999809698 0 0 0 0 + tauc_H1 7.44552461454 10.5549993187 7.99126139228 0 0 0 0 + tauc_H2 5.65126238443 12.0780984491 9.77141848626 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0735501370135 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0738938727992 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0894675062225 (SEC) + + DONE : INIT CHARGE Time : 0.131737289916 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375208 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000495 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098 + + Density error is 0.217497000313 + + Energy Rydberg eV + E_KohnSham -34.1824194502 -465.075675949 + E_Harris -34.3799324914 -467.762978738 + E_Fermi -0.412209529194 -5.60839836693 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000812142022353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116576677786 + + Density error is 0.0980946307096 + + Energy Rydberg eV + E_KohnSham -34.2737138291 -466.317799697 + E_Harris -34.2803778317 -466.408468104 + E_Fermi -0.219631586106 -2.98824103181 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000789784535151 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111442262151 + + Density error is 0.0627757098858 + + Energy Rydberg eV + E_KohnSham -34.2739659019 -466.321229324 + E_Harris -34.278237804 -466.379351533 + E_Fermi -0.207078993956 -2.81745425391 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000766971185754 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103743219375 + + Density error is 0.00210145297825 + + Energy Rydberg eV + E_KohnSham -34.2739797616 -466.321417894 + E_Harris -34.2739826858 -466.32145768 + E_Fermi -0.171542073712 -2.33394964922 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000767125333511 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103652927898 + + Density error is 0.000879061730577 + + Energy Rydberg eV + E_KohnSham -34.2739193383 -466.320595793 + E_Harris -34.2739202678 -466.320608439 + E_Fermi -0.170646647842 -2.32176675525 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000766580771306 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103542014594 + + Density error is 0.00019195306676 + + Energy Rydberg eV + E_KohnSham -34.2739554659 -466.321087335 + E_Harris -34.2739555599 -466.321088614 + E_Fermi -0.170688655817 -2.32233830307 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00076689902132 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103565304909 + + Density error is 4.83525029143e-05 + + Energy Rydberg eV + E_KohnSham -34.2739414389 -466.320896488 + E_Harris -34.2739414518 -466.320896662 + E_Fermi -0.170520146949 -2.32004562231 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000766796037156 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010355497766 + + Density error is 1.75352647469e-05 + + Energy Rydberg eV + E_KohnSham -34.2739470206 -466.32097243 + E_Harris -34.2739470217 -466.320972445 + E_Fermi -0.170570837991 -2.32073530931 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000766799145886 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103553889041 + + Density error is 2.72653928001e-06 + + Energy Rydberg eV + E_KohnSham -34.2739454182 -466.320950628 + E_Harris -34.2739454182 -466.320950628 + E_Fermi -0.170552941449 -2.32049181437 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000766802992638 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103554111073 + + Density error is 4.45086546924e-07 + + Energy Rydberg eV + E_KohnSham -34.2739456008 -466.320953113 + E_Harris -34.2739456008 -466.320953113 + E_Fermi -0.170550432461 -2.32045767784 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000766803659809 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103554175475 + + Density error is 1.84116545917e-07 + + Energy Rydberg eV + E_KohnSham -34.2739456434 -466.320953693 + E_Harris -34.2739456434 -466.320953693 + E_Fermi -0.170550300226 -2.32045587869 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00076680395153 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103554193438 + + Density error is 1.19935648482e-08 + + Energy Rydberg eV + E_KohnSham -34.2739456441 -466.320953703 + E_Harris -34.2739456441 -466.320953703 + E_band -7.98480748427 -108.638879219 + E_one_elec -69.4886328402 -945.441352856 + E_Hartree +36.1406987891 +491.719433234 + E_xc -8.22632595572 -111.924906603 + E_Ewald +7.4242949876 +101.012715464 + E_demet -3.2796628544e-80 -4.46221023388e-79 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195176016192 -2.65550593315 + E_Fermi -0.170550120914 -2.32045343901 + + charge density convergence is achieved + final etot is -466.320953703 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3305 2.00000 + 2 -13.3301 2.00000 + 3 -8.91250 2.00000 + 4 -6.74639 2.00000 + 5 1.31545 0.00000 + 6 4.63492 0.00000 + 7 11.0533 0.00000 + 8 11.2679 0.00000 + + EFERMI = -2.320453439013079 eV + OUT.ABACUS/ final etot is -466.3209537025852 eV + correction force for each atom along direction 1 is 0.000116846 + correction force for each atom along direction 2 is -3.63112e-05 + correction force for each atom along direction 3 is 6.48868e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -2.2547088 +2.9428739 +1.0163351 + H1 +1.5385441 -2.6666598 +0.098339408 + H2 +0.71616470 -0.27621407 -1.1146745 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3209537025852 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5578 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5508 1 7.6 1.e+02% + Potential init_pot 0.24253 2 0.12 3.2% + PW_Basis recip2real 0.23978 17 0.014 3.2% + PW_Basis gathers_scatterp 0.11319 17 0.0067 1.5% + Potential v_of_rho 0.94409 14 0.067 12.% + XC_Functional v_xc 0.29994 15 0.020 4.0% + H_Hartree_pw v_hartree 0.60862 14 0.043 8.1% + PW_Basis real2recip 0.64215 41 0.016 8.5% + PW_Basis gatherp_scatters 0.27497 41 0.0067 3.6% + ORB_control set_orb_tables 0.90243 1 0.90 12.% + ORB_gen_tables gen_tables 0.90243 1 0.90 12.% + ORB_table_phi init_Table 0.37847 1 0.38 5.0% + ORB_table_phi cal_ST_Phi12_R 0.37426 126 0.0030 5.0% + ORB_table_beta init_Table_Beta 0.15609 1 0.16 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15477 56 0.0028 2.0% + ORB_table_alpha init_Table_Alpha 0.21010 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20850 66 0.0032 2.8% + LOOP_ions opt_ions 6.2029 1 6.2 82.% + ESolver_KS_LCAO Run 5.6536 1 5.7 75.% + HSolverLCAO solve 3.3262 12 0.28 44.% + HamiltLCAO updateHk 1.6545 12 0.14 22.% + LCAO_Hamilt cal_Hgamma 1.6292 12 0.14 22.% + Gint_interface cal_gint 1.6191 25 0.065 21.% + Gint_Gamma distri_vl_value 0.62632 12 0.052 8.3% + Gint_Gamma distri_vl 2.9345 6 0.49 39.% + LCAO_Deepks cal_projected_DM 5.9451 14 0.42 79.% + LCAO_gen_fixedH add_v_delta 2.8069 6 0.47 37.% + LCAO_DESCRIPTOR add_v_delta 2.8070 6 0.47 37.% + ElecStateLCAO psiToRho 1.6536 12 0.14 22.% + Charge mix_rho 0.81631 11 0.074 11.% + LOOP_ions force_stress 0.54918 1 0.55 7.3% + Force_Stress_LCAO getForceStress 0.54915 1 0.55 7.3% + Force_LCAO_gamma ftable_gamma 0.35179 1 0.35 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.25314 1 0.25 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:40 2022 + Finish Time : Wed Sep 28 11:06:47 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2d2c534c024d6078528cb36a8bb04b7b5b2c303e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123564 ima = 3.6834e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123591089851 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112711287443 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113183156105 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113436221741 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011338724302 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113416292034 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113406296042 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113409701133 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113409104962 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113408992014 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113408980777 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113408971623 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/STRU new file mode 100644 index 0000000000000000000000000000000000000000..6a629c9111df6ceb11efac50c068dd7a23815aca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.482461313737 12.028391466318 8.089998096965 0 0 0 +H +0.0 +2 +-20.554475385457 10.554999318639 7.991261392281 0 0 0 +-22.348737615588 12.078098449077 9.771418486277 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/conv new file mode 100644 index 0000000000000000000000000000000000000000..714a174e578cb7f726b54ee7d1671f95fc1c01aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/conv @@ -0,0 +1 @@ +103 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d454a167bb22c185afd107f49a67600b53358fae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74578451 0.01258917816 1.275294797 1.383129518 1.469692213 0.008076439044 0.02015353247 0.03895756227 +1.980820518e-18 0.001166146762 0.002492270194 0.01231682764 0.04445785618 -2.347645078e-19 1.631570441e-06 5.191332506e-06 +0.001717204907 0.005640001561 + +H atom_index 1 n_descriptor 18 +1.312403613 0.03179685689 0.1318640298 0.182591313 0.3397933543 0.02457923338 0.03196276337 0.03621369113 +-3.223957262e-17 4.704777006e-05 0.1074544056 0.1270731926 0.1564667771 -2.359714944e-18 1.208720476e-06 0.01397535614 +0.02821504224 0.03317828814 + +H atom_index 2 n_descriptor 18 +1.194623612 0.03567357466 0.09060728668 0.1270240203 0.303639402 0.0194454918 0.02522445077 0.03904240263 +1.208205514e-17 3.703445014e-05 0.0875641435 0.1087798014 0.1131058111 4.395465308e-18 6.501457203e-06 0.01401984522 +0.02400503287 0.02814649876 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0d1f5e7a10cfb1c4baa895fede2b15c9d43c5ed7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:40 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0735646 SEC) : SETUP UNITCELL + DONE(0.0739042 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0894801 SEC) : INIT PLANEWAVE + DONE(0.131858 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.375256 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650757e+02 0.000000e+00 2.175e-01 5.402e-01 + GE2 -4.663178e+02 -1.242124e+00 9.809e-02 5.201e-01 + GE3 -4.663212e+02 -3.429627e-03 6.278e-02 5.846e-01 + GE4 -4.663214e+02 -1.885702e-04 2.101e-03 4.574e-01 + GE5 -4.663206e+02 8.221009e-04 8.791e-04 4.567e-01 + GE6 -4.663211e+02 -4.915416e-04 1.920e-04 4.545e-01 + GE7 -4.663209e+02 1.908473e-04 4.835e-05 4.485e-01 + GE8 -4.663210e+02 -7.594255e-05 1.754e-05 4.399e-01 + GE9 -4.663210e+02 2.180233e-05 2.727e-06 4.437e-01 + GE10 -4.663210e+02 -2.484553e-06 4.451e-07 4.405e-01 + GE11 -4.663210e+02 -5.800070e-07 1.841e-07 4.415e-01 + GE12 -4.663210e+02 -1.002039e-08 1.199e-08 3.728e-01 +E_delta_band = -7.11953912e-02 Ry = -9.68662992e-01 eV +E_delta_NN= -1.95176016e-01 Ry = -2.65550593e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5578 11 0.69 1e+02 % + Run_lcao lcao_line 7.5508 1 7.6 1e+02 % + Potential init_pot 0.24253 2 0.12 3.2 % + PW_Basis recip2real 0.23978 17 0.014 3.2 % + PW_Basis gathers_scatterp 0.11319 17 0.0067 1.5 % + Potential v_of_rho 0.94409 14 0.067 12 % + XC_Functional v_xc 0.29994 15 0.02 4 % + H_Hartree_pw v_hartree 0.60862 14 0.043 8.1 % + PW_Basis real2recip 0.64215 41 0.016 8.5 % + PW_Basis gatherp_scatters 0.27497 41 0.0067 3.6 % + ORB_control set_orb_tables 0.90243 1 0.9 12 % + ORB_gen_tables gen_tables 0.90243 1 0.9 12 % + ORB_table_phi init_Table 0.37847 1 0.38 5 % + ORB_table_phi cal_ST_Phi12_R 0.37426 126 0.003 5 % + ORB_table_beta init_Table_Beta 0.15609 1 0.16 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15477 56 0.0028 2 % + ORB_table_alpha init_Table_Alpha 0.2101 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.2085 66 0.0032 2.8 % + LOOP_ions opt_ions 6.2029 1 6.2 82 % + ESolver_KS_LCAO Run 5.6536 1 5.7 75 % + HSolverLCAO solve 3.3262 12 0.28 44 % + HamiltLCAO updateHk 1.6545 12 0.14 22 % + LCAO_Hamilt cal_Hgamma 1.6292 12 0.14 22 % + Gint_interface cal_gint 1.6191 25 0.065 21 % + Gint_Gamma distri_vl_value 0.62632 12 0.052 8.3 % + Gint_Gamma distri_vl 2.9345 6 0.49 39 % + LCAO_Deepks cal_projected_DM 5.9451 14 0.42 79 % + LCAO_gen_fixedH add_v_delta 2.8069 6 0.47 37 % + LCAO_DESCRIPTOR add_v_delta 2.807 6 0.47 37 % + ElecStateLCAO psiToRho 1.6536 12 0.14 22 % + Charge mix_rho 0.81631 11 0.074 11 % + LOOP_ions force_stress 0.54918 1 0.55 7.3 % + Force_Stress_LCAO getForceStress 0.54915 1 0.55 7.3 % + Force_LCAO_gamma ftable_gamma 0.35179 1 0.35 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.25314 1 0.25 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:40 2022 + FINISH Time : Wed Sep 28 11:06:47 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/103/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c959eb2d9f353b84ce932a36861be63c0928db22 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.246375 0.425869 0.288102 +H 0.293382 0.381422 0.28792 +H 0.194902 0.393375 0.309367 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..11bac1fd479ecf0e50df8907ddd10f8d0256ff10 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4566 2 + 2 -13.1499 2 + 3 -9.16992 2 + 4 -6.78229 2 + 5 1.43077 0 + 6 4.64095 0 + 7 11.0363 0 + 8 11.2901 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..8751d2377f5d4e5f3b7a31a772cc460d847f8605 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:08 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.89850795071 11.9243238684 8.06684745907 0 0 0 0 + tauc_H1 8.21468860553 10.6798297668 8.06176598134 0 0 0 0 + tauc_H2 5.4572499007 11.0145077997 8.66226980283 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.073487349498 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0845593632364 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.10095791542 (SEC) + + DONE : INIT CHARGE Time : 0.142729193962 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.390508 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000821 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00149 + + Density error is 0.216541247409 + + Energy Rydberg eV + E_KohnSham -34.1893932393 -465.170559217 + E_Harris -34.3846022631 -467.826514242 + E_Fermi -0.414704143183 -5.64233933149 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00097561878682 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132515676211 + + Density error is 0.0976211849518 + + Energy Rydberg eV + E_KohnSham -34.2798865272 -466.401783564 + E_Harris -34.2865490559 -466.492431916 + E_Fermi -0.222697117791 -3.02994973013 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000924257872422 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122349814139 + + Density error is 0.0624471982557 + + Energy Rydberg eV + E_KohnSham -34.2801718968 -466.405666216 + E_Harris -34.2844640999 -466.464064634 + E_Fermi -0.209672075976 -2.85273494476 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000852911259487 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104705285356 + + Density error is 0.00201175770268 + + Energy Rydberg eV + E_KohnSham -34.2801948491 -466.405978498 + E_Harris -34.2801962331 -466.405997329 + E_Fermi -0.17394488154 -2.36664152688 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000854855367013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104500742219 + + Density error is 0.00092210295473 + + Energy Rydberg eV + E_KohnSham -34.2801214653 -466.40498006 + E_Harris -34.2801238849 -466.40501298 + E_Fermi -0.172904849978 -2.35249117154 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000853637104746 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104330842422 + + Density error is 0.0001230177289 + + Energy Rydberg eV + E_KohnSham -34.280171868 -466.405665824 + E_Harris -34.280171896 -466.405666204 + E_Fermi -0.173113570736 -2.35533096314 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00085368498745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104308445204 + + Density error is 4.41765650382e-05 + + Energy Rydberg eV + E_KohnSham -34.2801544211 -466.405428447 + E_Harris -34.280154432 -466.405428594 + E_Fermi -0.172972076321 -2.35340583286 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000853651597003 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104308905876 + + Density error is 1.39101234622e-05 + + Energy Rydberg eV + E_KohnSham -34.2801579892 -466.405476993 + E_Harris -34.28015799 -466.405477004 + E_Fermi -0.173023825891 -2.35410992188 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000853653653122 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104306607971 + + Density error is 1.94239794107e-06 + + Energy Rydberg eV + E_KohnSham -34.2801565636 -466.405457598 + E_Harris -34.2801565637 -466.405457598 + E_Fermi -0.173009543783 -2.35391560383 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000853652541782 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104306328973 + + Density error is 1.46760760849e-07 + + Energy Rydberg eV + E_KohnSham -34.2801567459 -466.405460078 + E_Harris -34.2801567459 -466.405460078 + E_Fermi -0.173007506676 -2.35388788757 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000853652908641 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104306376952 + + Density error is 4.5984146468e-08 + + Energy Rydberg eV + E_KohnSham -34.2801567811 -466.405460556 + E_Harris -34.2801567811 -466.405460556 + E_band -8.01998716285 -109.117523302 + E_one_elec -69.6108468262 -947.104159442 + E_Hartree +36.1890775579 +492.377660151 + E_xc -8.23371350107 -112.025419314 + E_Ewald +7.49898518455 +102.028927727 + E_demet -1.11099543316e-86 -1.5115868343e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19540492669 -2.65862042026 + E_Fermi -0.173007514107 -2.35388798867 + + charge density convergence is achieved + final etot is -466.405460556 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4566 2.00000 + 2 -13.1499 2.00000 + 3 -9.16992 2.00000 + 4 -6.78229 2.00000 + 5 1.43077 0.00000 + 6 4.64095 0.00000 + 7 11.0363 0.00000 + 8 11.2901 0.00000 + + EFERMI = -2.353887988668229 eV + OUT.ABACUS/ final etot is -466.4054605562311 eV + correction force for each atom along direction 1 is 2.15171e-06 + correction force for each atom along direction 2 is -0.000146366 + correction force for each atom along direction 3 is 0.000113283 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.19942208 +0.99844231 -0.30491240 + H1 +0.72103804 -0.54384955 -0.040582950 + H2 -0.92046012 -0.45459276 +0.34549535 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4054605562311 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0536 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0459 1 7.0 1.e+02% + Potential init_pot 0.24578 2 0.12 3.5% + PW_Basis recip2real 0.22770 16 0.014 3.2% + PW_Basis gathers_scatterp 0.10774 16 0.0067 1.5% + Potential v_of_rho 0.86501 13 0.067 12.% + XC_Functional v_xc 0.27040 14 0.019 3.8% + H_Hartree_pw v_hartree 0.56114 13 0.043 8.0% + PW_Basis real2recip 0.59562 38 0.016 8.4% + PW_Basis gatherp_scatters 0.24587 38 0.0065 3.5% + ORB_control set_orb_tables 0.90313 1 0.90 13.% + ORB_gen_tables gen_tables 0.90313 1 0.90 13.% + ORB_table_phi init_Table 0.37530 1 0.38 5.3% + ORB_table_phi cal_ST_Phi12_R 0.37109 126 0.0029 5.3% + ORB_table_beta init_Table_Beta 0.15766 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15632 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.21123 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20954 66 0.0032 3.0% + LOOP_ions opt_ions 5.6823 1 5.7 81.% + ESolver_KS_LCAO Run 5.1379 1 5.1 73.% + HSolverLCAO solve 2.9942 11 0.27 42.% + HamiltLCAO updateHk 1.5077 11 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.4844 11 0.13 21.% + Gint_interface cal_gint 1.6306 23 0.071 23.% + Gint_Gamma distri_vl_value 0.49317 11 0.045 7.0% + Gint_Gamma distri_vl 2.4532 6 0.41 35.% + LCAO_Deepks cal_projected_DM 5.4406 13 0.42 77.% + LCAO_gen_fixedH add_v_delta 2.3253 6 0.39 33.% + LCAO_DESCRIPTOR add_v_delta 2.3253 6 0.39 33.% + ElecStateLCAO psiToRho 1.4699 11 0.13 21.% + Charge mix_rho 0.75638 10 0.076 11.% + LOOP_ions force_stress 0.54420 1 0.54 7.7% + Force_Stress_LCAO getForceStress 0.54418 1 0.54 7.7% + Force_LCAO_gamma ftable_gamma 0.34939 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.26510 1 0.27 3.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:08 2022 + Finish Time : Wed Sep 28 11:08:15 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..13cbeb2bda128b8fd6146e6a67bd970bcb1743bb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124079 ima = 3.68344e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122897074061 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011193783545 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240771202 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112680219706 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112610974117 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112651374205 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112645514494 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112648553869 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112647995157 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112647906753 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112647900344 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/STRU new file mode 100644 index 0000000000000000000000000000000000000000..db87956cb4b3824ea7803b40baf986d1431c4def --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.101492049302 11.924323868425 8.066847459055 0 0 0 +H +0.0 +2 +-19.785311394452 10.679829766808 8.061765981349 0 0 0 +-22.542750099273 11.014507799697 8.662269802834 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/conv new file mode 100644 index 0000000000000000000000000000000000000000..2ec9395fd5f5df651b0845d6d92b99782af46393 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/conv @@ -0,0 +1 @@ +104 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..eb5ce0910753d870c34c6cef1c51b443d8bb38bd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749659553 0.01279538538 1.286180389 1.371270412 1.470097827 0.008695096914 0.01867724063 0.03903632818 +-2.496681839e-18 0.001113795246 0.002719104862 0.01293838217 0.04693062238 -2.018122171e-19 2.313179395e-06 6.454913727e-06 +0.001647721238 0.005994763968 + +H atom_index 1 n_descriptor 18 +1.263234364 0.03383129728 0.1135720049 0.156083983 0.3247830952 0.02307698163 0.02905943707 0.037024279 +1.982634503e-17 5.023169218e-05 0.1058418837 0.1159799173 0.1341162219 8.786078788e-18 3.350527165e-06 0.01317089326 +0.02717736651 0.03135953052 + +H atom_index 2 n_descriptor 18 +1.267955916 0.03367211956 0.1152945181 0.1583752537 0.3262264834 0.02329709037 0.02933246537 0.03691009966 +4.949058479e-17 5.068755983e-05 0.1065966558 0.1165828588 0.1360783499 -2.838880831e-18 3.078286006e-06 0.0131830219 +0.02734198882 0.03155826082 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4fc8aeb784e8ec31c2b874099c978d3609d933b5 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..938096990da31ee8bfe8122daa87a7f1248a9f8e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..43577d2b270cd3f369a2ce1a79947d427adf7096 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..a36c752b067c893b1d124a51c89452dfad134517 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..b3fab60fa86632597852af9c164607ae7ad12d1b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:08 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0735031 SEC) : SETUP UNITCELL + DONE(0.0845714 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.100972 SEC) : INIT PLANEWAVE + DONE(0.142833 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.390553 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651706e+02 0.000000e+00 2.165e-01 5.332e-01 + GE2 -4.664018e+02 -1.231224e+00 9.762e-02 5.156e-01 + GE3 -4.664057e+02 -3.882652e-03 6.245e-02 5.756e-01 + GE4 -4.664060e+02 -3.122825e-04 2.012e-03 4.536e-01 + GE5 -4.664050e+02 9.984386e-04 9.221e-04 4.509e-01 + GE6 -4.664057e+02 -6.857648e-04 1.230e-04 4.480e-01 + GE7 -4.664054e+02 2.373774e-04 4.418e-05 4.367e-01 + GE8 -4.664055e+02 -4.854638e-05 1.391e-05 4.339e-01 + GE9 -4.664055e+02 1.939584e-05 1.942e-06 4.353e-01 + GE10 -4.664055e+02 -2.480198e-06 1.468e-07 4.369e-01 + GE11 -4.664055e+02 -4.784209e-07 4.598e-08 3.646e-01 +E_delta_band = -7.17457305e-02 Ry = -9.76150742e-01 eV +E_delta_NN= -1.95404927e-01 Ry = -2.65862042e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0536 11 0.64 1e+02 % + Run_lcao lcao_line 7.0459 1 7 1e+02 % + Potential init_pot 0.24578 2 0.12 3.5 % + PW_Basis recip2real 0.2277 16 0.014 3.2 % + PW_Basis gathers_scatterp 0.10774 16 0.0067 1.5 % + Potential v_of_rho 0.86501 13 0.067 12 % + XC_Functional v_xc 0.2704 14 0.019 3.8 % + H_Hartree_pw v_hartree 0.56114 13 0.043 8 % + PW_Basis real2recip 0.59562 38 0.016 8.4 % + PW_Basis gatherp_scatters 0.24587 38 0.0065 3.5 % + ORB_control set_orb_tables 0.90313 1 0.9 13 % + ORB_gen_tables gen_tables 0.90313 1 0.9 13 % + ORB_table_phi init_Table 0.3753 1 0.38 5.3 % + ORB_table_phi cal_ST_Phi12_R 0.37109 126 0.0029 5.3 % + ORB_table_beta init_Table_Beta 0.15766 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15632 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.21123 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20954 66 0.0032 3 % + LOOP_ions opt_ions 5.6823 1 5.7 81 % + ESolver_KS_LCAO Run 5.1379 1 5.1 73 % + HSolverLCAO solve 2.9942 11 0.27 42 % + HamiltLCAO updateHk 1.5077 11 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.4844 11 0.13 21 % + Gint_interface cal_gint 1.6306 23 0.071 23 % + Gint_Gamma distri_vl_value 0.49317 11 0.045 7 % + Gint_Gamma distri_vl 2.4532 6 0.41 35 % + LCAO_Deepks cal_projected_DM 5.4406 13 0.42 77 % + LCAO_gen_fixedH add_v_delta 2.3253 6 0.39 33 % + LCAO_DESCRIPTOR add_v_delta 2.3253 6 0.39 33 % + ElecStateLCAO psiToRho 1.4699 11 0.13 21 % + Charge mix_rho 0.75638 10 0.076 11 % + LOOP_ions force_stress 0.5442 1 0.54 7.7 % + Force_Stress_LCAO getForceStress 0.54418 1 0.54 7.7 % + Force_LCAO_gamma ftable_gamma 0.34939 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.2651 1 0.27 3.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:08 2022 + FINISH Time : Wed Sep 28 11:08:15 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/104/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..6e1f321286c48b73ab5115537d1ca06318ab337a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.25685 0.421621 0.279705 +H 0.297426 0.378639 0.316869 +H 0.199057 0.392443 0.289232 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..a2233dd3c53877428cf600bc88c83c161a24a9f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0528 2 + 2 -12.5174 2 + 3 -9.31512 2 + 4 -6.69455 2 + 5 0.917719 0 + 6 3.91517 0 + 7 11.1448 0 + 8 11.4043 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..12d0e978713145f5ad5ea9fe38e93323ffd815b7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:18 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.19181167502 11.8053926503 7.83174967908 0 0 0 0 + tauc_H1 8.32794110674 10.6018935824 8.87233333467 0 0 0 0 + tauc_H2 5.57360170715 10.9884060532 8.0984999642 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0738385194329 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0741210085887 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0903301657592 (SEC) + + DONE : INIT CHARGE Time : 0.131401435165 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.386308 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 144 25 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000874 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00166 + + Density error is 0.210865725217 + + Energy Rydberg eV + E_KohnSham -34.1864964203 -465.131145972 + E_Harris -34.3704651852 -467.63416943 + E_Fermi -0.386379822873 -5.2569671833 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00108366545887 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013892498006 + + Density error is 0.0987682288503 + + Energy Rydberg eV + E_KohnSham -34.2749198775 -466.334208828 + E_Harris -34.2822379398 -466.433776172 + E_Fermi -0.198190663492 -2.69652231389 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00103016483394 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128218767425 + + Density error is 0.0638473754736 + + Energy Rydberg eV + E_KohnSham -34.275438011 -466.341258396 + E_Harris -34.2800940528 -466.404607095 + E_Fermi -0.192458007409 -2.61852552649 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000959206932169 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107359728488 + + Density error is 0.00190841721914 + + Energy Rydberg eV + E_KohnSham -34.2753198191 -466.339650312 + E_Harris -34.2753209664 -466.339665922 + E_Fermi -0.15701466463 -2.13629410853 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000961322895074 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107330003208 + + Density error is 0.000974458458653 + + Energy Rydberg eV + E_KohnSham -34.2752881378 -466.339219266 + E_Harris -34.2752885536 -466.339224924 + E_Fermi -0.15716401555 -2.13832613204 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000960249542603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106994080958 + + Density error is 0.00017181768244 + + Energy Rydberg eV + E_KohnSham -34.2752986878 -466.339362806 + E_Harris -34.275298692 -466.339362864 + E_Fermi -0.156634851677 -2.1311264882 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000960376952188 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107002854169 + + Density error is 2.7933378019e-05 + + Energy Rydberg eV + E_KohnSham -34.2752963077 -466.339330423 + E_Harris -34.2752963089 -466.339330439 + E_Fermi -0.156633979054 -2.13111461555 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000960355242479 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010699691501 + + Density error is 1.03165998024e-05 + + Energy Rydberg eV + E_KohnSham -34.2752981622 -466.339355655 + E_Harris -34.2752981627 -466.339355661 + E_Fermi -0.156642022486 -2.13122405205 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000960356698808 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106995726708 + + Density error is 3.15907914904e-06 + + Energy Rydberg eV + E_KohnSham -34.2752973839 -466.339345066 + E_Harris -34.275297384 -466.339345066 + E_Fermi -0.15663389902 -2.13111352663 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000960350643857 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106994529057 + + Density error is 5.1984127358e-07 + + Energy Rydberg eV + E_KohnSham -34.2752975124 -466.339346814 + E_Harris -34.2752975124 -466.339346814 + E_Fermi -0.156630868093 -2.13107228876 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000960351189732 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106994535071 + + Density error is 1.9741711821e-07 + + Energy Rydberg eV + E_KohnSham -34.2752975353 -466.339347125 + E_Harris -34.2752975353 -466.339347125 + E_Fermi -0.156630630758 -2.13106905964 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000960351313275 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106994506946 + + Density error is 1.1712325102e-08 + + Energy Rydberg eV + E_KohnSham -34.2752975384 -466.339347168 + E_Harris -34.2752975384 -466.339347168 + E_band -7.87609739452 -107.159802568 + E_one_elec -68.6048119945 -933.416353345 + E_Hartree +35.7071988821 +485.821364416 + E_xc -8.15669986668 -110.977595063 + E_Ewald +6.90467960458 +93.9429854867 + E_demet -3.42674751891e-57 -4.66232918645e-56 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193721005202 -2.63570949304 + E_Fermi -0.156630449002 -2.13106658672 + + charge density convergence is achieved + final etot is -466.339347168 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0528 2.00000 + 2 -12.5174 2.00000 + 3 -9.31512 2.00000 + 4 -6.69455 2.00000 + 5 0.917719 0.00000 + 6 3.91517 0.00000 + 7 11.1448 0.00000 + 8 11.4043 0.00000 + + EFERMI = -2.131066586722911 eV + OUT.ABACUS/ final etot is -466.3393471679686 eV + correction force for each atom along direction 1 is 1.44405e-05 + correction force for each atom along direction 2 is -3.54856e-05 + correction force for each atom along direction 3 is 0.000170275 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.6377570 -1.5444267 +1.3755982 + H1 -1.0928615 +1.5460242 -1.2727943 + H2 -0.54489545 -0.0015974761 -0.10280382 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3393471679686 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4723 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4646 1 7.5 1.e+02% + Potential init_pot 0.25269 2 0.13 3.4% + PW_Basis recip2real 0.23712 17 0.014 3.2% + PW_Basis gathers_scatterp 0.11255 17 0.0066 1.5% + Potential v_of_rho 0.93467 14 0.067 13.% + XC_Functional v_xc 0.29434 15 0.020 3.9% + H_Hartree_pw v_hartree 0.60447 14 0.043 8.1% + PW_Basis real2recip 0.63915 41 0.016 8.6% + PW_Basis gatherp_scatters 0.26239 41 0.0064 3.5% + ORB_control set_orb_tables 0.89385 1 0.89 12.% + ORB_gen_tables gen_tables 0.89385 1 0.89 12.% + ORB_table_phi init_Table 0.37234 1 0.37 5.0% + ORB_table_phi cal_ST_Phi12_R 0.36813 126 0.0029 4.9% + ORB_table_beta init_Table_Beta 0.15412 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15281 56 0.0027 2.0% + ORB_table_alpha init_Table_Alpha 0.20950 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20778 66 0.0031 2.8% + LOOP_ions opt_ions 6.1151 1 6.1 82.% + ESolver_KS_LCAO Run 5.5725 1 5.6 75.% + HSolverLCAO solve 3.2405 12 0.27 43.% + HamiltLCAO updateHk 1.6148 12 0.13 22.% + LCAO_Hamilt cal_Hgamma 1.5896 12 0.13 21.% + Gint_interface cal_gint 1.7802 25 0.071 24.% + Gint_Gamma distri_vl_value 0.52852 12 0.044 7.1% + Gint_Gamma distri_vl 2.8872 6 0.48 39.% + LCAO_Deepks cal_projected_DM 5.8780 14 0.42 79.% + LCAO_gen_fixedH add_v_delta 2.7608 6 0.46 37.% + LCAO_DESCRIPTOR add_v_delta 2.7608 6 0.46 37.% + ElecStateLCAO psiToRho 1.6075 12 0.13 22.% + Charge mix_rho 0.82518 11 0.075 11.% + LOOP_ions force_stress 0.54238 1 0.54 7.3% + Force_Stress_LCAO getForceStress 0.54236 1 0.54 7.3% + Force_LCAO_gamma ftable_gamma 0.34812 1 0.35 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.26658 1 0.27 3.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:18 2022 + Finish Time : Wed Sep 28 11:07:26 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8c4a665b3ef22301bfee5c84639dfd22b376fc88 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123379 ima = 3.68628e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123328982859 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111742284447 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112590951641 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112804666091 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112792657271 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112800200671 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112797432348 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112798951213 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112798523898 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112798451306 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112798432655 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112798422551 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a6846d4a31da7352247aef459a812a8dff29103e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.808188324959 11.805392650298 7.831749679082 0 0 0 +H +0.0 +2 +-19.672058893280 10.601893582390 8.872333334683 0 0 0 +-22.426398292866 10.988406053221 8.098499964217 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/conv new file mode 100644 index 0000000000000000000000000000000000000000..2b0e7ff48c8c2b9432f5df112eb9ef0da2c769af --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/conv @@ -0,0 +1 @@ +105 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d5503efbc486ff35b4ebea5cdc3d16575c2718f3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753904964 0.01244846307 1.236741023 1.335983103 1.468436375 0.009181035904 0.01664605124 0.03923946845 +3.513280448e-18 0.0007991452641 0.002558046116 0.01185799182 0.04277136817 3.660028322e-19 1.967399944e-06 5.892495741e-06 +0.001547539527 0.00594513407 + +H atom_index 1 n_descriptor 18 +1.15432607 0.03757666769 0.07976473563 0.1103413151 0.2844184621 0.01800628681 0.02265354254 0.04160392564 +1.94044164e-18 3.490004816e-05 0.0752797956 0.09362724218 0.110695323 8.641277099e-18 6.749676943e-06 0.01586549049 +0.02200150627 0.02565657427 + +H atom_index 2 n_descriptor 18 +1.250158851 0.03472499814 0.1091928759 0.1498328174 0.3207310759 0.02257654701 0.02827464133 0.03793678771 +5.167242073e-17 4.304670918e-05 0.09921824601 0.1157200257 0.1283252731 -7.199015988e-18 3.293391257e-06 0.01330778818 +0.02595666109 0.03072112705 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..34b8b0e0c7420449ecfc015a76542ec97891a72b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:18 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0738535 SEC) : SETUP UNITCELL + DONE(0.0741304 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0903419 SEC) : INIT PLANEWAVE + DONE(0.131504 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.386355 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651311e+02 0.000000e+00 2.109e-01 5.335e-01 + GE2 -4.663342e+02 -1.203063e+00 9.877e-02 5.141e-01 + GE3 -4.663413e+02 -7.049568e-03 6.385e-02 5.730e-01 + GE4 -4.663397e+02 1.608084e-03 1.908e-03 4.508e-01 + GE5 -4.663392e+02 4.310461e-04 9.745e-04 4.501e-01 + GE6 -4.663394e+02 -1.435397e-04 1.718e-04 4.509e-01 + GE7 -4.663393e+02 3.238297e-05 2.793e-05 4.351e-01 + GE8 -4.663394e+02 -2.523285e-05 1.032e-05 4.351e-01 + GE9 -4.663393e+02 1.058950e-05 3.159e-06 4.383e-01 + GE10 -4.663393e+02 -1.747886e-06 5.198e-07 4.389e-01 + GE11 -4.663393e+02 -3.110317e-07 1.974e-07 4.351e-01 + GE12 -4.663393e+02 -4.313221e-08 1.171e-08 3.644e-01 +E_delta_band = -6.80568413e-02 Ry = -9.25960829e-01 eV +E_delta_NN= -1.93721005e-01 Ry = -2.63570949e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4723 11 0.68 1e+02 % + Run_lcao lcao_line 7.4646 1 7.5 1e+02 % + Potential init_pot 0.25269 2 0.13 3.4 % + PW_Basis recip2real 0.23712 17 0.014 3.2 % + PW_Basis gathers_scatterp 0.11255 17 0.0066 1.5 % + Potential v_of_rho 0.93467 14 0.067 13 % + XC_Functional v_xc 0.29434 15 0.02 3.9 % + H_Hartree_pw v_hartree 0.60447 14 0.043 8.1 % + PW_Basis real2recip 0.63915 41 0.016 8.6 % + PW_Basis gatherp_scatters 0.26239 41 0.0064 3.5 % + ORB_control set_orb_tables 0.89385 1 0.89 12 % + ORB_gen_tables gen_tables 0.89385 1 0.89 12 % + ORB_table_phi init_Table 0.37234 1 0.37 5 % + ORB_table_phi cal_ST_Phi12_R 0.36813 126 0.0029 4.9 % + ORB_table_beta init_Table_Beta 0.15412 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15281 56 0.0027 2 % + ORB_table_alpha init_Table_Alpha 0.2095 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20778 66 0.0031 2.8 % + LOOP_ions opt_ions 6.1151 1 6.1 82 % + ESolver_KS_LCAO Run 5.5725 1 5.6 75 % + HSolverLCAO solve 3.2405 12 0.27 43 % + HamiltLCAO updateHk 1.6148 12 0.13 22 % + LCAO_Hamilt cal_Hgamma 1.5896 12 0.13 21 % + Gint_interface cal_gint 1.7802 25 0.071 24 % + Gint_Gamma distri_vl_value 0.52852 12 0.044 7.1 % + Gint_Gamma distri_vl 2.8872 6 0.48 39 % + LCAO_Deepks cal_projected_DM 5.878 14 0.42 79 % + LCAO_gen_fixedH add_v_delta 2.7608 6 0.46 37 % + LCAO_DESCRIPTOR add_v_delta 2.7608 6 0.46 37 % + ElecStateLCAO psiToRho 1.6075 12 0.13 22 % + Charge mix_rho 0.82518 11 0.075 11 % + LOOP_ions force_stress 0.54238 1 0.54 7.3 % + Force_Stress_LCAO getForceStress 0.54236 1 0.54 7.3 % + Force_LCAO_gamma ftable_gamma 0.34812 1 0.35 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.26658 1 0.27 3.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:18 2022 + FINISH Time : Wed Sep 28 11:07:26 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/105/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fe3a009c627a6d1d7a8234d96f1b257544ac56a0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.261808 0.428724 0.272343 +H 0.29151 0.428215 0.327054 +H 0.205389 0.459319 0.284622 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8fee0ea7e4e35e653b4ab5b19a6585304268d034 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5888 2 + 2 -13.3125 2 + 3 -9.14323 2 + 4 -6.80904 2 + 5 1.51664 0 + 6 4.85419 0 + 7 11.0014 0 + 8 11.2405 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b6f45fec1cf682456ac74f114e33b227ad7cb55f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:07 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.33061772616 12.0042692168 7.62561223465 0 0 0 0 + tauc_H1 8.16226935484 11.9900163113 9.15752119046 0 0 0 0 + tauc_H2 5.75087832328 12.8609190276 7.96940372371 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.086845791036 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0977402803435 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116375228377 (SEC) + + DONE : INIT CHARGE Time : 0.165991916848 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44745 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 144 25 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.001 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00162 + + Density error is 0.219049609388 + + Energy Rydberg eV + E_KohnSham -34.1824431541 -465.075998456 + E_Harris -34.3836933432 -467.814147753 + E_Fermi -0.42473222025 -5.77877831959 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00131211895655 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00142095237995 + + Density error is 0.0975050044761 + + Energy Rydberg eV + E_KohnSham -34.2753355135 -466.339863845 + E_Harris -34.2819652942 -466.43006664 + E_Fermi -0.230293413056 -3.13330262943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00125045545936 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013107260225 + + Density error is 0.0622312358377 + + Energy Rydberg eV + E_KohnSham -34.2756562291 -466.344227406 + E_Harris -34.2798948129 -466.401896295 + E_Fermi -0.215925941398 -2.93782314903 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00115873888867 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112395056114 + + Density error is 0.00208392560137 + + Energy Rydberg eV + E_KohnSham -34.2757058623 -466.3449027 + E_Harris -34.2757083154 -466.344936075 + E_Fermi -0.179987143751 -2.44885072175 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116054973192 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112142999694 + + Density error is 0.000957911210639 + + Energy Rydberg eV + E_KohnSham -34.275622957 -466.343774715 + E_Harris -34.2756254641 -466.343808825 + E_Fermi -0.178764165422 -2.43221124796 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00115904107426 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111968634299 + + Density error is 0.000125286199826 + + Energy Rydberg eV + E_KohnSham -34.2756764747 -466.344502861 + E_Harris -34.2756765164 -466.344503427 + E_Fermi -0.179048844452 -2.43608450487 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00115915754979 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111944404529 + + Density error is 5.28198805833e-05 + + Energy Rydberg eV + E_KohnSham -34.2756583728 -466.344256572 + E_Harris -34.2756583884 -466.344256784 + E_Fermi -0.178885297621 -2.43385933608 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00115906516889 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111946190201 + + Density error is 1.63256062147e-05 + + Energy Rydberg eV + E_KohnSham -34.2756624232 -466.34431168 + E_Harris -34.2756624241 -466.344311693 + E_Fermi -0.178948667655 -2.43472152961 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00115905234845 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111942735545 + + Density error is 2.43754587129e-06 + + Energy Rydberg eV + E_KohnSham -34.2756608273 -466.344289966 + E_Harris -34.2756608273 -466.344289966 + E_Fermi -0.178931717607 -2.43449091239 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00115905466273 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111942374043 + + Density error is 1.60094857318e-07 + + Energy Rydberg eV + E_KohnSham -34.2756609825 -466.344292078 + E_Harris -34.2756609825 -466.344292078 + E_Fermi -0.178928995131 -2.4344538712 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00115905465433 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011194240166 + + Density error is 3.76614423235e-08 + + Energy Rydberg eV + E_KohnSham -34.2756610381 -466.344292835 + E_Harris -34.2756610381 -466.344292835 + E_band -8.06332832686 -109.70721009 + E_one_elec -69.894700738 -950.966190041 + E_Hartree +36.3239554263 +494.212767696 + E_xc -8.25586710638 -112.326834578 + E_Ewald +7.67405794252 +104.4109148 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195979041048 -2.66643164683 + E_Fermi -0.178929156883 -2.43445607195 + + charge density convergence is achieved + final etot is -466.344292835 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5888 2.00000 + 2 -13.3125 2.00000 + 3 -9.14323 2.00000 + 4 -6.80904 2.00000 + 5 1.51664 0.00000 + 6 4.85419 0.00000 + 7 11.0014 0.00000 + 8 11.2405 0.00000 + + EFERMI = -2.434456071949620 eV + OUT.ABACUS/ final etot is -466.3442928346259 eV + correction force for each atom along direction 1 is -4.71323e-05 + correction force for each atom along direction 2 is 0.000115627 + correction force for each atom along direction 3 is 0.000135790 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.2691483 -0.080626054 -2.7511139 + H1 +1.5690184 -0.062440615 +2.7564934 + H2 -0.29987009 +0.14306667 -0.0053794758 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3442928346259 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5360 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5261 1 7.5 1.e+02% + Potential init_pot 0.28446 2 0.14 3.8% + PW_Basis recip2real 0.26482 16 0.017 3.5% + PW_Basis gathers_scatterp 0.12159 16 0.0076 1.6% + Potential v_of_rho 0.97091 13 0.075 13.% + XC_Functional v_xc 0.29904 14 0.021 4.0% + H_Hartree_pw v_hartree 0.63121 13 0.049 8.4% + PW_Basis real2recip 0.64740 38 0.017 8.6% + PW_Basis gatherp_scatters 0.27312 38 0.0072 3.6% + ORB_control set_orb_tables 1.1033 1 1.1 15.% + ORB_gen_tables gen_tables 1.1033 1 1.1 15.% + ORB_table_phi init_Table 0.47954 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47438 126 0.0038 6.3% + ORB_table_beta init_Table_Beta 0.18726 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18572 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24961 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24763 66 0.0038 3.3% + LOOP_ions opt_ions 5.8979 1 5.9 78.% + ESolver_KS_LCAO Run 5.3145 1 5.3 71.% + HSolverLCAO solve 3.0555 11 0.28 41.% + HamiltLCAO updateHk 1.5367 11 0.14 20.% + LCAO_Hamilt cal_Hgamma 1.5094 11 0.14 20.% + Gint_interface cal_gint 1.6898 23 0.073 22.% + Gint_Gamma distri_vl_value 0.46347 11 0.042 6.2% + Gint_Gamma distri_vl 2.5544 6 0.43 34.% + LCAO_Deepks cal_projected_DM 5.6427 13 0.43 75.% + LCAO_gen_fixedH add_v_delta 2.4105 6 0.40 32.% + LCAO_DESCRIPTOR add_v_delta 2.4105 6 0.40 32.% + ElecStateLCAO psiToRho 1.4940 11 0.14 20.% + Charge mix_rho 0.76838 10 0.077 10.% + LOOP_ions force_stress 0.58322 1 0.58 7.7% + Force_Stress_LCAO getForceStress 0.58320 1 0.58 7.7% + Force_LCAO_gamma ftable_gamma 0.36828 1 0.37 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.28481 1 0.28 3.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:07 2022 + Finish Time : Wed Sep 28 11:13:15 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b351e36a3722008af9bc3b7ed96e12704b08ffd3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124004 ima = 3.68234e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012303718046 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112081689261 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112505373701 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112810516471 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112733905705 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112776133342 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112769716666 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773154528 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112772614138 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112772489953 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011277249466 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/STRU new file mode 100644 index 0000000000000000000000000000000000000000..73204f4af11589d0770a3498ea8257e259094aa1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.669382273821 12.004269216840 7.625612234670 0 0 0 +H +0.0 +2 +-19.837730645183 11.990016311302 9.157521190444 0 0 0 +-22.249121676708 12.860919027613 7.969403723694 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/conv new file mode 100644 index 0000000000000000000000000000000000000000..db81174323a557dfcd4cfc9609486099c0abb5e3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/conv @@ -0,0 +1 @@ +106 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b028583665cc906864020295065444d5d4a0fb0d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749116956 0.01280719571 1.294408902 1.385397854 1.47081946 0.008734219434 0.01930332957 0.03903717051 +8.470868161e-18 0.001200053703 0.002773499303 0.0131876862 0.04812387094 5.255835946e-19 2.338718953e-06 6.534725533e-06 +0.001652115713 0.005904376354 + +H atom_index 1 n_descriptor 18 +1.316068014 0.03213187484 0.1343912136 0.1835632054 0.3393000549 0.02547464332 0.03205270157 0.03645108348 +4.43770817e-18 5.687451996e-05 0.1076949654 0.1300543706 0.1574167475 -2.54875261e-18 7.570739568e-07 0.01430309415 +0.02901974338 0.03328150357 + +H atom_index 2 n_descriptor 18 +1.247829517 0.0342457571 0.1082096412 0.148859596 0.3199111394 0.02236239792 0.02817163957 0.03732958643 +-9.310004219e-18 5.029377534e-05 0.1036420206 0.114583209 0.1280238728 -3.446822664e-18 4.372258454e-06 0.01321169758 +0.02683138546 0.03070423527 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..31c301ee047b4a989775b0d1886bfac416a27959 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..b65cb83cd8ad69f75558c78298b1cae009576c03 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:07 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0868708 SEC) : SETUP UNITCELL + DONE(0.0977591 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116395 SEC) : INIT PLANEWAVE + DONE(0.166119 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447514 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650760e+02 0.000000e+00 2.190e-01 5.797e-01 + GE2 -4.663399e+02 -1.263865e+00 9.751e-02 5.341e-01 + GE3 -4.663442e+02 -4.363561e-03 6.223e-02 6.036e-01 + GE4 -4.663449e+02 -6.752943e-04 2.084e-03 4.679e-01 + GE5 -4.663438e+02 1.127985e-03 9.579e-04 4.649e-01 + GE6 -4.663445e+02 -7.281464e-04 1.253e-04 4.517e-01 + GE7 -4.663443e+02 2.462889e-04 5.282e-05 4.508e-01 + GE8 -4.663443e+02 -5.510810e-05 1.633e-05 4.410e-01 + GE9 -4.663443e+02 2.171407e-05 2.438e-06 4.420e-01 + GE10 -4.663443e+02 -2.112381e-06 1.601e-07 4.428e-01 + GE11 -4.663443e+02 -7.561354e-07 3.766e-08 3.743e-01 +E_delta_band = -7.28724785e-02 Ry = -9.91480935e-01 eV +E_delta_NN= -1.95979041e-01 Ry = -2.66643165e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.536 11 0.69 1e+02 % + Run_lcao lcao_line 7.5261 1 7.5 1e+02 % + Potential init_pot 0.28446 2 0.14 3.8 % + PW_Basis recip2real 0.26482 16 0.017 3.5 % + PW_Basis gathers_scatterp 0.12159 16 0.0076 1.6 % + Potential v_of_rho 0.97091 13 0.075 13 % + XC_Functional v_xc 0.29904 14 0.021 4 % + H_Hartree_pw v_hartree 0.63121 13 0.049 8.4 % + PW_Basis real2recip 0.6474 38 0.017 8.6 % + PW_Basis gatherp_scatters 0.27312 38 0.0072 3.6 % + ORB_control set_orb_tables 1.1033 1 1.1 15 % + ORB_gen_tables gen_tables 1.1033 1 1.1 15 % + ORB_table_phi init_Table 0.47954 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47438 126 0.0038 6.3 % + ORB_table_beta init_Table_Beta 0.18726 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18572 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24961 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24763 66 0.0038 3.3 % + LOOP_ions opt_ions 5.8979 1 5.9 78 % + ESolver_KS_LCAO Run 5.3145 1 5.3 71 % + HSolverLCAO solve 3.0555 11 0.28 41 % + HamiltLCAO updateHk 1.5367 11 0.14 20 % + LCAO_Hamilt cal_Hgamma 1.5094 11 0.14 20 % + Gint_interface cal_gint 1.6898 23 0.073 22 % + Gint_Gamma distri_vl_value 0.46347 11 0.042 6.2 % + Gint_Gamma distri_vl 2.5544 6 0.43 34 % + LCAO_Deepks cal_projected_DM 5.6427 13 0.43 75 % + LCAO_gen_fixedH add_v_delta 2.4105 6 0.4 32 % + LCAO_DESCRIPTOR add_v_delta 2.4105 6 0.4 32 % + ElecStateLCAO psiToRho 1.494 11 0.14 20 % + Charge mix_rho 0.76838 10 0.077 10 % + LOOP_ions force_stress 0.58322 1 0.58 7.7 % + Force_Stress_LCAO getForceStress 0.5832 1 0.58 7.7 % + Force_LCAO_gamma ftable_gamma 0.36828 1 0.37 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.28481 1 0.28 3.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:07 2022 + FINISH Time : Wed Sep 28 11:13:15 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/106/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..dde1c1fd11779bf70812b03b39beca2990fff1ec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.265225 0.448426 0.272254 +H 0.32378 0.473119 0.252398 +H 0.228275 0.501158 0.277668 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d4626317556696d371a7a1cb72eb2d74c494a159 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2972 2 + 2 -12.9767 2 + 3 -9.17139 2 + 4 -6.74677 2 + 5 1.27485 0 + 6 4.39673 0 + 7 11.0766 0 + 8 11.3323 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..cecb8cc54a8160270410cc93acde238949f62080 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/running_scf.log @@ -0,0 +1,780 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:28 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.42630282816 12.5559244962 7.62309947527 0 0 0 0 + tauc_H1 9.06584379968 13.2473373264 7.0671509608 0 0 0 0 + tauc_H2 6.39171071556 14.0324292917 7.77471188307 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0863109860559 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0868333716035 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104853123302 (SEC) + + DONE : INIT CHARGE Time : 0.147777788669 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44652 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 144 0 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00131 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108 + + Density error is 0.21448721156 + + Energy Rydberg eV + E_KohnSham -34.1909334943 -465.191515462 + E_Harris -34.3817725639 -467.788014209 + E_Fermi -0.404314164411 -5.5009764181 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00123677667659 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111822020932 + + Density error is 0.0979793471455 + + Energy Rydberg eV + E_KohnSham -34.2803501993 -466.408092146 + E_Harris -34.2871400014 -466.500472142 + E_Fermi -0.213807322312 -2.90899785757 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00114676891187 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104881941889 + + Density error is 0.0628940745625 + + Energy Rydberg eV + E_KohnSham -34.2806631137 -466.412349565 + E_Harris -34.2850534554 -466.472083228 + E_Fermi -0.203045521581 -2.76257604689 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000995204400099 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00093303326588 + + Density error is 0.00197008484575 + + Energy Rydberg eV + E_KohnSham -34.2806428841 -466.412074327 + E_Harris -34.2806440892 -466.412090723 + E_Fermi -0.167442686047 -2.27817461867 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000994919761045 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000932349582097 + + Density error is 0.000900524882344 + + Energy Rydberg eV + E_KohnSham -34.2805858889 -466.411298867 + E_Harris -34.280586905 -466.411312692 + E_Fermi -0.166837270185 -2.26993751328 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000993110230138 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000930911857995 + + Density error is 0.000142445466446 + + Energy Rydberg eV + E_KohnSham -34.2806204951 -466.411769709 + E_Harris -34.2806205206 -466.411770055 + E_Fermi -0.166762912714 -2.26892582799 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000993090926502 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000930942702343 + + Density error is 3.86475110098e-05 + + Energy Rydberg eV + E_KohnSham -34.2806085313 -466.411606933 + E_Harris -34.2806085392 -466.411607041 + E_Fermi -0.166651405315 -2.267408692 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00099307341854 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000930895235374 + + Density error is 1.49149696747e-05 + + Energy Rydberg eV + E_KohnSham -34.2806122117 -466.411657007 + E_Harris -34.2806122126 -466.41165702 + E_Fermi -0.166690720906 -2.26794360806 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000993056103298 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00093088000445 + + Density error is 1.7814237472e-06 + + Energy Rydberg eV + E_KohnSham -34.2806108243 -466.411638131 + E_Harris -34.2806108243 -466.411638131 + E_Fermi -0.166675132718 -2.26773151988 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000993052762381 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000930880093328 + + Density error is 1.96159244525e-07 + + Energy Rydberg eV + E_KohnSham -34.2806110337 -466.41164098 + E_Harris -34.2806110337 -466.41164098 + E_Fermi -0.166673533543 -2.26770976198 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000993053074789 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000930880668779 + + Density error is 3.53808127447e-08 + + Energy Rydberg eV + E_KohnSham -34.2806110627 -466.411641374 + E_Harris -34.2806110627 -466.411641374 + E_band -7.96608124268 -108.384095631 + E_one_elec -69.2627700737 -942.368332266 + E_Hartree +36.0244963683 +490.13841819 + E_xc -8.20719460042 -111.664611161 + E_Ewald +7.28924034471 +99.1752027796 + E_demet -2.79263518042e-76 -3.7995750889e-75 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194775563318 -2.65005749228 + E_Fermi -0.166673476075 -2.26770898008 + + charge density convergence is achieved + final etot is -466.411641374 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2972 2.00000 + 2 -12.9767 2.00000 + 3 -9.17139 2.00000 + 4 -6.74677 2.00000 + 5 1.27485 0.00000 + 6 4.39673 0.00000 + 7 11.0766 0.00000 + 8 11.3323 0.00000 + + EFERMI = -2.267708980081815 eV + OUT.ABACUS/ final etot is -466.4116413740049 eV + correction force for each atom along direction 1 is 3.93025e-05 + correction force for each atom along direction 2 is 9.80473e-05 + correction force for each atom along direction 3 is 0.000109192 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.0526175 -0.48167186 -0.25401477 + H1 -0.40510443 -0.27582114 +0.14492394 + H2 -0.64751304 +0.75749300 +0.10909083 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4116413740049 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7054 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6963 1 6.7 1.e+02% + Potential init_pot 0.30006 2 0.15 4.5% + PW_Basis recip2real 0.25467 16 0.016 3.8% + PW_Basis gathers_scatterp 0.11392 16 0.0071 1.7% + Charge atomic_rho 0.11475 1 0.11 1.7% + Potential v_of_rho 0.93333 13 0.072 14.% + XC_Functional v_xc 0.29259 14 0.021 4.4% + H_Hartree_pw v_hartree 0.59828 13 0.046 8.9% + PW_Basis real2recip 0.67114 38 0.018 10.% + PW_Basis gatherp_scatters 0.25941 38 0.0068 3.9% + ORB_control set_orb_tables 1.0970 1 1.1 16.% + ORB_gen_tables gen_tables 1.0970 1 1.1 16.% + ORB_table_phi init_Table 0.47392 1 0.47 7.1% + ORB_table_phi cal_ST_Phi12_R 0.46865 126 0.0037 7.0% + ORB_table_beta init_Table_Beta 0.18446 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18293 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24942 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.24750 66 0.0037 3.7% + LOOP_ions opt_ions 5.0760 1 5.1 76.% + ESolver_KS_LCAO Run 4.5345 1 4.5 68.% + HSolverLCAO solve 2.1631 11 0.20 32.% + HamiltLCAO updateHk 1.1510 11 0.10 17.% + LCAO_Hamilt cal_Hgamma 1.1237 11 0.10 17.% + Gint_interface cal_gint 1.3404 23 0.058 20.% + Gint_Gamma distri_vl_value 0.22525 11 0.020 3.4% + Gint_Gamma distri_vl 2.1902 6 0.37 33.% + LCAO_Deepks cal_projected_DM 4.8475 13 0.37 72.% + LCAO_gen_fixedH add_v_delta 2.0424 6 0.34 30.% + LCAO_DESCRIPTOR add_v_delta 2.0424 6 0.34 30.% + ElecStateLCAO psiToRho 0.98859 11 0.090 15.% + Charge mix_rho 0.89301 10 0.089 13.% + LOOP_ions force_stress 0.54130 1 0.54 8.1% + Force_Stress_LCAO getForceStress 0.54127 1 0.54 8.1% + Force_LCAO_gamma ftable_gamma 0.33443 1 0.33 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.24375 1 0.24 3.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:28 2022 + Finish Time : Wed Sep 28 11:04:35 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2aebbf4a0179d5aa8a6ebb556446b10cfa2a1192 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123676 ima = 3.67821e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123079826782 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011198978381 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112560072259 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112803214346 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756203774 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112783476236 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011277727601 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112780157456 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112779530905 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011277945302 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112779442608 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1b68a17bd20520641f97ff3af772024092e16614 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.573697171827 12.555924496160 7.623099475291 0 0 0 +H +0.0 +2 +-18.934156200303 13.247337326399 7.067150960825 0 0 0 +-21.608289284454 14.032429291674 7.774711883090 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/conv new file mode 100644 index 0000000000000000000000000000000000000000..643e0cfde261481902b534c7af0e5ca54948d340 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/conv @@ -0,0 +1 @@ +107 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c1ffa300c2878944dcd9696d81059ce4357a157d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750192278 0.01268770226 1.270310442 1.360176954 1.469351316 0.008665769937 0.01820336049 0.039061568 +-1.002709484e-18 0.001020770054 0.002631406452 0.01246148192 0.04527795348 -2.203255677e-19 2.124741333e-06 6.098093208e-06 +0.001629812209 0.005987294539 + +H atom_index 1 n_descriptor 18 +1.222078433 0.03530436322 0.09921733373 0.1373836351 0.3114054095 0.02104405269 0.02666552326 0.03849191249 +-2.23784451e-18 4.370849254e-05 0.09445619618 0.1140650441 0.117781563 4.700325085e-18 5.416187171e-06 0.01361782311 +0.02527133446 0.02942434165 + +H atom_index 2 n_descriptor 18 +1.265514125 0.03382283023 0.114058503 0.1572607762 0.3257605807 0.02308084927 0.02919928665 0.03707625462 +1.754904026e-17 4.773793881e-05 0.1049331886 0.1162249513 0.134984052 -2.630468997e-19 3.134581132e-06 0.01316523473 +0.02690808512 0.03143930847 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e2ccc6fb8c9bc62bdd1174966ce25a09aa502541 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..63ba17b6682d128573084f02ba641a036f1d9f1e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..d81c14b2d4654c6898414f85a8e23efa00a04b06 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..61ff451d9a1f8259d7c9639d7e3285fd1a2d3539 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..0404f49e92d77a74098dd41c4cd5c8e5ffd00d9e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:28 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0863332 SEC) : SETUP UNITCELL + DONE(0.0868488 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104874 SEC) : INIT PLANEWAVE + DONE(0.147915 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446586 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651915e+02 0.000000e+00 2.145e-01 5.041e-01 + GE2 -4.664081e+02 -1.216577e+00 9.798e-02 4.642e-01 + GE3 -4.664123e+02 -4.257418e-03 6.289e-02 5.346e-01 + GE4 -4.664121e+02 2.752379e-04 1.970e-03 3.923e-01 + GE5 -4.664113e+02 7.754598e-04 9.005e-04 3.943e-01 + GE6 -4.664118e+02 -4.708423e-04 1.424e-04 3.899e-01 + GE7 -4.664116e+02 1.627758e-04 3.865e-05 3.764e-01 + GE8 -4.664117e+02 -5.007374e-05 1.491e-05 3.719e-01 + GE9 -4.664116e+02 1.887632e-05 1.781e-06 3.713e-01 + GE10 -4.664116e+02 -2.849004e-06 1.962e-07 3.705e-01 + GE11 -4.664116e+02 -3.941169e-07 3.538e-08 3.025e-01 +E_delta_band = -7.03924617e-02 Ry = -9.57738576e-01 eV +E_delta_NN= -1.94775563e-01 Ry = -2.65005749e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7054 11 0.61 1e+02 % + Run_lcao lcao_line 6.6963 1 6.7 1e+02 % + Potential init_pot 0.30006 2 0.15 4.5 % + PW_Basis recip2real 0.25467 16 0.016 3.8 % + PW_Basis gathers_scatterp 0.11392 16 0.0071 1.7 % + Charge atomic_rho 0.11475 1 0.11 1.7 % + Potential v_of_rho 0.93333 13 0.072 14 % + XC_Functional v_xc 0.29259 14 0.021 4.4 % + H_Hartree_pw v_hartree 0.59828 13 0.046 8.9 % + PW_Basis real2recip 0.67114 38 0.018 10 % + PW_Basis gatherp_scatters 0.25941 38 0.0068 3.9 % + ORB_control set_orb_tables 1.097 1 1.1 16 % + ORB_gen_tables gen_tables 1.097 1 1.1 16 % + ORB_table_phi init_Table 0.47392 1 0.47 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.46865 126 0.0037 7 % + ORB_table_beta init_Table_Beta 0.18446 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18293 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24942 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.2475 66 0.0037 3.7 % + LOOP_ions opt_ions 5.076 1 5.1 76 % + ESolver_KS_LCAO Run 4.5345 1 4.5 68 % + HSolverLCAO solve 2.1631 11 0.2 32 % + HamiltLCAO updateHk 1.151 11 0.1 17 % + LCAO_Hamilt cal_Hgamma 1.1237 11 0.1 17 % + Gint_interface cal_gint 1.3404 23 0.058 20 % + Gint_Gamma distri_vl_value 0.22525 11 0.02 3.4 % + Gint_Gamma distri_vl 2.1902 6 0.37 33 % + LCAO_Deepks cal_projected_DM 4.8475 13 0.37 72 % + LCAO_gen_fixedH add_v_delta 2.0424 6 0.34 30 % + LCAO_DESCRIPTOR add_v_delta 2.0424 6 0.34 30 % + ElecStateLCAO psiToRho 0.98859 11 0.09 15 % + Charge mix_rho 0.89301 10 0.089 13 % + LOOP_ions force_stress 0.5413 1 0.54 8.1 % + Force_Stress_LCAO getForceStress 0.54127 1 0.54 8.1 % + Force_LCAO_gamma ftable_gamma 0.33443 1 0.33 5 % + Force_LCAO_gamma cal_fvl_dphi 0.24375 1 0.24 3.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:28 2022 + FINISH Time : Wed Sep 28 11:04:35 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/107/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ad31ec9b6a69deaddac907b95bbdbc24c523641f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.28336 0.46228 0.266662 +H 0.255838 0.466783 0.205664 +H 0.271099 0.523002 0.290929 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..de4bbf785913a6c1306a2d5d1ba213c572f9a724 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1273 2 + 2 -12.7226 2 + 3 -9.23394 2 + 4 -6.71159 2 + 5 1.10698 0 + 6 4.08065 0 + 7 11.1218 0 + 8 11.3868 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e8ced87ee57a973fee3f9c531f69cb7d733f31e3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:35 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.93408698242 12.9438529573 7.46652970056 0 0 0 0 + tauc_H1 7.16346279361 13.0699349733 5.75858279122 0 0 0 0 + tauc_H2 7.59076611687 14.6440534974 8.14602122528 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0856400058815 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0885676201517 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106858314079 (SEC) + + DONE : INIT CHARGE Time : 0.156590065644 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.435387 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 144 9 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000998 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000853 + + Density error is 0.21140457526 + + Energy Rydberg eV + E_KohnSham -34.1930723604 -465.220616228 + E_Harris -34.3774837054 -467.729661296 + E_Fermi -0.392050413098 -5.33411952139 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00122088466077 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114896974721 + + Density error is 0.0982337920935 + + Energy Rydberg eV + E_KohnSham -34.2803268869 -466.407774964 + E_Harris -34.2873006965 -466.502658512 + E_Fermi -0.203815118499 -2.77304695014 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116478852556 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110662820004 + + Density error is 0.063245305429 + + Energy Rydberg eV + E_KohnSham -34.2806335478 -466.411947301 + E_Harris -34.2851340342 -466.473179559 + E_Fermi -0.19542261892 -2.65886113539 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00109307573837 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106222299903 + + Density error is 0.00192794878232 + + Energy Rydberg eV + E_KohnSham -34.2805634297 -466.410993295 + E_Harris -34.2805645215 -466.411008149 + E_Fermi -0.160063475569 -2.17777530943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00109446005073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106245028996 + + Density error is 0.000842211983874 + + Energy Rydberg eV + E_KohnSham -34.2805285944 -466.410519336 + E_Harris -34.2805289631 -466.410524352 + E_Fermi -0.159854114998 -2.17492681272 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00109346597058 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106200441797 + + Density error is 0.000147200330935 + + Energy Rydberg eV + E_KohnSham -34.2805467226 -466.410765982 + E_Harris -34.2805467245 -466.410766008 + E_Fermi -0.1595374427 -2.17061826506 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00109357124511 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106225977791 + + Density error is 2.68994808994e-05 + + Energy Rydberg eV + E_KohnSham -34.2805414948 -466.410694855 + E_Harris -34.2805414973 -466.410694888 + E_Fermi -0.159484263859 -2.16989472982 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00109350721442 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106216969552 + + Density error is 1.28380521049e-05 + + Energy Rydberg eV + E_KohnSham -34.2805438309 -466.410726639 + E_Harris -34.2805438317 -466.41072665 + E_Fermi -0.159503122369 -2.17015131301 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00109351375745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106217695972 + + Density error is 2.03882453818e-06 + + Energy Rydberg eV + E_KohnSham -34.2805428068 -466.410712705 + E_Harris -34.2805428068 -466.410712705 + E_Fermi -0.159491083913 -2.16998752142 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00109351104025 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106217827392 + + Density error is 3.97189669124e-07 + + Energy Rydberg eV + E_KohnSham -34.2805430199 -466.410715604 + E_Harris -34.2805430199 -466.410715604 + E_Fermi -0.159489285913 -2.16996305837 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00109351190472 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010621787994 + + Density error is 1.405828587e-07 + + Energy Rydberg eV + E_KohnSham -34.2805430369 -466.410715836 + E_Harris -34.2805430369 -466.410715836 + E_Fermi -0.159489123507 -2.16996084872 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00109351208655 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106217893928 + + Density error is 1.10837566073e-08 + + Energy Rydberg eV + E_KohnSham -34.2805430402 -466.410715881 + E_Harris -34.2805430402 -466.410715881 + E_band -7.90778536265 -107.590939493 + E_one_elec -68.857255622 -936.851025102 + E_Hartree +35.8302455378 +487.495500053 + E_xc -8.17590985765 -111.238960398 + E_Ewald +7.04758050799 +95.8872520225 + E_demet -1.17538684543e-65 -1.59919584521e-64 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194060001802 -2.6403217784 + E_Fermi -0.159488994865 -2.16995909845 + + charge density convergence is achieved + final etot is -466.410715881 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1273 2.00000 + 2 -12.7226 2.00000 + 3 -9.23394 2.00000 + 4 -6.71159 2.00000 + 5 1.10698 0.00000 + 6 4.08065 0.00000 + 7 11.1218 0.00000 + 8 11.3868 0.00000 + + EFERMI = -2.169959098452582 eV + OUT.ABACUS/ final etot is -466.4107158813985 eV + correction force for each atom along direction 1 is -0.000197138 + correction force for each atom along direction 2 is 1.72999e-05 + correction force for each atom along direction 3 is -8.05304e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.52372367 +0.62516218 -0.66956617 + H1 +0.36459746 -0.21829284 +0.66016008 + H2 +0.15912621 -0.40686934 +0.0094060906 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4107158813985 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6495 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6399 1 6.6 1.e+02% + Potential init_pot 0.28292 2 0.14 4.3% + PW_Basis recip2real 0.27803 17 0.016 4.2% + PW_Basis gathers_scatterp 0.11710 17 0.0069 1.8% + Charge atomic_rho 0.10001 1 0.10 1.5% + Potential v_of_rho 0.92963 14 0.066 14.% + XC_Functional v_xc 0.25095 15 0.017 3.8% + H_Hartree_pw v_hartree 0.63712 14 0.046 9.6% + PW_Basis real2recip 0.60097 41 0.015 9.0% + PW_Basis gatherp_scatters 0.23372 41 0.0057 3.5% + ORB_control set_orb_tables 1.1144 1 1.1 17.% + ORB_gen_tables gen_tables 1.1144 1 1.1 17.% + ORB_table_phi init_Table 0.48565 1 0.49 7.3% + ORB_table_phi cal_ST_Phi12_R 0.48068 126 0.0038 7.2% + ORB_table_beta init_Table_Beta 0.18987 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18838 56 0.0034 2.8% + ORB_table_alpha init_Table_Alpha 0.25803 1 0.26 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25613 66 0.0039 3.9% + LOOP_ions opt_ions 5.0136 1 5.0 75.% + ESolver_KS_LCAO Run 4.4844 1 4.5 67.% + HSolverLCAO solve 2.3413 12 0.20 35.% + HamiltLCAO updateHk 1.2249 12 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1856 12 0.099 18.% + Gint_interface cal_gint 1.9776 25 0.079 30.% + Gint_Gamma distri_vl 2.3271 6 0.39 35.% + LCAO_Deepks cal_projected_DM 4.8346 14 0.35 73.% + LCAO_gen_fixedH add_v_delta 2.1955 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.1955 6 0.37 33.% + ElecStateLCAO psiToRho 1.0993 12 0.092 17.% + Charge mix_rho 0.72343 11 0.066 11.% + LOOP_ions force_stress 0.52904 1 0.53 8.0% + Force_Stress_LCAO getForceStress 0.52901 1 0.53 8.0% + Force_LCAO_gamma ftable_gamma 0.31855 1 0.32 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.29308 1 0.29 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:35 2022 + Finish Time : Wed Sep 28 11:13:41 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..9744a3f085eb3bd3f7ef940a1d1b2473fa03060a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/OUT.ABACUS/warning.log @@ -0,0 +1,77 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123475 ima = 3.67049e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 3 + 3 1 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123065856916 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111879573662 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112562732138 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112768206057 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112746246581 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112759227088 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755541235 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112757521862 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756902241 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756847614 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756831943 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756825091 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/STRU new file mode 100644 index 0000000000000000000000000000000000000000..390650428309d2dfff5dd632b91b536216f13f75 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.065913017568 12.943852957295 7.466529700572 0 0 0 +H +0.0 +2 +-20.836537206374 13.069934973344 5.758582791202 0 0 0 +-20.409233883151 14.644053497367 8.146021225301 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/conv new file mode 100644 index 0000000000000000000000000000000000000000..d75195d262fa1954289e0593740e7f21d0c714c0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/conv @@ -0,0 +1 @@ +108 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..038c4e4440d6792d92a7ca908b3433b2413e9e97 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751841751 0.01257674949 1.254600464 1.341748592 1.468601292 0.008825093918 0.01732615507 0.03912817455 +-3.849970305e-18 0.0008951076933 0.002564539692 0.01209542183 0.04356048133 -5.221787831e-19 2.034240813e-06 5.895065166e-06 +0.00159513495 0.006006825367 + +H atom_index 1 n_descriptor 18 +1.21281642 0.03579023301 0.09636908853 0.1333396601 0.3079013754 0.02064794679 0.02610130821 0.03908323624 +1.034927948e-17 4.094909813e-05 0.09062334077 0.1140238154 0.1140819148 4.674006384e-18 5.454899485e-06 0.01389361813 +0.02462672258 0.02891364996 + +H atom_index 2 n_descriptor 18 +1.224716944 0.03539948845 0.100163744 0.1384392278 0.3121955343 0.0212131738 0.02680098205 0.03861906572 +2.244064084e-17 4.200739595e-05 0.09372637026 0.1144593214 0.1185440496 1.497682466e-18 4.934564949e-06 0.01362153904 +0.02510711952 0.0295193363 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5e30daa6e41c74746b7af830aac4e55b14ac8396 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:35 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0856645 SEC) : SETUP UNITCELL + DONE(0.088583 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106878 SEC) : INIT PLANEWAVE + DONE(0.156716 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.435464 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652206e+02 0.000000e+00 2.114e-01 4.935e-01 + GE2 -4.664078e+02 -1.187159e+00 9.823e-02 4.136e-01 + GE3 -4.664119e+02 -4.172336e-03 6.325e-02 4.682e-01 + GE4 -4.664110e+02 9.540057e-04 1.928e-03 3.651e-01 + GE5 -4.664105e+02 4.739588e-04 8.422e-04 3.625e-01 + GE6 -4.664108e+02 -2.466462e-04 1.472e-04 3.561e-01 + GE7 -4.664107e+02 7.112764e-05 2.690e-05 3.362e-01 + GE8 -4.664107e+02 -3.178458e-05 1.284e-05 3.389e-01 + GE9 -4.664107e+02 1.393409e-05 2.039e-06 3.356e-01 + GE10 -4.664107e+02 -2.898965e-06 3.972e-07 3.378e-01 + GE11 -4.664107e+02 -2.320635e-07 1.406e-07 3.387e-01 + GE12 -4.664107e+02 -4.508029e-08 1.108e-08 2.770e-01 +E_delta_band = -6.88563955e-02 Ry = -9.36839322e-01 eV +E_delta_NN= -1.94060002e-01 Ry = -2.64032178e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6495 11 0.6 1e+02 % + Run_lcao lcao_line 6.6399 1 6.6 1e+02 % + Potential init_pot 0.28292 2 0.14 4.3 % + PW_Basis recip2real 0.27803 17 0.016 4.2 % + PW_Basis gathers_scatterp 0.1171 17 0.0069 1.8 % + Charge atomic_rho 0.10001 1 0.1 1.5 % + Potential v_of_rho 0.92963 14 0.066 14 % + XC_Functional v_xc 0.25095 15 0.017 3.8 % + H_Hartree_pw v_hartree 0.63712 14 0.046 9.6 % + PW_Basis real2recip 0.60097 41 0.015 9 % + PW_Basis gatherp_scatters 0.23372 41 0.0057 3.5 % + ORB_control set_orb_tables 1.1144 1 1.1 17 % + ORB_gen_tables gen_tables 1.1144 1 1.1 17 % + ORB_table_phi init_Table 0.48565 1 0.49 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.48068 126 0.0038 7.2 % + ORB_table_beta init_Table_Beta 0.18987 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18838 56 0.0034 2.8 % + ORB_table_alpha init_Table_Alpha 0.25803 1 0.26 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25613 66 0.0039 3.9 % + LOOP_ions opt_ions 5.0136 1 5 75 % + ESolver_KS_LCAO Run 4.4844 1 4.5 67 % + HSolverLCAO solve 2.3413 12 0.2 35 % + HamiltLCAO updateHk 1.2249 12 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1856 12 0.099 18 % + Gint_interface cal_gint 1.9776 25 0.079 30 % + Gint_Gamma distri_vl 2.3271 6 0.39 35 % + LCAO_Deepks cal_projected_DM 4.8346 14 0.35 73 % + LCAO_gen_fixedH add_v_delta 2.1955 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.1955 6 0.37 33 % + ElecStateLCAO psiToRho 1.0993 12 0.092 17 % + Charge mix_rho 0.72343 11 0.066 11 % + LOOP_ions force_stress 0.52904 1 0.53 8 % + Force_Stress_LCAO getForceStress 0.52901 1 0.53 8 % + Force_LCAO_gamma ftable_gamma 0.31855 1 0.32 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.29308 1 0.29 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:35 2022 + FINISH Time : Wed Sep 28 11:13:41 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/108/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4849113cd6550f4cea5b547882dacdbff779b8a4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.30945 0.483213 0.257099 +H 0.257217 0.500025 0.221406 +H 0.286385 0.477537 0.315778 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6d1bdf7246b12bec94f50211a66236686e88705e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4947 2 + 2 -13.1885 2 + 3 -9.16606 2 + 4 -6.78957 2 + 5 1.44634 0 + 6 4.70073 0 + 7 11.0268 0 + 8 11.2757 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e70d324314fe102f48eddc436bf2ac82be6098da --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:34 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 8.66460002024 13.5299684296 7.19878170352 0 0 0 0 + tauc_H1 7.2020646126 14.0006870979 6.1993649131 0 0 0 0 + tauc_H2 8.01879345461 13.3710440183 8.84177459979 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0733057746834 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0736099694605 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0898884225886 (SEC) + + DONE : INIT CHARGE Time : 0.131351914213 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374244 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000874 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00078 + + Density error is 0.217720004761 + + Energy Rydberg eV + E_KohnSham -34.1860645673 -465.125270312 + E_Harris -34.3841211436 -467.819968275 + E_Fermi -0.418606908746 -5.69543918112 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00132731174314 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000916507475365 + + Density error is 0.0977581079907 + + Energy Rydberg eV + E_KohnSham -34.2783011217 -466.380213015 + E_Harris -34.2849826996 -466.471120546 + E_Fermi -0.224380215016 -3.05284944268 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00127388791958 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000875145361378 + + Density error is 0.0625829598923 + + Energy Rydberg eV + E_KohnSham -34.2786507306 -466.384969688 + E_Harris -34.2829523924 -466.443496799 + E_Fermi -0.211528497254 -2.87799285203 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00120424214303 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000822387523541 + + Density error is 0.00203458237226 + + Energy Rydberg eV + E_KohnSham -34.2786729558 -466.385272078 + E_Harris -34.2786747369 -466.38529631 + E_Fermi -0.17565787497 -2.38994799816 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00120858066659 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000825004944289 + + Density error is 0.00096706311835 + + Energy Rydberg eV + E_KohnSham -34.2785948057 -466.384208791 + E_Harris -34.2785969032 -466.384237329 + E_Fermi -0.174661807829 -2.37639580946 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00120699284806 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000823959482419 + + Density error is 0.000114546057701 + + Energy Rydberg eV + E_KohnSham -34.2786439124 -466.384876922 + E_Harris -34.2786439331 -466.384877203 + E_Fermi -0.174818052502 -2.37852162729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00120698036904 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000823991465163 + + Density error is 4.84796386319e-05 + + Energy Rydberg eV + E_KohnSham -34.2786278256 -466.384658049 + E_Harris -34.2786278394 -466.384658237 + E_Fermi -0.174675761388 -2.37658565736 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00120690464791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000823953309895 + + Density error is 1.5247209507e-05 + + Energy Rydberg eV + E_KohnSham -34.2786313205 -466.3847056 + E_Harris -34.2786313214 -466.384705613 + E_Fermi -0.174735360319 -2.37739654242 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00120691182893 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000823960045198 + + Density error is 2.19482483846e-06 + + Energy Rydberg eV + E_KohnSham -34.2786297497 -466.384684228 + E_Harris -34.2786297497 -466.384684228 + E_Fermi -0.174719580785 -2.37718185085 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00120691194975 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000823959709339 + + Density error is 1.2356594961e-07 + + Energy Rydberg eV + E_KohnSham -34.2786299355 -466.384686757 + E_Harris -34.2786299355 -466.384686757 + E_Fermi -0.174717242623 -2.37715003852 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00120691245548 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000823959975473 + + Density error is 4.73248326311e-08 + + Energy Rydberg eV + E_KohnSham -34.2786299808 -466.384687373 + E_Harris -34.2786299808 -466.384687373 + E_band -8.03176123728 -109.277717803 + E_one_elec -69.6863828211 -948.131879376 + E_Hartree +36.2248661308 +492.864588666 + E_xc -8.23963396254 -112.105971325 + E_Ewald +7.54603765487 +102.669109429 + E_demet -3.12867317539e-88 -4.25677823651e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195565663899 -2.66080736218 + E_Fermi -0.174717292796 -2.37715072116 + + charge density convergence is achieved + final etot is -466.384687373 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4947 2.00000 + 2 -13.1885 2.00000 + 3 -9.16606 2.00000 + 4 -6.78957 2.00000 + 5 1.44634 0.00000 + 6 4.70073 0.00000 + 7 11.0268 0.00000 + 8 11.2757 0.00000 + + EFERMI = -2.377150721157687 eV + OUT.ABACUS/ final etot is -466.3846873728695 eV + correction force for each atom along direction 1 is -9.07633e-05 + correction force for each atom along direction 2 is 0.000132700 + correction force for each atom along direction 3 is 5.74079e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.84482122 +0.15019180 -1.7853217 + H1 -0.15982941 +0.069673190 -0.23067168 + H2 -0.68499181 -0.21986499 +2.0159934 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3846873728695 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6293 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6222 1 6.6 1.e+02% + Potential init_pot 0.23898 2 0.12 3.6% + PW_Basis recip2real 0.23251 16 0.015 3.5% + PW_Basis gathers_scatterp 0.10318 16 0.0064 1.6% + Potential v_of_rho 0.87205 13 0.067 13.% + XC_Functional v_xc 0.26930 14 0.019 4.1% + H_Hartree_pw v_hartree 0.56816 13 0.044 8.6% + PW_Basis real2recip 0.58693 38 0.015 8.9% + PW_Basis gatherp_scatters 0.21791 38 0.0057 3.3% + ORB_control set_orb_tables 0.89215 1 0.89 13.% + ORB_gen_tables gen_tables 0.89214 1 0.89 13.% + ORB_table_phi init_Table 0.37220 1 0.37 5.6% + ORB_table_phi cal_ST_Phi12_R 0.36803 126 0.0029 5.6% + ORB_table_beta init_Table_Beta 0.15488 1 0.15 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15358 56 0.0027 2.3% + ORB_table_alpha init_Table_Alpha 0.20738 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20577 66 0.0031 3.1% + LOOP_ions opt_ions 5.2850 1 5.3 80.% + ESolver_KS_LCAO Run 4.7612 1 4.8 72.% + HSolverLCAO solve 2.6013 11 0.24 39.% + HamiltLCAO updateHk 1.3318 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3086 11 0.12 20.% + Gint_interface cal_gint 2.0378 23 0.089 31.% + Gint_Gamma distri_vl_value 0.17218 11 0.016 2.6% + Gint_Gamma distri_vl 2.2939 6 0.38 35.% + LCAO_Deepks cal_projected_DM 5.0999 13 0.39 77.% + LCAO_gen_fixedH add_v_delta 2.1664 6 0.36 33.% + LCAO_DESCRIPTOR add_v_delta 2.1665 6 0.36 33.% + ElecStateLCAO psiToRho 1.2531 11 0.11 19.% + Charge mix_rho 0.75494 10 0.075 11.% + LOOP_ions force_stress 0.52358 1 0.52 7.9% + Force_Stress_LCAO getForceStress 0.52356 1 0.52 7.9% + Force_LCAO_gamma ftable_gamma 0.32524 1 0.33 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.28344 1 0.28 4.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:34 2022 + Finish Time : Wed Sep 28 11:04:41 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..110657cb5e6983bd5d694a82101325d4fc45ca17 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123877 ima = 3.66649e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123033610933 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111944083254 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112433668947 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112722784384 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112652419818 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112690932552 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011268564575 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112688990857 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112688398786 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112688290271 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112688287044 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0e2a3cc4cbc56d6c3b39e6ade9232240d55c47ec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-19.335399979737 13.529968429578 7.198781703538 0 0 0 +H +0.0 +2 +-20.797935387402 14.000687097843 6.199364913120 0 0 0 +-19.981206545379 13.371044018314 8.841774599790 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/conv new file mode 100644 index 0000000000000000000000000000000000000000..9f0f1e13da4a3d4f85a9a553cc40629991bd8642 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/conv @@ -0,0 +1 @@ +109 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..fa58cb4678a21e3c27b87e176f83c4acb247d077 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749592942 0.01279398726 1.287452669 1.375767811 1.470303148 0.008723598799 0.01882857971 0.03904031579 +3.363881835e-19 0.00113441835 0.002738135722 0.01299372001 0.04729526958 -2.114405995e-19 2.323069252e-06 6.489527355e-06 +0.001645912242 0.005968046014 + +H atom_index 1 n_descriptor 18 +1.246025161 0.03439857643 0.1075174131 0.1479918587 0.3193099395 0.02227718284 0.02806074594 0.0374961376 +2.25735806e-17 4.904448315e-05 0.1024305551 0.114623666 0.1271782927 6.06444764e-18 4.369960718e-06 0.01324343746 +0.02660813606 0.03060297959 + +H atom_index 2 n_descriptor 18 +1.293726432 0.03282810631 0.1251533386 0.1714280616 0.3336189127 0.0244889372 0.03080583509 0.03648896176 +-5.148124304e-17 5.363674373e-05 0.1083682348 0.1223819772 0.1471849904 1.209412074e-17 1.686388207e-06 0.01353770977 +0.02823625163 0.03255522033 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..8e4b0994eb2ef1154bb47243fb27b400bfb86206 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..c0ce903606d1c2d5bf69ecbd74f3d57a542cbfbe Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..bf6dd8b875ae8d63ccf53ec4eb0c426262d4bc00 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..66745a03c6b51c72eb9f59a7948275e82e5c106b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..0a0944f10f732c165f362ff9c3b5fa98380f244f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:34 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733212 SEC) : SETUP UNITCELL + DONE(0.0736194 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0899025 SEC) : INIT PLANEWAVE + DONE(0.131482 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374291 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651253e+02 0.000000e+00 2.177e-01 5.060e-01 + GE2 -4.663802e+02 -1.254943e+00 9.776e-02 4.797e-01 + GE3 -4.663850e+02 -4.756674e-03 6.258e-02 5.431e-01 + GE4 -4.663853e+02 -3.023894e-04 2.035e-03 4.216e-01 + GE5 -4.663842e+02 1.063287e-03 9.671e-04 4.187e-01 + GE6 -4.663849e+02 -6.681315e-04 1.145e-04 3.995e-01 + GE7 -4.663847e+02 2.188731e-04 4.848e-05 4.107e-01 + GE8 -4.663847e+02 -4.755083e-05 1.525e-05 4.002e-01 + GE9 -4.663847e+02 2.137198e-05 2.195e-06 4.002e-01 + GE10 -4.663847e+02 -2.528673e-06 1.236e-07 3.980e-01 + GE11 -4.663847e+02 -6.161758e-07 4.732e-08 3.298e-01 +E_delta_band = -7.20486811e-02 Ry = -9.80272596e-01 eV +E_delta_NN= -1.95565664e-01 Ry = -2.66080736e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6293 11 0.6 1e+02 % + Run_lcao lcao_line 6.6222 1 6.6 1e+02 % + Potential init_pot 0.23898 2 0.12 3.6 % + PW_Basis recip2real 0.23251 16 0.015 3.5 % + PW_Basis gathers_scatterp 0.10318 16 0.0064 1.6 % + Potential v_of_rho 0.87205 13 0.067 13 % + XC_Functional v_xc 0.2693 14 0.019 4.1 % + H_Hartree_pw v_hartree 0.56816 13 0.044 8.6 % + PW_Basis real2recip 0.58693 38 0.015 8.9 % + PW_Basis gatherp_scatters 0.21791 38 0.0057 3.3 % + ORB_control set_orb_tables 0.89215 1 0.89 13 % + ORB_gen_tables gen_tables 0.89214 1 0.89 13 % + ORB_table_phi init_Table 0.3722 1 0.37 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.36803 126 0.0029 5.6 % + ORB_table_beta init_Table_Beta 0.15488 1 0.15 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15358 56 0.0027 2.3 % + ORB_table_alpha init_Table_Alpha 0.20738 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20577 66 0.0031 3.1 % + LOOP_ions opt_ions 5.285 1 5.3 80 % + ESolver_KS_LCAO Run 4.7612 1 4.8 72 % + HSolverLCAO solve 2.6013 11 0.24 39 % + HamiltLCAO updateHk 1.3318 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3086 11 0.12 20 % + Gint_interface cal_gint 2.0378 23 0.089 31 % + Gint_Gamma distri_vl_value 0.17218 11 0.016 2.6 % + Gint_Gamma distri_vl 2.2939 6 0.38 35 % + LCAO_Deepks cal_projected_DM 5.0999 13 0.39 77 % + LCAO_gen_fixedH add_v_delta 2.1664 6 0.36 33 % + LCAO_DESCRIPTOR add_v_delta 2.1665 6 0.36 33 % + ElecStateLCAO psiToRho 1.2531 11 0.11 19 % + Charge mix_rho 0.75494 10 0.075 11 % + LOOP_ions force_stress 0.52358 1 0.52 7.9 % + Force_Stress_LCAO getForceStress 0.52356 1 0.52 7.9 % + Force_LCAO_gamma ftable_gamma 0.32524 1 0.33 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.28344 1 0.28 4.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:34 2022 + FINISH Time : Wed Sep 28 11:04:41 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/109/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..746d6ab909252fd8612bf50324504b45915b07b1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.569396 0.212817 0.376278 +H 0.563741 0.21121 0.312033 +H 0.619846 0.25734 0.386621 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6770b02418f3410720175f04e55f8b34998612ff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.181 2 + 2 -12.8994 2 + 3 -9.13096 2 + 4 -6.71928 2 + 5 1.14986 0 + 6 4.24938 0 + 7 11.1033 0 + 8 11.3512 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1e003e67609c585a355e9e8ef998b1d54ef384de --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:35 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.9430830214 5.95887060485 10.535792843 0 0 0 0 + tauc_H1 15.7847533095 5.91388709666 8.73693444274 0 0 0 0 + tauc_H2 17.3556921075 7.20551569062 10.8253742429 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0730421827492 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0733736060117 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0905673188955 (SEC) + + DONE : INIT CHARGE Time : 0.132780097963 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375171 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132 + + Density error is 0.213704541583 + + Energy Rydberg eV + E_KohnSham -34.1891244302 -465.166901882 + E_Harris -34.3785136825 -467.743674853 + E_Fermi -0.398304821651 -5.41921511533 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125481082427 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128590325326 + + Density error is 0.0984020315704 + + Energy Rydberg eV + E_KohnSham -34.2786273523 -466.384651609 + E_Harris -34.2855564575 -466.478926922 + E_Fermi -0.207785132902 -2.82706176716 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118550204716 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120643072847 + + Density error is 0.063321357925 + + Energy Rydberg eV + E_KohnSham -34.2789980376 -466.389695042 + E_Harris -34.2834642409 -466.450460855 + E_Fermi -0.198780011206 -2.70454080091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107446356085 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107463893488 + + Density error is 0.0019759127949 + + Energy Rydberg eV + E_KohnSham -34.2789458115 -466.38898447 + E_Harris -34.2789467409 -466.388997114 + E_Fermi -0.163277317835 -2.22150187671 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107360885256 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107343112137 + + Density error is 0.000912014343501 + + Energy Rydberg eV + E_KohnSham -34.2788971397 -466.388322255 + E_Harris -34.2788982295 -466.388337084 + E_Fermi -0.162903263966 -2.21641261273 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107211509417 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107165868728 + + Density error is 0.000168657942931 + + Energy Rydberg eV + E_KohnSham -34.2789230059 -466.388674183 + E_Harris -34.2789228823 -466.388672502 + E_Fermi -0.162661596391 -2.2131245567 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010723380412 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107183454075 + + Density error is 3.4816593785e-05 + + Energy Rydberg eV + E_KohnSham -34.2789137769 -466.388548616 + E_Harris -34.2789137818 -466.388548683 + E_Fermi -0.162590425904 -2.21215623254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010722522938 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107176086921 + + Density error is 1.53780712271e-05 + + Energy Rydberg eV + E_KohnSham -34.2789173634 -466.388597414 + E_Harris -34.2789175246 -466.388599607 + E_Fermi -0.162618267001 -2.21253503009 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107224578289 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107174981369 + + Density error is 2.84721879781e-06 + + Energy Rydberg eV + E_KohnSham -34.2789161167 -466.388580451 + E_Harris -34.2789161167 -466.388580452 + E_Fermi -0.162603752633 -2.21233755199 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107224400147 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107174678717 + + Density error is 4.49580537019e-07 + + Energy Rydberg eV + E_KohnSham -34.2789163132 -466.388583124 + E_Harris -34.2789163132 -466.388583124 + E_Fermi -0.162600892535 -2.21229863837 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001072244226 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107174688278 + + Density error is 1.73021001958e-07 + + Energy Rydberg eV + E_KohnSham -34.2789163485 -466.388583605 + E_Harris -34.2789163485 -466.388583605 + E_Fermi -0.162600706346 -2.21229610513 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010722442351 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107174681716 + + Density error is 1.07544827105e-08 + + Energy Rydberg eV + E_KohnSham -34.2789163501 -466.388583627 + E_Harris -34.2789163501 -466.388583627 + E_band -7.92764820974 -107.861187392 + E_one_elec -69.0280197038 -939.174389628 + E_Hartree +35.914826235 +488.646279476 + E_xc -8.1897419772 -111.42715604 + E_Ewald +7.14887721976 +97.2654644912 + E_demet -5.64826399927e-69 -7.68485741983e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194377732828 -2.64464473079 + E_Fermi -0.162600546449 -2.21229392962 + + charge density convergence is achieved + final etot is -466.388583627 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1810 2.00000 + 2 -12.8994 2.00000 + 3 -9.13096 2.00000 + 4 -6.71928 2.00000 + 5 1.14986 0.00000 + 6 4.24938 0.00000 + 7 11.1033 0.00000 + 8 11.3512 0.00000 + + EFERMI = -2.212293929621358 eV + OUT.ABACUS/ final etot is -466.3885836267669 eV + correction force for each atom along direction 1 is 0.000107905 + correction force for each atom along direction 2 is -5.37875e-05 + correction force for each atom along direction 3 is -0.000118538 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.2061323 +1.0014326 +1.2717334 + H1 -0.11933465 -0.044829407 -1.0795977 + H2 -1.0867977 -0.95660322 -0.19213573 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3885836267669 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9165 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9095 1 6.9 1.e+02% + Potential init_pot 0.23974 2 0.12 3.5% + PW_Basis recip2real 0.23734 17 0.014 3.4% + PW_Basis gathers_scatterp 0.11227 17 0.0066 1.6% + Potential v_of_rho 0.94380 14 0.067 14.% + XC_Functional v_xc 0.30247 15 0.020 4.4% + H_Hartree_pw v_hartree 0.60722 14 0.043 8.8% + PW_Basis real2recip 0.64939 41 0.016 9.4% + PW_Basis gatherp_scatters 0.29274 41 0.0071 4.2% + ORB_control set_orb_tables 0.89390 1 0.89 13.% + ORB_gen_tables gen_tables 0.89389 1 0.89 13.% + ORB_table_phi init_Table 0.37553 1 0.38 5.4% + ORB_table_phi cal_ST_Phi12_R 0.37136 126 0.0029 5.4% + ORB_table_beta init_Table_Beta 0.15309 1 0.15 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15174 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20725 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20559 66 0.0031 3.0% + LOOP_ions opt_ions 5.5710 1 5.6 81.% + ESolver_KS_LCAO Run 5.0177 1 5.0 73.% + HSolverLCAO solve 2.6587 12 0.22 38.% + HamiltLCAO updateHk 1.3448 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.3196 12 0.11 19.% + Gint_interface cal_gint 0.64106 25 0.026 9.3% + Gint_Gamma distri_vl_value 0.69173 12 0.058 10.% + Gint_Gamma distri_vl 2.6079 6 0.43 38.% + LCAO_Deepks cal_projected_DM 5.2013 14 0.37 75.% + LCAO_gen_fixedH add_v_delta 2.4784 6 0.41 36.% + LCAO_DESCRIPTOR add_v_delta 2.4784 6 0.41 36.% + ElecStateLCAO psiToRho 1.2958 12 0.11 19.% + Charge mix_rho 0.81526 11 0.074 12.% + LOOP_ions force_stress 0.55316 1 0.55 8.0% + Force_Stress_LCAO getForceStress 0.55314 1 0.55 8.0% + Force_LCAO_gamma ftable_gamma 0.36020 1 0.36 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.12960 1 0.13 1.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:35 2022 + Finish Time : Wed Sep 28 11:03:42 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..7a9c13424e42e9b3a323f048e458c4d0546a56fa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123513 ima = 3.69121e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123344155108 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112093119765 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011274958453 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112978125752 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112944560539 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112965183317 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112958567773 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112961079154 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112960454152 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001129603561 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112960342763 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112960333721 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/STRU new file mode 100644 index 0000000000000000000000000000000000000000..dd01dd91566126b114fb0c17405b3345bfe4ea7e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.056916978544 5.958870604835 10.535792843020 0 0 0 +H +0.0 +2 +-12.215246690541 5.913887096648 8.736934442740 0 0 0 +-10.644307892449 7.205515690615 10.825374242856 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/conv new file mode 100644 index 0000000000000000000000000000000000000000..829da12b797422047c3461a20bb2cf33e1fc3fca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/conv @@ -0,0 +1 @@ +11 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..90fa1603e25cab553bcd42bee53145ee7e42d457 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750050689 0.01256902533 1.257860514 1.355886499 1.468873604 0.008570478502 0.01816911593 0.03907505991 +2.709751369e-19 0.0009759602266 0.002543590553 0.01201684 0.0439335567 -4.377044156e-19 1.88780019e-06 5.654335573e-06 +0.001619941043 0.005912067473 + +H atom_index 1 n_descriptor 18 +1.267586595 0.03371571182 0.1143064434 0.1584463452 0.3268142719 0.0229906878 0.0293412673 0.03703143868 +-1.296477317e-17 4.533585579e-05 0.1043501054 0.1163476709 0.1359221056 3.33299892e-18 3.04815851e-06 0.01313594789 +0.02666901561 0.03152435708 + +H atom_index 2 n_descriptor 18 +1.188763678 0.0363315743 0.08861101298 0.1237847649 0.2995539343 0.01933008275 0.0247390054 0.0398395831 +-2.167900905e-17 3.835348167e-05 0.08462208647 0.1057452826 0.112928294 7.270241923e-18 6.56052341e-06 0.01448071145 +0.0235845442 0.02768217043 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ede1017c0fe021e881540439cedbee4ac73efad8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:35 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0730565 SEC) : SETUP UNITCELL + DONE(0.0733839 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0905817 SEC) : INIT PLANEWAVE + DONE(0.132882 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.375214 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651669e+02 0.000000e+00 2.137e-01 4.975e-01 + GE2 -4.663847e+02 -1.217750e+00 9.840e-02 4.659e-01 + GE3 -4.663897e+02 -5.043433e-03 6.332e-02 5.294e-01 + GE4 -4.663890e+02 7.105724e-04 1.976e-03 4.047e-01 + GE5 -4.663883e+02 6.622141e-04 9.120e-04 4.043e-01 + GE6 -4.663887e+02 -3.519280e-04 1.687e-04 4.031e-01 + GE7 -4.663885e+02 1.255672e-04 3.482e-05 3.910e-01 + GE8 -4.663886e+02 -4.879737e-05 1.538e-05 3.882e-01 + GE9 -4.663886e+02 1.696217e-05 2.847e-06 3.878e-01 + GE10 -4.663886e+02 -2.672749e-06 4.496e-07 3.866e-01 + GE11 -4.663886e+02 -4.805076e-07 1.730e-07 3.845e-01 + GE12 -4.663886e+02 -2.204899e-08 1.075e-08 3.198e-01 +E_delta_band = -6.95196089e-02 Ry = -9.45862804e-01 eV +E_delta_NN= -1.94377733e-01 Ry = -2.64464473e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9165 11 0.63 1e+02 % + Run_lcao lcao_line 6.9095 1 6.9 1e+02 % + Potential init_pot 0.23974 2 0.12 3.5 % + PW_Basis recip2real 0.23734 17 0.014 3.4 % + PW_Basis gathers_scatterp 0.11227 17 0.0066 1.6 % + Potential v_of_rho 0.9438 14 0.067 14 % + XC_Functional v_xc 0.30247 15 0.02 4.4 % + H_Hartree_pw v_hartree 0.60722 14 0.043 8.8 % + PW_Basis real2recip 0.64939 41 0.016 9.4 % + PW_Basis gatherp_scatters 0.29274 41 0.0071 4.2 % + ORB_control set_orb_tables 0.8939 1 0.89 13 % + ORB_gen_tables gen_tables 0.89389 1 0.89 13 % + ORB_table_phi init_Table 0.37553 1 0.38 5.4 % + ORB_table_phi cal_ST_Phi12_R 0.37136 126 0.0029 5.4 % + ORB_table_beta init_Table_Beta 0.15309 1 0.15 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15174 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20725 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20559 66 0.0031 3 % + LOOP_ions opt_ions 5.571 1 5.6 81 % + ESolver_KS_LCAO Run 5.0177 1 5 73 % + HSolverLCAO solve 2.6587 12 0.22 38 % + HamiltLCAO updateHk 1.3448 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.3196 12 0.11 19 % + Gint_interface cal_gint 0.64106 25 0.026 9.3 % + Gint_Gamma distri_vl_value 0.69173 12 0.058 10 % + Gint_Gamma distri_vl 2.6079 6 0.43 38 % + LCAO_Deepks cal_projected_DM 5.2013 14 0.37 75 % + LCAO_gen_fixedH add_v_delta 2.4784 6 0.41 36 % + LCAO_DESCRIPTOR add_v_delta 2.4784 6 0.41 36 % + ElecStateLCAO psiToRho 1.2958 12 0.11 19 % + Charge mix_rho 0.81526 11 0.074 12 % + LOOP_ions force_stress 0.55316 1 0.55 8 % + Force_Stress_LCAO getForceStress 0.55314 1 0.55 8 % + Force_LCAO_gamma ftable_gamma 0.3602 1 0.36 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.1296 1 0.13 1.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:35 2022 + FINISH Time : Wed Sep 28 11:03:42 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/11/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..0526d0b7c8bcddc28e0b61625f9111fab6809588 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.322214 0.498454 0.242218 +H 0.285884 0.553243 0.231068 +H 0.282534 0.476172 0.292086 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..90553687455a8d28751b7c8af9e8dfe9584805ae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2252 2 + 2 -12.3277 2 + 3 -9.59455 2 + 4 -6.73716 2 + 5 1.01014 0 + 6 3.97466 0 + 7 11.1205 0 + 8 11.4204 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..6369143cde8f9e676aba26368ecef8fd755c5eb3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:22 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.02199452819 13.956706671 6.78210019768 0 0 0 0 + tauc_H1 8.00474766986 15.4908060687 6.46989750532 0 0 0 0 + tauc_H2 7.91094232756 13.3328054905 8.17839542709 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.08782094386 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0882351349023 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106392973287 (SEC) + + DONE : INIT CHARGE Time : 0.151063966575 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.428202 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000743 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107 + + Density error is 0.209787745984 + + Energy Rydberg eV + E_KohnSham -34.1886304455 -465.160180875 + E_Harris -34.3708806744 -467.63982245 + E_Fermi -0.391081886207 -5.320942037 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00104675253886 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111899724181 + + Density error is 0.0979180765419 + + Energy Rydberg eV + E_KohnSham -34.2758155393 -466.346394931 + E_Harris -34.2830013785 -466.444163289 + E_Fermi -0.203611389911 -2.77027508049 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000997710970394 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105354403956 + + Density error is 0.0631544324482 + + Energy Rydberg eV + E_KohnSham -34.2762237293 -466.351948641 + E_Harris -34.2808409717 -466.414769447 + E_Fermi -0.196593718704 -2.67479476539 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000938611938011 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959626613725 + + Density error is 0.00185820681194 + + Energy Rydberg eV + E_KohnSham -34.2761229417 -466.350577356 + E_Harris -34.2761224207 -466.350570267 + E_Fermi -0.160990478169 -2.19038782684 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000940308732474 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000961586815207 + + Density error is 0.000939578814332 + + Energy Rydberg eV + E_KohnSham -34.2760898119 -466.350126602 + E_Harris -34.2760905082 -466.350136076 + E_Fermi -0.161153948194 -2.19261195064 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000939305814731 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000960163203143 + + Density error is 9.5469781374e-05 + + Energy Rydberg eV + E_KohnSham -34.2761063398 -466.350351475 + E_Harris -34.2761063405 -466.350351485 + E_Fermi -0.16070959346 -2.18656619432 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000939128716672 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959987351966 + + Density error is 2.06179485889e-05 + + Energy Rydberg eV + E_KohnSham -34.2761029256 -466.350305022 + E_Harris -34.2761029277 -466.350305051 + E_Fermi -0.16062525069 -2.18541865206 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000939105493516 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00095997930462 + + Density error is 7.79724688147e-06 + + Energy Rydberg eV + E_KohnSham -34.2761036588 -466.350314998 + E_Harris -34.276103659 -466.350315002 + E_Fermi -0.160647674635 -2.18572374549 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000939116921338 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959988204489 + + Density error is 1.75352256844e-06 + + Energy Rydberg eV + E_KohnSham -34.2761029262 -466.35030503 + E_Harris -34.2761029262 -466.350305031 + E_Fermi -0.16064196209 -2.18564602232 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000939117803903 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959986387986 + + Density error is 2.9754250761e-07 + + Energy Rydberg eV + E_KohnSham -34.2761030512 -466.350306732 + E_Harris -34.2761030512 -466.350306732 + E_Fermi -0.160640458113 -2.18562555967 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000939118298738 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959986789636 + + Density error is 5.39542172957e-08 + + Energy Rydberg eV + E_KohnSham -34.2761030722 -466.350307018 + E_Harris -34.2761030722 -466.350307018 + E_band -7.92089213436 -107.769266271 + E_one_elec -68.7965861803 -936.025575 + E_Hartree +35.7888067042 +486.931695798 + E_xc -8.1690220956 -111.145247588 + E_Ewald +7.02597054424 +95.5932333818 + E_demet -1.41840216573e-62 -1.92983515095e-61 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193975844644 -2.63917676152 + E_Fermi -0.160640259739 -2.18562286065 + + charge density convergence is achieved + final etot is -466.350307018 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2252 2.00000 + 2 -12.3277 2.00000 + 3 -9.59455 2.00000 + 4 -6.73716 2.00000 + 5 1.01014 0.00000 + 6 3.97466 0.00000 + 7 11.1205 0.00000 + 8 11.4204 0.00000 + + EFERMI = -2.185622860654937 eV + OUT.ABACUS/ final etot is -466.3503070177163 eV + correction force for each atom along direction 1 is -0.000185438 + correction force for each atom along direction 2 is 0.000108755 + correction force for each atom along direction 3 is 2.58070e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.5538100 +0.35570696 +1.0224178 + H1 +0.62990303 -0.040557880 -0.49255536 + H2 +0.92390701 -0.31514908 -0.52986242 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3503070177163 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2025 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1927 1 6.2 1.e+02% + Potential init_pot 0.27844 2 0.14 4.5% + PW_Basis recip2real 0.26703 16 0.017 4.3% + PW_Basis gathers_scatterp 0.11833 16 0.0074 1.9% + Potential v_of_rho 0.96365 13 0.074 16.% + XC_Functional v_xc 0.27975 14 0.020 4.5% + H_Hartree_pw v_hartree 0.63952 13 0.049 10.% + PW_Basis real2recip 0.68864 38 0.018 11.% + PW_Basis gatherp_scatters 0.27022 38 0.0071 4.4% + ORB_control set_orb_tables 1.0908 1 1.1 18.% + ORB_gen_tables gen_tables 1.0908 1 1.1 18.% + ORB_table_phi init_Table 0.47298 1 0.47 7.6% + ORB_table_phi cal_ST_Phi12_R 0.46782 126 0.0037 7.5% + ORB_table_beta init_Table_Beta 0.18226 1 0.18 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18069 56 0.0032 2.9% + ORB_table_alpha init_Table_Alpha 0.24860 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.24662 66 0.0037 4.0% + LOOP_ions opt_ions 4.5968 1 4.6 74.% + ESolver_KS_LCAO Run 4.1232 1 4.1 66.% + HSolverLCAO solve 1.7003 11 0.15 27.% + HamiltLCAO updateHk 0.95838 11 0.087 15.% + LCAO_Hamilt cal_Hgamma 0.93091 11 0.085 15.% + Gint_interface cal_gint 1.4255 23 0.062 23.% + Gint_Gamma distri_vl 2.0014 6 0.33 32.% + LCAO_Deepks cal_projected_DM 4.4601 13 0.34 72.% + LCAO_gen_fixedH add_v_delta 1.8534 6 0.31 30.% + LCAO_DESCRIPTOR add_v_delta 1.8534 6 0.31 30.% + ElecStateLCAO psiToRho 0.72219 11 0.066 12.% + Charge mix_rho 0.90193 10 0.090 15.% + LOOP_ions force_stress 0.47342 1 0.47 7.6% + Force_Stress_LCAO getForceStress 0.47340 1 0.47 7.6% + Force_LCAO_gamma ftable_gamma 0.26182 1 0.26 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.25365 1 0.25 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:22 2022 + Finish Time : Wed Sep 28 11:09:28 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..03f4ce4e8face2a4ef5077c55413644513c2f037 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123455 ima = 3.66264e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122676403841 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111242859802 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112040272413 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112262562254 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112240830463 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112251887659 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112251281474 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112252787968 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112252395945 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112252331346 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112252314643 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/STRU new file mode 100644 index 0000000000000000000000000000000000000000..027a15721427a5c2bbff17503c39a609187a228d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.978005471816 13.956706671022 6.782100197702 0 0 0 +H +0.0 +2 +-19.995252330130 15.490806068630 6.469897505313 0 0 0 +-20.089057672416 13.332805490497 8.178395427074 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/conv new file mode 100644 index 0000000000000000000000000000000000000000..b3e56b9bb81ecdc5ea914b8f6525940e9ae60a11 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/conv @@ -0,0 +1 @@ +110 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..09b77d826c7fd55e5a9e9164e650db00c3908652 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.757228978 0.01268389994 1.250615257 1.326500224 1.468966569 0.0100183938 0.01525825846 0.03929919203 +-1.340430556e-18 0.0007161889353 0.002797214818 0.01331764932 0.04445434462 3.187226162e-19 2.72949837e-06 7.51736793e-06 +0.001584568439 0.006119974249 + +H atom_index 1 n_descriptor 18 +1.225315438 0.03606731649 0.1049803006 0.1385385746 0.3108361047 0.02252353677 0.02677486999 0.0392479688 +-2.335026997e-17 4.28908785e-05 0.09595248593 0.1146591083 0.1184070501 2.709560367e-18 3.188172396e-06 0.0138522414 +0.02599784477 0.02952736096 + +H atom_index 2 n_descriptor 18 +1.207151041 0.03663769146 0.09898116155 0.1307684013 0.3040708048 0.02159971192 0.025698946 0.03995635467 +2.668019997e-17 4.137643831e-05 0.09140411531 0.1116096834 0.1137154599 1.271745514e-19 4.016748817e-06 0.01429735877 +0.02525730494 0.02858416471 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..6bc4b7eae761da2197fda8f07ba9d27c53101251 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:22 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0878434 SEC) : SETUP UNITCELL + DONE(0.088253 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106412 SEC) : INIT PLANEWAVE + DONE(0.151203 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.42827 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651602e+02 0.000000e+00 2.098e-01 4.777e-01 + GE2 -4.663464e+02 -1.186214e+00 9.792e-02 4.306e-01 + GE3 -4.663519e+02 -5.553710e-03 6.315e-02 4.996e-01 + GE4 -4.663506e+02 1.371285e-03 1.858e-03 3.583e-01 + GE5 -4.663501e+02 4.507541e-04 9.396e-04 3.554e-01 + GE6 -4.663504e+02 -2.248734e-04 9.547e-05 3.394e-01 + GE7 -4.663503e+02 4.645346e-05 2.062e-05 3.319e-01 + GE8 -4.663503e+02 -9.975966e-06 7.797e-06 3.338e-01 + GE9 -4.663503e+02 9.967617e-06 1.754e-06 3.352e-01 + GE10 -4.663503e+02 -1.701342e-06 2.975e-07 3.336e-01 + GE11 -4.663503e+02 -2.859950e-07 5.395e-08 2.646e-01 +E_delta_band = -6.87037998e-02 Ry = -9.34763152e-01 eV +E_delta_NN= -1.93975845e-01 Ry = -2.63917676e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2025 11 0.56 1e+02 % + Run_lcao lcao_line 6.1927 1 6.2 1e+02 % + Potential init_pot 0.27844 2 0.14 4.5 % + PW_Basis recip2real 0.26703 16 0.017 4.3 % + PW_Basis gathers_scatterp 0.11833 16 0.0074 1.9 % + Potential v_of_rho 0.96365 13 0.074 16 % + XC_Functional v_xc 0.27975 14 0.02 4.5 % + H_Hartree_pw v_hartree 0.63952 13 0.049 10 % + PW_Basis real2recip 0.68864 38 0.018 11 % + PW_Basis gatherp_scatters 0.27022 38 0.0071 4.4 % + ORB_control set_orb_tables 1.0908 1 1.1 18 % + ORB_gen_tables gen_tables 1.0908 1 1.1 18 % + ORB_table_phi init_Table 0.47298 1 0.47 7.6 % + ORB_table_phi cal_ST_Phi12_R 0.46782 126 0.0037 7.5 % + ORB_table_beta init_Table_Beta 0.18226 1 0.18 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18069 56 0.0032 2.9 % + ORB_table_alpha init_Table_Alpha 0.2486 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.24662 66 0.0037 4 % + LOOP_ions opt_ions 4.5968 1 4.6 74 % + ESolver_KS_LCAO Run 4.1232 1 4.1 66 % + HSolverLCAO solve 1.7003 11 0.15 27 % + HamiltLCAO updateHk 0.95838 11 0.087 15 % + LCAO_Hamilt cal_Hgamma 0.93091 11 0.085 15 % + Gint_interface cal_gint 1.4255 23 0.062 23 % + Gint_Gamma distri_vl 2.0014 6 0.33 32 % + LCAO_Deepks cal_projected_DM 4.4601 13 0.34 72 % + LCAO_gen_fixedH add_v_delta 1.8534 6 0.31 30 % + LCAO_DESCRIPTOR add_v_delta 1.8534 6 0.31 30 % + ElecStateLCAO psiToRho 0.72219 11 0.066 12 % + Charge mix_rho 0.90193 10 0.09 15 % + LOOP_ions force_stress 0.47342 1 0.47 7.6 % + Force_Stress_LCAO getForceStress 0.4734 1 0.47 7.6 % + Force_LCAO_gamma ftable_gamma 0.26182 1 0.26 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.25365 1 0.25 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:22 2022 + FINISH Time : Wed Sep 28 11:09:28 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/110/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..55a44bddbb371b3f34a37d4eee8c813b8798b39c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.336198 0.511225 0.225374 +H 0.344845 0.575255 0.230999 +H 0.302137 0.48788 0.273616 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..eb752ea707816ebe9f6b7b14d727fb69c4a003f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3643 2 + 2 -13.5939 2 + 3 -8.77559 2 + 4 -6.75917 2 + 5 1.50363 0 + 6 4.78132 0 + 7 11.033 0 + 8 11.242 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..63b1b5cde59e13bbacfefa5a6a0ba3edff6c0ac7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:26 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.41353255822 14.3142898819 6.31046290975 0 0 0 0 + tauc_H1 9.65565772625 16.1071306975 6.46797823596 0 0 0 0 + tauc_H2 8.45982869478 13.6606470971 7.66123716017 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.114806259314 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.115404055505 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.145028433841 (SEC) + + DONE : INIT CHARGE Time : 0.189095358882 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.470219 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 144 0 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000737 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125 + + Density error is 0.218183547412 + + Energy Rydberg eV + E_KohnSham -34.1865569358 -465.131969328 + E_Harris -34.3849276601 -467.830941496 + E_Fermi -0.416974709941 -5.67323197709 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000929930423021 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138341905718 + + Density error is 0.0976020718921 + + Energy Rydberg eV + E_KohnSham -34.2767318865 -466.358862474 + E_Harris -34.2832297236 -466.447270084 + E_Fermi -0.224136350066 -3.04953148981 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000882488617656 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131087762003 + + Density error is 0.0621888364122 + + Energy Rydberg eV + E_KohnSham -34.2768825579 -466.360912465 + E_Harris -34.280987816 -466.416767367 + E_Fermi -0.209075901503 -2.84462357493 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000807864499043 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119935498384 + + Density error is 0.00215801506785 + + Energy Rydberg eV + E_KohnSham -34.27693989 -466.361692508 + E_Harris -34.2769438969 -466.361747024 + E_Fermi -0.173892860982 -2.36593375088 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000807085479468 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120034591514 + + Density error is 0.000860356928068 + + Energy Rydberg eV + E_KohnSham -34.2768720575 -466.3607696 + E_Harris -34.2768740037 -466.360796078 + E_Fermi -0.172526641357 -2.34734537926 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000806261165336 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001198931601 + + Density error is 0.000252303627772 + + Energy Rydberg eV + E_KohnSham -34.2769213224 -466.361439882 + E_Harris -34.2769215778 -466.361443357 + E_Fermi -0.172905751311 -2.3525034348 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000806381585335 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119908564955 + + Density error is 4.47844230954e-05 + + Energy Rydberg eV + E_KohnSham -34.2769001299 -466.361151544 + E_Harris -34.2769001404 -466.361151686 + E_Fermi -0.172640160772 -2.34888989014 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000806354499686 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011990512382 + + Density error is 1.7220751053e-05 + + Energy Rydberg eV + E_KohnSham -34.2769071858 -466.361247545 + E_Harris -34.2769071868 -466.361247558 + E_Fermi -0.172693865307 -2.34962057783 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000806342527077 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011990365695 + + Density error is 2.63364840998e-06 + + Energy Rydberg eV + E_KohnSham -34.2769057788 -466.3612284 + E_Harris -34.2769057788 -466.361228401 + E_Fermi -0.17267634959 -2.34938226427 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000806340518403 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119903114843 + + Density error is 4.16460594454e-07 + + Energy Rydberg eV + E_KohnSham -34.2769059541 -466.361230785 + E_Harris -34.2769059541 -466.361230785 + E_Fermi -0.172673653398 -2.34934558069 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000806341132456 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119903185574 + + Density error is 1.69513597158e-07 + + Energy Rydberg eV + E_KohnSham -34.2769059879 -466.361231245 + E_Harris -34.2769059879 -466.361231245 + E_Fermi -0.172673500692 -2.34934350302 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000806341293037 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011990319582 + + Density error is 9.24815778215e-09 + + Energy Rydberg eV + E_KohnSham -34.2769059891 -466.361231263 + E_Harris -34.2769059891 -466.361231263 + E_band -8.01032697908 -108.986089759 + E_one_elec -69.7167978963 -948.545697704 + E_Hartree +36.2535458273 +493.254795955 + E_xc -8.24379479636 -112.162582373 + E_Ewald +7.55365458007 +102.772743013 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195423186832 -2.65886886224 + E_Fermi -0.172673341384 -2.34934133552 + + charge density convergence is achieved + final etot is -466.361231263 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3643 2.00000 + 2 -13.5939 2.00000 + 3 -8.77559 2.00000 + 4 -6.75917 2.00000 + 5 1.50363 0.00000 + 6 4.78132 0.00000 + 7 11.0330 0.00000 + 8 11.2420 0.00000 + + EFERMI = -2.349341335524622 eV + OUT.ABACUS/ final etot is -466.3612312625931 eV + correction force for each atom along direction 1 is -4.13837e-05 + correction force for each atom along direction 2 is 5.51881e-05 + correction force for each atom along direction 3 is 0.000139918 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.1403684 -0.32689821 -1.9533287 + H1 -0.17460966 +0.52663311 +0.44464099 + H2 -0.96575872 -0.19973490 +1.5086878 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3612312625931 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3599 11 0.58 1.0e+02% + Run_lcao lcao_line 6.3493 1 6.3 1.e+02% + Potential init_pot 0.28124 2 0.14 4.4% + PW_Basis recip2real 0.28376 17 0.017 4.5% + PW_Basis gathers_scatterp 0.12722 17 0.0075 2.0% + Potential v_of_rho 1.0410 14 0.074 16.% + XC_Functional v_xc 0.31369 15 0.021 4.9% + H_Hartree_pw v_hartree 0.68242 14 0.049 11.% + PW_Basis real2recip 0.73581 41 0.018 12.% + PW_Basis gatherp_scatters 0.28363 41 0.0069 4.5% + ORB_control set_orb_tables 1.0931 1 1.1 17.% + ORB_gen_tables gen_tables 1.0931 1 1.1 17.% + ORB_table_phi init_Table 0.47357 1 0.47 7.4% + ORB_table_phi cal_ST_Phi12_R 0.46832 126 0.0037 7.4% + ORB_table_beta init_Table_Beta 0.18300 1 0.18 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18151 56 0.0032 2.9% + ORB_table_alpha init_Table_Alpha 0.24796 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.24598 66 0.0037 3.9% + LOOP_ions opt_ions 4.7106 1 4.7 74.% + ESolver_KS_LCAO Run 4.2613 1 4.3 67.% + HSolverLCAO solve 1.6321 12 0.14 26.% + HamiltLCAO updateHk 0.92788 12 0.077 15.% + LCAO_Hamilt cal_Hgamma 0.89855 12 0.075 14.% + Gint_interface cal_gint 1.2058 25 0.048 19.% + Gint_Gamma distri_vl 2.2404 6 0.37 35.% + LCAO_Deepks cal_projected_DM 4.5680 14 0.33 72.% + LCAO_gen_fixedH add_v_delta 2.0917 6 0.35 33.% + LCAO_DESCRIPTOR add_v_delta 2.0918 6 0.35 33.% + ElecStateLCAO psiToRho 0.68448 12 0.057 11.% + Charge mix_rho 0.98686 11 0.090 16.% + LOOP_ions force_stress 0.44910 1 0.45 7.1% + Force_Stress_LCAO getForceStress 0.44907 1 0.45 7.1% + Force_LCAO_gamma ftable_gamma 0.23470 1 0.23 3.7% + Force_LCAO_gamma cal_fvl_dphi 0.21492 1 0.21 3.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:26 2022 + Finish Time : Wed Sep 28 11:12:33 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..35d6e74504e81c829c44719be1fa2168ed8cd62f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123811 ima = 3.69389e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123469019295 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112971191269 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113302157366 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113555573281 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113491737611 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113533256856 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113519228115 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113522171715 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113521627623 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113521536634 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113521525243 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113521517407 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0ad0c6148109083105f38bde1a5878f0776b24d5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.586467441787 14.314289881892 6.310462909758 0 0 0 +H +0.0 +2 +-18.344342273779 16.107130697449 6.467978235966 0 0 0 +-19.540171305229 13.660647097089 7.661237160141 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/conv new file mode 100644 index 0000000000000000000000000000000000000000..2b9447e844491ca7d9072927ffbf93fc7e954f4e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/conv @@ -0,0 +1 @@ +111 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..212149717d4f90108ccf9aedd25b73bae571e460 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742527452 0.01269652275 1.296445178 1.38649191 1.469903436 0.007642614897 0.02123729275 0.03883967271 +2.110190923e-18 0.001260031139 0.002403980572 0.01295171811 0.0437154167 1.016219507e-18 1.548038726e-06 4.910049506e-06 +0.001832819729 0.005525937841 + +H atom_index 1 n_descriptor 18 +1.251908449 0.03335168895 0.110086555 0.1525979016 0.3239919351 0.02200535054 0.02864418563 0.03653474512 +-1.033976575e-17 3.936508551e-05 0.1039499259 0.1148675039 0.1311792349 -3.185824039e-19 4.07742576e-06 0.01281313787 +0.02648851726 0.03101602444 + +H atom_index 2 n_descriptor 18 +1.282275166 0.0323034409 0.1211377207 0.1673923342 0.3326677371 0.02327188502 0.03037006974 0.03591953357 +1.862668699e-17 4.18296055e-05 0.1079771215 0.11947637 0.143815823 5.917557092e-18 2.599227632e-06 0.01301538147 +0.02752671478 0.03223048117 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..718cebcd30b564501221c740cd3c97d5569a749f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:26 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.114845 SEC) : SETUP UNITCELL + DONE(0.115423 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.145049 SEC) : INIT PLANEWAVE + DONE(0.189236 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.470288 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651320e+02 0.000000e+00 2.182e-01 4.597e-01 + GE2 -4.663589e+02 -1.226893e+00 9.760e-02 4.121e-01 + GE3 -4.663609e+02 -2.049990e-03 6.219e-02 4.820e-01 + GE4 -4.663617e+02 -7.800432e-04 2.158e-03 3.418e-01 + GE5 -4.663608e+02 9.229081e-04 8.604e-04 3.401e-01 + GE6 -4.663614e+02 -6.702827e-04 2.523e-04 3.316e-01 + GE7 -4.663612e+02 2.883384e-04 4.478e-05 3.287e-01 + GE8 -4.663612e+02 -9.600068e-05 1.722e-05 3.136e-01 + GE9 -4.663612e+02 1.914423e-05 2.634e-06 3.157e-01 + GE10 -4.663612e+02 -2.385058e-06 4.165e-07 3.135e-01 + GE11 -4.663612e+02 -4.599390e-07 1.695e-07 3.161e-01 + GE12 -4.663612e+02 -1.718608e-08 9.248e-09 2.434e-01 +E_delta_band = -7.19094830e-02 Ry = -9.78378708e-01 eV +E_delta_NN= -1.95423187e-01 Ry = -2.65886886e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3599 11 0.58 1e+02 % + Run_lcao lcao_line 6.3493 1 6.3 1e+02 % + Potential init_pot 0.28124 2 0.14 4.4 % + PW_Basis recip2real 0.28376 17 0.017 4.5 % + PW_Basis gathers_scatterp 0.12722 17 0.0075 2 % + Potential v_of_rho 1.041 14 0.074 16 % + XC_Functional v_xc 0.31369 15 0.021 4.9 % + H_Hartree_pw v_hartree 0.68242 14 0.049 11 % + PW_Basis real2recip 0.73581 41 0.018 12 % + PW_Basis gatherp_scatters 0.28363 41 0.0069 4.5 % + ORB_control set_orb_tables 1.0931 1 1.1 17 % + ORB_gen_tables gen_tables 1.0931 1 1.1 17 % + ORB_table_phi init_Table 0.47357 1 0.47 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.46832 126 0.0037 7.4 % + ORB_table_beta init_Table_Beta 0.183 1 0.18 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18151 56 0.0032 2.9 % + ORB_table_alpha init_Table_Alpha 0.24796 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.24598 66 0.0037 3.9 % + LOOP_ions opt_ions 4.7106 1 4.7 74 % + ESolver_KS_LCAO Run 4.2613 1 4.3 67 % + HSolverLCAO solve 1.6321 12 0.14 26 % + HamiltLCAO updateHk 0.92788 12 0.077 15 % + LCAO_Hamilt cal_Hgamma 0.89855 12 0.075 14 % + Gint_interface cal_gint 1.2058 25 0.048 19 % + Gint_Gamma distri_vl 2.2404 6 0.37 35 % + LCAO_Deepks cal_projected_DM 4.568 14 0.33 72 % + LCAO_gen_fixedH add_v_delta 2.0917 6 0.35 33 % + LCAO_DESCRIPTOR add_v_delta 2.0918 6 0.35 33 % + ElecStateLCAO psiToRho 0.68448 12 0.057 11 % + Charge mix_rho 0.98686 11 0.09 16 % + LOOP_ions force_stress 0.4491 1 0.45 7.1 % + Force_Stress_LCAO getForceStress 0.44907 1 0.45 7.1 % + Force_LCAO_gamma ftable_gamma 0.2347 1 0.23 3.7 % + Force_LCAO_gamma cal_fvl_dphi 0.21492 1 0.21 3.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:26 2022 + FINISH Time : Wed Sep 28 11:12:33 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/111/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5e34b738ba024db0b628a5e748c0bb9a4b6fe96a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.336089 0.53464 0.223931 +H 0.378811 0.554573 0.270087 +H 0.366548 0.476979 0.209707 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bc83afcb0f6fd932f6d11b736117b6d1c6324c9a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2997 2 + 2 -12.5442 2 + 3 -9.48919 2 + 4 -6.75107 2 + 5 1.13413 0 + 6 4.1688 0 + 7 11.0964 0 + 8 11.387 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..caf13fd6ff6915e769453d27246e0e9eaaf899b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:51 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.41047906713 14.9699210042 6.27007003917 0 0 0 0 + tauc_H1 10.6067076847 15.5280433893 7.56244171614 0 0 0 0 + tauc_H2 10.2633338828 13.3554082877 5.87179633814 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.106081618628 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.10642157935 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124456561497 (SEC) + + DONE : INIT CHARGE Time : 0.167603426476 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451318 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00145 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000892 + + Density error is 0.211354960786 + + Energy Rydberg eV + E_KohnSham -34.1906478736 -465.187629393 + E_Harris -34.3758618889 -467.707595351 + E_Fermi -0.397967763371 -5.41462920216 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00140623080765 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103868722666 + + Density error is 0.0978007899358 + + Energy Rydberg eV + E_KohnSham -34.2783690142 -466.38113674 + E_Harris -34.2853548878 -466.476184427 + E_Fermi -0.20935945575 -2.84848152838 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00130184932266 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000987691418037 + + Density error is 0.0628941893433 + + Energy Rydberg eV + E_KohnSham -34.278692315 -466.385535473 + E_Harris -34.2832115311 -466.447022563 + E_Fermi -0.200427945494 -2.72696209715 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111354880597 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000922765336229 + + Density error is 0.00188774071815 + + Energy Rydberg eV + E_KohnSham -34.2786308055 -466.384698593 + E_Harris -34.2786305392 -466.38469497 + E_Fermi -0.164749453239 -2.24153130644 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111304698343 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000923837495121 + + Density error is 0.000886097789334 + + Energy Rydberg eV + E_KohnSham -34.2785864066 -466.384094515 + E_Harris -34.2785874364 -466.384108526 + E_Fermi -0.164552168916 -2.23884711552 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111071025472 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000922960185731 + + Density error is 9.94525066581e-05 + + Energy Rydberg eV + E_KohnSham -34.2786132532 -466.384459781 + E_Harris -34.2786132547 -466.384459803 + E_Fermi -0.16429813599 -2.23539082024 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111047694036 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000923022551602 + + Density error is 2.6668445958e-05 + + Energy Rydberg eV + E_KohnSham -34.2786061608 -466.384363285 + E_Harris -34.2786061641 -466.384363329 + E_Fermi -0.164214503307 -2.23425293922 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111045008862 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000922957175485 + + Density error is 1.32966585355e-05 + + Energy Rydberg eV + E_KohnSham -34.2786073221 -466.384379085 + E_Harris -34.2786073229 -466.384379096 + E_Fermi -0.164242310914 -2.23463128112 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111044143905 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000922964157556 + + Density error is 2.42092662625e-06 + + Energy Rydberg eV + E_KohnSham -34.2786062482 -466.384364474 + E_Harris -34.2786062482 -466.384364474 + E_Fermi -0.164231221695 -2.23448040455 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111043825555 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000922965642305 + + Density error is 2.16683927994e-07 + + Energy Rydberg eV + E_KohnSham -34.2786064464 -466.38436717 + E_Harris -34.2786064464 -466.38436717 + E_Fermi -0.164229029341 -2.23445057604 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111043832328 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000922965787823 + + Density error is 4.59395087571e-08 + + Energy Rydberg eV + E_KohnSham -34.2786064911 -466.384367779 + E_Harris -34.2786064911 -466.384367779 + E_band -7.95021925106 -108.168282164 + E_one_elec -69.0323061963 -939.232710351 + E_Hartree +35.9042712614 +488.502671692 + E_xc -8.18761546613 -111.398223372 + E_Ewald +7.16185401541 +97.4420228537 + E_demet -3.14758504461e-69 -4.28250915463e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194390038482 -2.64481215779 + E_Fermi -0.164228905825 -2.23444889553 + + charge density convergence is achieved + final etot is -466.384367779 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2997 2.00000 + 2 -12.5442 2.00000 + 3 -9.48919 2.00000 + 4 -6.75107 2.00000 + 5 1.13413 0.00000 + 6 4.16880 0.00000 + 7 11.0964 0.00000 + 8 11.3870 0.00000 + + EFERMI = -2.234448895532133 eV + OUT.ABACUS/ final etot is -466.3843677791162 eV + correction force for each atom along direction 1 is 5.27837e-05 + correction force for each atom along direction 2 is -8.92427e-05 + correction force for each atom along direction 3 is 0.000130096 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.83190542 -0.76998030 +0.14642366 + H1 -0.23319984 +0.53222623 +0.16492716 + H2 -0.59870558 +0.23775407 -0.31135082 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3843677791162 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2714 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2616 1 6.3 1.e+02% + Potential init_pot 0.28443 2 0.14 4.5% + PW_Basis recip2real 0.28506 16 0.018 4.5% + PW_Basis gathers_scatterp 0.12220 16 0.0076 1.9% + Potential v_of_rho 1.0085 13 0.078 16.% + XC_Functional v_xc 0.29078 14 0.021 4.6% + H_Hartree_pw v_hartree 0.67479 13 0.052 11.% + PW_Basis real2recip 0.70108 38 0.018 11.% + PW_Basis gatherp_scatters 0.26854 38 0.0071 4.3% + ORB_control set_orb_tables 1.0916 1 1.1 17.% + ORB_gen_tables gen_tables 1.0916 1 1.1 17.% + ORB_table_phi init_Table 0.47335 1 0.47 7.5% + ORB_table_phi cal_ST_Phi12_R 0.46811 126 0.0037 7.5% + ORB_table_beta init_Table_Beta 0.18354 1 0.18 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18200 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.24497 1 0.24 3.9% + ORB_table_alpha S_PhiAlpha_R 0.24302 66 0.0037 3.9% + LOOP_ions opt_ions 4.6264 1 4.6 74.% + ESolver_KS_LCAO Run 4.1474 1 4.1 66.% + HSolverLCAO solve 1.6889 11 0.15 27.% + HamiltLCAO updateHk 0.94744 11 0.086 15.% + LCAO_Hamilt cal_Hgamma 0.92004 11 0.084 15.% + Gint_interface cal_gint 1.4101 23 0.061 22.% + Gint_Gamma distri_vl 2.0139 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.4897 13 0.35 72.% + LCAO_gen_fixedH add_v_delta 1.8658 6 0.31 30.% + LCAO_DESCRIPTOR add_v_delta 1.8659 6 0.31 30.% + ElecStateLCAO psiToRho 0.72322 11 0.066 12.% + Charge mix_rho 0.90378 10 0.090 14.% + LOOP_ions force_stress 0.47884 1 0.48 7.6% + Force_Stress_LCAO getForceStress 0.47881 1 0.48 7.6% + Force_LCAO_gamma ftable_gamma 0.26064 1 0.26 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.25260 1 0.25 4.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:51 2022 + Finish Time : Wed Sep 28 11:10:57 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8ca41b8f8c292681cd290f9f0f66cd9161bac1ed --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123758 ima = 3.69596e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012261982383 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111368445942 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112057698049 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011229223149 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112255126919 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112274803942 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112273859636 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112275936273 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112275290542 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112275173051 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112275161295 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c65b33b98473fbf56b273960f07636a915f215e8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.589520932879 14.969921004209 6.270070039168 0 0 0 +H +0.0 +2 +-17.393292315250 15.528043389310 7.562441716155 0 0 0 +-17.736666117164 13.355408287732 5.871796338126 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/conv new file mode 100644 index 0000000000000000000000000000000000000000..3052fb553d8c544c32450e3297c394e498e6e05b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/conv @@ -0,0 +1 @@ +112 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..88e841e91a38bfb9d393894d1740147b9fec635d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75533754 0.01273148304 1.259948961 1.33976199 1.469247279 0.009643350346 0.01610453136 0.03921906751 +1.938858416e-18 0.0008167864192 0.002800523671 0.0131502885 0.04553211496 8.966922943e-19 2.709460675e-06 7.324715052e-06 +0.00158227893 0.006145928654 + +H atom_index 1 n_descriptor 18 +1.239528636 0.03537575849 0.1081247569 0.1447672523 0.3160599538 0.02283430298 0.02761641522 0.03850019157 +1.008623425e-18 4.666184001e-05 0.09968021331 0.1150841241 0.1239788409 9.721807604e-18 3.250059137e-06 0.01354904385 +0.02647186187 0.03023367139 + +H atom_index 2 n_descriptor 18 +1.22269233 0.03592939522 0.1024067549 0.1372884792 0.310085415 0.02199072354 0.02662201157 0.03911823333 +4.811817489e-17 4.514382897e-05 0.09548656937 0.1142673287 0.1174720559 -4.098395224e-18 4.112742679e-06 0.01385509694 +0.02581024132 0.02940050359 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3ad32c2e3c48e7f0f6f76bb38b0923d0f7035efd Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..7da8c50c99632da08a626fc96669f8ebbd29a86d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/f_base.npy differ diff --git 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new file mode 100644 index 0000000000000000000000000000000000000000..e5ae1c8c54e151d3f7f45e6ec7f9fcef527db1e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:51 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.106105 SEC) : SETUP UNITCELL + DONE(0.106436 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124476 SEC) : INIT PLANEWAVE + DONE(0.167741 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451381 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651876e+02 0.000000e+00 2.114e-01 4.785e-01 + GE2 -4.663811e+02 -1.193507e+00 9.780e-02 4.298e-01 + GE3 -4.663855e+02 -4.398733e-03 6.289e-02 5.044e-01 + GE4 -4.663847e+02 8.368795e-04 1.888e-03 3.599e-01 + GE5 -4.663841e+02 6.040785e-04 8.861e-04 3.566e-01 + GE6 -4.663845e+02 -3.652668e-04 9.945e-05 3.486e-01 + GE7 -4.663844e+02 9.649688e-05 2.667e-05 3.366e-01 + GE8 -4.663844e+02 -1.580067e-05 1.330e-05 3.354e-01 + GE9 -4.663844e+02 1.461135e-05 2.421e-06 3.369e-01 + GE10 -4.663844e+02 -2.696161e-06 2.167e-07 3.368e-01 + GE11 -4.663844e+02 -6.090504e-07 4.594e-08 2.616e-01 +E_delta_band = -6.95799330e-02 Ry = -9.46683556e-01 eV +E_delta_NN= -1.94390038e-01 Ry = -2.64481216e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2714 11 0.57 1e+02 % + Run_lcao lcao_line 6.2616 1 6.3 1e+02 % + Potential init_pot 0.28443 2 0.14 4.5 % + PW_Basis recip2real 0.28506 16 0.018 4.5 % + PW_Basis gathers_scatterp 0.1222 16 0.0076 1.9 % + Potential v_of_rho 1.0085 13 0.078 16 % + XC_Functional v_xc 0.29078 14 0.021 4.6 % + H_Hartree_pw v_hartree 0.67479 13 0.052 11 % + PW_Basis real2recip 0.70108 38 0.018 11 % + PW_Basis gatherp_scatters 0.26854 38 0.0071 4.3 % + ORB_control set_orb_tables 1.0916 1 1.1 17 % + ORB_gen_tables gen_tables 1.0916 1 1.1 17 % + ORB_table_phi init_Table 0.47335 1 0.47 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.46811 126 0.0037 7.5 % + ORB_table_beta init_Table_Beta 0.18354 1 0.18 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.182 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.24497 1 0.24 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.24302 66 0.0037 3.9 % + LOOP_ions opt_ions 4.6264 1 4.6 74 % + ESolver_KS_LCAO Run 4.1474 1 4.1 66 % + HSolverLCAO solve 1.6889 11 0.15 27 % + HamiltLCAO updateHk 0.94744 11 0.086 15 % + LCAO_Hamilt cal_Hgamma 0.92004 11 0.084 15 % + Gint_interface cal_gint 1.4101 23 0.061 22 % + Gint_Gamma distri_vl 2.0139 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.4897 13 0.35 72 % + LCAO_gen_fixedH add_v_delta 1.8658 6 0.31 30 % + LCAO_DESCRIPTOR add_v_delta 1.8659 6 0.31 30 % + ElecStateLCAO psiToRho 0.72322 11 0.066 12 % + Charge mix_rho 0.90378 10 0.09 14 % + LOOP_ions force_stress 0.47884 1 0.48 7.6 % + Force_Stress_LCAO getForceStress 0.47881 1 0.48 7.6 % + Force_LCAO_gamma ftable_gamma 0.26064 1 0.26 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.2526 1 0.25 4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:51 2022 + FINISH Time : Wed Sep 28 11:10:57 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/112/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3d02f8976321f159170a1bbea9ad1447647dd37b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.339208 0.539556 0.220277 +H 0.365409 0.555348 0.277357 +H 0.354118 0.586638 0.177198 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f3c7c307087bbc13b251a7476c45186da030700a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2651 2 + 2 -13.2891 2 + 3 -8.91961 2 + 4 -6.73729 2 + 5 1.36354 0 + 6 4.52914 0 + 7 11.0688 0 + 8 11.2996 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..23c582f6293a44fe5f4e2656a015834e724391b3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:57 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.49782041847 15.1075763896 6.16775183578 0 0 0 0 + tauc_H1 10.2314443846 15.5497506274 7.76600620888 0 0 0 0 + tauc_H2 9.91529446388 16.4258523968 4.96155278351 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0787082731105 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0790132667676 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.095053065656 (SEC) + + DONE : INIT CHARGE Time : 0.14645406965 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.407927 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00117 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000854 + + Density error is 0.216133299254 + + Energy Rydberg eV + E_KohnSham -34.1903218831 -465.183194064 + E_Harris -34.3841851257 -467.820838796 + E_Fermi -0.407698793257 -5.54702665602 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00121992294183 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113386437043 + + Density error is 0.0979798485629 + + Energy Rydberg eV + E_KohnSham -34.2801523743 -466.405400598 + E_Harris -34.286793675 -466.49576013 + E_Fermi -0.215774610336 -2.9357641843 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00114460730288 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109440740673 + + Density error is 0.0627467667616 + + Energy Rydberg eV + E_KohnSham -34.2804055759 -466.408845583 + E_Harris -34.284673346 -466.466911574 + E_Fermi -0.203594284474 -2.77004234908 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102329046368 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104590044903 + + Density error is 0.00206851372981 + + Energy Rydberg eV + E_KohnSham -34.2804121726 -466.408935337 + E_Harris -34.2804153476 -466.408978534 + E_Fermi -0.168260433392 -2.28930064208 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102244133576 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104664440491 + + Density error is 0.000864779324283 + + Energy Rydberg eV + E_KohnSham -34.2803530359 -466.40813074 + E_Harris -34.2803541574 -466.408145999 + E_Fermi -0.167355028709 -2.27698197939 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102110494243 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104582144206 + + Density error is 0.000198803134858 + + Energy Rydberg eV + E_KohnSham -34.280391331 -466.408651772 + E_Harris -34.2803914307 -466.408653129 + E_Fermi -0.167431202841 -2.27801838163 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102121549359 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104620035953 + + Density error is 3.96863236211e-05 + + Energy Rydberg eV + E_KohnSham -34.2803760932 -466.408444451 + E_Harris -34.2803761013 -466.408444561 + E_Fermi -0.167265380736 -2.27576225615 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102117515823 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104610454245 + + Density error is 1.69587046901e-05 + + Energy Rydberg eV + E_KohnSham -34.2803814182 -466.408516901 + E_Harris -34.2803814193 -466.408516916 + E_Fermi -0.167309768471 -2.27636618227 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0010211570725 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104610170836 + + Density error is 2.21489446564e-06 + + Energy Rydberg eV + E_KohnSham -34.2803800267 -466.408497968 + E_Harris -34.2803800267 -466.408497968 + E_Fermi -0.167292260888 -2.27612797938 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102115537326 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104610370382 + + Density error is 3.45820819635e-07 + + Energy Rydberg eV + E_KohnSham -34.2803802404 -466.408500876 + E_Harris -34.2803802404 -466.408500876 + E_Fermi -0.167290051466 -2.27609791866 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102115536504 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104610407461 + + Density error is 1.52695314108e-07 + + Energy Rydberg eV + E_KohnSham -34.2803802694 -466.408501271 + E_Harris -34.2803802694 -466.408501271 + E_Fermi -0.167289976682 -2.27609690117 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102115524068 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104610421215 + + Density error is 9.74013603161e-09 + + Energy Rydberg eV + E_KohnSham -34.2803802698 -466.408501276 + E_Harris -34.2803802698 -466.408501276 + E_band -7.96888306522 -108.422216383 + E_one_elec -69.3904425668 -944.10540565 + E_Hartree +36.0941670869 +491.086336946 + E_xc -8.2181545568 -111.813729017 + E_Ewald +7.35820754759 +100.113549714 + E_demet -2.27169206661e-80 -3.09079562073e-79 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194892469974 -2.65164808894 + E_Fermi -0.167289829699 -2.27609490136 + + charge density convergence is achieved + final etot is -466.408501276 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2651 2.00000 + 2 -13.2891 2.00000 + 3 -8.91961 2.00000 + 4 -6.73729 2.00000 + 5 1.36354 0.00000 + 6 4.52914 0.00000 + 7 11.0688 0.00000 + 8 11.2996 0.00000 + + EFERMI = -2.276094901360611 eV + OUT.ABACUS/ final etot is -466.4085012756377 eV + correction force for each atom along direction 1 is 2.29379e-05 + correction force for each atom along direction 2 is 3.11079e-05 + correction force for each atom along direction 3 is -2.41719e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.55924172 -0.62102177 -0.65593030 + H1 +0.39826493 +0.40770111 +0.53497504 + H2 +0.16097679 +0.21332067 +0.12095526 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4085012756377 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0090 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0015 1 7.0 1.e+02% + Potential init_pot 0.25884 2 0.13 3.7% + PW_Basis recip2real 0.26947 17 0.016 3.8% + PW_Basis gathers_scatterp 0.11731 17 0.0069 1.7% + Potential v_of_rho 0.97661 14 0.070 14.% + XC_Functional v_xc 0.28549 15 0.019 4.1% + H_Hartree_pw v_hartree 0.64980 14 0.046 9.3% + PW_Basis real2recip 0.69187 41 0.017 9.9% + PW_Basis gatherp_scatters 0.28128 41 0.0069 4.0% + ORB_control set_orb_tables 0.93574 1 0.94 13.% + ORB_gen_tables gen_tables 0.93574 1 0.94 13.% + ORB_table_phi init_Table 0.39213 1 0.39 5.6% + ORB_table_phi cal_ST_Phi12_R 0.38773 126 0.0031 5.5% + ORB_table_beta init_Table_Beta 0.16335 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.16197 56 0.0029 2.3% + ORB_table_alpha init_Table_Alpha 0.21736 1 0.22 3.1% + ORB_table_alpha S_PhiAlpha_R 0.21558 66 0.0033 3.1% + LOOP_ions opt_ions 5.5808 1 5.6 80.% + ESolver_KS_LCAO Run 5.0590 1 5.1 72.% + HSolverLCAO solve 2.6841 12 0.22 38.% + HamiltLCAO updateHk 1.3687 12 0.11 20.% + LCAO_Hamilt cal_Hgamma 1.3423 12 0.11 19.% + Gint_interface cal_gint 2.5382 25 0.10 36.% + Gint_Gamma distri_vl 2.6252 6 0.44 37.% + LCAO_Deepks cal_projected_DM 5.4313 14 0.39 77.% + LCAO_gen_fixedH add_v_delta 2.4921 6 0.42 36.% + LCAO_DESCRIPTOR add_v_delta 2.4920 6 0.42 36.% + ElecStateLCAO psiToRho 1.2971 12 0.11 19.% + Charge mix_rho 0.84695 11 0.077 12.% + LOOP_ions force_stress 0.52166 1 0.52 7.4% + Force_Stress_LCAO getForceStress 0.52163 1 0.52 7.4% + Force_LCAO_gamma ftable_gamma 0.32631 1 0.33 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.31902 1 0.32 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:57 2022 + Finish Time : Wed Sep 28 11:05:04 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e330f6f079aec21f6309054dad4ae589db1765e9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012368 ima = 3.71053e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012338352698 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011251007167 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011298485238 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113221204359 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113171216363 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113202571242 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113192567718 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113195432068 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113194792688 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113194714947 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113194706322 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113194698885 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4b0e5ef321e8bd155ff1b1ba984bcf563b621606 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.502179581539 15.107576389582 6.167751835771 0 0 0 +H +0.0 +2 +-17.768555615335 15.549750627383 7.766006208875 0 0 0 +-18.084705536095 16.425852396758 4.961552783491 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/conv new file mode 100644 index 0000000000000000000000000000000000000000..fe76388b8d084b9a0b0b6f40547b93cbd9b281e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/conv @@ -0,0 +1 @@ +113 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..fd2d69cc2efa03279e2d418165c2d623d5b4c19e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745632355 0.01265749404 1.280288438 1.371126246 1.469262338 0.007948777061 0.01986069289 0.03891563108 +-1.286120377e-18 0.001143311953 0.002459420868 0.01241151906 0.04386277011 -4.233831194e-19 1.691465024e-06 5.200602819e-06 +0.001739156099 0.005752158851 + +H atom_index 1 n_descriptor 18 +1.257828854 0.03354089982 0.1110165298 0.1545436301 0.3248430581 0.02228488289 0.02888221402 0.03677528863 +4.290566606e-17 4.210716981e-05 0.1037999828 0.115298578 0.1327316093 -1.484043911e-18 3.842003176e-06 0.0129496301 +0.02646425256 0.03118523117 + +H atom_index 2 n_descriptor 18 +1.240577174 0.03414751382 0.1050829435 0.1465454227 0.3194263302 0.02152110004 0.02788556198 0.03729730511 +1.61570707e-17 4.062552438e-05 0.09963607532 0.1145031215 0.1258289448 -1.94378406e-18 4.691635885e-06 0.01305857598 +0.02582836199 0.03041692327 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..86e0aee05c912321d065f7254ae9e0df31df9675 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:57 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0787237 SEC) : SETUP UNITCELL + DONE(0.0790227 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0950669 SEC) : INIT PLANEWAVE + DONE(0.146554 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.407969 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651832e+02 0.000000e+00 2.161e-01 4.954e-01 + GE2 -4.664054e+02 -1.222207e+00 9.798e-02 4.689e-01 + GE3 -4.664088e+02 -3.444984e-03 6.275e-02 5.358e-01 + GE4 -4.664089e+02 -8.975388e-05 2.069e-03 4.136e-01 + GE5 -4.664081e+02 8.045960e-04 8.648e-04 4.124e-01 + GE6 -4.664087e+02 -5.210314e-04 1.988e-04 4.044e-01 + GE7 -4.664084e+02 2.073209e-04 3.969e-05 3.991e-01 + GE8 -4.664085e+02 -7.244981e-05 1.696e-05 3.890e-01 + GE9 -4.664085e+02 1.893279e-05 2.215e-06 3.915e-01 + GE10 -4.664085e+02 -2.907588e-06 3.458e-07 3.933e-01 + GE11 -4.664085e+02 -3.954988e-07 1.527e-07 3.833e-01 + GE12 -4.664085e+02 -4.528901e-09 9.740e-09 3.169e-01 +E_delta_band = -7.07346893e-02 Ry = -9.62394821e-01 eV +E_delta_NN= -1.94892470e-01 Ry = -2.65164809e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.009 11 0.64 1e+02 % + Run_lcao lcao_line 7.0015 1 7 1e+02 % + Potential init_pot 0.25884 2 0.13 3.7 % + PW_Basis recip2real 0.26947 17 0.016 3.8 % + PW_Basis gathers_scatterp 0.11731 17 0.0069 1.7 % + Potential v_of_rho 0.97661 14 0.07 14 % + XC_Functional v_xc 0.28549 15 0.019 4.1 % + H_Hartree_pw v_hartree 0.6498 14 0.046 9.3 % + PW_Basis real2recip 0.69187 41 0.017 9.9 % + PW_Basis gatherp_scatters 0.28128 41 0.0069 4 % + ORB_control set_orb_tables 0.93574 1 0.94 13 % + ORB_gen_tables gen_tables 0.93574 1 0.94 13 % + ORB_table_phi init_Table 0.39213 1 0.39 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.38773 126 0.0031 5.5 % + ORB_table_beta init_Table_Beta 0.16335 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.16197 56 0.0029 2.3 % + ORB_table_alpha init_Table_Alpha 0.21736 1 0.22 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.21558 66 0.0033 3.1 % + LOOP_ions opt_ions 5.5808 1 5.6 80 % + ESolver_KS_LCAO Run 5.059 1 5.1 72 % + HSolverLCAO solve 2.6841 12 0.22 38 % + HamiltLCAO updateHk 1.3687 12 0.11 20 % + LCAO_Hamilt cal_Hgamma 1.3423 12 0.11 19 % + Gint_interface cal_gint 2.5382 25 0.1 36 % + Gint_Gamma distri_vl 2.6252 6 0.44 37 % + LCAO_Deepks cal_projected_DM 5.4313 14 0.39 77 % + LCAO_gen_fixedH add_v_delta 2.4921 6 0.42 36 % + LCAO_DESCRIPTOR add_v_delta 2.492 6 0.42 36 % + ElecStateLCAO psiToRho 1.2971 12 0.11 19 % + Charge mix_rho 0.84695 11 0.077 12 % + LOOP_ions force_stress 0.52166 1 0.52 7.4 % + Force_Stress_LCAO getForceStress 0.52163 1 0.52 7.4 % + Force_LCAO_gamma ftable_gamma 0.32631 1 0.33 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.31902 1 0.32 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:57 2022 + FINISH Time : Wed Sep 28 11:05:04 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/113/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..f51ab4aab9c3647ca2ca37c8b3db325fe7dc2c1c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.33198 0.550201 0.218853 +H 0.34321 0.502511 0.263158 +H 0.337671 0.606465 0.252347 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..4721baa76589969470bd24a09100cc457526a207 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1997 2 + 2 -13.0387 2 + 3 -9.05408 2 + 4 -6.72423 2 + 5 1.25191 0 + 6 4.329 0 + 7 11.0939 0 + 8 11.3405 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9281fb04f9c507720a997d749290ef60a0a3f6fd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:08 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.29543157444 15.4056402418 6.12788969025 0 0 0 0 + tauc_H1 9.60988964797 14.0703088583 7.36841272988 0 0 0 0 + tauc_H2 9.45479085857 16.9810072136 7.06571396053 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0974785468122 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.110309235234 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.128446391281 (SEC) + + DONE : INIT CHARGE Time : 0.171570350579 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.453955 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 144 0 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00141 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000903 + + Density error is 0.213193976399 + + Energy Rydberg eV + E_KohnSham -34.1940756498 -465.23426668 + E_Harris -34.3819577252 -467.790533457 + E_Fermi -0.399915867299 -5.44113451588 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0013149222562 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012398067858 + + Density error is 0.0979971699969 + + Energy Rydberg eV + E_KohnSham -34.2813206345 -466.421295594 + E_Harris -34.2880422866 -466.512748363 + E_Fermi -0.210938950511 -2.86997165708 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00121107203376 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011973896871 + + Density error is 0.0627832258588 + + Energy Rydberg eV + E_KohnSham -34.2814677362 -466.423297016 + E_Harris -34.2858103353 -466.482381108 + E_Fermi -0.19970971832 -2.71719011512 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00102332158074 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114750125446 + + Density error is 0.00199545824492 + + Energy Rydberg eV + E_KohnSham -34.2814506636 -466.423064731 + E_Harris -34.2814522994 -466.423086987 + E_Fermi -0.164429581969 -2.23717923453 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00101978327773 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114863946347 + + Density error is 0.000781700009087 + + Energy Rydberg eV + E_KohnSham -34.2814065006 -466.422463863 + E_Harris -34.2814072129 -466.422473554 + E_Fermi -0.163758678772 -2.22805112826 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00101782347416 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114779178246 + + Density error is 0.000179507133894 + + Energy Rydberg eV + E_KohnSham -34.2814370438 -466.422879424 + E_Harris -34.2814371362 -466.422880682 + E_Fermi -0.163700597398 -2.22726089062 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0010178483233 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114816896561 + + Density error is 3.48683509663e-05 + + Energy Rydberg eV + E_KohnSham -34.2814245275 -466.422709131 + E_Harris -34.2814245335 -466.422709213 + E_Fermi -0.163590626856 -2.22576466463 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00101783564446 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011480712199 + + Density error is 1.5096699295e-05 + + Energy Rydberg eV + E_KohnSham -34.2814292684 -466.422773635 + E_Harris -34.2814292693 -466.422773647 + E_Fermi -0.163626123074 -2.22624761545 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00101779815798 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114807005744 + + Density error is 1.62207189965e-06 + + Energy Rydberg eV + E_KohnSham -34.2814279958 -466.422756319 + E_Harris -34.2814279958 -466.422756319 + E_Fermi -0.163609555209 -2.22602219808 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00101779638588 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114807226489 + + Density error is 1.80547464885e-07 + + Energy Rydberg eV + E_KohnSham -34.2814281987 -466.42275908 + E_Harris -34.2814281987 -466.42275908 + E_Fermi -0.163608219317 -2.22600402234 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00101779675097 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114807288208 + + Density error is 2.99979335292e-08 + + Energy Rydberg eV + E_KohnSham -34.2814282239 -466.422759423 + E_Harris -34.2814282239 -466.422759423 + E_band -7.94031262743 -108.033495634 + E_one_elec -69.1475486778 -940.80066475 + E_Hartree +35.9743302299 +489.45587286 + E_xc -8.19894766645 -111.552405867 + E_Ewald +7.21537549155 +98.1702198946 + E_demet -1.28096077359e-73 -1.74283654353e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194512833492 -2.64648286962 + E_Fermi -0.163608137085 -2.22600290352 + + charge density convergence is achieved + final etot is -466.422759423 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1997 2.00000 + 2 -13.0387 2.00000 + 3 -9.05408 2.00000 + 4 -6.72423 2.00000 + 5 1.25191 0.00000 + 6 4.32900 0.00000 + 7 11.0939 0.00000 + 8 11.3405 0.00000 + + EFERMI = -2.226002903524718 eV + OUT.ABACUS/ final etot is -466.4227594228766 eV + correction force for each atom along direction 1 is 3.35340e-05 + correction force for each atom along direction 2 is -3.58043e-06 + correction force for each atom along direction 3 is 7.46570e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.00050077433 -0.20037707 -0.032729931 + H1 -0.020610689 +0.18845129 -0.066158323 + H2 +0.021111463 +0.011925783 +0.098888255 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4227594228766 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1446 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1351 1 6.1 1.e+02% + Potential init_pot 0.28330 2 0.14 4.6% + PW_Basis recip2real 0.27203 16 0.017 4.4% + PW_Basis gathers_scatterp 0.12270 16 0.0077 2.0% + Potential v_of_rho 0.99944 13 0.077 16.% + XC_Functional v_xc 0.31344 14 0.022 5.1% + H_Hartree_pw v_hartree 0.64418 13 0.050 10.% + PW_Basis real2recip 0.69398 38 0.018 11.% + PW_Basis gatherp_scatters 0.26824 38 0.0071 4.4% + ORB_control set_orb_tables 1.0941 1 1.1 18.% + ORB_gen_tables gen_tables 1.0941 1 1.1 18.% + ORB_table_phi init_Table 0.47418 1 0.47 7.7% + ORB_table_phi cal_ST_Phi12_R 0.46900 126 0.0037 7.6% + ORB_table_beta init_Table_Beta 0.18236 1 0.18 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18085 56 0.0032 2.9% + ORB_table_alpha init_Table_Alpha 0.24809 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.24611 66 0.0037 4.0% + LOOP_ions opt_ions 4.5032 1 4.5 73.% + ESolver_KS_LCAO Run 4.0417 1 4.0 66.% + HSolverLCAO solve 1.5944 11 0.14 26.% + HamiltLCAO updateHk 0.90141 11 0.082 15.% + LCAO_Hamilt cal_Hgamma 0.87408 11 0.079 14.% + Gint_interface cal_gint 1.1502 23 0.050 19.% + Gint_Gamma distri_vl 1.9714 6 0.33 32.% + LCAO_Deepks cal_projected_DM 4.3561 13 0.34 71.% + LCAO_gen_fixedH add_v_delta 1.8242 6 0.30 30.% + LCAO_DESCRIPTOR add_v_delta 1.8242 6 0.30 30.% + ElecStateLCAO psiToRho 0.67497 11 0.061 11.% + Charge mix_rho 0.89983 10 0.090 15.% + LOOP_ions force_stress 0.46131 1 0.46 7.5% + Force_Stress_LCAO getForceStress 0.46128 1 0.46 7.5% + Force_LCAO_gamma ftable_gamma 0.24542 1 0.25 4.0% + Force_LCAO_gamma cal_fvl_dphi 0.21961 1 0.22 3.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:08 2022 + Finish Time : Wed Sep 28 11:14:14 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..650a3e5633ddc5a9f49f1f1adbaab558c3f46f86 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123774 ima = 3.70644e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123098130696 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112282915901 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112804465954 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113017133693 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112979801151 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113005335528 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112996123285 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112998715708 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112998122258 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112998053183 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112998041879 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9857ceee8df51b21cdc3a083554dd2c2871031ec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.704568425560 15.405640241814 6.127889690227 0 0 0 +H +0.0 +2 +-18.390110352033 14.070308858266 7.368412729870 0 0 0 +-18.545209141449 16.981007213590 7.065713960546 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/conv new file mode 100644 index 0000000000000000000000000000000000000000..054cbbf6059536626c971d18d6715e4f271ccbf6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/conv @@ -0,0 +1 @@ +114 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a0e16cec49358789ed663004cebca55731a1cefb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748365834 0.01262367532 1.268347724 1.358350501 1.468902642 0.008292862368 0.0187292095 0.03900016807 +9.891700802e-18 0.001037583269 0.002508589677 0.01216216059 0.0438717345 7.949296019e-19 1.839186036e-06 5.49328896e-06 +0.001666621265 0.005896011695 + +H atom_index 1 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:08 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0975049 SEC) : SETUP UNITCELL + DONE(0.110325 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.128468 SEC) : INIT PLANEWAVE + DONE(0.171702 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.454036 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652343e+02 0.000000e+00 2.132e-01 4.721e-01 + GE2 -4.664213e+02 -1.187029e+00 9.800e-02 4.209e-01 + GE3 -4.664233e+02 -2.001422e-03 6.278e-02 4.905e-01 + GE4 -4.664231e+02 2.322851e-04 1.995e-03 3.504e-01 + GE5 -4.664225e+02 6.008680e-04 7.817e-04 3.463e-01 + GE6 -4.664229e+02 -4.155612e-04 1.795e-04 3.391e-01 + GE7 -4.664227e+02 1.702930e-04 3.487e-05 3.345e-01 + GE8 -4.664228e+02 -6.450374e-05 1.510e-05 3.280e-01 + GE9 -4.664228e+02 1.731529e-05 1.622e-06 3.254e-01 + GE10 -4.664228e+02 -2.761032e-06 1.805e-07 3.225e-01 + GE11 -4.664228e+02 -3.426209e-07 3.000e-08 2.500e-01 +E_delta_band = -6.98752324e-02 Ry = -9.50701309e-01 eV +E_delta_NN= -1.94512833e-01 Ry = -2.64648287e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1446 11 0.56 1e+02 % + Run_lcao lcao_line 6.1351 1 6.1 1e+02 % + Potential init_pot 0.2833 2 0.14 4.6 % + PW_Basis recip2real 0.27203 16 0.017 4.4 % + PW_Basis gathers_scatterp 0.1227 16 0.0077 2 % + Potential v_of_rho 0.99944 13 0.077 16 % + XC_Functional v_xc 0.31344 14 0.022 5.1 % + H_Hartree_pw v_hartree 0.64418 13 0.05 10 % + PW_Basis real2recip 0.69398 38 0.018 11 % + PW_Basis gatherp_scatters 0.26824 38 0.0071 4.4 % + ORB_control set_orb_tables 1.0941 1 1.1 18 % + ORB_gen_tables gen_tables 1.0941 1 1.1 18 % + ORB_table_phi init_Table 0.47418 1 0.47 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.469 126 0.0037 7.6 % + ORB_table_beta init_Table_Beta 0.18236 1 0.18 3 % + ORB_table_beta VNL_PhiBeta_R 0.18085 56 0.0032 2.9 % + ORB_table_alpha init_Table_Alpha 0.24809 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.24611 66 0.0037 4 % + LOOP_ions opt_ions 4.5032 1 4.5 73 % + ESolver_KS_LCAO Run 4.0417 1 4 66 % + HSolverLCAO solve 1.5944 11 0.14 26 % + HamiltLCAO updateHk 0.90141 11 0.082 15 % + LCAO_Hamilt cal_Hgamma 0.87408 11 0.079 14 % + Gint_interface cal_gint 1.1502 23 0.05 19 % + Gint_Gamma distri_vl 1.9714 6 0.33 32 % + LCAO_Deepks cal_projected_DM 4.3561 13 0.34 71 % + LCAO_gen_fixedH add_v_delta 1.8242 6 0.3 30 % + LCAO_DESCRIPTOR add_v_delta 1.8242 6 0.3 30 % + ElecStateLCAO psiToRho 0.67497 11 0.061 11 % + Charge mix_rho 0.89983 10 0.09 15 % + LOOP_ions force_stress 0.46131 1 0.46 7.5 % + Force_Stress_LCAO getForceStress 0.46128 1 0.46 7.5 % + Force_LCAO_gamma ftable_gamma 0.24542 1 0.25 4 % + Force_LCAO_gamma cal_fvl_dphi 0.21961 1 0.22 3.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:08 2022 + FINISH Time : Wed Sep 28 11:14:14 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/114/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e5f63fb80d50fcc930507ba840d75ec0c9d69021 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.331273 0.557603 0.212801 +H 0.336917 0.494339 0.194515 +H 0.32959 0.558144 0.277989 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d38e008c190d1c1fc60c24ba778142c026437136 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2103 2 + 2 -13.1435 2 + 3 -8.9835 2 + 4 -6.72553 2 + 5 1.28749 0 + 6 4.39823 0 + 7 11.087 0 + 8 11.3256 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..5a0149328ee0fc2c383aba07ba73ab94efa68c6c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.27564290955 15.6128896935 5.95844046935 0 0 0 0 + tauc_H1 9.43368511822 13.8414983793 5.44642167884 0 0 0 0 + tauc_H2 9.22850638421 15.6280411585 7.78370561996 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0728619603326 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0731941193309 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0889338147113 (SEC) + + DONE : INIT CHARGE Time : 0.130655716353 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374896 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 0 81 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000896 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000923 + + Density error is 0.21437849318 + + Energy Rydberg eV + E_KohnSham -34.192599408 -465.21418138 + E_Harris -34.3827493701 -467.801304339 + E_Fermi -0.402277716486 -5.47326912264 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00123985650784 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127446282445 + + Density error is 0.0979860097947 + + Energy Rydberg eV + E_KohnSham -34.2808801132 -466.415301995 + E_Harris -34.2875781673 -466.506433695 + E_Fermi -0.212207813245 -2.88723542025 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00120010595855 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122857872333 + + Density error is 0.0628005030365 + + Energy Rydberg eV + E_KohnSham -34.2810777131 -466.417990479 + E_Harris -34.2853912996 -466.476679834 + E_Fermi -0.200739120486 -2.73119585011 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115308594528 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117269433438 + + Density error is 0.00203412540232 + + Energy Rydberg eV + E_KohnSham -34.281068251 -466.41786174 + E_Harris -34.2810706505 -466.417894388 + E_Fermi -0.165468748468 -2.25131782009 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115314826842 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117504829002 + + Density error is 0.000816658404649 + + Energy Rydberg eV + E_KohnSham -34.2810196384 -466.417200332 + E_Harris -34.2810202493 -466.417208644 + E_Fermi -0.164717899444 -2.24110199503 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115246733997 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117400773939 + + Density error is 0.000185251915449 + + Energy Rydberg eV + E_KohnSham -34.2810515508 -466.417634523 + E_Harris -34.2810517784 -466.417637619 + E_Fermi -0.164699327492 -2.24084931065 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115287349653 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117430911961 + + Density error is 3.64041279476e-05 + + Energy Rydberg eV + E_KohnSham -34.2810389949 -466.417463691 + E_Harris -34.2810390016 -466.417463782 + E_Fermi -0.164566190644 -2.23903789091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115275223818 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117422332532 + + Density error is 1.76072534944e-05 + + Energy Rydberg eV + E_KohnSham -34.2810437423 -466.417528283 + E_Harris -34.2810437438 -466.417528302 + E_Fermi -0.164604869034 -2.23956413741 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115275739689 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117423367326 + + Density error is 2.35273830049e-06 + + Energy Rydberg eV + E_KohnSham -34.2810423055 -466.417508734 + E_Harris -34.2810423055 -466.417508734 + E_Fermi -0.164587275399 -2.23932476372 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115275885314 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117422971379 + + Density error is 5.02243648257e-07 + + Energy Rydberg eV + E_KohnSham -34.2810425866 -466.417512558 + E_Harris -34.2810425866 -466.417512558 + E_Fermi -0.164585108622 -2.23929528321 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115275953741 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117423099132 + + Density error is 1.67919179369e-07 + + Energy Rydberg eV + E_KohnSham -34.2810426045 -466.417512802 + E_Harris -34.2810426045 -466.417512802 + E_Fermi -0.164584873775 -2.23929208795 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115275975984 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011742312724 + + Density error is 1.02202650555e-08 + + Energy Rydberg eV + E_KohnSham -34.2810426084 -466.417512854 + E_Harris -34.2810426084 -466.417512854 + E_band -7.9470782624 -108.125546821 + E_one_elec -69.2224009678 -941.819082402 + E_Hartree +36.012382073 +489.973594745 + E_xc -8.20501989672 -111.635022799 + E_Ewald +7.25849121142 +98.7568393582 + E_demet -1.25875503664e-75 -1.71262408845e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194618426284 -2.64791953326 + E_Fermi -0.164584710652 -2.23928986855 + + charge density convergence is achieved + final etot is -466.417512854 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2103 2.00000 + 2 -13.1435 2.00000 + 3 -8.98350 2.00000 + 4 -6.72553 2.00000 + 5 1.28749 0.00000 + 6 4.39823 0.00000 + 7 11.0870 0.00000 + 8 11.3256 0.00000 + + EFERMI = -2.239289868549999 eV + OUT.ABACUS/ final etot is -466.4175128544557 eV + correction force for each atom along direction 1 is -8.17063e-05 + correction force for each atom along direction 2 is -0.000146431 + correction force for each atom along direction 3 is 2.13662e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.013727112 -0.021457093 -0.66351111 + H1 -0.020025010 +0.19821916 +0.24536505 + H2 +0.0062978976 -0.17676207 +0.41814605 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4175128544557 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0316 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0245 1 7.0 1.e+02% + Potential init_pot 0.24404 2 0.12 3.5% + PW_Basis recip2real 0.27988 17 0.016 4.0% + PW_Basis gathers_scatterp 0.11323 17 0.0067 1.6% + Potential v_of_rho 0.99049 14 0.071 14.% + XC_Functional v_xc 0.28894 15 0.019 4.1% + H_Hartree_pw v_hartree 0.65971 14 0.047 9.4% + PW_Basis real2recip 0.64324 41 0.016 9.1% + PW_Basis gatherp_scatters 0.23890 41 0.0058 3.4% + ORB_control set_orb_tables 0.90015 1 0.90 13.% + ORB_gen_tables gen_tables 0.90015 1 0.90 13.% + ORB_table_phi init_Table 0.37793 1 0.38 5.4% + ORB_table_phi cal_ST_Phi12_R 0.37368 126 0.0030 5.3% + ORB_table_beta init_Table_Beta 0.15573 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15440 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.20857 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20690 66 0.0031 2.9% + LOOP_ions opt_ions 5.6799 1 5.7 81.% + ESolver_KS_LCAO Run 5.1495 1 5.1 73.% + HSolverLCAO solve 2.7870 12 0.23 40.% + HamiltLCAO updateHk 1.4233 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3879 12 0.12 20.% + Gint_interface cal_gint 2.6416 25 0.11 38.% + Gint_Gamma distri_vl 2.6823 6 0.45 38.% + LCAO_Deepks cal_projected_DM 5.5293 14 0.39 79.% + LCAO_gen_fixedH add_v_delta 2.5543 6 0.43 36.% + LCAO_DESCRIPTOR add_v_delta 2.5543 6 0.43 36.% + ElecStateLCAO psiToRho 1.3463 12 0.11 19.% + Charge mix_rho 0.83677 11 0.076 12.% + LOOP_ions force_stress 0.53029 1 0.53 7.5% + Force_Stress_LCAO getForceStress 0.53025 1 0.53 7.5% + Force_LCAO_gamma ftable_gamma 0.33291 1 0.33 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.32567 1 0.33 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:17 2022 + Finish Time : Wed Sep 28 11:12:25 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6b40dd5981c2dde1fbd62fe78c6ed465e8bbf8da --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123855 ima = 3.70377e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123231996094 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112390873667 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011289894154 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113119867989 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011307919 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113105171409 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113096530836 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113099354228 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113098558026 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011309849805 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113098479524 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113098471096 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e50f6684bfa6e4bc8a62fd412c38cd6bb324cc45 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.724357090460 15.612889693485 5.958440469343 0 0 0 +H +0.0 +2 +-18.566314881775 13.841498379278 5.446421678835 0 0 0 +-18.771493615778 15.628041158504 7.783705619974 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/conv new file mode 100644 index 0000000000000000000000000000000000000000..91b9a7b6f070b19fb88d54a48d7160598e789fef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/conv @@ -0,0 +1 @@ +115 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4abba0415e645239b48451c619904719c577d75d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747031866 0.0126244318 1.272149678 1.363428282 1.468971682 0.008103551997 0.01924601735 0.03895890223 +2.303012452e-18 0.001080323019 0.002472188518 0.01219807517 0.04367135817 2.545201658e-19 1.738378845e-06 5.289945495e-06 +0.001699314261 0.005825540783 + +H atom_index 1 n_descriptor 18 +1.229654602 0.03469561986 0.1011902067 0.1413762528 0.3154002252 0.02105445353 0.02721058988 0.03786611229 +-3.498260288e-17 4.022870715e-05 0.09605190396 0.1143115492 0.121273339 4.862224163e-18 5.157798218e-06 0.0132852049 +0.02530115032 0.02986234501 + +H atom_index 2 n_descriptor 18 +1.249319682 0.03400901368 0.1077699442 0.1502653027 0.3218571368 0.02194295398 0.02835399995 0.03719776148 +-1.834837982e-19 4.193611547e-05 0.1011286323 0.1149356988 0.1289818037 -2.676719546e-18 4.225207683e-06 0.01304616292 +0.02604970672 0.03077988612 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c2479433f7d75550cd3934cb6af7bf7cec8d171c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/e_base.npy new file mode 100644 index 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TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0728773 SEC) : SETUP UNITCELL + DONE(0.0732077 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0889733 SEC) : INIT PLANEWAVE + DONE(0.130755 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374968 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652142e+02 0.000000e+00 2.144e-01 5.104e-01 + GE2 -4.664153e+02 -1.201121e+00 9.799e-02 4.841e-01 + GE3 -4.664180e+02 -2.688484e-03 6.280e-02 5.439e-01 + GE4 -4.664179e+02 1.287389e-04 2.034e-03 4.181e-01 + GE5 -4.664172e+02 6.614078e-04 8.167e-04 4.160e-01 + GE6 -4.664176e+02 -4.341904e-04 1.853e-04 4.133e-01 + GE7 -4.664175e+02 1.708313e-04 3.640e-05 4.027e-01 + GE8 -4.664175e+02 -6.459199e-05 1.761e-05 4.017e-01 + GE9 -4.664175e+02 1.954939e-05 2.353e-06 3.977e-01 + GE10 -4.664175e+02 -3.824443e-06 5.022e-07 3.929e-01 + GE11 -4.664175e+02 -2.437140e-07 1.679e-07 3.893e-01 + GE12 -4.664175e+02 -5.251841e-08 1.022e-08 3.261e-01 +E_delta_band = -7.01233980e-02 Ry = -9.54077776e-01 eV +E_delta_NN= -1.94618426e-01 Ry = -2.64791953e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0316 11 0.64 1e+02 % + Run_lcao lcao_line 7.0245 1 7 1e+02 % + Potential init_pot 0.24404 2 0.12 3.5 % + PW_Basis recip2real 0.27988 17 0.016 4 % + PW_Basis gathers_scatterp 0.11323 17 0.0067 1.6 % + Potential v_of_rho 0.99049 14 0.071 14 % + XC_Functional v_xc 0.28894 15 0.019 4.1 % + H_Hartree_pw v_hartree 0.65971 14 0.047 9.4 % + PW_Basis real2recip 0.64324 41 0.016 9.1 % + PW_Basis gatherp_scatters 0.2389 41 0.0058 3.4 % + ORB_control set_orb_tables 0.90015 1 0.9 13 % + ORB_gen_tables gen_tables 0.90015 1 0.9 13 % + ORB_table_phi init_Table 0.37793 1 0.38 5.4 % + ORB_table_phi cal_ST_Phi12_R 0.37368 126 0.003 5.3 % + ORB_table_beta init_Table_Beta 0.15573 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.1544 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.20857 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.2069 66 0.0031 2.9 % + LOOP_ions opt_ions 5.6799 1 5.7 81 % + ESolver_KS_LCAO Run 5.1495 1 5.1 73 % + HSolverLCAO solve 2.787 12 0.23 40 % + HamiltLCAO updateHk 1.4233 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3879 12 0.12 20 % + Gint_interface cal_gint 2.6416 25 0.11 38 % + Gint_Gamma distri_vl 2.6823 6 0.45 38 % + LCAO_Deepks cal_projected_DM 5.5293 14 0.39 79 % + LCAO_gen_fixedH add_v_delta 2.5543 6 0.43 36 % + LCAO_DESCRIPTOR add_v_delta 2.5543 6 0.43 36 % + ElecStateLCAO psiToRho 1.3463 12 0.11 19 % + Charge mix_rho 0.83677 11 0.076 12 % + LOOP_ions force_stress 0.53029 1 0.53 7.5 % + Force_Stress_LCAO getForceStress 0.53025 1 0.53 7.5 % + Force_LCAO_gamma ftable_gamma 0.33291 1 0.33 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.32567 1 0.33 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:17 2022 + FINISH Time : Wed Sep 28 11:12:25 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/115/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e3177cfbc2c7ea3e615476c740a93c2bef78c28b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.334207 0.549996 0.202207 +H 0.395667 0.532754 0.181268 +H 0.317074 0.504715 0.246288 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6f670f8fc4046a102d39fdc8d131cbccdb35c5ae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1181 2 + 2 -13.0048 2 + 3 -9.01112 2 + 4 -6.70526 2 + 5 1.18142 0 + 6 4.23394 0 + 7 11.1114 0 + 8 11.3543 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..be2baecbfa5ccd7e268773248eb85449ee6272f1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:02 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.35780603772 15.3998907236 5.66180784086 0 0 0 0 + tauc_H1 11.0786768698 14.9171156677 5.07550331243 0 0 0 0 + tauc_H2 8.87805826027 14.1320215517 6.89605015728 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.102485518634 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.108013152182 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.125997349374 (SEC) + + DONE : INIT CHARGE Time : 0.169213775964 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449424 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 0 81 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00165 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000745 + + Density error is 0.213933456538 + + Energy Rydberg eV + E_KohnSham -34.1910545245 -465.193162161 + E_Harris -34.3803039387 -467.768032538 + E_Fermi -0.396541206289 -5.39521989732 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00137920620963 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920498231021 + + Density error is 0.0984940896641 + + Energy Rydberg eV + E_KohnSham -34.2803326254 -466.407853041 + E_Harris -34.2872175797 -466.50152765 + E_Fermi -0.205840509085 -2.80060380278 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0012757597452 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000881847586264 + + Density error is 0.0633591634464 + + Energy Rydberg eV + E_KohnSham -34.2806932705 -466.412759868 + E_Harris -34.2851286652 -466.47310651 + E_Fermi -0.196776441364 -2.67728083471 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0010868612465 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00082859915112 + + Density error is 0.00201384339414 + + Energy Rydberg eV + E_KohnSham -34.280644301 -466.412093604 + E_Harris -34.2806467434 -466.412126835 + E_Fermi -0.161459393363 -2.19676774536 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108492976174 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000828003289904 + + Density error is 0.00091400197648 + + Energy Rydberg eV + E_KohnSham -34.280597049 -466.411450708 + E_Harris -34.2805975504 -466.411457531 + E_Fermi -0.161028399366 -2.19090377119 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108240035658 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000827329342411 + + Density error is 0.000180055051252 + + Energy Rydberg eV + E_KohnSham -34.2806220231 -466.411790498 + E_Harris -34.2806220484 -466.411790843 + E_Fermi -0.160804445338 -2.18785672032 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108232371986 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000827537666704 + + Density error is 3.41868142031e-05 + + Energy Rydberg eV + E_KohnSham -34.2806132846 -466.411671606 + E_Harris -34.2806132899 -466.411671678 + E_Fermi -0.160714629255 -2.18663470983 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108229421004 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000827476230961 + + Density error is 1.51993211071e-05 + + Energy Rydberg eV + E_KohnSham -34.2806171074 -466.411723617 + E_Harris -34.2806171084 -466.411723631 + E_Fermi -0.160745097631 -2.18704925334 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108226755062 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000827473125676 + + Density error is 1.70788013257e-06 + + Energy Rydberg eV + E_KohnSham -34.2806158393 -466.411706363 + E_Harris -34.2806158393 -466.411706363 + E_Fermi -0.160729248321 -2.18683361243 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108226372439 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000827474218563 + + Density error is 1.72322662385e-07 + + Energy Rydberg eV + E_KohnSham -34.2806160597 -466.411709363 + E_Harris -34.2806160597 -466.411709363 + E_Fermi -0.160727655776 -2.18681194474 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108226409187 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000827474716093 + + Density error is 3.49405852979e-08 + + Energy Rydberg eV + E_KohnSham -34.2806160861 -466.411709721 + E_Harris -34.2806160861 -466.411709721 + E_band -7.91423067158 -107.67863242 + E_one_elec -68.9974242835 -938.758117579 + E_Hartree +35.9049879954 +488.512423359 + E_xc -8.18784650513 -111.401366819 + E_Ewald +7.12461670395 +96.9353832396 + E_demet -3.25019509724e-69 -4.42211729341e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194238302118 -2.64274767865 + E_Fermi -0.160727621243 -2.18681147489 + + charge density convergence is achieved + final etot is -466.411709721 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1181 2.00000 + 2 -13.0048 2.00000 + 3 -9.01112 2.00000 + 4 -6.70526 2.00000 + 5 1.18142 0.00000 + 6 4.23394 0.00000 + 7 11.1114 0.00000 + 8 11.3543 0.00000 + + EFERMI = -2.186811474887766 eV + OUT.ABACUS/ final etot is -466.4117097208147 eV + correction force for each atom along direction 1 is 0.000122151 + correction force for each atom along direction 2 is -0.000182916 + correction force for each atom along direction 3 is 8.65595e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.82419400 +0.099235985 -0.53219981 + H1 -0.88594853 +0.13737415 +0.38637668 + H2 +0.061754527 -0.23661014 +0.14582313 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4117097208147 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3475 11 0.58 1.0e+02% + Run_lcao lcao_line 6.3370 1 6.3 1.e+02% + Potential init_pot 0.28219 2 0.14 4.4% + PW_Basis recip2real 0.27381 16 0.017 4.3% + PW_Basis gathers_scatterp 0.12509 16 0.0078 2.0% + Potential v_of_rho 0.99203 13 0.076 16.% + XC_Functional v_xc 0.30294 14 0.022 4.8% + H_Hartree_pw v_hartree 0.64480 13 0.050 10.% + PW_Basis real2recip 0.68311 38 0.018 11.% + PW_Basis gatherp_scatters 0.25819 38 0.0068 4.1% + ORB_control set_orb_tables 1.1008 1 1.1 17.% + ORB_gen_tables gen_tables 1.1008 1 1.1 17.% + ORB_table_phi init_Table 0.47623 1 0.48 7.5% + ORB_table_phi cal_ST_Phi12_R 0.47114 126 0.0037 7.4% + ORB_table_beta init_Table_Beta 0.18495 1 0.18 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18338 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.24895 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.24701 66 0.0037 3.9% + LOOP_ions opt_ions 4.7061 1 4.7 74.% + ESolver_KS_LCAO Run 4.2142 1 4.2 66.% + HSolverLCAO solve 1.7788 11 0.16 28.% + HamiltLCAO updateHk 0.99043 11 0.090 16.% + LCAO_Hamilt cal_Hgamma 0.96291 11 0.088 15.% + Gint_interface cal_gint 1.5293 23 0.066 24.% + Gint_Gamma distri_vl 2.0428 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.5629 13 0.35 72.% + LCAO_gen_fixedH add_v_delta 1.8957 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.8958 6 0.32 30.% + ElecStateLCAO psiToRho 0.77208 11 0.070 12.% + Charge mix_rho 0.90218 10 0.090 14.% + LOOP_ions force_stress 0.49170 1 0.49 7.7% + Force_Stress_LCAO getForceStress 0.49167 1 0.49 7.7% + Force_LCAO_gamma ftable_gamma 0.27594 1 0.28 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.26790 1 0.27 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:02 2022 + Finish Time : Wed Sep 28 11:06:08 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8f36b90027a69101e4bfcf11e3126d2a367b937a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123492 ima = 3.67489e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123513458619 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112317176012 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112951324468 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113169645929 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113137414879 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113156805408 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113150241608 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113152799031 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113152143079 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113152072877 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113152063975 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0d1b8c768bdb11cf79029e83523f2c86db49390b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.642193962301 15.399890723624 5.661807840876 0 0 0 +H +0.0 +2 +-16.921323130171 14.917115667691 5.075503312455 0 0 0 +-19.121941739720 14.132021551719 6.896050157292 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/conv new file mode 100644 index 0000000000000000000000000000000000000000..b1efa81ecb1395ead6ce9db36c5998343728a47b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/conv @@ -0,0 +1 @@ +116 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7bcaa7d34f6db9fc79ac332563a1b0c309ad6092 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747946512 0.01254937334 1.261532445 1.35523225 1.468568714 0.008177945813 0.01879145458 0.03899991014 +1.333182183e-18 0.001013128967 0.002440662495 0.01189576925 0.04286373081 -2.059878636e-19 1.682345945e-06 5.162137543e-06 +0.001670325808 0.005837486441 + +H atom_index 1 n_descriptor 18 +1.206544615 0.03557727927 0.09366482909 0.1314133196 0.3071718895 0.01996710733 0.02584701924 0.03890384351 +7.433837937e-18 3.748709965e-05 0.08902898142 0.1124766892 0.1137693158 3.612589352e-19 5.957741474e-06 0.01383242576 +0.02418609442 0.02867777778 + +H atom_index 2 n_descriptor 18 +1.244400395 0.03428663724 0.1058239129 0.147905859 0.3202223134 0.02169178732 0.02805578959 0.03748462796 +3.121946069e-17 4.070587867e-05 0.09898716281 0.1148933187 0.1268653949 -1.251097518e-18 4.37737315e-06 0.01311774477 +0.02567986985 0.0305361992 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..dc1ce774ac5ca393f8045565f082f80325962bad Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..717c66c4e4395d01b8f2af4de1129237eb3d2332 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:02 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.10251 SEC) : SETUP UNITCELL + DONE(0.108029 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.126017 SEC) : INIT PLANEWAVE + DONE(0.169349 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449487 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651932e+02 0.000000e+00 2.139e-01 4.896e-01 + GE2 -4.664079e+02 -1.214691e+00 9.849e-02 4.338e-01 + GE3 -4.664128e+02 -4.906827e-03 6.336e-02 5.043e-01 + GE4 -4.664121e+02 6.662642e-04 2.014e-03 3.657e-01 + GE5 -4.664115e+02 6.428962e-04 9.140e-04 3.646e-01 + GE6 -4.664118e+02 -3.397902e-04 1.801e-04 3.589e-01 + GE7 -4.664117e+02 1.188927e-04 3.419e-05 3.465e-01 + GE8 -4.664117e+02 -5.201185e-05 1.520e-05 3.404e-01 + GE9 -4.664117e+02 1.725442e-05 1.708e-06 3.405e-01 + GE10 -4.664117e+02 -2.999596e-06 1.723e-07 3.402e-01 + GE11 -4.664117e+02 -3.582654e-07 3.494e-08 2.673e-01 +E_delta_band = -6.92883053e-02 Ry = -9.42715757e-01 eV +E_delta_NN= -1.94238302e-01 Ry = -2.64274768e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3475 11 0.58 1e+02 % + Run_lcao lcao_line 6.337 1 6.3 1e+02 % + Potential init_pot 0.28219 2 0.14 4.4 % + PW_Basis recip2real 0.27381 16 0.017 4.3 % + PW_Basis gathers_scatterp 0.12509 16 0.0078 2 % + Potential v_of_rho 0.99203 13 0.076 16 % + XC_Functional v_xc 0.30294 14 0.022 4.8 % + H_Hartree_pw v_hartree 0.6448 13 0.05 10 % + PW_Basis real2recip 0.68311 38 0.018 11 % + PW_Basis gatherp_scatters 0.25819 38 0.0068 4.1 % + ORB_control set_orb_tables 1.1008 1 1.1 17 % + ORB_gen_tables gen_tables 1.1008 1 1.1 17 % + ORB_table_phi init_Table 0.47623 1 0.48 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.47114 126 0.0037 7.4 % + ORB_table_beta init_Table_Beta 0.18495 1 0.18 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18338 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.24895 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.24701 66 0.0037 3.9 % + LOOP_ions opt_ions 4.7061 1 4.7 74 % + ESolver_KS_LCAO Run 4.2142 1 4.2 66 % + HSolverLCAO solve 1.7788 11 0.16 28 % + HamiltLCAO updateHk 0.99043 11 0.09 16 % + LCAO_Hamilt cal_Hgamma 0.96291 11 0.088 15 % + Gint_interface cal_gint 1.5293 23 0.066 24 % + Gint_Gamma distri_vl 2.0428 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.5629 13 0.35 72 % + LCAO_gen_fixedH add_v_delta 1.8957 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.8958 6 0.32 30 % + ElecStateLCAO psiToRho 0.77208 11 0.07 12 % + Charge mix_rho 0.90218 10 0.09 14 % + LOOP_ions force_stress 0.4917 1 0.49 7.7 % + Force_Stress_LCAO getForceStress 0.49167 1 0.49 7.7 % + Force_LCAO_gamma ftable_gamma 0.27594 1 0.28 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.2679 1 0.27 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:02 2022 + FINISH Time : Wed Sep 28 11:06:08 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/116/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ec98e4bd7d0e56ed81d3f2c8002cce1b333713e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.321642 0.54493 0.201204 +H 0.373584 0.543495 0.238446 +H 0.281856 0.504935 0.235783 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9f675fa5e395c83484394e3166f7d849d1a9ddd3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4622 2 + 2 -12.8915 2 + 3 -9.35149 2 + 4 -6.78302 2 + 5 1.32737 0 + 6 4.52148 0 + 7 11.0482 0 + 8 11.3191 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..893e4b69f92214af88a92be430d504295037ee8b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:30 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.0059750477 15.2580451195 5.6337023696 0 0 0 0 + tauc_H1 10.460363326 15.2178497742 6.67648563222 0 0 0 0 + tauc_H2 7.8919733522 14.1381684081 6.60192878096 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.095093761475 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.106582060688 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124605094217 (SEC) + + DONE : INIT CHARGE Time : 0.169136301191 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44857 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 337 ; sender_size of each process is: +144 144 0 49 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000488 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109 + + Density error is 0.215400364583 + + Energy Rydberg eV + E_KohnSham -34.1877609884 -465.148351304 + E_Harris -34.3811325489 -467.779306358 + E_Fermi -0.411494785119 -5.5986737749 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000582136295451 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113588464141 + + Density error is 0.097654843612 + + Energy Rydberg eV + E_KohnSham -34.2784889635 -466.382768733 + E_Harris -34.2852960585 -466.475384013 + E_Fermi -0.219917360245 -2.99212918846 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000600942110872 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106684914385 + + Density error is 0.0626606377244 + + Energy Rydberg eV + E_KohnSham -34.2788487189 -466.387663457 + E_Harris -34.2832528901 -466.447585281 + E_Fermi -0.208527136406 -2.83715724274 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000643127014215 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954807953076 + + Density error is 0.00196698457381 + + Energy Rydberg eV + E_KohnSham -34.2788408032 -466.387555758 + E_Harris -34.2788424363 -466.387577978 + E_Fermi -0.1725939358 -2.34826096713 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000643625238563 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000955082316434 + + Density error is 0.000967072656217 + + Energy Rydberg eV + E_KohnSham -34.2787713902 -466.386611346 + E_Harris -34.2787730898 -466.386634471 + E_Fermi -0.171889443499 -2.33867585763 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000643974075698 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000953415809496 + + Density error is 0.000102512213688 + + Energy Rydberg eV + E_KohnSham -34.2788159365 -466.387217429 + E_Harris -34.2788161082 -466.387219766 + E_Fermi -0.171909068892 -2.33894287481 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000643969710791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000953278305283 + + Density error is 4.04300018333e-05 + + Energy Rydberg eV + E_KohnSham -34.2788017254 -466.387024078 + E_Harris -34.2788017344 -466.3870242 + E_Fermi -0.17179981661 -2.33745642125 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000643959827944 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000953236986509 + + Density error is 1.77305732403e-05 + + Energy Rydberg eV + E_KohnSham -34.2788043193 -466.387059369 + E_Harris -34.2788043206 -466.387059388 + E_Fermi -0.171847316229 -2.33810268672 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000643970793606 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000953230485394 + + Density error is 2.51797093232e-06 + + Energy Rydberg eV + E_KohnSham -34.2788028015 -466.387038719 + E_Harris -34.2788028015 -466.387038719 + E_Fermi -0.17182937459 -2.33785857819 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00064397245088 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000953231733188 + + Density error is 1.83594808343e-07 + + Energy Rydberg eV + E_KohnSham -34.2788030436 -466.387042012 + E_Harris -34.2788030436 -466.387042012 + E_Fermi -0.171826958361 -2.33782570372 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000643972221664 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000953231662858 + + Density error is 7.23223966922e-08 + + Energy Rydberg eV + E_KohnSham -34.2788030935 -466.387042692 + E_Harris -34.2788030935 -466.387042692 + E_band -8.00962179483 -108.976495235 + E_one_elec -69.4720694366 -945.215996189 + E_Hartree +36.1172369817 +491.400218968 + E_xc -8.22214623761 -111.868038621 + E_Ewald +7.4221061101 +100.982934258 + E_demet -1.82650240329e-81 -2.48508400955e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.1951977044 -2.65580101636 + E_Fermi -0.171826920356 -2.33782518664 + + charge density convergence is achieved + final etot is -466.387042692 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4622 2.00000 + 2 -12.8915 2.00000 + 3 -9.35149 2.00000 + 4 -6.78302 2.00000 + 5 1.32737 0.00000 + 6 4.52148 0.00000 + 7 11.0482 0.00000 + 8 11.3191 0.00000 + + EFERMI = -2.337825186635483 eV + OUT.ABACUS/ final etot is -466.3870426919165 eV + correction force for each atom along direction 1 is -3.44363e-05 + correction force for each atom along direction 2 is 5.72778e-05 + correction force for each atom along direction 3 is 0.000186697 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.3513074 -0.32715469 -0.39390703 + H1 +1.5499760 +0.20463924 +0.72396639 + H2 -0.19866862 +0.12251545 -0.33005936 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3870426919165 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0327 11 0.55 1.0e+02% + Run_lcao lcao_line 6.0228 1 6.0 1.e+02% + Potential init_pot 0.28195 2 0.14 4.7% + PW_Basis recip2real 0.27627 16 0.017 4.6% + PW_Basis gathers_scatterp 0.11933 16 0.0075 2.0% + Potential v_of_rho 1.0169 13 0.078 17.% + XC_Functional v_xc 0.30215 14 0.022 5.0% + H_Hartree_pw v_hartree 0.67149 13 0.052 11.% + PW_Basis real2recip 0.71995 38 0.019 12.% + PW_Basis gatherp_scatters 0.28645 38 0.0075 4.7% + ORB_control set_orb_tables 1.0985 1 1.1 18.% + ORB_gen_tables gen_tables 1.0985 1 1.1 18.% + ORB_table_phi init_Table 0.47293 1 0.47 7.8% + ORB_table_phi cal_ST_Phi12_R 0.46781 126 0.0037 7.8% + ORB_table_beta init_Table_Beta 0.18613 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18461 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.24887 1 0.25 4.1% + ORB_table_alpha S_PhiAlpha_R 0.24689 66 0.0037 4.1% + LOOP_ions opt_ions 4.3944 1 4.4 73.% + ESolver_KS_LCAO Run 3.9378 1 3.9 65.% + HSolverLCAO solve 1.4687 11 0.13 24.% + HamiltLCAO updateHk 0.85204 11 0.077 14.% + LCAO_Hamilt cal_Hgamma 0.82455 11 0.075 14.% + Gint_interface cal_gint 1.1760 23 0.051 19.% + Gint_Gamma distri_vl 1.9152 6 0.32 32.% + LCAO_Deepks cal_projected_DM 4.2608 13 0.33 71.% + LCAO_gen_fixedH add_v_delta 1.7680 6 0.29 29.% + LCAO_DESCRIPTOR add_v_delta 1.7681 6 0.29 29.% + ElecStateLCAO psiToRho 0.59898 11 0.054 9.9% + Charge mix_rho 0.90800 10 0.091 15.% + LOOP_ions force_stress 0.45640 1 0.46 7.6% + Force_Stress_LCAO getForceStress 0.45637 1 0.46 7.6% + Force_LCAO_gamma ftable_gamma 0.23476 1 0.23 3.9% + Force_LCAO_gamma cal_fvl_dphi 0.22663 1 0.23 3.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:30 2022 + Finish Time : Wed Sep 28 11:02:36 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e1e5ea96a3e01cad86d63b401436be77ba4fd498 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123823 ima = 3.67945e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122766480093 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111558841716 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112131718483 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112410259295 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011234593836 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112381506095 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011237812095 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112381168615 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112380399607 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112380276714 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112380271659 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/STRU new file mode 100644 index 0000000000000000000000000000000000000000..834fb4e316cce4edf691cee7d5268b29dda702d1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.994024952294 15.258045119446 5.633702369603 0 0 0 +H +0.0 +2 +-17.539636674005 15.217849774180 6.676485632209 0 0 0 +-20.108026647823 14.138168408070 6.601928780958 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/conv new file mode 100644 index 0000000000000000000000000000000000000000..55f4c32208d41a0a9f86d40d5d179f53a967d266 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/conv @@ -0,0 +1 @@ +117 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0fdeccde706ab1ecc39a125f40ac98c42188c530 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752750989 0.012801592 1.276315202 1.362845834 1.470003816 0.009247455242 0.01745603952 0.03912604918 +2.649518992e-18 0.0009891183506 0.002832470612 0.01317156184 0.04737026074 3.278017506e-19 2.675110028e-06 7.165491871e-06 +0.001597671013 0.006106544735 + +H atom_index 1 n_descriptor 18 +1.282539317 0.03362174935 0.1222121496 0.165398472 0.3299438176 0.02451973057 0.03013255836 0.03701326579 +3.328999448e-17 5.382320495e-05 0.1079381124 0.1198545126 0.1419197799 -8.214979852e-20 1.704808905e-06 0.01343417362 +0.02806784129 0.03212786984 + +H atom_index 2 n_descriptor 18 +1.233238316 0.03525764455 0.1043786831 0.1419094525 0.314147398 0.02211858171 0.02726008498 0.03836918976 +8.438659203e-18 4.907538052e-05 0.09916307019 0.1143049235 0.1217417479 2.805024803e-18 4.463622565e-06 0.01356353767 +0.02629761857 0.0299565192 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..96262db3928828c09880bde5a6d8164ecc2c3ffb Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..47d0a4651a0faa0dd805e1fb0b3aa8f83542d4f9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:30 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0951186 SEC) : SETUP UNITCELL + DONE(0.106599 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124624 SEC) : INIT PLANEWAVE + DONE(0.169268 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448634 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651484e+02 0.000000e+00 2.154e-01 4.621e-01 + GE2 -4.663828e+02 -1.234417e+00 9.765e-02 4.108e-01 + GE3 -4.663877e+02 -4.894724e-03 6.266e-02 4.817e-01 + GE4 -4.663876e+02 1.076985e-04 1.967e-03 3.389e-01 + GE5 -4.663866e+02 9.444124e-04 9.671e-04 3.373e-01 + GE6 -4.663872e+02 -6.060834e-04 1.025e-04 3.322e-01 + GE7 -4.663870e+02 1.933511e-04 4.043e-05 3.240e-01 + GE8 -4.663871e+02 -3.529089e-05 1.773e-05 3.171e-01 + GE9 -4.663870e+02 2.065021e-05 2.518e-06 3.144e-01 + GE10 -4.663870e+02 -3.293632e-06 1.836e-07 3.162e-01 + GE11 -4.663870e+02 -6.794652e-07 7.232e-08 2.396e-01 +E_delta_band = -7.12671932e-02 Ry = -9.69639908e-01 eV +E_delta_NN= -1.95197704e-01 Ry = -2.65580102e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0327 11 0.55 1e+02 % + Run_lcao lcao_line 6.0228 1 6 1e+02 % + Potential init_pot 0.28195 2 0.14 4.7 % + PW_Basis recip2real 0.27627 16 0.017 4.6 % + PW_Basis gathers_scatterp 0.11933 16 0.0075 2 % + Potential v_of_rho 1.0169 13 0.078 17 % + XC_Functional v_xc 0.30215 14 0.022 5 % + H_Hartree_pw v_hartree 0.67149 13 0.052 11 % + PW_Basis real2recip 0.71995 38 0.019 12 % + PW_Basis gatherp_scatters 0.28645 38 0.0075 4.7 % + ORB_control set_orb_tables 1.0985 1 1.1 18 % + ORB_gen_tables gen_tables 1.0985 1 1.1 18 % + ORB_table_phi init_Table 0.47293 1 0.47 7.8 % + ORB_table_phi cal_ST_Phi12_R 0.46781 126 0.0037 7.8 % + ORB_table_beta init_Table_Beta 0.18613 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18461 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.24887 1 0.25 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.24689 66 0.0037 4.1 % + LOOP_ions opt_ions 4.3944 1 4.4 73 % + ESolver_KS_LCAO Run 3.9378 1 3.9 65 % + HSolverLCAO solve 1.4687 11 0.13 24 % + HamiltLCAO updateHk 0.85204 11 0.077 14 % + LCAO_Hamilt cal_Hgamma 0.82455 11 0.075 14 % + Gint_interface cal_gint 1.176 23 0.051 19 % + Gint_Gamma distri_vl 1.9152 6 0.32 32 % + LCAO_Deepks cal_projected_DM 4.2608 13 0.33 71 % + LCAO_gen_fixedH add_v_delta 1.768 6 0.29 29 % + LCAO_DESCRIPTOR add_v_delta 1.7681 6 0.29 29 % + ElecStateLCAO psiToRho 0.59898 11 0.054 9.9 % + Charge mix_rho 0.908 10 0.091 15 % + LOOP_ions force_stress 0.4564 1 0.46 7.6 % + Force_Stress_LCAO getForceStress 0.45637 1 0.46 7.6 % + Force_LCAO_gamma ftable_gamma 0.23476 1 0.23 3.9 % + Force_LCAO_gamma cal_fvl_dphi 0.22663 1 0.23 3.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:30 2022 + FINISH Time : Wed Sep 28 11:02:36 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/117/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ea73084dd1c3ff384b0280671353b60b72f4a3e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.315573 0.543323 0.198525 +H 0.309896 0.598282 0.236176 +H 0.25678 0.515108 0.204569 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9422e1acfcb4b8bbf71051cecd2faf6890eda979 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1963 2 + 2 -12.8973 2 + 3 -9.15472 2 + 4 -6.72486 2 + 5 1.19901 0 + 6 4.25032 0 + 7 11.1004 0 + 8 11.3569 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e219c2f3aebc76fd2423e957beb62b059ea781ed --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:19 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 8.83603080553 15.2130338582 5.55869438651 0 0 0 0 + tauc_H1 8.67708447172 16.7518890757 6.61292683602 0 0 0 0 + tauc_H2 7.18983877865 14.4230284943 5.72792202038 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0735500140333 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0738170229686 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0900341484411 (SEC) + + DONE : INIT CHARGE Time : 0.131134524522 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.373663 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000858 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00164 + + Density error is 0.213061938667 + + Energy Rydberg eV + E_KohnSham -34.1924682532 -465.212396928 + E_Harris -34.3802924512 -467.767876243 + E_Fermi -0.398662159382 -5.42407694458 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107711203973 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00137020991375 + + Density error is 0.0981306531759 + + Energy Rydberg eV + E_KohnSham -34.2808080509 -466.414321536 + E_Harris -34.2876599452 -466.507546341 + E_Fermi -0.208610161556 -2.83828685787 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00102140911515 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126493140841 + + Density error is 0.0630986536134 + + Energy Rydberg eV + E_KohnSham -34.2810934823 -466.41820503 + E_Harris -34.2855232157 -466.478474645 + E_Fermi -0.198898581566 -2.70615403341 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000936326226589 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107933355647 + + Density error is 0.00196168901584 + + Energy Rydberg eV + E_KohnSham -34.2810515913 -466.417635074 + E_Harris -34.2810527071 -466.417650255 + E_Fermi -0.163462462999 -2.22402090589 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000936644618303 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107892427869 + + Density error is 0.000865174981269 + + Energy Rydberg eV + E_KohnSham -34.2810051381 -466.417003046 + E_Harris -34.2810058008 -466.417012062 + E_Fermi -0.163017780699 -2.21797069282 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000935470811668 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107651923161 + + Density error is 0.000153034345232 + + Energy Rydberg eV + E_KohnSham -34.2810322952 -466.417372536 + E_Harris -34.2810323185 -466.417372854 + E_Fermi -0.162834783084 -2.21548088254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000935564556846 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107644856453 + + Density error is 3.18223970232e-05 + + Energy Rydberg eV + E_KohnSham -34.2810229341 -466.417245172 + E_Harris -34.2810229384 -466.417245231 + E_Fermi -0.162752208432 -2.21435739676 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000935511295917 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107643864554 + + Density error is 1.63684861562e-05 + + Energy Rydberg eV + E_KohnSham -34.2810262988 -466.417290952 + E_Harris -34.2810263 -466.417290969 + E_Fermi -0.162782168259 -2.21476502112 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000935511748639 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107642213409 + + Density error is 2.60329277863e-06 + + Energy Rydberg eV + E_KohnSham -34.2810250169 -466.41727351 + E_Harris -34.2810250169 -466.41727351 + E_Fermi -0.162766707973 -2.21455467313 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000935508685871 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107641330305 + + Density error is 4.63770826305e-07 + + Energy Rydberg eV + E_KohnSham -34.2810252726 -466.41727699 + E_Harris -34.2810252726 -466.41727699 + E_Fermi -0.162764158666 -2.21451998803 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000935509491456 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107641348394 + + Density error is 1.63667540855e-07 + + Energy Rydberg eV + E_KohnSham -34.2810252995 -466.417277355 + E_Harris -34.2810252995 -466.417277355 + E_Fermi -0.162763964351 -2.21451734424 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000935509645541 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107641320927 + + Density error is 1.06662097728e-08 + + Energy Rydberg eV + E_KohnSham -34.2810253029 -466.417277402 + E_Harris -34.2810253029 -466.417277402 + E_band -7.93391163771 -107.946405701 + E_one_elec -69.0615722247 -939.630895094 + E_Hartree +35.929885066 +488.851165382 + E_xc -8.1918895531 -111.456375309 + E_Ewald +7.16734972197 +97.5167957775 + E_demet -5.12962391727e-71 -6.9792113872e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194402473446 -2.64498134415 + E_Fermi -0.162763810448 -2.21451525029 + + charge density convergence is achieved + final etot is -466.417277402 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1963 2.00000 + 2 -12.8973 2.00000 + 3 -9.15472 2.00000 + 4 -6.72486 2.00000 + 5 1.19901 0.00000 + 6 4.25032 0.00000 + 7 11.1004 0.00000 + 8 11.3569 0.00000 + + EFERMI = -2.214515250290294 eV + OUT.ABACUS/ final etot is -466.4172774022502 eV + correction force for each atom along direction 1 is -0.000149533 + correction force for each atom along direction 2 is 6.10524e-05 + correction force for each atom along direction 3 is 3.27296e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.12657956 +0.72761346 +0.41196293 + H1 +0.12246203 -0.54658117 -0.39963029 + H2 -0.24904159 -0.18103230 -0.012332636 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4172774022502 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3210 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3138 1 7.3 1.e+02% + Potential init_pot 0.23958 2 0.12 3.3% + PW_Basis recip2real 0.28271 17 0.017 3.9% + PW_Basis gathers_scatterp 0.11342 17 0.0067 1.5% + Potential v_of_rho 0.99325 14 0.071 14.% + XC_Functional v_xc 0.28929 15 0.019 4.0% + H_Hartree_pw v_hartree 0.66306 14 0.047 9.1% + PW_Basis real2recip 0.64493 41 0.016 8.8% + PW_Basis gatherp_scatters 0.23882 41 0.0058 3.3% + ORB_control set_orb_tables 0.90147 1 0.90 12.% + ORB_gen_tables gen_tables 0.90147 1 0.90 12.% + ORB_table_phi init_Table 0.37897 1 0.38 5.2% + ORB_table_phi cal_ST_Phi12_R 0.37468 126 0.0030 5.1% + ORB_table_beta init_Table_Beta 0.15490 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15353 56 0.0027 2.1% + ORB_table_alpha init_Table_Alpha 0.20731 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20564 66 0.0031 2.8% + LOOP_ions opt_ions 5.9685 1 6.0 82.% + ESolver_KS_LCAO Run 5.4271 1 5.4 74.% + HSolverLCAO solve 3.0685 12 0.26 42.% + HamiltLCAO updateHk 1.5349 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.4998 12 0.12 20.% + Gint_interface cal_gint 2.9407 25 0.12 40.% + Gint_Gamma distri_vl 2.8191 6 0.47 39.% + LCAO_Deepks cal_projected_DM 5.8120 14 0.42 79.% + LCAO_gen_fixedH add_v_delta 2.6937 6 0.45 37.% + LCAO_DESCRIPTOR add_v_delta 2.6938 6 0.45 37.% + ElecStateLCAO psiToRho 1.5148 12 0.13 21.% + Charge mix_rho 0.82452 11 0.075 11.% + LOOP_ions force_stress 0.54132 1 0.54 7.4% + Force_Stress_LCAO getForceStress 0.54129 1 0.54 7.4% + Force_LCAO_gamma ftable_gamma 0.34457 1 0.34 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.33725 1 0.34 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:19 2022 + Finish Time : Wed Sep 28 11:05:26 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..156b86b8bdaeee9bf3e12354424c84823ad0cf16 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012393 ima = 3.67474e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123115029538 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111977350865 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112592495576 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112814057574 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112778777198 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112800047429 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112794295836 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112796774971 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112796017273 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112795936722 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112795919385 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011279591126 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a4d704d4b3949900f76cfd2fbe7be8441cdf9545 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-19.163969194496 15.213033858174 5.558694386491 0 0 0 +H +0.0 +2 +-19.322915528284 16.751889075662 6.612926836014 0 0 0 +-20.810161221332 14.423028494237 5.727922020357 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/conv new file mode 100644 index 0000000000000000000000000000000000000000..b634284291235e6bf884b023da337c9195b93424 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/conv @@ -0,0 +1 @@ +118 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9358056980a0f0ac9bd75a69f4f2bb9c9b93913a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750222508 0.01262137407 1.262999069 1.352628489 1.468886328 0.008591612656 0.01803487385 0.03906466265 +-8.899297545e-19 0.0009771940549 0.00256370591 0.01218281805 0.0441592157 -2.183449962e-19 1.987985515e-06 5.806653014e-06 +0.001625873096 0.005970237387 + +H atom_index 1 n_descriptor 18 +1.215940609 0.03551274759 0.09702681566 0.134830582 0.3094404694 0.0206660356 0.0263158488 0.03876124358 +1.533815233e-17 4.144623849e-05 0.09198212256 0.114006701 0.1154772387 1.157304798e-17 5.594449186e-06 0.01374246733 +0.02480927061 0.02910684016 + +H atom_index 2 n_descriptor 18 +1.246229686 0.03448475085 0.1069846507 0.1482302246 0.3198732823 0.02208438459 0.02808937028 0.0376563572 +2.603289244e-17 4.417619627e-05 0.09984532453 0.1150285247 0.1271421424 5.089430379e-19 4.149660673e-06 0.01322520851 +0.02599335753 0.030581047 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c5b3b4da51026ddfad9bebfec6bdce62950e3511 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:19 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0735654 SEC) : SETUP UNITCELL + DONE(0.073826 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0900475 SEC) : INIT PLANEWAVE + DONE(0.131244 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.373709 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652124e+02 0.000000e+00 2.131e-01 5.250e-01 + GE2 -4.664143e+02 -1.201925e+00 9.813e-02 5.053e-01 + GE3 -4.664182e+02 -3.883494e-03 6.310e-02 5.634e-01 + GE4 -4.664176e+02 5.699564e-04 1.962e-03 4.396e-01 + GE5 -4.664170e+02 6.320278e-04 8.652e-04 4.423e-01 + GE6 -4.664174e+02 -3.694901e-04 1.530e-04 4.385e-01 + GE7 -4.664172e+02 1.273643e-04 3.182e-05 4.245e-01 + GE8 -4.664173e+02 -4.578026e-05 1.637e-05 4.190e-01 + GE9 -4.664173e+02 1.744220e-05 2.603e-06 4.198e-01 + GE10 -4.664173e+02 -3.480006e-06 4.638e-07 4.235e-01 + GE11 -4.664173e+02 -3.651059e-07 1.637e-07 4.203e-01 + GE12 -4.664173e+02 -4.720567e-08 1.067e-08 3.525e-01 +E_delta_band = -6.96041603e-02 Ry = -9.47013185e-01 eV +E_delta_NN= -1.94402473e-01 Ry = -2.64498134e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.321 11 0.67 1e+02 % + Run_lcao lcao_line 7.3138 1 7.3 1e+02 % + Potential init_pot 0.23958 2 0.12 3.3 % + PW_Basis recip2real 0.28271 17 0.017 3.9 % + PW_Basis gathers_scatterp 0.11342 17 0.0067 1.5 % + Potential v_of_rho 0.99325 14 0.071 14 % + XC_Functional v_xc 0.28929 15 0.019 4 % + H_Hartree_pw v_hartree 0.66306 14 0.047 9.1 % + PW_Basis real2recip 0.64493 41 0.016 8.8 % + PW_Basis gatherp_scatters 0.23882 41 0.0058 3.3 % + ORB_control set_orb_tables 0.90147 1 0.9 12 % + ORB_gen_tables gen_tables 0.90147 1 0.9 12 % + ORB_table_phi init_Table 0.37897 1 0.38 5.2 % + ORB_table_phi cal_ST_Phi12_R 0.37468 126 0.003 5.1 % + ORB_table_beta init_Table_Beta 0.1549 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15353 56 0.0027 2.1 % + ORB_table_alpha init_Table_Alpha 0.20731 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20564 66 0.0031 2.8 % + LOOP_ions opt_ions 5.9685 1 6 82 % + ESolver_KS_LCAO Run 5.4271 1 5.4 74 % + HSolverLCAO solve 3.0685 12 0.26 42 % + HamiltLCAO updateHk 1.5349 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.4998 12 0.12 20 % + Gint_interface cal_gint 2.9407 25 0.12 40 % + Gint_Gamma distri_vl 2.8191 6 0.47 39 % + LCAO_Deepks cal_projected_DM 5.812 14 0.42 79 % + LCAO_gen_fixedH add_v_delta 2.6937 6 0.45 37 % + LCAO_DESCRIPTOR add_v_delta 2.6938 6 0.45 37 % + ElecStateLCAO psiToRho 1.5148 12 0.13 21 % + Charge mix_rho 0.82452 11 0.075 11 % + LOOP_ions force_stress 0.54132 1 0.54 7.4 % + Force_Stress_LCAO getForceStress 0.54129 1 0.54 7.4 % + Force_LCAO_gamma ftable_gamma 0.34457 1 0.34 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.33725 1 0.34 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:19 2022 + FINISH Time : Wed Sep 28 11:05:26 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/118/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..acc0b89a3bd1e589ce9a228e439cec71481612a7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.301208 0.548465 0.193974 +H 0.326531 0.582771 0.14548 +H 0.272685 0.492536 0.170991 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..cfc17a39e4e49a18a3050117442dd2ef1a07969b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1265 2 + 2 -13.3167 2 + 3 -8.77698 2 + 4 -6.70242 2 + 5 1.26436 0 + 6 4.42115 0 + 7 11.0964 0 + 8 11.314 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f2890404ec52b6f3d73d8ed67946aa797ab6e1d7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:18 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 8.43382769547 15.3570315985 5.43128136735 0 0 0 0 + tauc_H1 9.14285842043 16.3175933119 4.07343295597 0 0 0 0 + tauc_H2 7.63516620479 13.7910006597 4.78775690151 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.11444141137 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.115052855061 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.14579563311 (SEC) + + DONE : INIT CHARGE Time : 0.197583128055 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.503852 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00137 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101 + + Density error is 0.215298970415 + + Energy Rydberg eV + E_KohnSham -34.189425781 -465.17100197 + E_Harris -34.3815102593 -467.784445371 + E_Fermi -0.401291424683 -5.45984993423 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013362132156 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012167476821 + + Density error is 0.0982848447478 + + Energy Rydberg eV + E_KohnSham -34.2783066899 -466.380288774 + E_Harris -34.2849789041 -466.471068906 + E_Fermi -0.210251303026 -2.86061573308 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00124250501895 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116601416318 + + Density error is 0.0629971816414 + + Energy Rydberg eV + E_KohnSham -34.278501843 -466.382943969 + E_Harris -34.2827829586 -466.441191534 + E_Fermi -0.198852185842 -2.70552278721 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107519724062 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109187872482 + + Density error is 0.0021203083467 + + Energy Rydberg eV + E_KohnSham -34.2784932547 -466.382827118 + E_Harris -34.2784974474 -466.382884163 + E_Fermi -0.16376880002 -2.22818883489 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107116561498 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109026360175 + + Density error is 0.000826265584612 + + Energy Rydberg eV + E_KohnSham -34.2784467503 -466.382194394 + E_Harris -34.27844736 -466.382202689 + E_Fermi -0.162970320681 -2.21732496615 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106932868393 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108932143075 + + Density error is 0.000210803747375 + + Energy Rydberg eV + E_KohnSham -34.2784771915 -466.382608567 + E_Harris -34.2784773108 -466.382610191 + E_Fermi -0.162931782645 -2.21680062927 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106931351431 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010896212773 + + Density error is 3.71163428937e-05 + + Energy Rydberg eV + E_KohnSham -34.2784643759 -466.382434203 + E_Harris -34.2784643829 -466.382434297 + E_Fermi -0.162788108177 -2.21484583785 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106928580997 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010895280375 + + Density error is 1.72727031912e-05 + + Energy Rydberg eV + E_KohnSham -34.2784698734 -466.382508999 + E_Harris -34.2784698745 -466.382509015 + E_Fermi -0.162827793511 -2.21538578451 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106925589819 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010895218027 + + Density error is 2.44445367461e-06 + + Energy Rydberg eV + E_KohnSham -34.2784685005 -466.38249032 + E_Harris -34.2784685005 -466.38249032 + E_Fermi -0.162810160541 -2.21514587565 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106925133151 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108952203105 + + Density error is 4.99529572025e-07 + + Energy Rydberg eV + E_KohnSham -34.2784687371 -466.38249354 + E_Harris -34.2784687371 -466.38249354 + E_Fermi -0.162807868322 -2.21511468842 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106925133672 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108952254345 + + Density error is 1.80053622347e-07 + + Energy Rydberg eV + E_KohnSham -34.2784687585 -466.382493831 + E_Harris -34.2784687585 -466.382493831 + E_Fermi -0.162807652117 -2.21511174679 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106925113307 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108952267634 + + Density error is 9.69195020202e-09 + + Energy Rydberg eV + E_KohnSham -34.278468761 -466.382493865 + E_Harris -34.278468761 -466.382493865 + E_band -7.92646404439 -107.845075996 + E_one_elec -69.1855983383 -941.31835694 + E_Hartree +36.00315701 +489.848081325 + E_xc -8.2032975321 -111.611588826 + E_Ewald +7.23187853698 +98.3947553468 + E_demet -1.10742904382e-73 -1.50673451266e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194446761303 -2.64558391136 + E_Fermi -0.162807475234 -2.21510934018 + + charge density convergence is achieved + final etot is -466.382493865 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1265 2.00000 + 2 -13.3167 2.00000 + 3 -8.77698 2.00000 + 4 -6.70242 2.00000 + 5 1.26436 0.00000 + 6 4.42115 0.00000 + 7 11.0964 0.00000 + 8 11.3140 0.00000 + + EFERMI = -2.215109340176490 eV + OUT.ABACUS/ final etot is -466.3824938647687 eV + correction force for each atom along direction 1 is 3.03128e-05 + correction force for each atom along direction 2 is -7.98976e-05 + correction force for each atom along direction 3 is -2.95886e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.68295224 -0.98457313 +1.0702403 + H1 +0.18395222 +0.11951921 -0.94661733 + H2 +0.49900001 +0.86505392 -0.12362298 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3824938647687 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2909 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2807 1 7.3 1.e+02% + Potential init_pot 0.30563 2 0.15 4.2% + PW_Basis recip2real 0.30456 17 0.018 4.2% + PW_Basis gathers_scatterp 0.12985 17 0.0076 1.8% + Charge atomic_rho 0.10979 1 0.11 1.5% + Potential v_of_rho 1.0988 14 0.078 15.% + XC_Functional v_xc 0.32213 15 0.021 4.4% + H_Hartree_pw v_hartree 0.72894 14 0.052 10.% + PW_Basis real2recip 0.75353 41 0.018 10.% + PW_Basis gatherp_scatters 0.28789 41 0.0070 3.9% + ORB_control set_orb_tables 1.1004 1 1.1 15.% + ORB_gen_tables gen_tables 1.1004 1 1.1 15.% + ORB_table_phi init_Table 0.47562 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47034 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18347 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18193 56 0.0032 2.5% + ORB_table_alpha init_Table_Alpha 0.24677 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24475 66 0.0037 3.4% + LOOP_ions opt_ions 5.5994 1 5.6 77.% + ESolver_KS_LCAO Run 5.0686 1 5.1 70.% + HSolverLCAO solve 2.3834 12 0.20 33.% + HamiltLCAO updateHk 1.2648 12 0.11 17.% + LCAO_Hamilt cal_Hgamma 1.2352 12 0.10 17.% + Gint_interface cal_gint 2.1504 25 0.086 29.% + Gint_Gamma distri_vl 2.6462 6 0.44 36.% + LCAO_Deepks cal_projected_DM 5.4503 14 0.39 75.% + LCAO_gen_fixedH add_v_delta 2.4981 6 0.42 34.% + LCAO_DESCRIPTOR add_v_delta 2.4982 6 0.42 34.% + ElecStateLCAO psiToRho 1.1004 12 0.092 15.% + Charge mix_rho 0.99088 11 0.090 14.% + LOOP_ions force_stress 0.53056 1 0.53 7.3% + Force_Stress_LCAO getForceStress 0.53053 1 0.53 7.3% + Force_LCAO_gamma ftable_gamma 0.31067 1 0.31 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.30237 1 0.30 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:18 2022 + Finish Time : Wed Sep 28 11:12:26 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..5c398fee9f2e1433bc61e045a7c5d3065d8c7a62 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012362 ima = 3.66781e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123709966232 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112905278237 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113397060277 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011360524842 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113567963398 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113593277593 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113582724804 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113585484543 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113584798172 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113584731704 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113584716057 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113584706945 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/STRU new file mode 100644 index 0000000000000000000000000000000000000000..831ea53cd523554916b967f6347f499e3401e287 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-19.566172304546 15.357031598491 5.431281367357 0 0 0 +H +0.0 +2 +-18.857141579569 16.317593311866 4.073432955951 0 0 0 +-20.364833795213 13.791000659708 4.787756901502 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/conv new file mode 100644 index 0000000000000000000000000000000000000000..02d7de2ebd41425c57d70a5e1612a82ad86f3eeb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/conv @@ -0,0 +1 @@ +119 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..82915afaebc1d0badcfa946cfd28b2a738a55f05 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.743377501 0.01253430029 1.272064504 1.36985374 1.468624697 0.007563201386 0.02045633159 0.0388532501 +4.860437352e-19 0.001120279373 0.002303486987 0.01211615997 0.04164516545 3.028141098e-20 1.380616743e-06 4.497541315e-06 +0.001795431247 0.005566372927 + +H atom_index 1 n_descriptor 18 +1.259493272 0.03324937397 0.1118318167 0.1562322343 0.3265259234 0.02214459673 0.02908911434 0.03656502175 +-1.249282115e-17 3.723184079e-05 0.1037614303 0.1153910911 0.1340907984 7.88866538e-18 3.617774669e-06 0.01281919115 +0.02627318932 0.03130987729 + +H atom_index 2 n_descriptor 18 +1.208309033 0.03505317155 0.09499084803 0.1334035153 0.3099158338 0.01992571581 0.02613373605 0.0383275844 +7.00964541e-18 3.32989094e-05 0.09057408423 0.1137952126 0.114271303 1.960031231e-18 5.617558837e-06 0.01349397049 +0.02431327666 0.02892310168 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e687140d9419fb63c317febef34d48d40d08af6f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:18 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.11448 SEC) : SETUP UNITCELL + DONE(0.115072 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.145825 SEC) : INIT PLANEWAVE + DONE(0.197753 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.50393 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651710e+02 0.000000e+00 2.153e-01 5.143e-01 + GE2 -4.663803e+02 -1.209287e+00 9.828e-02 4.794e-01 + GE3 -4.663829e+02 -2.655195e-03 6.300e-02 5.513e-01 + GE4 -4.663828e+02 1.168507e-04 2.120e-03 4.078e-01 + GE5 -4.663822e+02 6.327244e-04 8.263e-04 4.058e-01 + GE6 -4.663826e+02 -4.141733e-04 2.108e-04 4.017e-01 + GE7 -4.663824e+02 1.743643e-04 3.712e-05 3.947e-01 + GE8 -4.663825e+02 -7.479648e-05 1.727e-05 3.855e-01 + GE9 -4.663825e+02 1.867890e-05 2.444e-06 3.842e-01 + GE10 -4.663825e+02 -3.219601e-06 4.995e-07 3.855e-01 + GE11 -4.663825e+02 -2.910403e-07 1.801e-07 3.865e-01 + GE12 -4.663825e+02 -3.400180e-08 9.692e-09 3.096e-01 +E_delta_band = -6.98383237e-02 Ry = -9.50199141e-01 eV +E_delta_NN= -1.94446761e-01 Ry = -2.64558391e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2909 11 0.66 1e+02 % + Run_lcao lcao_line 7.2807 1 7.3 1e+02 % + Potential init_pot 0.30563 2 0.15 4.2 % + PW_Basis recip2real 0.30456 17 0.018 4.2 % + PW_Basis gathers_scatterp 0.12985 17 0.0076 1.8 % + Charge atomic_rho 0.10979 1 0.11 1.5 % + Potential v_of_rho 1.0988 14 0.078 15 % + XC_Functional v_xc 0.32213 15 0.021 4.4 % + H_Hartree_pw v_hartree 0.72894 14 0.052 10 % + PW_Basis real2recip 0.75353 41 0.018 10 % + PW_Basis gatherp_scatters 0.28789 41 0.007 3.9 % + ORB_control set_orb_tables 1.1004 1 1.1 15 % + ORB_gen_tables gen_tables 1.1004 1 1.1 15 % + ORB_table_phi init_Table 0.47562 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.47034 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.18347 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18193 56 0.0032 2.5 % + ORB_table_alpha init_Table_Alpha 0.24677 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24475 66 0.0037 3.4 % + LOOP_ions opt_ions 5.5994 1 5.6 77 % + ESolver_KS_LCAO Run 5.0686 1 5.1 70 % + HSolverLCAO solve 2.3834 12 0.2 33 % + HamiltLCAO updateHk 1.2648 12 0.11 17 % + LCAO_Hamilt cal_Hgamma 1.2352 12 0.1 17 % + Gint_interface cal_gint 2.1504 25 0.086 29 % + Gint_Gamma distri_vl 2.6462 6 0.44 36 % + LCAO_Deepks cal_projected_DM 5.4503 14 0.39 75 % + LCAO_gen_fixedH add_v_delta 2.4981 6 0.42 34 % + LCAO_DESCRIPTOR add_v_delta 2.4982 6 0.42 34 % + ElecStateLCAO psiToRho 1.1004 12 0.092 15 % + Charge mix_rho 0.99088 11 0.09 14 % + LOOP_ions force_stress 0.53056 1 0.53 7.3 % + Force_Stress_LCAO getForceStress 0.53053 1 0.53 7.3 % + Force_LCAO_gamma ftable_gamma 0.31067 1 0.31 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.30237 1 0.3 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:18 2022 + FINISH Time : Wed Sep 28 11:12:26 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/119/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a7542bb97f94e5e2a6614960876a65253f9a4424 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.571651 0.227465 0.363101 +H 0.580004 0.188261 0.313226 +H 0.628164 0.255293 0.369723 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..943845c30b2763d767bc31fe737610cfd1b2ef95 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6235 2 + 2 -13.2844 2 + 3 -9.19726 2 + 4 -6.8184 2 + 5 1.556 0 + 6 4.86942 0 + 7 10.9959 0 + 8 11.2461 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3feafb7ae231222c4ac2d39946834ab956819a9f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:39 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.0062375181 6.36902742533 10.1668200865 0 0 0 0 + tauc_H1 16.2401246692 5.27129856208 8.77033625379 0 0 0 0 + tauc_H2 17.5885815572 7.14820357763 10.3522303556 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105460229706 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105884185208 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124046062889 (SEC) + + DONE : INIT CHARGE Time : 0.168379037504 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450156 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000984 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0017 + + Density error is 0.218398819708 + + Energy Rydberg eV + E_KohnSham -34.1853433731 -465.115457961 + E_Harris -34.3850640386 -467.83279702 + E_Fermi -0.425634120112 -5.79104929674 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00126893686417 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00142614754832 + + Density error is 0.0972702890089 + + Energy Rydberg eV + E_KohnSham -34.2770209276 -466.36279508 + E_Harris -34.2836278296 -466.452686595 + E_Fermi -0.231710805735 -3.15258724617 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120204453064 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130905580267 + + Density error is 0.0620084049517 + + Energy Rydberg eV + E_KohnSham -34.2772723641 -466.366216049 + E_Harris -34.2814813775 -466.423482615 + E_Fermi -0.216582052979 -2.94675000505 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110057368817 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111759297552 + + Density error is 0.00207286816803 + + Energy Rydberg eV + E_KohnSham -34.2773326926 -466.367036861 + E_Harris -34.2773352879 -466.367072172 + E_Fermi -0.180711054297 -2.45870003003 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110340894534 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111606681338 + + Density error is 0.000942247450253 + + Energy Rydberg eV + E_KohnSham -34.2772482355 -466.365887763 + E_Harris -34.277251577 -466.365933226 + E_Fermi -0.179303892682 -2.43955461406 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110167680462 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111456950223 + + Density error is 0.00010383492388 + + Energy Rydberg eV + E_KohnSham -34.277308327 -466.36670535 + E_Harris -34.277308345 -466.366705595 + E_Fermi -0.179724366315 -2.44527545132 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110140140702 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111420231451 + + Density error is 5.40383213994e-05 + + Energy Rydberg eV + E_KohnSham -34.2772887473 -466.366438954 + E_Harris -34.277288762 -466.366439155 + E_Fermi -0.179572355524 -2.44320723841 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110139976485 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111428761998 + + Density error is 1.14162574452e-05 + + Energy Rydberg eV + E_KohnSham -34.2772916073 -466.366477867 + E_Harris -34.2772916078 -466.366477874 + E_Fermi -0.179638909426 -2.4441127507 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110140962008 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111427605854 + + Density error is 2.08084905075e-06 + + Energy Rydberg eV + E_KohnSham -34.2772902146 -466.366458918 + E_Harris -34.2772902146 -466.366458918 + E_Fermi -0.179627890369 -2.44396282874 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110141046065 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111427086257 + + Density error is 1.82121163046e-07 + + Energy Rydberg eV + E_KohnSham -34.2772903559 -466.36646084 + E_Harris -34.2772903559 -466.36646084 + E_Fermi -0.179625948772 -2.44393641195 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110141071703 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111427115687 + + Density error is 8.94093998986e-08 + + Energy Rydberg eV + E_KohnSham -34.2772903936 -466.366461353 + E_Harris -34.2772903936 -466.366461353 + E_band -8.07361031797 -109.847103756 + E_one_elec -69.9412897397 -951.600065928 + E_Hartree +36.344125937 +494.487201573 + E_xc -8.25892736831 -112.368471577 + E_Ewald +7.70178451522 +104.788154175 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196049489297 -2.66739014443 + E_Fermi -0.17962592748 -2.44393612226 + + charge density convergence is achieved + final etot is -466.366461353 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6235 2.00000 + 2 -13.2844 2.00000 + 3 -9.19726 2.00000 + 4 -6.81840 2.00000 + 5 1.55600 0.00000 + 6 4.86942 0.00000 + 7 10.9959 0.00000 + 8 11.2461 0.00000 + + EFERMI = -2.443936122258971 eV + OUT.ABACUS/ final etot is -466.3664613532528 eV + correction force for each atom along direction 1 is 2.03937e-05 + correction force for each atom along direction 2 is -6.57853e-05 + correction force for each atom along direction 3 is -0.000105822 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.8628310 -0.043458723 +0.80680003 + H1 +0.046972778 -0.96195849 -1.1508646 + H2 +1.8158583 +1.0054172 +0.34406458 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3664613532528 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9102 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9002 1 6.9 1.e+02% + Potential init_pot 0.28323 2 0.14 4.1% + PW_Basis recip2real 0.25455 16 0.016 3.7% + PW_Basis gathers_scatterp 0.11114 16 0.0069 1.6% + Potential v_of_rho 0.78193 13 0.060 11.% + XC_Functional v_xc 0.18262 14 0.013 2.6% + H_Hartree_pw v_hartree 0.56622 13 0.044 8.2% + PW_Basis real2recip 0.66079 38 0.017 9.6% + PW_Basis gatherp_scatters 0.27721 38 0.0073 4.0% + ORB_control set_orb_tables 1.0962 1 1.1 16.% + ORB_gen_tables gen_tables 1.0962 1 1.1 16.% + ORB_table_phi init_Table 0.47553 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47033 126 0.0037 6.8% + ORB_table_beta init_Table_Beta 0.18350 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18191 56 0.0032 2.6% + ORB_table_alpha init_Table_Alpha 0.24744 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24551 66 0.0037 3.6% + LOOP_ions opt_ions 5.2779 1 5.3 76.% + ESolver_KS_LCAO Run 4.7104 1 4.7 68.% + HSolverLCAO solve 2.5079 11 0.23 36.% + HamiltLCAO updateHk 1.3091 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2817 11 0.12 19.% + Gint_interface cal_gint 0.72299 23 0.031 10.% + Gint_Gamma distri_vl_value 0.58626 11 0.053 8.5% + Gint_Gamma distri_vl 2.2667 6 0.38 33.% + LCAO_Deepks cal_projected_DM 4.9147 13 0.38 71.% + LCAO_gen_fixedH add_v_delta 2.1204 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.1206 6 0.35 31.% + ElecStateLCAO psiToRho 1.1799 11 0.11 17.% + Charge mix_rho 0.86773 10 0.087 13.% + LOOP_ions force_stress 0.56737 1 0.57 8.2% + Force_Stress_LCAO getForceStress 0.56735 1 0.57 8.2% + Force_LCAO_gamma ftable_gamma 0.37526 1 0.38 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.16301 1 0.16 2.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:39 2022 + Finish Time : Wed Sep 28 11:14:46 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a345ab6d165e53e7e784199604461a228bcabdba --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124134 ima = 3.6583e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122775373757 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111954437859 + charge after normalized = 7.99999999999996 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112340854433 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112642884794 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112558090896 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112605400825 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112601455828 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112604470683 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112604012707 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112603922056 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112603918373 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4d3ad3295f95e208cc4af57c9b7a9720e310a946 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.993762481883 6.369027425313 10.166820086501 0 0 0 +H +0.0 +2 +-11.759875330763 5.271298562065 8.770336253769 0 0 0 +-10.411418442834 7.148203577633 10.352230355642 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/conv new file mode 100644 index 0000000000000000000000000000000000000000..9fe2e3c1870fbc866c2d968a304c8085682d2f5f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/conv @@ -0,0 +1 @@ +12 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..18db2b36895035f781255587a743ef638214a9ef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749826704 0.01286652088 1.299247953 1.382159141 1.470912366 0.008864849951 0.01900769015 0.03904198066 +-8.399165638e-19 0.001191422419 0.002827400011 0.01340817166 0.0486972902 -8.886619756e-21 2.539055066e-06 6.873441521e-06 +0.001645011564 0.005982105303 + +H atom_index 1 n_descriptor 18 +1.278673896 0.03331871793 0.1197661214 0.1635539296 0.3290133929 0.02396654476 0.0299324486 0.03665334448 +-1.623750698e-17 5.503372857e-05 0.1085759749 0.119096324 0.1406288561 3.187628783e-18 2.442863441e-06 0.01330918307 +0.02808827568 0.03200552314 + +H atom_index 2 n_descriptor 18 +1.292933397 0.0328754185 0.1253146166 0.1708788476 0.3330439546 0.0246274389 0.03074519461 0.03647777825 +5.235358446e-19 5.643636015e-05 0.1087446902 0.1230101726 0.1468256984 9.472197333e-19 1.664874587e-06 0.01356128471 +0.02853898937 0.03253789109 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..b3b0725f002028c589b4f4ec51810f1fa7c5fab4 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..f85175f2956e02a79e9a83f753cc3ad62736c413 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..892bb66c86d84f0721c360a78bcaba982b065c7d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..f01b182cc212d2bf86aff614d3695924d3ae6e0b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..bb9276c346c4d19a34e899b9177c60cb957700ee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:39 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105482 SEC) : SETUP UNITCELL + DONE(0.105903 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124065 SEC) : INIT PLANEWAVE + DONE(0.168514 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450237 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651155e+02 0.000000e+00 2.184e-01 5.261e-01 + GE2 -4.663628e+02 -1.247337e+00 9.727e-02 4.783e-01 + GE3 -4.663662e+02 -3.420969e-03 6.201e-02 5.445e-01 + GE4 -4.663670e+02 -8.208115e-04 2.073e-03 4.052e-01 + GE5 -4.663659e+02 1.149098e-03 9.422e-04 4.059e-01 + GE6 -4.663667e+02 -8.175864e-04 1.038e-04 3.910e-01 + GE7 -4.663664e+02 2.663956e-04 5.404e-05 3.961e-01 + GE8 -4.663665e+02 -3.891291e-05 1.142e-05 3.907e-01 + GE9 -4.663665e+02 1.894927e-05 2.081e-06 3.887e-01 + GE10 -4.663665e+02 -1.922515e-06 1.821e-07 3.885e-01 + GE11 -4.663665e+02 -5.130619e-07 8.941e-08 3.353e-01 +E_delta_band = -7.30657514e-02 Ry = -9.94110548e-01 eV +E_delta_NN= -1.96049489e-01 Ry = -2.66739014e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9102 11 0.63 1e+02 % + Run_lcao lcao_line 6.9002 1 6.9 1e+02 % + Potential init_pot 0.28323 2 0.14 4.1 % + PW_Basis recip2real 0.25455 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.11114 16 0.0069 1.6 % + Potential v_of_rho 0.78193 13 0.06 11 % + XC_Functional v_xc 0.18262 14 0.013 2.6 % + H_Hartree_pw v_hartree 0.56622 13 0.044 8.2 % + PW_Basis real2recip 0.66079 38 0.017 9.6 % + PW_Basis gatherp_scatters 0.27721 38 0.0073 4 % + ORB_control set_orb_tables 1.0962 1 1.1 16 % + ORB_gen_tables gen_tables 1.0962 1 1.1 16 % + ORB_table_phi init_Table 0.47553 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47033 126 0.0037 6.8 % + ORB_table_beta init_Table_Beta 0.1835 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18191 56 0.0032 2.6 % + ORB_table_alpha init_Table_Alpha 0.24744 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24551 66 0.0037 3.6 % + LOOP_ions opt_ions 5.2779 1 5.3 76 % + ESolver_KS_LCAO Run 4.7104 1 4.7 68 % + HSolverLCAO solve 2.5079 11 0.23 36 % + HamiltLCAO updateHk 1.3091 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2817 11 0.12 19 % + Gint_interface cal_gint 0.72299 23 0.031 10 % + Gint_Gamma distri_vl_value 0.58626 11 0.053 8.5 % + Gint_Gamma distri_vl 2.2667 6 0.38 33 % + LCAO_Deepks cal_projected_DM 4.9147 13 0.38 71 % + LCAO_gen_fixedH add_v_delta 2.1204 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.1206 6 0.35 31 % + ElecStateLCAO psiToRho 1.1799 11 0.11 17 % + Charge mix_rho 0.86773 10 0.087 13 % + LOOP_ions force_stress 0.56737 1 0.57 8.2 % + Force_Stress_LCAO getForceStress 0.56735 1 0.57 8.2 % + Force_LCAO_gamma ftable_gamma 0.37526 1 0.38 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.16301 1 0.16 2.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:39 2022 + FINISH Time : Wed Sep 28 11:14:46 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/12/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b02dae458587f1c288d3ad5cc95cc58748ce22ca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.282752 0.551309 0.184005 +H 0.334683 0.547757 0.142215 +H 0.254894 0.493861 0.167862 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..27147e18f0b37ac87ffdc1ba5974484f544ecfc7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2915 2 + 2 -12.5962 2 + 3 -9.44584 2 + 4 -6.74888 2 + 5 1.14895 0 + 6 4.1869 0 + 7 11.0956 0 + 8 11.3817 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..434aef51c1dd6b990fcee3e0f63cf716fedad6e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:25 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.91706668428 15.43664786 5.15214845357 0 0 0 0 + tauc_H1 9.37112494552 15.337185063 3.9820095456 0 0 0 0 + tauc_H2 7.13704309149 13.8281219348 4.70013546212 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0862659701764 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0866248147779 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104884335192 (SEC) + + DONE : INIT CHARGE Time : 0.154575535383 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438768 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00147 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943 + + Density error is 0.211959393209 + + Energy Rydberg eV + E_KohnSham -34.1906349525 -465.187453592 + E_Harris -34.3767599063 -467.719813504 + E_Fermi -0.39799398022 -5.41498590069 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00139994785153 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112111607509 + + Density error is 0.0979494692796 + + Energy Rydberg eV + E_KohnSham -34.2788824489 -466.388122377 + E_Harris -34.2858678479 -466.483163606 + E_Fermi -0.209362218707 -2.84851912033 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00129518410254 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106413524277 + + Density error is 0.0630014888935 + + Energy Rydberg eV + E_KohnSham -34.2792398814 -466.392985496 + E_Harris -34.2837606068 -466.45449312 + E_Fermi -0.200476423018 -2.7276216677 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110784451254 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000982759198372 + + Density error is 0.00189581191753 + + Energy Rydberg eV + E_KohnSham -34.2791807791 -466.392181368 + E_Harris -34.2791805008 -466.392177582 + E_Fermi -0.164785453273 -2.24202111202 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011077064969 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000983798423864 + + Density error is 0.000926080864108 + + Energy Rydberg eV + E_KohnSham -34.2791329223 -466.391530243 + E_Harris -34.2791339553 -466.391544297 + E_Fermi -0.164568885272 -2.23907455321 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110531556959 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000982564884544 + + Density error is 9.89056939963e-05 + + Energy Rydberg eV + E_KohnSham -34.2791605639 -466.391906326 + E_Harris -34.2791605642 -466.39190633 + E_Fermi -0.164316498236 -2.23564065142 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110515306952 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000982515635465 + + Density error is 2.85393397929e-05 + + Energy Rydberg eV + E_KohnSham -34.2791532003 -466.39180614 + E_Harris -34.2791532045 -466.391806196 + E_Fermi -0.164230439941 -2.23446976825 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110512657943 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098245660108 + + Density error is 1.20407383749e-05 + + Energy Rydberg eV + E_KohnSham -34.2791546014 -466.391825203 + E_Harris -34.2791546021 -466.391825212 + E_Fermi -0.164260537828 -2.234879271 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110511607657 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000982459614405 + + Density error is 2.24689516847e-06 + + Energy Rydberg eV + E_KohnSham -34.2791535113 -466.39181037 + E_Harris -34.2791535113 -466.39181037 + E_Fermi -0.164250469296 -2.2347422816 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110511145891 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000982460320333 + + Density error is 2.2612320124e-07 + + Energy Rydberg eV + E_KohnSham -34.2791536971 -466.391812899 + E_Harris -34.2791536971 -466.391812899 + E_Fermi -0.164248215092 -2.23471161159 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110511157726 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098246068808 + + Density error is 5.91361300903e-08 + + Energy Rydberg eV + E_KohnSham -34.279153732 -466.391813373 + E_Harris -34.279153732 -466.391813373 + E_band -7.94996411485 -108.164810858 + E_one_elec -69.0472342402 -939.435816808 + E_Hartree +35.9127864976 +488.618527424 + E_xc -8.18901613145 -111.417280402 + E_Ewald +7.16909562494 +97.540550006 + E_demet -7.96116097744e-70 -1.08317151989e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194417736909 -2.64518901423 + E_Fermi -0.164248103342 -2.23471009115 + + charge density convergence is achieved + final etot is -466.391813373 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2915 2.00000 + 2 -12.5962 2.00000 + 3 -9.44584 2.00000 + 4 -6.74888 2.00000 + 5 1.14895 0.00000 + 6 4.18690 0.00000 + 7 11.0956 0.00000 + 8 11.3817 0.00000 + + EFERMI = -2.234710091147233 eV + OUT.ABACUS/ final etot is -466.3918133727087 eV + correction force for each atom along direction 1 is -2.62923e-05 + correction force for each atom along direction 2 is -8.21679e-05 + correction force for each atom along direction 3 is -7.77065e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.63605161 -0.40333110 -0.74770090 + H1 -0.17666472 +0.48073268 +0.44741089 + H2 -0.45938690 -0.077401582 +0.30029001 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3918133727087 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8995 11 0.72 1.0e+02% + Run_lcao lcao_line 7.8905 1 7.9 1.e+02% + Potential init_pot 0.28763 2 0.14 3.6% + PW_Basis recip2real 0.28819 16 0.018 3.6% + PW_Basis gathers_scatterp 0.12325 16 0.0077 1.6% + Potential v_of_rho 0.99708 13 0.077 13.% + XC_Functional v_xc 0.28798 14 0.021 3.6% + H_Hartree_pw v_hartree 0.66769 13 0.051 8.5% + PW_Basis real2recip 0.65571 38 0.017 8.3% + PW_Basis gatherp_scatters 0.25322 38 0.0067 3.2% + ORB_control set_orb_tables 1.0968 1 1.1 14.% + ORB_gen_tables gen_tables 1.0968 1 1.1 14.% + ORB_table_phi init_Table 0.47653 1 0.48 6.0% + ORB_table_phi cal_ST_Phi12_R 0.47136 126 0.0037 6.0% + ORB_table_beta init_Table_Beta 0.18434 1 0.18 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18273 56 0.0033 2.3% + ORB_table_alpha init_Table_Alpha 0.24893 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24694 66 0.0037 3.1% + LOOP_ions opt_ions 6.2749 1 6.3 79.% + ESolver_KS_LCAO Run 5.6548 1 5.7 72.% + HSolverLCAO solve 3.3509 11 0.30 42.% + HamiltLCAO updateHk 1.6750 11 0.15 21.% + LCAO_Hamilt cal_Hgamma 1.6416 11 0.15 21.% + Gint_interface cal_gint 3.2277 23 0.14 41.% + Gint_Gamma distri_vl 2.7061 6 0.45 34.% + LCAO_Deepks cal_projected_DM 6.0850 13 0.47 77.% + LCAO_gen_fixedH add_v_delta 2.5591 6 0.43 32.% + LCAO_DESCRIPTOR add_v_delta 2.5591 6 0.43 32.% + ElecStateLCAO psiToRho 1.6596 11 0.15 21.% + Charge mix_rho 0.79177 10 0.079 10.% + LOOP_ions force_stress 0.61992 1 0.62 7.8% + Force_Stress_LCAO getForceStress 0.61988 1 0.62 7.8% + Force_LCAO_gamma ftable_gamma 0.39911 1 0.40 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.39117 1 0.39 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:25 2022 + Finish Time : Wed Sep 28 11:12:33 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ed6ef5d61a7692e51ae8f7c8a42642ef08656549 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123959 ima = 3.68813e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122718626101 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011141831466 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112108028154 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112347065302 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112308214807 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112328699495 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112327160021 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112329367541 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011232878501 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112328690755 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112328678656 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8002da05a93e36385a7a2385026c10453de81568 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.082933315710 15.436647859983 5.152148453559 0 0 0 +H +0.0 +2 +-18.628875054467 15.337185062996 3.982009545605 0 0 0 +-20.862956908530 13.828121934764 4.700135462137 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/conv new file mode 100644 index 0000000000000000000000000000000000000000..19bbc2c7296b36cf171335fdf03eab21841be39b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/conv @@ -0,0 +1 @@ +120 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9c4e1fc550bba2cfdd18060208b63391b0d4d24b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754701135 0.01272001398 1.260645209 1.341937179 1.469223247 0.009501499218 0.01636071343 0.03919890438 +-1.755489623e-18 0.0008415287859 0.002773894438 0.01299539475 0.04547845181 1.464732034e-19 2.621191431e-06 7.125785357e-06 +0.001581885027 0.006133928567 + +H atom_index 1 n_descriptor 18 +1.222080798 0.0358626534 0.1016056668 0.1370241839 0.3100383177 0.02179929302 0.02659104794 0.03905776579 +2.886388956e-17 4.512250577e-05 0.0950542553 0.1142259666 0.1172732147 2.570889739e-18 4.38078326e-06 0.01384025718 +0.02567678115 0.02937078454 + +H atom_index 2 n_descriptor 18 +1.241779687 0.03521152425 0.1082707033 0.1457823605 0.316981051 0.02277719772 0.02775252084 0.03833850884 +-2.357675694e-17 4.69145215e-05 0.09998428261 0.1151391965 0.1248915652 -8.435287633e-19 3.364616234e-06 0.01349198363 +0.026448871 0.03034071861 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..2a774923b3cfe6d7bee337731fe93678ceb2816d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:25 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0862892 SEC) : SETUP UNITCELL + DONE(0.0866394 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104906 SEC) : INIT PLANEWAVE + DONE(0.154713 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438834 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651875e+02 0.000000e+00 2.120e-01 6.115e-01 + GE2 -4.663881e+02 -1.200669e+00 9.795e-02 5.658e-01 + GE3 -4.663930e+02 -4.863120e-03 6.300e-02 6.353e-01 + GE4 -4.663922e+02 8.041282e-04 1.896e-03 4.984e-01 + GE5 -4.663915e+02 6.511250e-04 9.261e-04 4.940e-01 + GE6 -4.663919e+02 -3.760831e-04 9.891e-05 4.868e-01 + GE7 -4.663918e+02 1.001866e-04 2.854e-05 4.721e-01 + GE8 -4.663918e+02 -1.906291e-05 1.204e-05 4.710e-01 + GE9 -4.663918e+02 1.483270e-05 2.247e-06 4.757e-01 + GE10 -4.663918e+02 -2.528944e-06 2.261e-07 4.742e-01 + GE11 -4.663918e+02 -4.739364e-07 5.914e-08 4.075e-01 +E_delta_band = -6.96322541e-02 Ry = -9.47395421e-01 eV +E_delta_NN= -1.94417737e-01 Ry = -2.64518901e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8995 11 0.72 1e+02 % + Run_lcao lcao_line 7.8905 1 7.9 1e+02 % + Potential init_pot 0.28763 2 0.14 3.6 % + PW_Basis recip2real 0.28819 16 0.018 3.6 % + PW_Basis gathers_scatterp 0.12325 16 0.0077 1.6 % + Potential v_of_rho 0.99708 13 0.077 13 % + XC_Functional v_xc 0.28798 14 0.021 3.6 % + H_Hartree_pw v_hartree 0.66769 13 0.051 8.5 % + PW_Basis real2recip 0.65571 38 0.017 8.3 % + PW_Basis gatherp_scatters 0.25322 38 0.0067 3.2 % + ORB_control set_orb_tables 1.0968 1 1.1 14 % + ORB_gen_tables gen_tables 1.0968 1 1.1 14 % + ORB_table_phi init_Table 0.47653 1 0.48 6 % + ORB_table_phi cal_ST_Phi12_R 0.47136 126 0.0037 6 % + ORB_table_beta init_Table_Beta 0.18434 1 0.18 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.18273 56 0.0033 2.3 % + ORB_table_alpha init_Table_Alpha 0.24893 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24694 66 0.0037 3.1 % + LOOP_ions opt_ions 6.2749 1 6.3 79 % + ESolver_KS_LCAO Run 5.6548 1 5.7 72 % + HSolverLCAO solve 3.3509 11 0.3 42 % + HamiltLCAO updateHk 1.675 11 0.15 21 % + LCAO_Hamilt cal_Hgamma 1.6416 11 0.15 21 % + Gint_interface cal_gint 3.2277 23 0.14 41 % + Gint_Gamma distri_vl 2.7061 6 0.45 34 % + LCAO_Deepks cal_projected_DM 6.085 13 0.47 77 % + LCAO_gen_fixedH add_v_delta 2.5591 6 0.43 32 % + LCAO_DESCRIPTOR add_v_delta 2.5591 6 0.43 32 % + ElecStateLCAO psiToRho 1.6596 11 0.15 21 % + Charge mix_rho 0.79177 10 0.079 10 % + LOOP_ions force_stress 0.61992 1 0.62 7.8 % + Force_Stress_LCAO getForceStress 0.61988 1 0.62 7.8 % + Force_LCAO_gamma ftable_gamma 0.39911 1 0.4 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.39117 1 0.39 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:25 2022 + FINISH Time : Wed Sep 28 11:12:33 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/120/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..49c9005940587543fd43ebc152dfe7a7bc8b73d3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.262691 0.547813 0.179285 +H 0.316585 0.574248 0.1516 +H 0.253362 0.492281 0.147427 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..efa8da8f9fcedc412f2f1d76024ea365aa92baf0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2927 2 + 2 -13.0892 2 + 3 -9.08772 2 + 4 -6.74519 2 + 5 1.31552 0 + 6 4.4506 0 + 7 11.0721 0 + 8 11.3201 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f8b2456f2dddb61155e82301467221c54e29ff10 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:36 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.35535330046 15.3387521664 5.01996925657 0 0 0 0 + tauc_H1 8.86439312476 16.0789549136 4.24478993267 0 0 0 0 + tauc_H2 7.09413333488 13.7838666614 4.12795844762 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0858990763798 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0862633003997 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104508023299 (SEC) + + DONE : INIT CHARGE Time : 0.152756522761 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.435246 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0015 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000748 + + Density error is 0.214828466172 + + Energy Rydberg eV + E_KohnSham -34.1915941171 -465.200503696 + E_Harris -34.3830443572 -467.805317845 + E_Fermi -0.405878399237 -5.52225892475 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00144448739912 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000985417264874 + + Density error is 0.0979026907036 + + Energy Rydberg eV + E_KohnSham -34.2807563459 -466.413618054 + E_Harris -34.2874705426 -466.504969386 + E_Fermi -0.215039228665 -2.92575880336 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00133519398606 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000948263079499 + + Density error is 0.0627739495568 + + Energy Rydberg eV + E_KohnSham -34.280996888 -466.416890796 + E_Harris -34.2853315018 -466.475866244 + E_Fermi -0.203457938375 -2.76818726523 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114293506813 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000901765823034 + + Density error is 0.00200287017506 + + Energy Rydberg eV + E_KohnSham -34.2809908916 -466.416809212 + E_Harris -34.2809921542 -466.416826391 + E_Fermi -0.167961967894 -2.28523981065 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114077510677 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000902563848214 + + Density error is 0.000864836631997 + + Energy Rydberg eV + E_KohnSham -34.2809336227 -466.416030028 + E_Harris -34.2809347035 -466.416044734 + E_Fermi -0.167209877703 -2.27500709865 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113874595753 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000901824426642 + + Density error is 0.000153114819602 + + Energy Rydberg eV + E_KohnSham -34.2809701778 -466.416527386 + E_Harris -34.2809702167 -466.416527915 + E_Fermi -0.167213895459 -2.27506176302 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113863977821 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000902057906249 + + Density error is 3.87689083708e-05 + + Energy Rydberg eV + E_KohnSham -34.2809570933 -466.416349362 + E_Harris -34.2809571014 -466.416349473 + E_Fermi -0.16708621062 -2.27332452166 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113862214872 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000901982821511 + + Density error is 1.58170445729e-05 + + Energy Rydberg eV + E_KohnSham -34.2809611621 -466.416404721 + E_Harris -34.2809611632 -466.416404736 + E_Fermi -0.167128678916 -2.27390233247 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011385893545 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000901981845792 + + Density error is 1.61554936736e-06 + + Energy Rydberg eV + E_KohnSham -34.2809597352 -466.416385308 + E_Harris -34.2809597352 -466.416385308 + E_Fermi -0.167111659972 -2.27367077786 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113858656688 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000901983569067 + + Density error is 2.16173589179e-07 + + Energy Rydberg eV + E_KohnSham -34.2809599728 -466.416388541 + E_Harris -34.2809599729 -466.416388541 + E_Fermi -0.16711023703 -2.27365141774 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113858699907 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000901984074862 + + Density error is 6.28543210397e-08 + + Energy Rydberg eV + E_KohnSham -34.2809599953 -466.416388847 + E_Harris -34.2809599953 -466.416388847 + E_band -7.96942737638 -108.429622116 + E_one_elec -69.3204436402 -943.153021395 + E_Hartree +36.0548458818 +490.551344504 + E_xc -8.21202015867 -111.730266249 + E_Ewald +7.32093366498 +99.6064125237 + E_demet -3.13314746438e-78 -4.26286581898e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194846062165 -2.65101667831 + E_Fermi -0.167110184389 -2.27365070152 + + charge density convergence is achieved + final etot is -466.416388847 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2927 2.00000 + 2 -13.0892 2.00000 + 3 -9.08772 2.00000 + 4 -6.74519 2.00000 + 5 1.31552 0.00000 + 6 4.45060 0.00000 + 7 11.0721 0.00000 + 8 11.3201 0.00000 + + EFERMI = -2.273650701517236 eV + OUT.ABACUS/ final etot is -466.4163888466884 eV + correction force for each atom along direction 1 is 0.000143830 + correction force for each atom along direction 2 is -8.17558e-05 + correction force for each atom along direction 3 is -1.20112e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.28685090 +0.85632812 +0.37569509 + H1 -0.17948446 -0.10757487 +0.074186508 + H2 -0.10736643 -0.74875325 -0.44988160 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4163888466884 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9682 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9585 1 7.0 1.e+02% + Potential init_pot 0.28924 2 0.14 4.2% + PW_Basis recip2real 0.27521 16 0.017 3.9% + PW_Basis gathers_scatterp 0.12303 16 0.0077 1.8% + Charge atomic_rho 0.10139 1 0.10 1.5% + Potential v_of_rho 0.88268 13 0.068 13.% + XC_Functional v_xc 0.25577 14 0.018 3.7% + H_Hartree_pw v_hartree 0.58910 13 0.045 8.5% + PW_Basis real2recip 0.55516 38 0.015 8.0% + PW_Basis gatherp_scatters 0.21437 38 0.0056 3.1% + ORB_control set_orb_tables 1.1026 1 1.1 16.% + ORB_gen_tables gen_tables 1.1026 1 1.1 16.% + ORB_table_phi init_Table 0.48056 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47571 126 0.0038 6.8% + ORB_table_beta init_Table_Beta 0.18825 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18676 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25339 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.25150 66 0.0038 3.6% + LOOP_ions opt_ions 5.3447 1 5.3 77.% + ESolver_KS_LCAO Run 4.7627 1 4.8 68.% + HSolverLCAO solve 2.7889 11 0.25 40.% + HamiltLCAO updateHk 1.4129 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3790 11 0.13 20.% + Gint_interface cal_gint 2.6998 23 0.12 39.% + Gint_Gamma distri_vl 2.2789 6 0.38 33.% + LCAO_Deepks cal_projected_DM 5.1590 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1455 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1454 6 0.36 31.% + ElecStateLCAO psiToRho 1.3619 11 0.12 20.% + Charge mix_rho 0.65594 10 0.066 9.4% + LOOP_ions force_stress 0.58181 1 0.58 8.3% + Force_Stress_LCAO getForceStress 0.58178 1 0.58 8.3% + Force_LCAO_gamma ftable_gamma 0.37263 1 0.37 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.36594 1 0.37 5.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:36 2022 + Finish Time : Wed Sep 28 11:02:43 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..189a9c45517444a6bed5309814599476d64a5b88 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123556 ima = 3.67362e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123116520813 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112180769977 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112699958643 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112939777692 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112890905901 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001129197997 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112912751395 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112915654749 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112914981553 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112914920514 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011291491048 + charge after normalized = 7.99999999999997 + charge before normalized = 7.99999999999997 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1dd194f35a65c315b8c4c7d4601fa52a353e4846 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.644646699556 15.338752166384 5.019969256578 0 0 0 +H +0.0 +2 +-19.135606875238 16.078954913624 4.244789932648 0 0 0 +-20.905866665094 13.783866661451 4.127958447610 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/conv new file mode 100644 index 0000000000000000000000000000000000000000..0d0d699f031c63a8bc2857f4486635d2f1c4462a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/conv @@ -0,0 +1 @@ +121 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e26ce95c758e005471508daf096bb9190597b37b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748688143 0.01268463187 1.274439945 1.36415414 1.4693425 0.008417005803 0.0187668553 0.03901052119 +7.494484076e-19 0.001069752423 0.002579283463 0.01241852405 0.04496087217 -5.938838778e-19 1.98161802e-06 5.803609608e-06 +0.001661814733 0.005923878856 + +H atom_index 1 n_descriptor 18 +1.231110807 0.03482504093 0.1018908917 0.1415769456 0.3150685334 0.02131493847 0.02723303447 0.03797418366 +-4.156348956e-17 4.331552738e-05 0.09689399136 0.114298358 0.1214777055 4.206785745e-18 5.114889846e-06 0.01336429883 +0.02556318787 0.02989795466 + +H atom_index 2 n_descriptor 18 +1.262367338 0.03374567284 0.1126188182 0.1559871536 0.325206361 0.02275454409 0.02905125313 0.03698480022 +3.727405527e-17 4.617083957e-05 0.1044553805 0.1157907957 0.1339325382 4.024089072e-18 3.479906996e-06 0.01309547344 +0.02672919339 0.03132444157 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..1384e48d2e75c0b5f5e6025e669583acdb8d7b01 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..5ec8ca196561f1de1a9535bb8923e657b615564b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..90456c5702855f94af448ee956a4d440cacfa19e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..b4d1e7015c93a07913c1835cf28313ed5430187c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:36 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0859208 SEC) : SETUP UNITCELL + DONE(0.0862843 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104531 SEC) : INIT PLANEWAVE + DONE(0.152886 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.435314 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652005e+02 0.000000e+00 2.148e-01 5.477e-01 + GE2 -4.664136e+02 -1.213114e+00 9.790e-02 4.748e-01 + GE3 -4.664169e+02 -3.272742e-03 6.277e-02 5.265e-01 + GE4 -4.664168e+02 8.158459e-05 2.003e-03 4.117e-01 + GE5 -4.664160e+02 7.791835e-04 8.648e-04 4.189e-01 + GE6 -4.664165e+02 -4.973575e-04 1.531e-04 4.054e-01 + GE7 -4.664163e+02 1.780235e-04 3.877e-05 3.986e-01 + GE8 -4.664164e+02 -5.535885e-05 1.582e-05 3.936e-01 + GE9 -4.664164e+02 1.941343e-05 1.616e-06 3.962e-01 + GE10 -4.664164e+02 -3.232921e-06 2.162e-07 3.912e-01 + GE11 -4.664164e+02 -3.060112e-07 6.285e-08 3.372e-01 +E_delta_band = -7.05703190e-02 Ry = -9.60158448e-01 eV +E_delta_NN= -1.94846062e-01 Ry = -2.65101668e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9682 11 0.63 1e+02 % + Run_lcao lcao_line 6.9585 1 7 1e+02 % + Potential init_pot 0.28924 2 0.14 4.2 % + PW_Basis recip2real 0.27521 16 0.017 3.9 % + PW_Basis gathers_scatterp 0.12303 16 0.0077 1.8 % + Charge atomic_rho 0.10139 1 0.1 1.5 % + Potential v_of_rho 0.88268 13 0.068 13 % + XC_Functional v_xc 0.25577 14 0.018 3.7 % + H_Hartree_pw v_hartree 0.5891 13 0.045 8.5 % + PW_Basis real2recip 0.55516 38 0.015 8 % + PW_Basis gatherp_scatters 0.21437 38 0.0056 3.1 % + ORB_control set_orb_tables 1.1026 1 1.1 16 % + ORB_gen_tables gen_tables 1.1026 1 1.1 16 % + ORB_table_phi init_Table 0.48056 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47571 126 0.0038 6.8 % + ORB_table_beta init_Table_Beta 0.18825 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18676 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.25339 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.2515 66 0.0038 3.6 % + LOOP_ions opt_ions 5.3447 1 5.3 77 % + ESolver_KS_LCAO Run 4.7627 1 4.8 68 % + HSolverLCAO solve 2.7889 11 0.25 40 % + HamiltLCAO updateHk 1.4129 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.379 11 0.13 20 % + Gint_interface cal_gint 2.6998 23 0.12 39 % + Gint_Gamma distri_vl 2.2789 6 0.38 33 % + LCAO_Deepks cal_projected_DM 5.159 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.1455 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1454 6 0.36 31 % + ElecStateLCAO psiToRho 1.3619 11 0.12 20 % + Charge mix_rho 0.65594 10 0.066 9.4 % + LOOP_ions force_stress 0.58181 1 0.58 8.3 % + Force_Stress_LCAO getForceStress 0.58178 1 0.58 8.3 % + Force_LCAO_gamma ftable_gamma 0.37263 1 0.37 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.36594 1 0.37 5.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:36 2022 + FINISH Time : Wed Sep 28 11:02:43 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/121/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..719014466a501335da5e697d08c01b844e1c31b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.253501 0.553769 0.178763 +H 0.313273 0.568468 0.158991 +H 0.227748 0.531569 0.124648 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..14f6194c94d3d6e39e98255b71192d202b1f14d0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5658 2 + 2 -13.0674 2 + 3 -9.30557 2 + 4 -6.80586 2 + 5 1.4551 0 + 6 4.70928 0 + 7 11.0188 0 + 8 11.2848 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..bbfec7110518c28ec9f132c668e926b1d3378db3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:28 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.09804046969 15.505531373 5.00536371738 0 0 0 0 + tauc_H1 8.77165216144 15.9171046917 4.45175490497 0 0 0 0 + tauc_H2 6.37693922284 14.8839368749 3.49013645276 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0878079655257 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0980350652003 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11620941364 (SEC) + + DONE : INIT CHARGE Time : 0.165649938888 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44736 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000979 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000878 + + Density error is 0.217262346212 + + Energy Rydberg eV + E_KohnSham -34.1863466379 -465.129108078 + E_Harris -34.3836973312 -467.814202011 + E_Fermi -0.419419838505 -5.7064996579 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00136016365021 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102909755006 + + Density error is 0.0975255219061 + + Energy Rydberg eV + E_KohnSham -34.2783052188 -466.380268758 + E_Harris -34.2850164083 -466.471579176 + E_Fermi -0.226155556393 -3.0770042013 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00129727382833 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973769747207 + + Density error is 0.0624067397124 + + Energy Rydberg eV + E_KohnSham -34.2786591334 -466.385084014 + E_Harris -34.2829870928 -466.443968922 + E_Fermi -0.213164637166 -2.90025367755 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120890861859 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000892154819434 + + Density error is 0.00201881513289 + + Energy Rydberg eV + E_KohnSham -34.2786836575 -466.385417681 + E_Harris -34.278685245 -466.385439281 + E_Fermi -0.177162791838 -2.41042344258 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121290826642 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00089429365486 + + Density error is 0.000992191511836 + + Energy Rydberg eV + E_KohnSham -34.2786019139 -466.384305502 + E_Harris -34.2786047421 -466.384343982 + E_Fermi -0.176143826064 -2.39655970199 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012110059793 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000892798273102 + + Density error is 9.83017689135e-05 + + Energy Rydberg eV + E_KohnSham -34.2786556892 -466.385037153 + E_Harris -34.2786558564 -466.385039428 + E_Fermi -0.176336153307 -2.39917644838 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121075138468 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000892546860249 + + Density error is 5.51322270718e-05 + + Energy Rydberg eV + E_KohnSham -34.278639307 -466.384814263 + E_Harris -34.2786393222 -466.384814469 + E_Fermi -0.176202093545 -2.39735247175 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121072489366 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000892544475626 + + Density error is 1.08875960303e-05 + + Energy Rydberg eV + E_KohnSham -34.2786413462 -466.384842007 + E_Harris -34.2786413467 -466.384842013 + E_Fermi -0.176268579903 -2.39825706505 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121073996897 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000892558829642 + + Density error is 2.19599132975e-06 + + Energy Rydberg eV + E_KohnSham -34.2786399683 -466.384823259 + E_Harris -34.2786399683 -466.38482326 + E_Fermi -0.176260219327 -2.39814331357 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121073979672 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000892559027181 + + Density error is 2.50354280684e-07 + + Energy Rydberg eV + E_KohnSham -34.2786401151 -466.384825257 + E_Harris -34.2786401151 -466.384825257 + E_Fermi -0.176257729532 -2.39810943818 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121074083636 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000892559810823 + + Density error is 2.99000850198e-08 + + Energy Rydberg eV + E_KohnSham -34.2786401523 -466.384825762 + E_Harris -34.2786401523 -466.384825762 + E_band -8.0473055593 -109.489209154 + E_one_elec -69.7332537553 -948.769591151 + E_Hartree +36.2423103194 +493.101929028 + E_xc -8.24233932608 -112.142779684 + E_Ewald +7.57803403906 +103.104442569 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195665905621 -2.66217122077 + E_Fermi -0.176257740767 -2.39810959103 + + charge density convergence is achieved + final etot is -466.384825762 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5658 2.00000 + 2 -13.0674 2.00000 + 3 -9.30557 2.00000 + 4 -6.80586 2.00000 + 5 1.45510 0.00000 + 6 4.70928 0.00000 + 7 11.0188 0.00000 + 8 11.2848 0.00000 + + EFERMI = -2.398109591033695 eV + OUT.ABACUS/ final etot is -466.3848257623841 eV + correction force for each atom along direction 1 is 4.55963e-05 + correction force for each atom along direction 2 is 8.45396e-05 + correction force for each atom along direction 3 is -3.30868e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.053170360 +0.30182298 +1.2450651 + H1 +1.0007199 +0.32610684 -0.0072558076 + H2 -0.94754958 -0.62792982 -1.2378093 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3848257623841 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9389 11 0.72 1.0e+02% + Run_lcao lcao_line 7.9291 1 7.9 1.e+02% + Potential init_pot 0.28468 2 0.14 3.6% + PW_Basis recip2real 0.28698 16 0.018 3.6% + PW_Basis gathers_scatterp 0.12197 16 0.0076 1.5% + Potential v_of_rho 0.98043 13 0.075 12.% + XC_Functional v_xc 0.27453 14 0.020 3.5% + H_Hartree_pw v_hartree 0.66472 13 0.051 8.4% + PW_Basis real2recip 0.64618 38 0.017 8.1% + PW_Basis gatherp_scatters 0.24666 38 0.0065 3.1% + ORB_control set_orb_tables 1.1012 1 1.1 14.% + ORB_gen_tables gen_tables 1.1012 1 1.1 14.% + ORB_table_phi init_Table 0.47720 1 0.48 6.0% + ORB_table_phi cal_ST_Phi12_R 0.47202 126 0.0037 5.9% + ORB_table_beta init_Table_Beta 0.18647 1 0.19 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18491 56 0.0033 2.3% + ORB_table_alpha init_Table_Alpha 0.25139 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24939 66 0.0038 3.1% + LOOP_ions opt_ions 6.2999 1 6.3 79.% + ESolver_KS_LCAO Run 5.6746 1 5.7 71.% + HSolverLCAO solve 3.3997 11 0.31 43.% + HamiltLCAO updateHk 1.7055 11 0.16 21.% + LCAO_Hamilt cal_Hgamma 1.6698 11 0.15 21.% + Gint_interface cal_gint 3.2802 23 0.14 41.% + Gint_Gamma distri_vl 2.7187 6 0.45 34.% + LCAO_Deepks cal_projected_DM 6.1077 13 0.47 77.% + LCAO_gen_fixedH add_v_delta 2.5736 6 0.43 32.% + LCAO_DESCRIPTOR add_v_delta 2.5737 6 0.43 32.% + ElecStateLCAO psiToRho 1.6779 11 0.15 21.% + Charge mix_rho 0.78368 10 0.078 9.9% + LOOP_ions force_stress 0.62506 1 0.63 7.9% + Force_Stress_LCAO getForceStress 0.62503 1 0.63 7.9% + Force_LCAO_gamma ftable_gamma 0.40410 1 0.40 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.39607 1 0.40 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:28 2022 + Finish Time : Wed Sep 28 11:02:35 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..5a56f945ae6b3b7ebdc9939fe69f881ef96fcda6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124026 ima = 3.67353e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122777818852 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111678043261 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112174968038 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112473944649 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112395553587 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112437527314 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112435485885 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112438488834 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112438007309 + charge after normalized = 8.00000000000004 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112437909785 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112437897478 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/STRU new file mode 100644 index 0000000000000000000000000000000000000000..bc6705ab83c4d958077cae8ebad96be5ba41984b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.901959530287 15.505531373006 5.005363717374 0 0 0 +H +0.0 +2 +-19.228347838543 15.917104691746 4.451754904948 0 0 0 +-21.623060777139 14.883936874959 3.490136452757 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/conv new file mode 100644 index 0000000000000000000000000000000000000000..774462476f543ce14accd3cb7034bef74df36a4d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/conv @@ -0,0 +1 @@ +122 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b631cda3fb63f89b6043064a6793f93e649b704a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751704411 0.01286230213 1.289236255 1.371904817 1.470523098 0.009133654302 0.01806380469 0.03909087002 +-5.324692301e-18 0.00108130852 0.002866180756 0.01339391564 0.04841712166 2.391279889e-19 2.731426117e-06 7.224771867e-06 +0.001614657442 0.006087442899 + +H atom_index 1 n_descriptor 18 +1.265782166 0.03402536667 0.115586945 0.157032703 0.3248320754 0.02362595185 0.02916624135 0.03719892242 +1.964608091e-17 5.399642609e-05 0.1071089315 0.1166469828 0.1349307313 3.158679123e-18 2.841995954e-06 0.01328604051 +0.02767603911 0.0314615844 + +H atom_index 2 n_descriptor 18 +1.282074023 0.03349676745 0.1217467633 0.1651370512 0.3297336669 0.02440927185 0.03010686541 0.03686924599 +1.447112847e-17 5.559872319e-05 0.1084703718 0.1199791872 0.1418358949 3.377377356e-18 1.918081853e-06 0.01341597574 +0.02822347373 0.03212232313 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5fdc413cce54e2b9e5eff3cacc591e824f775e78 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:28 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0878357 SEC) : SETUP UNITCELL + DONE(0.0980524 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116231 SEC) : INIT PLANEWAVE + DONE(0.165785 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44742 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651291e+02 0.000000e+00 2.173e-01 6.170e-01 + GE2 -4.663803e+02 -1.251161e+00 9.753e-02 5.726e-01 + GE3 -4.663851e+02 -4.815255e-03 6.241e-02 6.351e-01 + GE4 -4.663854e+02 -3.336678e-04 2.019e-03 4.978e-01 + GE5 -4.663843e+02 1.112179e-03 9.922e-04 4.955e-01 + GE6 -4.663850e+02 -7.316512e-04 9.830e-05 4.758e-01 + GE7 -4.663848e+02 2.228909e-04 5.513e-05 4.800e-01 + GE8 -4.663848e+02 -2.774395e-05 1.089e-05 4.742e-01 + GE9 -4.663848e+02 1.874709e-05 2.196e-06 4.762e-01 + GE10 -4.663848e+02 -1.997134e-06 2.504e-07 4.765e-01 + GE11 -4.663848e+02 -5.058386e-07 2.990e-08 4.116e-01 +E_delta_band = -7.22744762e-02 Ry = -9.83344697e-01 eV +E_delta_NN= -1.95665906e-01 Ry = -2.66217122e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9389 11 0.72 1e+02 % + Run_lcao lcao_line 7.9291 1 7.9 1e+02 % + Potential init_pot 0.28468 2 0.14 3.6 % + PW_Basis recip2real 0.28698 16 0.018 3.6 % + PW_Basis gathers_scatterp 0.12197 16 0.0076 1.5 % + Potential v_of_rho 0.98043 13 0.075 12 % + XC_Functional v_xc 0.27453 14 0.02 3.5 % + H_Hartree_pw v_hartree 0.66472 13 0.051 8.4 % + PW_Basis real2recip 0.64618 38 0.017 8.1 % + PW_Basis gatherp_scatters 0.24666 38 0.0065 3.1 % + ORB_control set_orb_tables 1.1012 1 1.1 14 % + ORB_gen_tables gen_tables 1.1012 1 1.1 14 % + ORB_table_phi init_Table 0.4772 1 0.48 6 % + ORB_table_phi cal_ST_Phi12_R 0.47202 126 0.0037 5.9 % + ORB_table_beta init_Table_Beta 0.18647 1 0.19 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.18491 56 0.0033 2.3 % + ORB_table_alpha init_Table_Alpha 0.25139 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24939 66 0.0038 3.1 % + LOOP_ions opt_ions 6.2999 1 6.3 79 % + ESolver_KS_LCAO Run 5.6746 1 5.7 71 % + HSolverLCAO solve 3.3997 11 0.31 43 % + HamiltLCAO updateHk 1.7055 11 0.16 21 % + LCAO_Hamilt cal_Hgamma 1.6698 11 0.15 21 % + Gint_interface cal_gint 3.2802 23 0.14 41 % + Gint_Gamma distri_vl 2.7187 6 0.45 34 % + LCAO_Deepks cal_projected_DM 6.1077 13 0.47 77 % + LCAO_gen_fixedH add_v_delta 2.5736 6 0.43 32 % + LCAO_DESCRIPTOR add_v_delta 2.5737 6 0.43 32 % + ElecStateLCAO psiToRho 1.6779 11 0.15 21 % + Charge mix_rho 0.78368 10 0.078 9.9 % + LOOP_ions force_stress 0.62506 1 0.63 7.9 % + Force_Stress_LCAO getForceStress 0.62503 1 0.63 7.9 % + Force_LCAO_gamma ftable_gamma 0.4041 1 0.4 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.39607 1 0.4 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:28 2022 + FINISH Time : Wed Sep 28 11:02:35 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/122/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c531c6c66b00b1858ca90cc214782d8085e54295 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.240648 0.57408 0.176166 +H 0.277977 0.626471 0.169819 +H 0.200226 0.572061 0.123512 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b96d64e558d9bbb48aa8a701cf12601794082fc9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2207 2 + 2 -13.1941 2 + 3 -8.95131 2 + 4 -6.72728 2 + 5 1.30003 0 + 6 4.4387 0 + 7 11.082 0 + 8 11.3168 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9201b44366947829bb332f964bde87d58bf2dda7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:47 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.73813049161 16.0742384023 4.93263495713 0 0 0 0 + tauc_H1 7.78335138848 17.5411960588 4.75494236253 0 0 0 0 + tauc_H2 5.60633806377 16.017720274 3.45834126364 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874846914862 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0982520791291 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116749923603 (SEC) + + DONE : INIT CHARGE Time : 0.166419724466 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451062 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000562 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012 + + Density error is 0.2154748692 + + Energy Rydberg eV + E_KohnSham -34.190317288 -465.183131545 + E_Harris -34.3828402431 -467.80254073 + E_Fermi -0.404070108684 -5.49765586959 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000887514493721 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124257651783 + + Density error is 0.0982145122122 + + Energy Rydberg eV + E_KohnSham -34.2801008525 -466.404699608 + E_Harris -34.2868155308 -466.496057494 + E_Fermi -0.212667118606 -2.89348459029 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00085897889395 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117244246141 + + Density error is 0.0629870434984 + + Energy Rydberg eV + E_KohnSham -34.2803857341 -466.408575621 + E_Harris -34.2847116141 -466.467432239 + E_Fermi -0.201529865495 -2.74195448791 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000827825289478 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105749383157 + + Density error is 0.00204706212964 + + Energy Rydberg eV + E_KohnSham -34.280374346 -466.408420679 + E_Harris -34.2803766279 -466.408451725 + E_Fermi -0.166165108144 -2.26079227955 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000828469190318 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105625004206 + + Density error is 0.000881735904386 + + Energy Rydberg eV + E_KohnSham -34.2803186621 -466.407663061 + E_Harris -34.2803196637 -466.407676687 + E_Fermi -0.165432771808 -2.25082833252 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000827880758656 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105478863827 + + Density error is 0.000185621484609 + + Energy Rydberg eV + E_KohnSham -34.2803521641 -466.408118878 + E_Harris -34.2803522267 -466.408119731 + E_Fermi -0.165393452864 -2.25029337084 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000828154029621 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105487138979 + + Density error is 3.96293118743e-05 + + Energy Rydberg eV + E_KohnSham -34.2803394345 -466.407945683 + E_Harris -34.2803394427 -466.407945794 + E_Fermi -0.165256268979 -2.24842688834 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00082807484378 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105481241801 + + Density error is 1.6331402413e-05 + + Energy Rydberg eV + E_KohnSham -34.2803442359 -466.40801101 + E_Harris -34.2803442371 -466.408011025 + E_Fermi -0.165297601033 -2.24898923978 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000828077315271 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105479460916 + + Density error is 1.65366525551e-06 + + Energy Rydberg eV + E_KohnSham -34.2803428156 -466.407991685 + E_Harris -34.2803428156 -466.407991685 + E_Fermi -0.165280053862 -2.24875049827 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000828079915537 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105479496257 + + Density error is 1.56629512441e-07 + + Energy Rydberg eV + E_KohnSham -34.2803430395 -466.407994731 + E_Harris -34.2803430395 -466.407994731 + E_Fermi -0.165278566889 -2.24873026697 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000828080278235 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105479539499 + + Density error is 3.55647415884e-08 + + Energy Rydberg eV + E_KohnSham -34.2803430668 -466.407995103 + E_Harris -34.2803430668 -466.407995103 + E_band -7.95158322918 -108.186840038 + E_one_elec -69.2650406456 -942.399224982 + E_Hartree +36.0337391691 +490.264172946 + E_xc -8.20848702342 -111.682195478 + E_Ewald +7.28385838424 +99.1019774507 + E_demet -1.5416787433e-76 -2.09756153943e-75 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194689249777 -2.64888313631 + E_Fermi -0.165278551987 -2.24873006421 + + charge density convergence is achieved + final etot is -466.407995103 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2207 2.00000 + 2 -13.1941 2.00000 + 3 -8.95131 2.00000 + 4 -6.72728 2.00000 + 5 1.30003 0.00000 + 6 4.43870 0.00000 + 7 11.0820 0.00000 + 8 11.3168 0.00000 + + EFERMI = -2.248730064207456 eV + OUT.ABACUS/ final etot is -466.4079951029595 eV + correction force for each atom along direction 1 is 6.21496e-05 + correction force for each atom along direction 2 is 9.67090e-05 + correction force for each atom along direction 3 is -8.97639e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.78969481 -0.95172814 -0.039571016 + H1 +0.39094815 +0.74919635 -0.28243635 + H2 +0.39874666 +0.20253179 +0.32200737 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4079951029595 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9370 11 0.72 1.0e+02% + Run_lcao lcao_line 7.9271 1 7.9 1.e+02% + Potential init_pot 0.28777 2 0.14 3.6% + PW_Basis recip2real 0.29027 16 0.018 3.7% + PW_Basis gathers_scatterp 0.12366 16 0.0077 1.6% + Potential v_of_rho 1.0094 13 0.078 13.% + XC_Functional v_xc 0.29768 14 0.021 3.8% + H_Hartree_pw v_hartree 0.67032 13 0.052 8.4% + PW_Basis real2recip 0.65318 38 0.017 8.2% + PW_Basis gatherp_scatters 0.25094 38 0.0066 3.2% + ORB_control set_orb_tables 1.0899 1 1.1 14.% + ORB_gen_tables gen_tables 1.0899 1 1.1 14.% + ORB_table_phi init_Table 0.47526 1 0.48 6.0% + ORB_table_phi cal_ST_Phi12_R 0.46998 126 0.0037 5.9% + ORB_table_beta init_Table_Beta 0.18212 1 0.18 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18058 56 0.0032 2.3% + ORB_table_alpha init_Table_Alpha 0.24597 1 0.25 3.1% + ORB_table_alpha S_PhiAlpha_R 0.24403 66 0.0037 3.1% + LOOP_ions opt_ions 6.3078 1 6.3 79.% + ESolver_KS_LCAO Run 5.6851 1 5.7 72.% + HSolverLCAO solve 3.3760 11 0.31 43.% + HamiltLCAO updateHk 1.6985 11 0.15 21.% + LCAO_Hamilt cal_Hgamma 1.6665 11 0.15 21.% + Gint_interface cal_gint 3.2600 23 0.14 41.% + Gint_Gamma distri_vl 2.7173 6 0.45 34.% + LCAO_Deepks cal_projected_DM 6.1168 13 0.47 77.% + LCAO_gen_fixedH add_v_delta 2.5737 6 0.43 32.% + LCAO_DESCRIPTOR add_v_delta 2.5738 6 0.43 32.% + ElecStateLCAO psiToRho 1.6621 11 0.15 21.% + Charge mix_rho 0.78487 10 0.078 9.9% + LOOP_ions force_stress 0.62253 1 0.62 7.8% + Force_Stress_LCAO getForceStress 0.62250 1 0.62 7.8% + Force_LCAO_gamma ftable_gamma 0.40094 1 0.40 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.39314 1 0.39 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:47 2022 + Finish Time : Wed Sep 28 11:10:55 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..857c711a9ce64cfa576941ecb3e2aa0f1c5c6cf6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123883 ima = 3.67683e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123419824706 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240641083 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112935979097 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113166810256 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113122724336 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113149601552 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113140924325 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113143856823 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113143196655 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001131431263 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113143119361 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b0cf15403c6a4014eb7951fec8a3cebe44604766 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.261869508400 16.074238402315 4.932634957129 0 0 0 +H +0.0 +2 +-20.216648611532 17.541196058806 4.754942362551 0 0 0 +-22.393661936231 16.017720274015 3.458341263635 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/conv new file mode 100644 index 0000000000000000000000000000000000000000..fc666d277f3dccb664d26b1214d91da9839cb439 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/conv @@ -0,0 +1 @@ +123 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9763a0bd1c143f44cb3acc8b25d6d427dace4433 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746436065 0.01262103641 1.273543312 1.366679488 1.46904691 0.008030487451 0.01950154732 0.0389451678 +-6.705938882e-19 0.001100741229 0.002458350241 0.0122221403 0.04361559695 -1.373497624e-19 1.691409861e-06 5.20147039e-06 +0.001713812872 0.005783098072 + +H atom_index 1 n_descriptor 18 +1.261348724 0.0335158606 0.112029454 0.156080732 0.3257805876 0.02244045427 0.02906745085 0.03678927452 +1.068532816e-18 4.244243731e-05 0.1040412918 0.1155833422 0.1340058403 1.426012456e-17 3.630991199e-06 0.01297835384 +0.02649084937 0.03131790702 + +H atom_index 2 n_descriptor 18 +1.221926644 0.0348921207 0.09876282891 0.1381585493 0.3130073051 0.02067536131 0.02678166182 0.03808384779 +-5.167622383e-18 3.906219367e-05 0.09415202151 0.1140803512 0.1184844571 2.293512194e-18 5.486244673e-06 0.01339337033 +0.02500355499 0.0295027313 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..590a7df1dd436530defca6931a7ac811bcb699ef Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..a08894fee0db67720915791d9922eff29ee217e3 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..b0b803b43b55e5b68c5633e8d689106411b7f0a8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..5126b032c58cfb01bc5eccb7ad1d6f84b6053e79 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..f9ad37b2b50ddb08ff83d09b6e21b32deb540b77 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:47 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087508 SEC) : SETUP UNITCELL + DONE(0.0982725 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116776 SEC) : INIT PLANEWAVE + DONE(0.166554 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451127 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651831e+02 0.000000e+00 2.155e-01 6.120e-01 + GE2 -4.664047e+02 -1.221568e+00 9.821e-02 5.719e-01 + GE3 -4.664086e+02 -3.876013e-03 6.299e-02 6.332e-01 + GE4 -4.664084e+02 1.549425e-04 2.047e-03 4.984e-01 + GE5 -4.664077e+02 7.576177e-04 8.817e-04 4.953e-01 + GE6 -4.664081e+02 -4.558173e-04 1.856e-04 4.915e-01 + GE7 -4.664079e+02 1.731953e-04 3.963e-05 4.817e-01 + GE8 -4.664080e+02 -6.532739e-05 1.633e-05 4.756e-01 + GE9 -4.664080e+02 1.932546e-05 1.654e-06 4.785e-01 + GE10 -4.664080e+02 -3.046434e-06 1.566e-07 4.777e-01 + GE11 -4.664080e+02 -3.716303e-07 3.556e-08 4.070e-01 +E_delta_band = -7.02762987e-02 Ry = -9.56158096e-01 eV +E_delta_NN= -1.94689250e-01 Ry = -2.64888314e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.937 11 0.72 1e+02 % + Run_lcao lcao_line 7.9271 1 7.9 1e+02 % + Potential init_pot 0.28777 2 0.14 3.6 % + PW_Basis recip2real 0.29027 16 0.018 3.7 % + PW_Basis gathers_scatterp 0.12366 16 0.0077 1.6 % + Potential v_of_rho 1.0094 13 0.078 13 % + XC_Functional v_xc 0.29768 14 0.021 3.8 % + H_Hartree_pw v_hartree 0.67032 13 0.052 8.4 % + PW_Basis real2recip 0.65318 38 0.017 8.2 % + PW_Basis gatherp_scatters 0.25094 38 0.0066 3.2 % + ORB_control set_orb_tables 1.0899 1 1.1 14 % + ORB_gen_tables gen_tables 1.0899 1 1.1 14 % + ORB_table_phi init_Table 0.47526 1 0.48 6 % + ORB_table_phi cal_ST_Phi12_R 0.46998 126 0.0037 5.9 % + ORB_table_beta init_Table_Beta 0.18212 1 0.18 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.18058 56 0.0032 2.3 % + ORB_table_alpha init_Table_Alpha 0.24597 1 0.25 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.24403 66 0.0037 3.1 % + LOOP_ions opt_ions 6.3078 1 6.3 79 % + ESolver_KS_LCAO Run 5.6851 1 5.7 72 % + HSolverLCAO solve 3.376 11 0.31 43 % + HamiltLCAO updateHk 1.6985 11 0.15 21 % + LCAO_Hamilt cal_Hgamma 1.6665 11 0.15 21 % + Gint_interface cal_gint 3.26 23 0.14 41 % + Gint_Gamma distri_vl 2.7173 6 0.45 34 % + LCAO_Deepks cal_projected_DM 6.1168 13 0.47 77 % + LCAO_gen_fixedH add_v_delta 2.5737 6 0.43 32 % + LCAO_DESCRIPTOR add_v_delta 2.5738 6 0.43 32 % + ElecStateLCAO psiToRho 1.6621 11 0.15 21 % + Charge mix_rho 0.78487 10 0.078 9.9 % + LOOP_ions force_stress 0.62253 1 0.62 7.8 % + Force_Stress_LCAO getForceStress 0.6225 1 0.62 7.8 % + Force_LCAO_gamma ftable_gamma 0.40094 1 0.4 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.39314 1 0.39 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:47 2022 + FINISH Time : Wed Sep 28 11:10:55 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/123/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4f847b6162069a63e6a3cf2cc0d6c117c37d2494 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.228656 0.597174 0.169862 +H 0.232808 0.662336 0.17129 +H 0.235282 0.582695 0.106851 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..525a767a382933ee298351588cd42112805b82e4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3552 2 + 2 -13.0745 2 + 3 -9.14794 2 + 4 -6.75973 2 + 5 1.35237 0 + 6 4.50242 0 + 7 11.0606 0 + 8 11.3142 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3f0226dbf366a8b4c79f7e71f85b58e9dac829b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:40 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.40235450894 16.7208679885 4.75614875179 0 0 0 0 + tauc_H1 6.51862209859 18.5454116853 4.79613169128 0 0 0 0 + tauc_H2 6.5878885608 16.3154506019 2.99181654206 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874227489457 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0880119334563 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106322790091 (SEC) + + DONE : INIT CHARGE Time : 0.15607425243 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437277 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000591 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000936 + + Density error is 0.214489082382 + + Energy Rydberg eV + E_KohnSham -34.1925999368 -465.214188575 + E_Harris -34.3835332375 -467.811969403 + E_Fermi -0.408035127544 -5.55160271875 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000848961953932 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129193276483 + + Density error is 0.097689013835 + + Energy Rydberg eV + E_KohnSham -34.2809414113 -466.416135997 + E_Harris -34.287612418 -466.506899701 + E_Fermi -0.21807357194 -2.96704316159 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813764701842 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124365408974 + + Density error is 0.0625041467499 + + Energy Rydberg eV + E_KohnSham -34.2811078632 -466.418400692 + E_Harris -34.2854062054 -466.476882639 + E_Fermi -0.205489418768 -2.79582697395 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000767140654836 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118356497816 + + Density error is 0.00199304499343 + + Energy Rydberg eV + E_KohnSham -34.2811176649 -466.418534051 + E_Harris -34.2811187374 -466.418548643 + E_Fermi -0.169998130598 -2.31294322548 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000768251583702 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118719333683 + + Density error is 0.000819851832463 + + Energy Rydberg eV + E_KohnSham -34.2810593805 -466.417741051 + E_Harris -34.2810609921 -466.417762979 + E_Fermi -0.169084978701 -2.30051915654 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000767411311194 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118574898618 + + Density error is 0.000142540971963 + + Energy Rydberg eV + E_KohnSham -34.2811009093 -466.41830608 + E_Harris -34.2811009493 -466.418306623 + E_Fermi -0.169211345754 -2.3022384685 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000767511002677 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118587737365 + + Density error is 3.86629521411e-05 + + Energy Rydberg eV + E_KohnSham -34.2810858886 -466.418101713 + E_Harris -34.2810858968 -466.418101824 + E_Fermi -0.169076835183 -2.3004083583 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000767457383318 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118579096918 + + Density error is 1.63716778437e-05 + + Energy Rydberg eV + E_KohnSham -34.2810898296 -466.418155333 + E_Harris -34.2810898308 -466.418155349 + E_Fermi -0.169121133617 -2.30101106942 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000767462948424 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118580298805 + + Density error is 2.37407874218e-06 + + Energy Rydberg eV + E_KohnSham -34.2810883802 -466.418135613 + E_Harris -34.2810883803 -466.418135613 + E_Fermi -0.169104818891 -2.30078909618 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000767463312447 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118580149517 + + Density error is 3.30586898835e-07 + + Energy Rydberg eV + E_KohnSham -34.2810886179 -466.418138846 + E_Harris -34.2810886179 -466.418138846 + E_Fermi -0.169102398665 -2.30075616731 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000767463921645 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118580251427 + + Density error is 1.23804146314e-07 + + Energy Rydberg eV + E_KohnSham -34.281088651 -466.418139296 + E_Harris -34.281088651 -466.418139296 + E_Fermi -0.169102287299 -2.30075465209 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000767464125447 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118580276156 + + Density error is 1.03452381241e-08 + + Energy Rydberg eV + E_KohnSham -34.2810886535 -466.41813933 + E_Harris -34.2810886535 -466.41813933 + E_band -7.98743652031 -108.67464909 + E_one_elec -69.4112803931 -944.388918822 + E_Hartree +36.0955686713 +491.10540648 + E_xc -8.21855536583 -111.819182304 + E_Ewald +7.37725482327 +100.372701194 + E_demet -6.02108931325e-81 -8.1921122827e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195025457944 -2.65345748309 + E_Fermi -0.169102180146 -2.30075319421 + + charge density convergence is achieved + final etot is -466.41813933 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3552 2.00000 + 2 -13.0745 2.00000 + 3 -9.14794 2.00000 + 4 -6.75973 2.00000 + 5 1.35237 0.00000 + 6 4.50242 0.00000 + 7 11.0606 0.00000 + 8 11.3142 0.00000 + + EFERMI = -2.300753194212967 eV + OUT.ABACUS/ final etot is -466.4181393301133 eV + correction force for each atom along direction 1 is -0.000137476 + correction force for each atom along direction 2 is 7.20304e-05 + correction force for each atom along direction 3 is -3.56444e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.086489785 -0.19108579 +0.55156608 + H1 +0.021538232 +0.40307366 +0.073886040 + H2 +0.064951553 -0.21198787 -0.62545212 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4181393301133 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3999 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3896 1 7.4 1.e+02% + Potential init_pot 0.28707 2 0.14 3.9% + PW_Basis recip2real 0.28443 17 0.017 3.8% + PW_Basis gathers_scatterp 0.11977 17 0.0070 1.6% + Charge atomic_rho 0.10065 1 0.10 1.4% + Potential v_of_rho 0.93451 14 0.067 13.% + XC_Functional v_xc 0.25867 15 0.017 3.5% + H_Hartree_pw v_hartree 0.63637 14 0.045 8.6% + PW_Basis real2recip 0.59687 41 0.015 8.1% + PW_Basis gatherp_scatters 0.22468 41 0.0055 3.0% + ORB_control set_orb_tables 1.1064 1 1.1 15.% + ORB_gen_tables gen_tables 1.1064 1 1.1 15.% + ORB_table_phi init_Table 0.47604 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47115 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18955 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18806 56 0.0034 2.5% + ORB_table_alpha init_Table_Alpha 0.25763 1 0.26 3.5% + ORB_table_alpha S_PhiAlpha_R 0.25578 66 0.0039 3.5% + LOOP_ions opt_ions 5.7693 1 5.8 78.% + ESolver_KS_LCAO Run 5.1784 1 5.2 70.% + HSolverLCAO solve 3.0442 12 0.25 41.% + HamiltLCAO updateHk 1.5350 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.4930 12 0.12 20.% + Gint_interface cal_gint 2.9453 25 0.12 40.% + Gint_Gamma distri_vl 2.6848 6 0.45 36.% + LCAO_Deepks cal_projected_DM 5.5806 14 0.40 75.% + LCAO_gen_fixedH add_v_delta 2.5529 6 0.43 34.% + LCAO_DESCRIPTOR add_v_delta 2.5529 6 0.43 34.% + ElecStateLCAO psiToRho 1.4947 12 0.12 20.% + Charge mix_rho 0.71908 11 0.065 9.7% + LOOP_ions force_stress 0.59065 1 0.59 8.0% + Force_Stress_LCAO getForceStress 0.59063 1 0.59 8.0% + Force_LCAO_gamma ftable_gamma 0.37797 1 0.38 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.37120 1 0.37 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:40 2022 + Finish Time : Wed Sep 28 11:03:48 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..241596579576b84dd194cd45e088d7e69bff73aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124036 ima = 3.70389e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122832439786 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112028554608 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112502371912 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112744452797 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011268928285 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112722608428 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112715818484 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112718747561 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112718038332 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112717948764 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112717936399 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112717930816 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/STRU new file mode 100644 index 0000000000000000000000000000000000000000..28fdd308cfc6fc5665ca1bb200a4b793c99519f5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.597645491064 16.720867988470 4.756148751803 0 0 0 +H +0.0 +2 +-21.481377901435 18.545411685318 4.796131691286 0 0 0 +-21.412111439192 16.315450601869 2.991816542038 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/conv new file mode 100644 index 0000000000000000000000000000000000000000..1f6e3b4a7484bb00255552eecc2e26d8e57a7315 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/conv @@ -0,0 +1 @@ +124 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..57dcac0013f61886170fb5610969a2f73e12717f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749538872 0.01273569954 1.278202382 1.364876782 1.469605906 0.008595305769 0.01852838258 0.03903158269 +3.239536489e-18 0.001070068321 0.002649272659 0.01264065463 0.04581403928 2.43680791e-19 2.162816586e-06 6.160890335e-06 +0.001647436396 0.00598317446 + +H atom_index 1 n_descriptor 18 +1.249555417 0.03429097017 0.1084310245 0.1497189969 0.3207422777 0.02232735761 0.02827884873 0.03743009468 +-9.679175625e-18 4.694009319e-05 0.1021042569 0.1149563711 0.1285610533 6.310515571e-19 4.114523074e-06 0.0131931085 +0.02644829154 0.03075149602 + +H atom_index 2 n_descriptor 18 +1.256584261 0.03404949381 0.1108978288 0.1530169645 0.322991657 0.0226552384 0.02868785098 0.03722132117 +1.789185925e-17 4.760195345e-05 0.1037097978 0.1153857544 0.1314034284 4.853698513e-18 3.72338179e-06 0.01315511055 +0.02670563591 0.03106554186 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4a785f144e46916e5bf4ca9488e754904f648deb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:40 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087448 SEC) : SETUP UNITCELL + DONE(0.0880329 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106345 SEC) : INIT PLANEWAVE + DONE(0.156218 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.437339 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652142e+02 0.000000e+00 2.145e-01 5.483e-01 + GE2 -4.664161e+02 -1.201947e+00 9.769e-02 4.745e-01 + GE3 -4.664184e+02 -2.264695e-03 6.250e-02 5.309e-01 + GE4 -4.664185e+02 -1.333587e-04 1.993e-03 4.213e-01 + GE5 -4.664177e+02 7.929999e-04 8.199e-04 4.189e-01 + GE6 -4.664183e+02 -5.650288e-04 1.425e-04 4.053e-01 + GE7 -4.664181e+02 2.043670e-04 3.866e-05 4.025e-01 + GE8 -4.664182e+02 -5.361963e-05 1.637e-05 3.954e-01 + GE9 -4.664181e+02 1.971964e-05 2.374e-06 3.952e-01 + GE10 -4.664181e+02 -3.233085e-06 3.306e-07 3.942e-01 + GE11 -4.664181e+02 -4.500949e-07 1.238e-07 3.963e-01 + GE12 -4.664181e+02 -3.404337e-08 1.035e-08 3.336e-01 +E_delta_band = -7.09490689e-02 Ry = -9.65311604e-01 eV +E_delta_NN= -1.95025458e-01 Ry = -2.65345748e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3999 11 0.67 1e+02 % + Run_lcao lcao_line 7.3896 1 7.4 1e+02 % + Potential init_pot 0.28707 2 0.14 3.9 % + PW_Basis recip2real 0.28443 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.11977 17 0.007 1.6 % + Charge atomic_rho 0.10065 1 0.1 1.4 % + Potential v_of_rho 0.93451 14 0.067 13 % + XC_Functional v_xc 0.25867 15 0.017 3.5 % + H_Hartree_pw v_hartree 0.63637 14 0.045 8.6 % + PW_Basis real2recip 0.59687 41 0.015 8.1 % + PW_Basis gatherp_scatters 0.22468 41 0.0055 3 % + ORB_control set_orb_tables 1.1064 1 1.1 15 % + ORB_gen_tables gen_tables 1.1064 1 1.1 15 % + ORB_table_phi init_Table 0.47604 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47115 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18955 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18806 56 0.0034 2.5 % + ORB_table_alpha init_Table_Alpha 0.25763 1 0.26 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.25578 66 0.0039 3.5 % + LOOP_ions opt_ions 5.7693 1 5.8 78 % + ESolver_KS_LCAO Run 5.1784 1 5.2 70 % + HSolverLCAO solve 3.0442 12 0.25 41 % + HamiltLCAO updateHk 1.535 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.493 12 0.12 20 % + Gint_interface cal_gint 2.9453 25 0.12 40 % + Gint_Gamma distri_vl 2.6848 6 0.45 36 % + LCAO_Deepks cal_projected_DM 5.5806 14 0.4 75 % + LCAO_gen_fixedH add_v_delta 2.5529 6 0.43 34 % + LCAO_DESCRIPTOR add_v_delta 2.5529 6 0.43 34 % + ElecStateLCAO psiToRho 1.4947 12 0.12 20 % + Charge mix_rho 0.71908 11 0.065 9.7 % + LOOP_ions force_stress 0.59065 1 0.59 8 % + Force_Stress_LCAO getForceStress 0.59063 1 0.59 8 % + Force_LCAO_gamma ftable_gamma 0.37797 1 0.38 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.3712 1 0.37 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:40 2022 + FINISH Time : Wed Sep 28 11:03:48 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/124/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..64c7a3cc7bc29cb8599ad3cf21efec95d91575e4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.220299 0.613076 0.167074 +H 0.183954 0.64316 0.122431 +H 0.279668 0.603191 0.138244 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..05347279c8fb4cca823a42d785851c7904475fbd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2015 2 + 2 -13.0676 2 + 3 -9.03071 2 + 4 -6.72389 2 + 5 1.25044 0 + 6 4.3504 0 + 7 11.092 0 + 8 11.335 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..6ee6eda3de0d0675cf8218d2ec468b31ac4c6536 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:15 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.16838113569 17.1661253914 4.67806003871 0 0 0 0 + tauc_H1 5.15070782589 18.0084891916 3.42805950988 0 0 0 0 + tauc_H2 7.83070933018 16.8893357714 3.87082635559 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101461467348 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101827356552 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119968379684 (SEC) + + DONE : INIT CHARGE Time : 0.164536677496 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445581 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00162 + + Density error is 0.215190103785 + + Energy Rydberg eV + E_KohnSham -34.1897904946 -465.175964152 + E_Harris -34.3818754977 -467.789414695 + E_Fermi -0.401743644918 -5.46600270617 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114306469592 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013565272724 + + Density error is 0.098423657997 + + Energy Rydberg eV + E_KohnSham -34.2804245328 -466.409103505 + E_Harris -34.287263228 -466.502148726 + E_Fermi -0.209835491749 -2.85495833042 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110148787058 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125383516318 + + Density error is 0.0632859727261 + + Energy Rydberg eV + E_KohnSham -34.2808243685 -466.414543549 + E_Harris -34.2852376061 -466.474588726 + E_Fermi -0.200156878196 -2.72327403736 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105332361471 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106394381134 + + Density error is 0.00201186765495 + + Energy Rydberg eV + E_KohnSham -34.2807898637 -466.414074087 + E_Harris -34.280791892 -466.414101683 + E_Fermi -0.164690255003 -2.24072587311 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105437771085 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010614840294 + + Density error is 0.00096220256891 + + Energy Rydberg eV + E_KohnSham -34.2807311421 -466.413275138 + E_Harris -34.2807321458 -466.413288794 + E_Fermi -0.164149918814 -2.23337422211 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105349179963 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105896319412 + + Density error is 0.000175340707065 + + Energy Rydberg eV + E_KohnSham -34.2807630529 -466.413709308 + E_Harris -34.2807630956 -466.413709889 + E_Fermi -0.164005284352 -2.23140636929 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105379483862 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105885614187 + + Density error is 3.86382933938e-05 + + Energy Rydberg eV + E_KohnSham -34.2807515271 -466.41355249 + E_Harris -34.2807515346 -466.413552593 + E_Fermi -0.163893052758 -2.22987938012 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105368898044 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105883478606 + + Density error is 1.66167942881e-05 + + Energy Rydberg eV + E_KohnSham -34.2807558668 -466.413611535 + E_Harris -34.280755868 -466.413611551 + E_Fermi -0.163931617565 -2.23040408124 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105369020343 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105880078888 + + Density error is 1.70797657172e-06 + + Energy Rydberg eV + E_KohnSham -34.2807544471 -466.413592219 + E_Harris -34.2807544471 -466.41359222 + E_Fermi -0.163913926379 -2.2301633803 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105369304412 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010587986168 + + Density error is 3.19441676099e-07 + + Energy Rydberg eV + E_KohnSham -34.2807546832 -466.413595432 + E_Harris -34.2807546832 -466.413595432 + E_Fermi -0.163912579751 -2.2301450585 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105369373629 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105879887389 + + Density error is 7.94393357888e-08 + + Energy Rydberg eV + E_KohnSham -34.2807547052 -466.413595731 + E_Harris -34.2807547052 -466.413595731 + E_band -7.94133269259 -108.047374333 + E_one_elec -69.1635482809 -941.018350518 + E_Hartree +35.9827497694 +489.570426573 + E_xc -8.20035317463 -111.571528787 + E_Ewald +7.22500551236 +98.3012430495 + E_demet -9.97230867199e-74 -1.35680220154e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194543755326 -2.64690358275 + E_Fermi -0.163912449614 -2.23014328789 + + charge density convergence is achieved + final etot is -466.413595731 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2015 2.00000 + 2 -13.0676 2.00000 + 3 -9.03071 2.00000 + 4 -6.72389 2.00000 + 5 1.25044 0.00000 + 6 4.35040 0.00000 + 7 11.0920 0.00000 + 8 11.3350 0.00000 + + EFERMI = -2.230143287885711 eV + OUT.ABACUS/ final etot is -466.4135957313724 eV + correction force for each atom along direction 1 is -1.36350e-05 + correction force for each atom along direction 2 is 3.17618e-05 + correction force for each atom along direction 3 is -0.000181641 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.91462092 -0.44969853 +0.32079450 + H1 -0.27624491 +0.30037562 -0.52154931 + H2 -0.63837602 +0.14932292 +0.20075482 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4135957313724 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5028 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4933 1 7.5 1.e+02% + Potential init_pot 0.28370 2 0.14 3.8% + PW_Basis recip2real 0.28003 16 0.018 3.7% + PW_Basis gathers_scatterp 0.12189 16 0.0076 1.6% + Potential v_of_rho 1.0161 13 0.078 14.% + XC_Functional v_xc 0.30819 14 0.022 4.1% + H_Hartree_pw v_hartree 0.66664 13 0.051 8.9% + PW_Basis real2recip 0.69817 38 0.018 9.3% + PW_Basis gatherp_scatters 0.26549 38 0.0070 3.5% + ORB_control set_orb_tables 1.0953 1 1.1 15.% + ORB_gen_tables gen_tables 1.0953 1 1.1 15.% + ORB_table_phi init_Table 0.47374 1 0.47 6.3% + ORB_table_phi cal_ST_Phi12_R 0.46861 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18509 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18357 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24724 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24527 66 0.0037 3.3% + LOOP_ions opt_ions 5.8767 1 5.9 78.% + ESolver_KS_LCAO Run 5.2624 1 5.3 70.% + HSolverLCAO solve 2.7962 11 0.25 37.% + HamiltLCAO updateHk 1.4282 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.4004 11 0.13 19.% + Gint_interface cal_gint 2.6628 23 0.12 35.% + Gint_Gamma distri_vl 2.5218 6 0.42 34.% + LCAO_Deepks cal_projected_DM 5.7034 13 0.44 76.% + LCAO_gen_fixedH add_v_delta 2.3761 6 0.40 32.% + LCAO_DESCRIPTOR add_v_delta 2.3762 6 0.40 32.% + ElecStateLCAO psiToRho 1.3521 11 0.12 18.% + Charge mix_rho 0.90771 10 0.091 12.% + LOOP_ions force_stress 0.61415 1 0.61 8.2% + Force_Stress_LCAO getForceStress 0.61412 1 0.61 8.2% + Force_LCAO_gamma ftable_gamma 0.39386 1 0.39 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.38573 1 0.39 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:15 2022 + Finish Time : Wed Sep 28 11:14:22 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1ec75608388dc5abe65af60e1d88c97f2ae38d2a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123814 ima = 3.68505e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123436093634 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011214806215 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112764383 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113005971425 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112962567239 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112988113656 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112980486998 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011298339819 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112982708303 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112982643367 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112982629144 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/STRU new file mode 100644 index 0000000000000000000000000000000000000000..df2da395ff484e52d36a2621d306f9f3359a98fd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.831618864340 17.166125391355 4.678060038708 0 0 0 +H +0.0 +2 +-22.849292174126 18.008489191612 3.428059509869 0 0 0 +-20.169290669839 16.889335771398 3.870826355577 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/conv new file mode 100644 index 0000000000000000000000000000000000000000..7270a2a57b6fb9dc5aba004dba45650a77a9b03b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/conv @@ -0,0 +1 @@ +125 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..221b59fd8a8ef62ff9fa34e3570cc2ee5027bc4a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74799006 0.01261263011 1.268163935 1.360699397 1.468931842 0.008242800447 0.0188954533 0.03899303491 +-3.66475689e-19 0.001049208251 0.002496466881 0.01213603858 0.04379775673 2.553010243e-20 1.79222045e-06 5.411412883e-06 +0.001673471555 0.005863834933 + +H atom_index 1 n_descriptor 18 +1.256008786 0.03388366353 0.1100419615 0.1531996388 0.3236885633 0.02230154593 0.02871513995 0.03710753321 +1.698184085e-17 4.322458608e-05 0.1024578516 0.1153201118 0.1314861529 8.91290941e-18 3.840606838e-06 0.01305531419 +0.02628060154 0.031057613 + +H atom_index 2 n_descriptor 18 +1.216426095 0.03524972131 0.09690992064 0.1354614547 0.3104857916 0.0204957378 0.0264102644 0.03848329698 +1.796990623e-17 3.975569561e-05 0.09228923855 0.1139789951 0.1160828362 2.777858659e-18 5.698289168e-06 0.01360271194 +0.02476012452 0.02918437976 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..66556ba5d75f3d7844304f47b03a67e52132f72c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:15 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101486 SEC) : SETUP UNITCELL + DONE(0.101842 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119989 SEC) : INIT PLANEWAVE + DONE(0.164671 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445646 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651760e+02 0.000000e+00 2.152e-01 5.711e-01 + GE2 -4.664091e+02 -1.233139e+00 9.842e-02 5.343e-01 + GE3 -4.664145e+02 -5.440044e-03 6.329e-02 6.002e-01 + GE4 -4.664141e+02 4.694624e-04 2.012e-03 4.602e-01 + GE5 -4.664133e+02 7.989482e-04 9.622e-04 4.615e-01 + GE6 -4.664137e+02 -4.341693e-04 1.753e-04 4.551e-01 + GE7 -4.664136e+02 1.568175e-04 3.864e-05 4.424e-01 + GE8 -4.664136e+02 -5.904538e-05 1.662e-05 4.372e-01 + GE9 -4.664136e+02 1.931598e-05 1.708e-06 4.365e-01 + GE10 -4.664136e+02 -3.212052e-06 3.194e-07 4.370e-01 + GE11 -4.664136e+02 -2.998255e-07 7.944e-08 3.645e-01 +E_delta_band = -6.99352238e-02 Ry = -9.51517535e-01 eV +E_delta_NN= -1.94543755e-01 Ry = -2.64690358e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5028 11 0.68 1e+02 % + Run_lcao lcao_line 7.4933 1 7.5 1e+02 % + Potential init_pot 0.2837 2 0.14 3.8 % + PW_Basis recip2real 0.28003 16 0.018 3.7 % + PW_Basis gathers_scatterp 0.12189 16 0.0076 1.6 % + Potential v_of_rho 1.0161 13 0.078 14 % + XC_Functional v_xc 0.30819 14 0.022 4.1 % + H_Hartree_pw v_hartree 0.66664 13 0.051 8.9 % + PW_Basis real2recip 0.69817 38 0.018 9.3 % + PW_Basis gatherp_scatters 0.26549 38 0.007 3.5 % + ORB_control set_orb_tables 1.0953 1 1.1 15 % + ORB_gen_tables gen_tables 1.0953 1 1.1 15 % + ORB_table_phi init_Table 0.47374 1 0.47 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.46861 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18509 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18357 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24724 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24527 66 0.0037 3.3 % + LOOP_ions opt_ions 5.8767 1 5.9 78 % + ESolver_KS_LCAO Run 5.2624 1 5.3 70 % + HSolverLCAO solve 2.7962 11 0.25 37 % + HamiltLCAO updateHk 1.4282 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.4004 11 0.13 19 % + Gint_interface cal_gint 2.6628 23 0.12 35 % + Gint_Gamma distri_vl 2.5218 6 0.42 34 % + LCAO_Deepks cal_projected_DM 5.7034 13 0.44 76 % + LCAO_gen_fixedH add_v_delta 2.3761 6 0.4 32 % + LCAO_DESCRIPTOR add_v_delta 2.3762 6 0.4 32 % + ElecStateLCAO psiToRho 1.3521 11 0.12 18 % + Charge mix_rho 0.90771 10 0.091 12 % + LOOP_ions force_stress 0.61415 1 0.61 8.2 % + Force_Stress_LCAO getForceStress 0.61412 1 0.61 8.2 % + Force_LCAO_gamma ftable_gamma 0.39386 1 0.39 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.38573 1 0.39 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:15 2022 + FINISH Time : Wed Sep 28 11:14:22 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/125/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a35473ca8c403a8e02d85f4c81d654ae79fddf6c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.213354 0.615016 0.157672 +H 0.22244 0.620813 0.0938512 +H 0.273262 0.601339 0.178568 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..09a9fe0a3ad675bb0a1bd1a5aec6f939629b10b7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4516 2 + 2 -13.0338 2 + 3 -9.24846 2 + 4 -6.78121 2 + 5 1.38965 0 + 6 4.57753 0 + 7 11.0434 0 + 8 11.306 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9062e55f68ec0d0c4daa42153dada8b60cc1fa71 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:24 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.97391848293 17.220452369 4.4148109117 0 0 0 0 + tauc_H1 6.22832175677 17.3827660426 2.62783273694 0 0 0 0 + tauc_H2 7.65134649113 16.837488691 4.99990721331 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0859584041818 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0950857464866 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.113268946021 (SEC) + + DONE : INIT CHARGE Time : 0.16192887466 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443673 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000878 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00171 + + Density error is 0.216302226391 + + Energy Rydberg eV + E_KohnSham -34.1883506113 -465.156373535 + E_Harris -34.3836321026 -467.813314531 + E_Fermi -0.413803361529 -5.63008356835 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00131581052393 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138553126407 + + Density error is 0.0977943153893 + + Energy Rydberg eV + E_KohnSham -34.2799481259 -466.402621657 + E_Harris -34.2867010705 -466.494500182 + E_Fermi -0.220527382783 -3.00042897088 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012618937049 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127239491293 + + Density error is 0.0627305515026 + + Energy Rydberg eV + E_KohnSham -34.280328695 -466.407799564 + E_Harris -34.2846958738 -466.467218081 + E_Fermi -0.208827052437 -2.84123780969 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119322988249 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107625497392 + + Density error is 0.00199510409735 + + Energy Rydberg eV + E_KohnSham -34.2803305467 -466.407824758 + E_Harris -34.2803316976 -466.407840418 + E_Fermi -0.172973871095 -2.35343025201 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119742371233 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107542636519 + + Density error is 0.00100610616082 + + Energy Rydberg eV + E_KohnSham -34.280253913 -466.406782104 + E_Harris -34.2802562236 -466.406813541 + E_Fermi -0.172139814634 -2.34208233169 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119569553398 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107321272986 + + Density error is 0.000100899441861 + + Energy Rydberg eV + E_KohnSham -34.2803023413 -466.407441004 + E_Harris -34.2803023441 -466.407441042 + E_Fermi -0.172219168322 -2.343161994 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119558348513 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107291999362 + + Density error is 4.41359185391e-05 + + Energy Rydberg eV + E_KohnSham -34.2802875689 -466.407240016 + E_Harris -34.2802874197 -466.407237985 + E_Fermi -0.172096007269 -2.3414863019 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119551578576 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107296656514 + + Density error is 1.16961907435e-05 + + Energy Rydberg eV + E_KohnSham -34.2802899142 -466.407271925 + E_Harris -34.2802899148 -466.407271934 + E_Fermi -0.172149995832 -2.342220854 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119552851581 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107295008238 + + Density error is 1.21887067632e-06 + + Energy Rydberg eV + E_KohnSham -34.2802885307 -466.407253102 + E_Harris -34.2802885307 -466.407253102 + E_Fermi -0.172137794931 -2.34205485222 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119552835776 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107294584035 + + Density error is 1.20556840265e-07 + + Energy Rydberg eV + E_KohnSham -34.2802887338 -466.407255865 + E_Harris -34.2802887338 -466.407255865 + E_Fermi -0.172136600405 -2.34203859985 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119552865228 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107294622314 + + Density error is 3.436866926e-08 + + Energy Rydberg eV + E_KohnSham -34.2802887548 -466.407256151 + E_Harris -34.2802887548 -466.407256151 + E_band -8.01355971617 -109.030073403 + E_one_elec -69.5387809677 -946.123653135 + E_Hartree +36.1523161787 +491.877495928 + E_xc -8.22774202014 -111.944173148 + E_Ewald +7.45771487814 +101.467416402 + E_demet -2.38111424091e-84 -3.23967212654e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.1952869524 -2.65701529769 + E_Fermi -0.172136639313 -2.34203912923 + + charge density convergence is achieved + final etot is -466.407256151 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4516 2.00000 + 2 -13.0338 2.00000 + 3 -9.24846 2.00000 + 4 -6.78121 2.00000 + 5 1.38965 0.00000 + 6 4.57753 0.00000 + 7 11.0434 0.00000 + 8 11.3060 0.00000 + + EFERMI = -2.342039129234180 eV + OUT.ABACUS/ final etot is -466.4072561506925 eV + correction force for each atom along direction 1 is 4.86972e-05 + correction force for each atom along direction 2 is 0.000142095 + correction force for each atom along direction 3 is -9.80491e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.54739436 +0.053975962 +0.47303663 + H1 -0.091355037 +0.12377049 -0.93697985 + H2 +0.63874940 -0.17774645 +0.46394322 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4072561506925 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0067 11 0.64 1.0e+02% + Run_lcao lcao_line 6.9969 1 7.0 1.e+02% + Potential init_pot 0.28671 2 0.14 4.1% + PW_Basis recip2real 0.27305 16 0.017 3.9% + PW_Basis gathers_scatterp 0.12026 16 0.0075 1.7% + Potential v_of_rho 0.85891 13 0.066 12.% + XC_Functional v_xc 0.23136 14 0.017 3.3% + H_Hartree_pw v_hartree 0.58927 13 0.045 8.4% + PW_Basis real2recip 0.55457 38 0.015 7.9% + PW_Basis gatherp_scatters 0.21508 38 0.0057 3.1% + ORB_control set_orb_tables 1.1182 1 1.1 16.% + ORB_gen_tables gen_tables 1.1182 1 1.1 16.% + ORB_table_phi init_Table 0.49062 1 0.49 7.0% + ORB_table_phi cal_ST_Phi12_R 0.48567 126 0.0039 6.9% + ORB_table_beta init_Table_Beta 0.19184 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.19036 56 0.0034 2.7% + ORB_table_alpha init_Table_Alpha 0.25630 1 0.26 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25438 66 0.0039 3.6% + LOOP_ions opt_ions 5.3578 1 5.4 76.% + ESolver_KS_LCAO Run 4.7731 1 4.8 68.% + HSolverLCAO solve 2.8214 11 0.26 40.% + HamiltLCAO updateHk 1.4294 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3956 11 0.13 20.% + Gint_interface cal_gint 2.7314 23 0.12 39.% + Gint_Gamma distri_vl 2.2823 6 0.38 33.% + LCAO_Deepks cal_projected_DM 5.1673 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1489 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1489 6 0.36 31.% + ElecStateLCAO psiToRho 1.3783 11 0.13 20.% + Charge mix_rho 0.66274 10 0.066 9.5% + LOOP_ions force_stress 0.58451 1 0.58 8.3% + Force_Stress_LCAO getForceStress 0.58448 1 0.58 8.3% + Force_LCAO_gamma ftable_gamma 0.37199 1 0.37 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.36529 1 0.37 5.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:24 2022 + Finish Time : Wed Sep 28 11:12:31 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ab6fb2e9c32c1fcbb856b2d1c342b78e69d7c888 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123933 ima = 3.71855e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122956570267 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111765017759 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112312500498 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112595587972 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112526005189 + charge after normalized = 8.00000000000005 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112563692028 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011256069947 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112563626921 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112563065573 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112563014889 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112563011377 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/STRU new file mode 100644 index 0000000000000000000000000000000000000000..66ae92a10d094973034a9e15397c981044e6f680 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.026081517071 17.220452368985 4.414810911714 0 0 0 +H +0.0 +2 +-21.771678243230 17.382766042604 2.627832736943 0 0 0 +-20.348653508868 16.837488690999 4.999907213313 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/conv new file mode 100644 index 0000000000000000000000000000000000000000..76748d31abfa41a8e915155b63108f6df400394e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/conv @@ -0,0 +1 @@ +126 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c65d2cda260a740b9632640779a907810ad7410e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751001071 0.012802121 1.282270099 1.366398362 1.470002949 0.008917435704 0.01811743318 0.03907002818 +4.980422684e-18 0.00105870319 0.002764743896 0.01300724864 0.04710019664 -1.517380116e-19 2.471106781e-06 6.752683758e-06 +0.001623795574 0.006059225264 + +H atom_index 1 n_descriptor 18 +1.263726363 0.0339969992 0.1142027011 0.1561692381 0.3246094532 0.02329747455 0.02906539035 0.03718414884 +-2.62691191e-18 5.119837791e-05 0.1058744716 0.1161883032 0.1341293697 -8.286645677e-18 3.101220332e-06 0.01323024267 +0.02727594397 0.03136701959 + +H atom_index 2 n_descriptor 18 +1.2597259 0.03413243294 0.1127521333 0.1542467092 0.3233586012 0.02310710245 0.02883298836 0.03729013918 +-5.993273332e-18 5.081083755e-05 0.1051506668 0.1157586583 0.1324797722 3.979894256e-18 3.332855469e-06 0.0132318776 +0.02713436078 0.03119434489 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a9134e8fb535a5fdb1111c7c5c038e0815e1d8f3 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/e_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..771a0284dadadbb0fdc2e98639dd80a1c13447ac Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/e_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/e_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/e_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..b271192223698f849b00f8d2e425e2537bf59392 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/e_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..0064bb923bdee9a5729fbbb560628c3227470c81 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..9dd358585dc5edcfd75cb14b011f64b95d05f55f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..2418de2ac84636850bf9065b741f2b0c60660499 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..7cd97bcbd7edacbcff07e690701b10d74671dc73 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:24 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0859812 SEC) : SETUP UNITCELL + DONE(0.0951031 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.113291 SEC) : INIT PLANEWAVE + DONE(0.162055 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443739 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651564e+02 0.000000e+00 2.163e-01 5.520e-01 + GE2 -4.664026e+02 -1.246248e+00 9.779e-02 4.741e-01 + GE3 -4.664078e+02 -5.177908e-03 6.273e-02 5.286e-01 + GE4 -4.664078e+02 -2.519365e-05 1.995e-03 4.187e-01 + GE5 -4.664068e+02 1.042654e-03 1.006e-03 4.204e-01 + GE6 -4.664074e+02 -6.589009e-04 1.009e-04 3.951e-01 + GE7 -4.664072e+02 2.009885e-04 4.414e-05 3.979e-01 + GE8 -4.664073e+02 -3.190928e-05 1.170e-05 3.973e-01 + GE9 -4.664073e+02 1.882357e-05 1.219e-06 3.931e-01 + GE10 -4.664073e+02 -2.763653e-06 1.206e-07 3.937e-01 + GE11 -4.664073e+02 -2.853830e-07 3.437e-08 3.394e-01 +E_delta_band = -7.14901286e-02 Ry = -9.72673100e-01 eV +E_delta_NN= -1.95286952e-01 Ry = -2.65701530e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0067 11 0.64 1e+02 % + Run_lcao lcao_line 6.9969 1 7 1e+02 % + Potential init_pot 0.28671 2 0.14 4.1 % + PW_Basis recip2real 0.27305 16 0.017 3.9 % + PW_Basis gathers_scatterp 0.12026 16 0.0075 1.7 % + Potential v_of_rho 0.85891 13 0.066 12 % + XC_Functional v_xc 0.23136 14 0.017 3.3 % + H_Hartree_pw v_hartree 0.58927 13 0.045 8.4 % + PW_Basis real2recip 0.55457 38 0.015 7.9 % + PW_Basis gatherp_scatters 0.21508 38 0.0057 3.1 % + ORB_control set_orb_tables 1.1182 1 1.1 16 % + ORB_gen_tables gen_tables 1.1182 1 1.1 16 % + ORB_table_phi init_Table 0.49062 1 0.49 7 % + ORB_table_phi cal_ST_Phi12_R 0.48567 126 0.0039 6.9 % + ORB_table_beta init_Table_Beta 0.19184 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.19036 56 0.0034 2.7 % + ORB_table_alpha init_Table_Alpha 0.2563 1 0.26 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25438 66 0.0039 3.6 % + LOOP_ions opt_ions 5.3578 1 5.4 76 % + ESolver_KS_LCAO Run 4.7731 1 4.8 68 % + HSolverLCAO solve 2.8214 11 0.26 40 % + HamiltLCAO updateHk 1.4294 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3956 11 0.13 20 % + Gint_interface cal_gint 2.7314 23 0.12 39 % + Gint_Gamma distri_vl 2.2823 6 0.38 33 % + LCAO_Deepks cal_projected_DM 5.1673 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.1489 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1489 6 0.36 31 % + ElecStateLCAO psiToRho 1.3783 11 0.13 20 % + Charge mix_rho 0.66274 10 0.066 9.5 % + LOOP_ions force_stress 0.58451 1 0.58 8.3 % + Force_Stress_LCAO getForceStress 0.58448 1 0.58 8.3 % + Force_LCAO_gamma ftable_gamma 0.37199 1 0.37 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.36529 1 0.37 5.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:24 2022 + FINISH Time : Wed Sep 28 11:12:31 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/126/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3ab2c8d133b90063f71027ef95664a5a5997fe38 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.197404 0.612954 0.130507 +H 0.250113 0.590636 0.0995894 +H 0.215088 0.618983 0.193004 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bb33145989b0cf8d0a7f0a0748c4dec47e07828b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3194 2 + 2 -13.1635 2 + 3 -9.05601 2 + 4 -6.75092 2 + 5 1.36055 0 + 6 4.51354 0 + 7 11.0637 0 + 8 11.3081 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f82bc24fe719389249788964cf7c164a2ffb36ad --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:38 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.52729841306 17.1627086055 3.65419449985 0 0 0 0 + tauc_H1 7.00316921133 16.5377963329 2.78850402995 0 0 0 0 + tauc_H2 6.02246202841 17.3315234636 5.40410993576 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0865073674818 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0989063117606 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117207662042 (SEC) + + DONE : INIT CHARGE Time : 0.167021862187 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451094 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000797 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000672 + + Density error is 0.216350517384 + + Energy Rydberg eV + E_KohnSham -34.189573826 -465.173016225 + E_Harris -34.384185072 -467.820838065 + E_Fermi -0.409390415111 -5.5700423521 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122835363452 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000851954288851 + + Density error is 0.0980984612246 + + Energy Rydberg eV + E_KohnSham -34.2807570254 -466.413627298 + E_Harris -34.2874815888 -466.505119678 + E_Fermi -0.216127581136 -2.9405665984 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118360807096 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000819436815989 + + Density error is 0.0629446916095 + + Energy Rydberg eV + E_KohnSham -34.2811158335 -466.418509134 + E_Harris -34.2854585705 -466.477595101 + E_Fermi -0.20485267171 -2.78716358579 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112890858466 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783167637063 + + Density error is 0.00202271257859 + + Energy Rydberg eV + E_KohnSham -34.2811098819 -466.418428157 + E_Harris -34.2811118727 -466.418455244 + E_Fermi -0.169269372868 -2.3030279679 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113102991034 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784662046953 + + Density error is 0.000957018386356 + + Energy Rydberg eV + E_KohnSham -34.2810416545 -466.417499877 + E_Harris -34.2810432372 -466.41752141 + E_Fermi -0.168486624939 -2.29237813596 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112988610838 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783925823814 + + Density error is 0.000159407231824 + + Energy Rydberg eV + E_KohnSham -34.28108271 -466.418058466 + E_Harris -34.2810827573 -466.418059109 + E_Fermi -0.16850730093 -2.29265944725 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113017450335 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784159880541 + + Density error is 4.1002761976e-05 + + Energy Rydberg eV + E_KohnSham -34.2810679597 -466.417857777 + E_Harris -34.281067969 -466.417857903 + E_Fermi -0.168368862889 -2.29077590106 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113006905854 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784094151956 + + Density error is 1.74232085559e-05 + + Energy Rydberg eV + E_KohnSham -34.281072328 -466.41791721 + E_Harris -34.2810723292 -466.417917228 + E_Fermi -0.168416340297 -2.29142186435 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001130069223 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784098387291 + + Density error is 1.47985727684e-06 + + Energy Rydberg eV + E_KohnSham -34.2810708193 -466.417896684 + E_Harris -34.2810708193 -466.417896684 + E_Fermi -0.16839719888 -2.29116143201 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011300714771 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784099900973 + + Density error is 2.00695343335e-07 + + Energy Rydberg eV + E_KohnSham -34.2810710778 -466.417900201 + E_Harris -34.2810710778 -466.417900201 + E_Fermi -0.168396013093 -2.29114529855 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113007214399 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784100265635 + + Density error is 4.04152644082e-08 + + Energy Rydberg eV + E_KohnSham -34.2810710981 -466.417900477 + E_Harris -34.2810710981 -466.417900477 + E_band -7.98044597749 -108.579537875 + E_one_elec -69.4048034748 -944.300795827 + E_Hartree +36.0958185228 +491.108805884 + E_xc -8.21854138108 -111.818992031 + E_Ewald +7.37055936252 +100.281604778 + E_demet -6.9301840355e-81 -9.42899910714e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194981405831 -2.65285812336 + E_Fermi -0.168395965636 -2.29114465287 + + charge density convergence is achieved + final etot is -466.417900477 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3194 2.00000 + 2 -13.1635 2.00000 + 3 -9.05601 2.00000 + 4 -6.75092 2.00000 + 5 1.36055 0.00000 + 6 4.51354 0.00000 + 7 11.0637 0.00000 + 8 11.3081 0.00000 + + EFERMI = -2.291144652866879 eV + OUT.ABACUS/ final etot is -466.4179004769348 eV + correction force for each atom along direction 1 is 3.98783e-05 + correction force for each atom along direction 2 is -7.06382e-05 + correction force for each atom along direction 3 is 9.07658e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.67127888 +0.17420757 -0.17961893 + H1 +0.49026584 -0.19035877 -0.20370066 + H2 +0.18101304 +0.016151195 +0.38331959 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4179004769348 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9420 11 0.72 1.0e+02% + Run_lcao lcao_line 7.9323 1 7.9 1.e+02% + Potential init_pot 0.28841 2 0.14 3.6% + PW_Basis recip2real 0.28764 16 0.018 3.6% + PW_Basis gathers_scatterp 0.12768 16 0.0080 1.6% + Potential v_of_rho 0.99128 13 0.076 12.% + XC_Functional v_xc 0.29249 14 0.021 3.7% + H_Hartree_pw v_hartree 0.65752 13 0.051 8.3% + PW_Basis real2recip 0.66423 38 0.017 8.4% + PW_Basis gatherp_scatters 0.25885 38 0.0068 3.3% + ORB_control set_orb_tables 1.1048 1 1.1 14.% + ORB_gen_tables gen_tables 1.1048 1 1.1 14.% + ORB_table_phi init_Table 0.47995 1 0.48 6.0% + ORB_table_phi cal_ST_Phi12_R 0.47469 126 0.0038 6.0% + ORB_table_beta init_Table_Beta 0.18785 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18630 56 0.0033 2.3% + ORB_table_alpha init_Table_Alpha 0.25162 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24963 66 0.0038 3.1% + LOOP_ions opt_ions 6.2947 1 6.3 79.% + ESolver_KS_LCAO Run 5.6819 1 5.7 72.% + HSolverLCAO solve 3.3947 11 0.31 43.% + HamiltLCAO updateHk 1.6982 11 0.15 21.% + LCAO_Hamilt cal_Hgamma 1.6707 11 0.15 21.% + Gint_interface cal_gint 3.2740 23 0.14 41.% + Gint_Gamma distri_vl 2.7186 6 0.45 34.% + LCAO_Deepks cal_projected_DM 6.1033 13 0.47 77.% + LCAO_gen_fixedH add_v_delta 2.5717 6 0.43 32.% + LCAO_DESCRIPTOR add_v_delta 2.5717 6 0.43 32.% + ElecStateLCAO psiToRho 1.6807 11 0.15 21.% + Charge mix_rho 0.79244 10 0.079 10.% + LOOP_ions force_stress 0.61256 1 0.61 7.7% + Force_Stress_LCAO getForceStress 0.61253 1 0.61 7.7% + Force_LCAO_gamma ftable_gamma 0.39704 1 0.40 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.38922 1 0.39 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:38 2022 + Finish Time : Wed Sep 28 11:10:46 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0a626a6969a7fc44c03726fafcf9430e1f9af665 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.01239 ima = 3.66927e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123267156941 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112116815517 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112660153183 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112920947819 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112864483037 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112897419278 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112889806337 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112892875269 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112892150364 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112892095014 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011289208446 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/STRU new file mode 100644 index 0000000000000000000000000000000000000000..abdf7e15d6ae05c3a95c091d49370bfa62e0af8c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.472701586913 17.162708605517 3.654194499869 0 0 0 +H +0.0 +2 +-20.996830788656 16.537796332887 2.788504029935 0 0 0 +-21.977537971601 17.331523463671 5.404109935740 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/conv new file mode 100644 index 0000000000000000000000000000000000000000..e52a6f6b24f01dc1d10c7fe2045bece17a0533e3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/conv @@ -0,0 +1 @@ +127 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a37b2df1d20437db2987ac33797bac36b8ca6dc9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748006013 0.0127053274 1.279153183 1.367382068 1.469465949 0.008328251397 0.01906180936 0.0389841385 +1.427866239e-18 0.001104152856 0.002573562214 0.01251011478 0.04509716719 -4.222956633e-20 1.961324792e-06 5.760564543e-06 +0.001680102156 0.00589977284 + +H atom_index 1 n_descriptor 18 +1.253718784 0.03396023626 0.1095795675 0.1519781452 0.3226430077 0.02232342248 0.02856412852 0.03713436049 +1.622284683e-17 4.526609664e-05 0.1029065655 0.1151172965 0.1305218828 -3.053392864e-18 4.011768175e-06 0.01308676132 +0.02646258494 0.03096087028 + +H atom_index 2 n_descriptor 18 +1.249854693 0.03409401796 0.1082360104 0.1501733121 0.3214160231 0.02214690346 0.02833986505 0.03724958335 +9.89700858e-18 4.491011571e-05 0.1019975786 0.1149107773 0.1289651305 -5.318203147e-18 4.218565251e-06 0.01310873331 +0.02632061923 0.0307884918 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..817408b6e418d6d4ca3355ca10363178498b3731 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:38 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0865326 SEC) : SETUP UNITCELL + DONE(0.098928 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11723 SEC) : INIT PLANEWAVE + DONE(0.167153 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451158 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651730e+02 0.000000e+00 2.164e-01 6.100e-01 + GE2 -4.664136e+02 -1.240611e+00 9.810e-02 5.720e-01 + GE3 -4.664185e+02 -4.881835e-03 6.294e-02 6.363e-01 + GE4 -4.664184e+02 8.097619e-05 2.023e-03 4.982e-01 + GE5 -4.664175e+02 9.282801e-04 9.570e-04 4.962e-01 + GE6 -4.664181e+02 -5.585883e-04 1.594e-04 4.921e-01 + GE7 -4.664179e+02 2.006886e-04 4.100e-05 4.829e-01 + GE8 -4.664179e+02 -5.943341e-05 1.742e-05 4.770e-01 + GE9 -4.664179e+02 2.052670e-05 1.480e-06 4.757e-01 + GE10 -4.664179e+02 -3.517365e-06 2.007e-07 4.737e-01 + GE11 -4.664179e+02 -2.759966e-07 4.042e-08 4.059e-01 +E_delta_band = -7.08772783e-02 Ry = -9.64334844e-01 eV +E_delta_NN= -1.94981406e-01 Ry = -2.65285812e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.942 11 0.72 1e+02 % + Run_lcao lcao_line 7.9323 1 7.9 1e+02 % + Potential init_pot 0.28841 2 0.14 3.6 % + PW_Basis recip2real 0.28764 16 0.018 3.6 % + PW_Basis gathers_scatterp 0.12768 16 0.008 1.6 % + Potential v_of_rho 0.99128 13 0.076 12 % + XC_Functional v_xc 0.29249 14 0.021 3.7 % + H_Hartree_pw v_hartree 0.65752 13 0.051 8.3 % + PW_Basis real2recip 0.66423 38 0.017 8.4 % + PW_Basis gatherp_scatters 0.25885 38 0.0068 3.3 % + ORB_control set_orb_tables 1.1048 1 1.1 14 % + ORB_gen_tables gen_tables 1.1048 1 1.1 14 % + ORB_table_phi init_Table 0.47995 1 0.48 6 % + ORB_table_phi cal_ST_Phi12_R 0.47469 126 0.0038 6 % + ORB_table_beta init_Table_Beta 0.18785 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.1863 56 0.0033 2.3 % + ORB_table_alpha init_Table_Alpha 0.25162 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24963 66 0.0038 3.1 % + LOOP_ions opt_ions 6.2947 1 6.3 79 % + ESolver_KS_LCAO Run 5.6819 1 5.7 72 % + HSolverLCAO solve 3.3947 11 0.31 43 % + HamiltLCAO updateHk 1.6982 11 0.15 21 % + LCAO_Hamilt cal_Hgamma 1.6707 11 0.15 21 % + Gint_interface cal_gint 3.274 23 0.14 41 % + Gint_Gamma distri_vl 2.7186 6 0.45 34 % + LCAO_Deepks cal_projected_DM 6.1033 13 0.47 77 % + LCAO_gen_fixedH add_v_delta 2.5717 6 0.43 32 % + LCAO_DESCRIPTOR add_v_delta 2.5717 6 0.43 32 % + ElecStateLCAO psiToRho 1.6807 11 0.15 21 % + Charge mix_rho 0.79244 10 0.079 10 % + LOOP_ions force_stress 0.61256 1 0.61 7.7 % + Force_Stress_LCAO getForceStress 0.61253 1 0.61 7.7 % + Force_LCAO_gamma ftable_gamma 0.39704 1 0.4 5 % + Force_LCAO_gamma cal_fvl_dphi 0.38922 1 0.39 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:38 2022 + FINISH Time : Wed Sep 28 11:10:46 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/127/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..eee6c9dda67e9daa7f45a00ac7c66dc4ed9f19f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.184833 0.61535 0.1163 +H 0.202765 0.55175 0.121188 +H 0.208167 0.645046 0.171381 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..5c8a8461f3475f06e55680e2ab7dbeda90445443 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0835 2 + 2 -12.9762 2 + 3 -9.00747 2 + 4 -6.69788 2 + 5 1.16085 0 + 6 4.18008 0 + 7 11.1198 0 + 8 11.3637 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..af4a74c0732e516d2e59ab64a5479cc6f5a2e4ca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:56 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.17531532321 17.2298109763 3.25640785855 0 0 0 0 + tauc_H1 5.67741599178 15.4490128441 3.39326885504 0 0 0 0 + tauc_H2 5.8286867382 18.0612922246 4.7986546314 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0866981509532 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0872488481075 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105259770279 (SEC) + + DONE : INIT CHARGE Time : 0.153171166728 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.432056 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000929 + + Density error is 0.212454043619 + + Energy Rydberg eV + E_KohnSham -34.193629339 -465.22819431 + E_Harris -34.3798233428 -467.761493696 + E_Fermi -0.393784282282 -5.35771002188 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000927617073882 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116934495121 + + Density error is 0.098309802363 + + Energy Rydberg eV + E_KohnSham -34.2807912332 -466.414092721 + E_Harris -34.2876228838 -466.507042094 + E_Fermi -0.204854382526 -2.78718686263 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000880559929848 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112165291694 + + Density error is 0.0631612201626 + + Energy Rydberg eV + E_KohnSham -34.2809980232 -466.416906243 + E_Harris -34.2854028394 -466.476836841 + E_Fermi -0.195243520876 -2.65642438149 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000805486091748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106231323103 + + Density error is 0.00200801679005 + + Energy Rydberg eV + E_KohnSham -34.2809513676 -466.416271461 + E_Harris -34.2809541795 -466.416309718 + E_Fermi -0.160073454767 -2.17791108338 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000803803961097 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106307609666 + + Density error is 0.000802844043973 + + Energy Rydberg eV + E_KohnSham -34.2809161842 -466.415792765 + E_Harris -34.2809166649 -466.415799306 + E_Fermi -0.159626886928 -2.17183521622 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000802924565131 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106228401265 + + Density error is 0.000171976013658 + + Energy Rydberg eV + E_KohnSham -34.2809371891 -466.416078552 + E_Harris -34.2809370586 -466.416076776 + E_Fermi -0.159396855474 -2.16870547772 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000803044965003 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106252302478 + + Density error is 2.97654626031e-05 + + Energy Rydberg eV + E_KohnSham -34.2809298035 -466.415978066 + E_Harris -34.2809298071 -466.415978115 + E_Fermi -0.159330084173 -2.16779700758 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00080299598917 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106245038453 + + Density error is 1.45121386333e-05 + + Energy Rydberg eV + E_KohnSham -34.2809332881 -466.416025476 + E_Harris -34.2809332891 -466.416025489 + E_Fermi -0.159355058611 -2.16813680223 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000802991254385 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106245528298 + + Density error is 1.78370051469e-06 + + Energy Rydberg eV + E_KohnSham -34.2809321284 -466.416009697 + E_Harris -34.2809321284 -466.416009697 + E_Fermi -0.159340262506 -2.1679354909 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00080299082645 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106245369447 + + Density error is 3.91399787369e-07 + + Energy Rydberg eV + E_KohnSham -34.2809323667 -466.416012939 + E_Harris -34.2809323667 -466.41601294 + E_Fermi -0.159338776851 -2.16791527753 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000802991396475 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010624545751 + + Density error is 1.256367565e-07 + + Energy Rydberg eV + E_KohnSham -34.2809323816 -466.416013142 + E_Harris -34.2809323816 -466.416013142 + E_Fermi -0.159338600642 -2.16791288007 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000802991492416 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106245476087 + + Density error is 1.04053560559e-08 + + Energy Rydberg eV + E_KohnSham -34.2809323853 -466.416013192 + E_Harris -34.2809323853 -466.416013192 + E_band -7.90331471317 -107.530113186 + E_one_elec -68.9289843307 -937.826944251 + E_Hartree +35.8727687608 +488.074058183 + E_xc -8.18260790867 -111.330092058 + E_Ewald +7.0829844296 +96.3689470878 + E_demet -1.15445353077e-67 -1.57071460946e-66 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194106379115 -2.64095277412 + E_Fermi -0.159338481472 -2.16791125869 + + charge density convergence is achieved + final etot is -466.416013192 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0835 2.00000 + 2 -12.9762 2.00000 + 3 -9.00747 2.00000 + 4 -6.69788 2.00000 + 5 1.16085 0.00000 + 6 4.18008 0.00000 + 7 11.1198 0.00000 + 8 11.3637 0.00000 + + EFERMI = -2.167911258689185 eV + OUT.ABACUS/ final etot is -466.4160131924257 eV + correction force for each atom along direction 1 is 0.000195906 + correction force for each atom along direction 2 is 5.18903e-06 + correction force for each atom along direction 3 is 0.000107627 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.21701414 +0.095997453 +0.42206185 + H1 -0.026898467 +0.34610206 +0.10736587 + H2 -0.19011567 -0.44209952 -0.52942772 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4160131924257 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4223 11 0.67 1.0e+02% + Run_lcao lcao_line 7.4127 1 7.4 1.e+02% + Potential init_pot 0.28539 2 0.14 3.8% + PW_Basis recip2real 0.28534 17 0.017 3.8% + PW_Basis gathers_scatterp 0.12198 17 0.0072 1.6% + Charge atomic_rho 0.10033 1 0.10 1.4% + Potential v_of_rho 0.94017 14 0.067 13.% + XC_Functional v_xc 0.26056 15 0.017 3.5% + H_Hartree_pw v_hartree 0.64023 14 0.046 8.6% + PW_Basis real2recip 0.59903 41 0.015 8.1% + PW_Basis gatherp_scatters 0.23009 41 0.0056 3.1% + ORB_control set_orb_tables 1.0987 1 1.1 15.% + ORB_gen_tables gen_tables 1.0987 1 1.1 15.% + ORB_table_phi init_Table 0.48174 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47684 126 0.0038 6.4% + ORB_table_beta init_Table_Beta 0.18744 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18596 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.25080 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24895 66 0.0038 3.4% + LOOP_ions opt_ions 5.8060 1 5.8 78.% + ESolver_KS_LCAO Run 5.2086 1 5.2 70.% + HSolverLCAO solve 3.0623 12 0.26 41.% + HamiltLCAO updateHk 1.5486 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.5074 12 0.13 20.% + Gint_interface cal_gint 2.9646 25 0.12 40.% + Gint_Gamma distri_vl 2.6948 6 0.45 36.% + LCAO_Deepks cal_projected_DM 5.6179 14 0.40 76.% + LCAO_gen_fixedH add_v_delta 2.5607 6 0.43 35.% + LCAO_DESCRIPTOR add_v_delta 2.5607 6 0.43 35.% + ElecStateLCAO psiToRho 1.4984 12 0.12 20.% + Charge mix_rho 0.71973 11 0.065 9.7% + LOOP_ions force_stress 0.59722 1 0.60 8.0% + Force_Stress_LCAO getForceStress 0.59720 1 0.60 8.0% + Force_LCAO_gamma ftable_gamma 0.38474 1 0.38 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.37805 1 0.38 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:56 2022 + Finish Time : Wed Sep 28 11:10:03 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1418d79d56e25ac85f137eb6aa6eeec4f823f054 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123469 ima = 3.67011e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012334796596 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112377967319 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112972068671 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113164037812 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011313983161 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011315581677 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113149637289 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113151894412 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113151217876 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113151168232 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113151152197 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113151145975 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7e690b971e35d7ff7721faefff0db326ae1e2a68 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.824684676805 17.229810976267 3.256407858540 0 0 0 +H +0.0 +2 +-22.322584008225 15.449012844085 3.393268855018 0 0 0 +-22.171313261776 18.061292224553 4.798654631376 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/conv new file mode 100644 index 0000000000000000000000000000000000000000..4523d3e1e5c4519d909580d3940796eb19f742a5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/conv @@ -0,0 +1 @@ +128 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ea8ccdb53d911c8e77a20b70f7c87ac34409ee3a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747974342 0.01252978431 1.259643731 1.35199264 1.468405207 0.008152590674 0.01871987677 0.03900049794 +-4.870796944e-18 0.0009975423495 0.002419517934 0.01181990004 0.04248625965 -8.67838194e-19 1.652196389e-06 5.076606625e-06 +0.001669469139 0.005837241716 + +H atom_index 1 n_descriptor 18 +1.227014657 0.03489796013 0.1000144197 0.1401476275 0.314465564 0.0208786223 0.02704549843 0.03811410227 +-2.716737293e-17 3.87352539e-05 0.09420551468 0.1144383076 0.1201019814 -3.332132667e-18 5.135623091e-06 0.01336700615 +0.02495153915 0.02970838312 + +H atom_index 2 n_descriptor 18 +1.215366228 0.03529328714 0.09632256052 0.1351323719 0.3103963258 0.02034780363 0.02636530553 0.03856452028 +-1.399403219e-18 3.775494756e-05 0.09112034992 0.1141020616 0.1157182116 1.607191417e-18 5.599176729e-06 0.0136116312 +0.02448668922 0.02912801573 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d6fb052a3a6881ef7716660ecf9b5f11acd98dbc Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:56 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.086723 SEC) : SETUP UNITCELL + DONE(0.0872634 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.10528 SEC) : INIT PLANEWAVE + DONE(0.153299 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.43212 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652282e+02 0.000000e+00 2.125e-01 5.482e-01 + GE2 -4.664141e+02 -1.185898e+00 9.831e-02 4.775e-01 + GE3 -4.664169e+02 -2.813522e-03 6.316e-02 5.357e-01 + GE4 -4.664163e+02 6.347821e-04 2.008e-03 4.217e-01 + GE5 -4.664158e+02 4.786953e-04 8.028e-04 4.198e-01 + GE6 -4.664161e+02 -2.857866e-04 1.720e-04 4.155e-01 + GE7 -4.664160e+02 1.004859e-04 2.977e-05 4.036e-01 + GE8 -4.664160e+02 -4.740995e-05 1.451e-05 3.985e-01 + GE9 -4.664160e+02 1.577878e-05 1.784e-06 3.995e-01 + GE10 -4.664160e+02 -3.242207e-06 3.914e-07 3.944e-01 + GE11 -4.664160e+02 -2.023261e-07 1.256e-07 3.951e-01 + GE12 -4.664160e+02 -5.061257e-08 1.041e-08 3.376e-01 +E_delta_band = -6.90130429e-02 Ry = -9.38970619e-01 eV +E_delta_NN= -1.94106379e-01 Ry = -2.64095277e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4223 11 0.67 1e+02 % + Run_lcao lcao_line 7.4127 1 7.4 1e+02 % + Potential init_pot 0.28539 2 0.14 3.8 % + PW_Basis recip2real 0.28534 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.12198 17 0.0072 1.6 % + Charge atomic_rho 0.10033 1 0.1 1.4 % + Potential v_of_rho 0.94017 14 0.067 13 % + XC_Functional v_xc 0.26056 15 0.017 3.5 % + H_Hartree_pw v_hartree 0.64023 14 0.046 8.6 % + PW_Basis real2recip 0.59903 41 0.015 8.1 % + PW_Basis gatherp_scatters 0.23009 41 0.0056 3.1 % + ORB_control set_orb_tables 1.0987 1 1.1 15 % + ORB_gen_tables gen_tables 1.0987 1 1.1 15 % + ORB_table_phi init_Table 0.48174 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.47684 126 0.0038 6.4 % + ORB_table_beta init_Table_Beta 0.18744 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18596 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.2508 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24895 66 0.0038 3.4 % + LOOP_ions opt_ions 5.806 1 5.8 78 % + ESolver_KS_LCAO Run 5.2086 1 5.2 70 % + HSolverLCAO solve 3.0623 12 0.26 41 % + HamiltLCAO updateHk 1.5486 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.5074 12 0.13 20 % + Gint_interface cal_gint 2.9646 25 0.12 40 % + Gint_Gamma distri_vl 2.6948 6 0.45 36 % + LCAO_Deepks cal_projected_DM 5.6179 14 0.4 76 % + LCAO_gen_fixedH add_v_delta 2.5607 6 0.43 35 % + LCAO_DESCRIPTOR add_v_delta 2.5607 6 0.43 35 % + ElecStateLCAO psiToRho 1.4984 12 0.12 20 % + Charge mix_rho 0.71973 11 0.065 9.7 % + LOOP_ions force_stress 0.59722 1 0.6 8 % + Force_Stress_LCAO getForceStress 0.5972 1 0.6 8 % + Force_LCAO_gamma ftable_gamma 0.38474 1 0.38 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.37805 1 0.38 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:56 2022 + FINISH Time : Wed Sep 28 11:10:03 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/128/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..729d99ca65238a1a5ba6c2a6c5f6f3163ef336e5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.181142 0.60942 0.110236 +H 0.163545 0.553744 0.137256 +H 0.241701 0.622575 0.133135 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ba729c642b460ddc83c3f3969c497bad5b20b130 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3001 2 + 2 -13.1832 2 + 3 -9.02344 2 + 4 -6.746 2 + 5 1.34491 0 + 6 4.50875 0 + 7 11.0662 0 + 8 11.3064 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0f6a4b01dd1f6317a5682cb37c9927119b4fd343 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:14 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.07197469389 17.0637552613 3.08661729092 0 0 0 0 + tauc_H1 4.5792527935 15.5048360228 3.84315854657 0 0 0 0 + tauc_H2 6.76763226545 17.4321119232 3.72776647366 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0864078038643 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0981471897217 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116309869737 (SEC) + + DONE : INIT CHARGE Time : 0.166196958643 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.444041 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000614 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00171 + + Density error is 0.215742904627 + + Energy Rydberg eV + E_KohnSham -34.1902693911 -465.182479875 + E_Harris -34.3836055605 -467.812953407 + E_Fermi -0.407868687846 -5.54933819049 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000917428786787 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00142355520671 + + Density error is 0.097986857776 + + Energy Rydberg eV + E_KohnSham -34.2802202907 -466.406324648 + E_Harris -34.2869040769 -466.497262225 + E_Fermi -0.2161959248 -2.94149646165 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883008198124 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131222740373 + + Density error is 0.0627805725792 + + Energy Rydberg eV + E_KohnSham -34.2804866242 -466.409948302 + E_Harris -34.2847968146 -466.468591451 + E_Fermi -0.204333905131 -2.78010540437 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000838697238567 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111684073215 + + Density error is 0.00203221947141 + + Energy Rydberg eV + E_KohnSham -34.2804875381 -466.409960737 + E_Harris -34.2804896089 -466.40998891 + E_Fermi -0.168843994143 -2.29724039343 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000839495829396 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111452396343 + + Density error is 0.000887626534111 + + Energy Rydberg eV + E_KohnSham -34.280426984 -466.409136855 + E_Harris -34.2804279394 -466.409149854 + E_Fermi -0.168030513929 -2.2861724273 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00083869493694 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011124261997 + + Density error is 0.000164691252629 + + Energy Rydberg eV + E_KohnSham -34.280464495 -466.409647219 + E_Harris -34.2804646994 -466.40965 + E_Fermi -0.168057919482 -2.28654529899 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000838872819928 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111222292022 + + Density error is 4.14314694561e-05 + + Energy Rydberg eV + E_KohnSham -34.2804509623 -466.409463097 + E_Harris -34.2804509717 -466.409463225 + E_Fermi -0.16791566187 -2.28460978487 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000838798942088 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111222086359 + + Density error is 1.66739665372e-05 + + Energy Rydberg eV + E_KohnSham -34.2804553721 -466.409523095 + E_Harris -34.2804553733 -466.409523111 + E_Fermi -0.16796149035 -2.28523331333 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000838800854569 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001112189019 + + Density error is 1.61128673261e-06 + + Energy Rydberg eV + E_KohnSham -34.2804538638 -466.409502573 + E_Harris -34.2804538638 -466.409502573 + E_Fermi -0.167943590471 -2.28498977298 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000838802329374 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111218486289 + + Density error is 2.12398266325e-07 + + Energy Rydberg eV + E_KohnSham -34.2804541154 -466.409505997 + E_Harris -34.2804541154 -466.409505997 + E_Fermi -0.167942141891 -2.28497006404 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000838802860549 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111218531116 + + Density error is 6.55943058498e-08 + + Energy Rydberg eV + E_KohnSham -34.2804541372 -466.409506294 + E_Harris -34.2804541372 -466.409506294 + E_band -7.97500312565 -108.505484077 + E_one_elec -69.3835790757 -944.012023063 + E_Hartree +36.0870465183 +490.98945664 + E_xc -8.21720227208 -111.800772519 + E_Ewald +7.35743741631 +100.10307154 + E_demet -5.92315857145e-80 -8.05887067293e-79 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194939919546 -2.65229367349 + E_Fermi -0.167942100513 -2.28496950107 + + charge density convergence is achieved + final etot is -466.409506294 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3001 2.00000 + 2 -13.1832 2.00000 + 3 -9.02344 2.00000 + 4 -6.74600 2.00000 + 5 1.34491 0.00000 + 6 4.50875 0.00000 + 7 11.0662 0.00000 + 8 11.3064 0.00000 + + EFERMI = -2.284969501070544 eV + OUT.ABACUS/ final etot is -466.4095062937313 eV + correction force for each atom along direction 1 is -9.85311e-06 + correction force for each atom along direction 2 is -4.32072e-05 + correction force for each atom along direction 3 is -3.70217e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.41894559 +1.1440734 -0.52841088 + H1 -0.20412968 -0.99644168 +0.54263232 + H2 -0.21481590 -0.14763175 -0.014221438 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4095062937313 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0136 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0042 1 7.0 1.e+02% + Potential init_pot 0.28376 2 0.14 4.0% + PW_Basis recip2real 0.26913 16 0.017 3.8% + PW_Basis gathers_scatterp 0.11529 16 0.0072 1.6% + Potential v_of_rho 0.88131 13 0.068 13.% + XC_Functional v_xc 0.25687 14 0.018 3.7% + H_Hartree_pw v_hartree 0.58894 13 0.045 8.4% + PW_Basis real2recip 0.55011 38 0.014 7.8% + PW_Basis gatherp_scatters 0.20885 38 0.0055 3.0% + ORB_control set_orb_tables 1.1057 1 1.1 16.% + ORB_gen_tables gen_tables 1.1057 1 1.1 16.% + ORB_table_phi init_Table 0.48097 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47600 126 0.0038 6.8% + ORB_table_beta init_Table_Beta 0.18839 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18693 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25830 1 0.26 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25639 66 0.0039 3.7% + LOOP_ions opt_ions 5.3783 1 5.4 77.% + ESolver_KS_LCAO Run 4.7879 1 4.8 68.% + HSolverLCAO solve 2.8265 11 0.26 40.% + HamiltLCAO updateHk 1.4326 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3968 11 0.13 20.% + Gint_interface cal_gint 2.7448 23 0.12 39.% + Gint_Gamma distri_vl 2.2916 6 0.38 33.% + LCAO_Deepks cal_projected_DM 5.1911 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1628 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1628 6 0.36 31.% + ElecStateLCAO psiToRho 1.3806 11 0.13 20.% + Charge mix_rho 0.65077 10 0.065 9.3% + LOOP_ions force_stress 0.59016 1 0.59 8.4% + Force_Stress_LCAO getForceStress 0.59013 1 0.59 8.4% + Force_LCAO_gamma ftable_gamma 0.38019 1 0.38 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.37318 1 0.37 5.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:14 2022 + Finish Time : Wed Sep 28 11:08:21 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..72184fc637d63840f98bb3353fe4295e2bc0b427 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123496 ima = 3.65741e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123280150265 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112352419954 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112854591305 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113099671611 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113048726908 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113078291738 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113070710725 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113073782198 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113073075402 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113073016768 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113073007339 + charge after normalized = 8.00000000000003 + charge before normalized = 8.00000000000003 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/STRU new file mode 100644 index 0000000000000000000000000000000000000000..510001d8c667a3692854c51bcf5e2309b1e11324 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.928025306128 17.063755261307 3.086617290946 0 0 0 +H +0.0 +2 +-23.420747206504 15.504836022767 3.843158546575 0 0 0 +-21.232367734556 17.432111923268 3.727766473674 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/conv new file mode 100644 index 0000000000000000000000000000000000000000..940234e8f501a62140d8920eca0379b552441cdc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/conv @@ -0,0 +1 @@ +129 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f90a852c60a1455f9f40bd77b36be2a1a0be9113 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747513679 0.01267962941 1.277567344 1.36865376 1.469411027 0.008246987213 0.01923747241 0.03897704555 +-9.812072804e-19 0.001109356983 0.002543772442 0.01242808068 0.04476116041 -2.76352449e-20 1.876270238e-06 5.598395423e-06 +0.001688934451 0.005857395947 + +H atom_index 1 n_descriptor 18 +1.269142848 0.03336876796 0.1150015686 0.1595109222 0.3275856841 0.02294751315 0.02947188536 0.0366902161 +-1.851381007e-17 4.571448505e-05 0.1058552945 0.1164320979 0.1369828635 -3.233242731e-18 3.202118836e-06 0.01306412975 +0.02694270759 0.03162594115 + +H atom_index 2 n_descriptor 18 +1.230706469 0.03470020945 0.1017150345 0.1416425883 0.3153709941 0.02120604687 0.02724465652 0.03784603092 +-2.317476809e-17 4.22636322e-05 0.09696340159 0.1142390013 0.1215664157 6.590522471e-18 5.187576802e-06 0.0133050083 +0.0255271668 0.02990616712 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..861d1f8ad65681787ca5455ddb071d1b0e9d411d Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..9ca816410b6e0bd792821330acffb4c3b50c3516 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:14 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0864305 SEC) : SETUP UNITCELL + DONE(0.0981676 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11633 SEC) : INIT PLANEWAVE + DONE(0.166326 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444098 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651825e+02 0.000000e+00 2.157e-01 5.482e-01 + GE2 -4.664063e+02 -1.223845e+00 9.799e-02 4.768e-01 + GE3 -4.664099e+02 -3.623654e-03 6.278e-02 5.290e-01 + GE4 -4.664100e+02 -1.243441e-05 2.032e-03 4.212e-01 + GE5 -4.664091e+02 8.238818e-04 8.876e-04 4.196e-01 + GE6 -4.664096e+02 -5.103635e-04 1.647e-04 4.086e-01 + GE7 -4.664095e+02 1.841219e-04 4.143e-05 4.040e-01 + GE8 -4.664095e+02 -5.999823e-05 1.667e-05 3.941e-01 + GE9 -4.664095e+02 2.052151e-05 1.611e-06 3.952e-01 + GE10 -4.664095e+02 -3.424059e-06 2.124e-07 3.913e-01 + GE11 -4.664095e+02 -2.963397e-07 6.559e-08 3.392e-01 +E_delta_band = -7.07831955e-02 Ry = -9.63054781e-01 eV +E_delta_NN= -1.94939920e-01 Ry = -2.65229367e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0136 11 0.64 1e+02 % + Run_lcao lcao_line 7.0042 1 7 1e+02 % + Potential init_pot 0.28376 2 0.14 4 % + PW_Basis recip2real 0.26913 16 0.017 3.8 % + PW_Basis gathers_scatterp 0.11529 16 0.0072 1.6 % + Potential v_of_rho 0.88131 13 0.068 13 % + XC_Functional v_xc 0.25687 14 0.018 3.7 % + H_Hartree_pw v_hartree 0.58894 13 0.045 8.4 % + PW_Basis real2recip 0.55011 38 0.014 7.8 % + PW_Basis gatherp_scatters 0.20885 38 0.0055 3 % + ORB_control set_orb_tables 1.1057 1 1.1 16 % + ORB_gen_tables gen_tables 1.1057 1 1.1 16 % + ORB_table_phi init_Table 0.48097 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.476 126 0.0038 6.8 % + ORB_table_beta init_Table_Beta 0.18839 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18693 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.2583 1 0.26 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25639 66 0.0039 3.7 % + LOOP_ions opt_ions 5.3783 1 5.4 77 % + ESolver_KS_LCAO Run 4.7879 1 4.8 68 % + HSolverLCAO solve 2.8265 11 0.26 40 % + HamiltLCAO updateHk 1.4326 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3968 11 0.13 20 % + Gint_interface cal_gint 2.7448 23 0.12 39 % + Gint_Gamma distri_vl 2.2916 6 0.38 33 % + LCAO_Deepks cal_projected_DM 5.1911 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.1628 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1628 6 0.36 31 % + ElecStateLCAO psiToRho 1.3806 11 0.13 20 % + Charge mix_rho 0.65077 10 0.065 9.3 % + LOOP_ions force_stress 0.59016 1 0.59 8.4 % + Force_Stress_LCAO getForceStress 0.59013 1 0.59 8.4 % + Force_LCAO_gamma ftable_gamma 0.38019 1 0.38 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.37318 1 0.37 5.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:14 2022 + FINISH Time : Wed Sep 28 11:08:21 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/129/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ca6c028b8a12bdf8c78e9574738ac74f56a29b7a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.57565 0.239909 0.358205 +H 0.614018 0.187036 0.341423 +H 0.618771 0.29149 0.361492 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c7f831fa4cb52bb08bdcf75d65c51b731a20364c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9713 2 + 2 -12.794 2 + 3 -9.05628 2 + 4 -6.67426 2 + 5 1.03379 0 + 6 3.96059 0 + 7 11.15 0 + 8 11.3985 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..bc811fe91270695507281fda241b103e1273b421 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:55 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.1182044056 6.71745605793 10.0297269644 0 0 0 0 + tauc_H1 17.1925092401 5.23702060161 9.55984977433 0 0 0 0 + tauc_H2 17.3255938275 8.16170903144 10.1217882914 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.102965980143 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.115857175593 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.133969828512 (SEC) + + DONE : INIT CHARGE Time : 0.177635630519 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.457136 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102 + + Density error is 0.210887896079 + + Energy Rydberg eV + E_KohnSham -34.1929994534 -465.219624277 + E_Harris -34.3759553589 -467.708867075 + E_Fermi -0.3864809096 -5.25834253878 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118485879256 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000988705498039 + + Density error is 0.0986489811247 + + Energy Rydberg eV + E_KohnSham -34.2795616123 -466.397362869 + E_Harris -34.2865887412 -466.492971862 + E_Fermi -0.197812900771 -2.6913825884 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110310420332 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000932629683615 + + Density error is 0.0635873799145 + + Energy Rydberg eV + E_KohnSham -34.2798321606 -466.401043868 + E_Harris -34.2843475478 -466.462478863 + E_Fermi -0.190302606534 -2.58919979312 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000949496249034 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000846227211822 + + Density error is 0.00198747074552 + + Energy Rydberg eV + E_KohnSham -34.2797453437 -466.399862664 + E_Harris -34.2797480117 -466.399898963 + E_Fermi -0.155222524976 -2.11191079762 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000946630066145 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000846148222402 + + Density error is 0.000827099883377 + + Energy Rydberg eV + E_KohnSham -34.2797215845 -466.399539403 + E_Harris -34.2797219173 -466.399543931 + E_Fermi -0.155080069711 -2.1099725943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000944438368476 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000845009459702 + + Density error is 0.000186378614379 + + Energy Rydberg eV + E_KohnSham -34.279732555 -466.399688664 + E_Harris -34.2797324244 -466.399686887 + E_Fermi -0.154624120765 -2.10376909065 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000944694405689 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000845244896228 + + Density error is 2.75841028362e-05 + + Energy Rydberg eV + E_KohnSham -34.2797298821 -466.399652297 + E_Harris -34.2797298837 -466.399652319 + E_Fermi -0.154653360947 -2.10416692373 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000944630707605 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000845204002717 + + Density error is 1.05952985688e-05 + + Energy Rydberg eV + E_KohnSham -34.2797320532 -466.399681837 + E_Harris -34.2797320537 -466.399681843 + E_Fermi -0.15466175857 -2.10428117925 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000944613071767 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000845199973976 + + Density error is 1.38660409404e-06 + + Energy Rydberg eV + E_KohnSham -34.2797312224 -466.399670533 + E_Harris -34.2797312224 -466.399670533 + E_Fermi -0.154650488569 -2.10412784302 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000944612384746 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000845198882214 + + Density error is 2.31651415133e-07 + + Energy Rydberg eV + E_KohnSham -34.2797313841 -466.399672733 + E_Harris -34.2797313841 -466.399672733 + E_Fermi -0.154649602912 -2.10411579304 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000944612739768 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000845199218014 + + Density error is 3.33240920385e-08 + + Energy Rydberg eV + E_KohnSham -34.2797314 -466.39967295 + E_Harris -34.2797314 -466.39967295 + E_band -7.86374291849 -106.991711299 + E_one_elec -68.6470172193 -933.990584886 + E_Hartree +35.7373077545 +486.231016641 + E_xc -8.16098571179 -111.035906977 + E_Ewald +6.91660872205 +94.1052894564 + E_demet -2.00099716005e-60 -2.72249630586e-59 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193644555977 -2.63466934797 + E_Fermi -0.154649475958 -2.10411406575 + + charge density convergence is achieved + final etot is -466.39967295 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9713 2.00000 + 2 -12.7940 2.00000 + 3 -9.05628 2.00000 + 4 -6.67426 2.00000 + 5 1.03379 0.00000 + 6 3.96059 0.00000 + 7 11.1500 0.00000 + 8 11.3985 0.00000 + + EFERMI = -2.104114065747322 eV + OUT.ABACUS/ final etot is -466.3996729500461 eV + correction force for each atom along direction 1 is 0.000197486 + correction force for each atom along direction 2 is 4.66033e-05 + correction force for each atom along direction 3 is 0.000115672 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.1169605 -0.081429725 -0.19073874 + H1 -0.54548401 +0.89432590 +0.26349495 + H2 -0.57147652 -0.81289617 -0.072756209 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3996729500461 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8368 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8264 1 6.8 1.e+02% + Potential init_pot 0.28114 2 0.14 4.1% + PW_Basis recip2real 0.25402 16 0.016 3.7% + PW_Basis gathers_scatterp 0.11644 16 0.0073 1.7% + Potential v_of_rho 0.79498 13 0.061 12.% + XC_Functional v_xc 0.20187 14 0.014 3.0% + H_Hartree_pw v_hartree 0.55723 13 0.043 8.2% + PW_Basis real2recip 0.64976 38 0.017 9.5% + PW_Basis gatherp_scatters 0.26617 38 0.0070 3.9% + ORB_control set_orb_tables 1.0925 1 1.1 16.% + ORB_gen_tables gen_tables 1.0925 1 1.1 16.% + ORB_table_phi init_Table 0.47419 1 0.47 6.9% + ORB_table_phi cal_ST_Phi12_R 0.46901 126 0.0037 6.9% + ORB_table_beta init_Table_Beta 0.18365 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18210 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24760 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24566 66 0.0037 3.6% + LOOP_ions opt_ions 5.1939 1 5.2 76.% + ESolver_KS_LCAO Run 4.6217 1 4.6 68.% + HSolverLCAO solve 2.4630 11 0.22 36.% + HamiltLCAO updateHk 1.2827 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2552 11 0.11 18.% + Gint_interface cal_gint 0.66280 23 0.029 9.7% + Gint_Gamma distri_vl_value 0.58913 11 0.054 8.6% + Gint_Gamma distri_vl 2.2148 6 0.37 32.% + LCAO_Deepks cal_projected_DM 4.8204 13 0.37 71.% + LCAO_gen_fixedH add_v_delta 2.0753 6 0.35 30.% + LCAO_DESCRIPTOR add_v_delta 2.0755 6 0.35 30.% + ElecStateLCAO psiToRho 1.1630 11 0.11 17.% + Charge mix_rho 0.81435 10 0.081 12.% + LOOP_ions force_stress 0.57202 1 0.57 8.4% + Force_Stress_LCAO getForceStress 0.57200 1 0.57 8.4% + Force_LCAO_gamma ftable_gamma 0.38040 1 0.38 5.6% + Force_LCAO_gamma cal_fvl_dphi 0.15749 1 0.16 2.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:55 2022 + Finish Time : Wed Sep 28 11:12:02 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..fdec87f7747c7081612511c1e031cebe757e00b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123402 ima = 3.67676e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123457506977 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112280367955 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112984566523 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113158040957 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113149003207 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113156246834 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113152470284 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113154100767 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113153623035 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113153573658 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113153559656 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e5de7948c6173ca0fa5cbffb9f1ed62f8a82659e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.881795594464 6.717456057905 10.029726964381 0 0 0 +H +0.0 +2 +-10.807490759961 5.237020601628 9.559849774341 0 0 0 +-10.674406172517 8.161709031444 10.121788291465 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/conv new file mode 100644 index 0000000000000000000000000000000000000000..c52bdb9e6a3ef168a29b44e6b5e4dd888a63b9a4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/conv @@ -0,0 +1 @@ +13 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..6552c809151a57f45f157aaae02312b8d5bd7593 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749419536 0.01243005531 1.247444762 1.339837543 1.467970452 0.008301325456 0.01809344651 0.03906848657 +9.94848913e-19 0.0009121077618 0.002382562627 0.0114965482 0.04146007111 -1.633251576e-19 1.597712786e-06 4.938104997e-06 +0.001628506911 0.005845157195 + +H atom_index 1 n_descriptor 18 +1.202095195 0.03586843898 0.09205737632 0.1294335322 0.3053146398 0.01972877192 0.02556107295 0.0392829007 +9.865746907e-18 3.589470712e-05 0.08661294427 0.1106219994 0.1138081245 2.835864269e-18 5.885035139e-06 0.01401785885 +0.02373953309 0.02840484758 + +H atom_index 2 n_descriptor 18 +1.205127422 0.03577119942 0.0929704288 0.1306790825 0.306431124 0.01986769759 0.02573823917 0.03915852254 +-9.546061316e-19 3.614130989e-05 0.08739822612 0.1117182381 0.113923745 4.602254231e-18 5.787433342e-06 0.01393408129 +0.02386445702 0.02856383106 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..eee9b598ee35bddb41cd82fc371c537ebf25ef8a Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..0d9d3e30a1e8045840b9e1e44f19485da5937c89 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..af5e1956b70f5fe0ba825ac24a953f3454b5a94c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..a24eb93706969585de98b9fb549d8fa16e894c66 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:55 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.103006 SEC) : SETUP UNITCELL + DONE(0.115875 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.133992 SEC) : INIT PLANEWAVE + DONE(0.177768 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.457205 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652196e+02 0.000000e+00 2.109e-01 5.179e-01 + GE2 -4.663974e+02 -1.177739e+00 9.865e-02 4.692e-01 + GE3 -4.664010e+02 -3.680999e-03 6.359e-02 5.327e-01 + GE4 -4.663999e+02 1.181205e-03 1.987e-03 4.011e-01 + GE5 -4.663995e+02 3.232605e-04 8.271e-04 3.960e-01 + GE6 -4.663997e+02 -1.492607e-04 1.864e-04 3.942e-01 + GE7 -4.663997e+02 3.636700e-05 2.758e-05 3.820e-01 + GE8 -4.663997e+02 -2.953971e-05 1.060e-05 3.792e-01 + GE9 -4.663997e+02 1.130389e-05 1.387e-06 3.809e-01 + GE10 -4.663997e+02 -2.200359e-06 2.317e-07 3.810e-01 + GE11 -4.663997e+02 -2.169544e-07 3.332e-08 3.273e-01 +E_delta_band = -6.79996104e-02 Ry = -9.25182164e-01 eV +E_delta_NN= -1.93644556e-01 Ry = -2.63466935e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8368 11 0.62 1e+02 % + Run_lcao lcao_line 6.8264 1 6.8 1e+02 % + Potential init_pot 0.28114 2 0.14 4.1 % + PW_Basis recip2real 0.25402 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.11644 16 0.0073 1.7 % + Potential v_of_rho 0.79498 13 0.061 12 % + XC_Functional v_xc 0.20187 14 0.014 3 % + H_Hartree_pw v_hartree 0.55723 13 0.043 8.2 % + PW_Basis real2recip 0.64976 38 0.017 9.5 % + PW_Basis gatherp_scatters 0.26617 38 0.007 3.9 % + ORB_control set_orb_tables 1.0925 1 1.1 16 % + ORB_gen_tables gen_tables 1.0925 1 1.1 16 % + ORB_table_phi init_Table 0.47419 1 0.47 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.46901 126 0.0037 6.9 % + ORB_table_beta init_Table_Beta 0.18365 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.1821 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.2476 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24566 66 0.0037 3.6 % + LOOP_ions opt_ions 5.1939 1 5.2 76 % + ESolver_KS_LCAO Run 4.6217 1 4.6 68 % + HSolverLCAO solve 2.463 11 0.22 36 % + HamiltLCAO updateHk 1.2827 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2552 11 0.11 18 % + Gint_interface cal_gint 0.6628 23 0.029 9.7 % + Gint_Gamma distri_vl_value 0.58913 11 0.054 8.6 % + Gint_Gamma distri_vl 2.2148 6 0.37 32 % + LCAO_Deepks cal_projected_DM 4.8204 13 0.37 71 % + LCAO_gen_fixedH add_v_delta 2.0753 6 0.35 30 % + LCAO_DESCRIPTOR add_v_delta 2.0755 6 0.35 30 % + ElecStateLCAO psiToRho 1.163 11 0.11 17 % + Charge mix_rho 0.81435 10 0.081 12 % + LOOP_ions force_stress 0.57202 1 0.57 8.4 % + Force_Stress_LCAO getForceStress 0.572 1 0.57 8.4 % + Force_LCAO_gamma ftable_gamma 0.3804 1 0.38 5.6 % + Force_LCAO_gamma cal_fvl_dphi 0.15749 1 0.16 2.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:55 2022 + FINISH Time : Wed Sep 28 11:12:02 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/13/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..24d3d8f99a7236434346e14c40064ec0b4b5f84b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.174405 0.60641 0.0956895 +H 0.14598 0.561891 0.137737 +H 0.235952 0.587888 0.0941027 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..7008779e1b77417c74a22ba61bb7c73cbbbcf04b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2494 2 + 2 -12.9428 2 + 3 -9.15343 2 + 4 -6.73484 2 + 5 1.21236 0 + 6 4.33796 0 + 7 11.0878 0 + 8 11.3384 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..544ccc075f514c0f038e8712b34e8ee493a21352 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:29 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.88335133454 16.9794784832 2.67930717489 0 0 0 0 + tauc_H1 4.08745100266 15.7329568627 3.85663194143 0 0 0 0 + tauc_H2 6.60665927315 16.4608551924 2.6348757107 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.087333784662 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877085852992 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105844716801 (SEC) + + DONE : INIT CHARGE Time : 0.155196714419 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.440558 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000752 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00187 + + Density error is 0.214396546313 + + Energy Rydberg eV + E_KohnSham -34.1892233636 -465.16824794 + E_Harris -34.3799814234 -467.763644492 + E_Fermi -0.402199011415 -5.47219828521 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104503024966 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00149494133124 + + Density error is 0.0981950721832 + + Energy Rydberg eV + E_KohnSham -34.2790862363 -466.390895047 + E_Harris -34.2859506574 -466.484290287 + E_Fermi -0.211213216285 -2.87370323439 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100026743933 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00136979370448 + + Density error is 0.0631419588161 + + Energy Rydberg eV + E_KohnSham -34.2794540191 -466.395898988 + E_Harris -34.2838879209 -466.456225318 + E_Fermi -0.20139229332 -2.74008272244 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000945598000617 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113904059413 + + Density error is 0.0019783753017 + + Energy Rydberg eV + E_KohnSham -34.2794175842 -466.395403267 + E_Harris -34.2794189578 -466.395421956 + E_Fermi -0.165796721285 -2.25578011919 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000948470742706 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113742080598 + + Density error is 0.000921887978004 + + Energy Rydberg eV + E_KohnSham -34.2793636482 -466.39466943 + E_Harris -34.2793644624 -466.394680507 + E_Fermi -0.165316315744 -2.24924386649 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947447712451 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113444390639 + + Density error is 0.000162940152455 + + Energy Rydberg eV + E_KohnSham -34.2793938999 -466.395081025 + E_Harris -34.2793939323 -466.395081466 + E_Fermi -0.165155522739 -2.24705616542 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00094759544248 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113429393704 + + Density error is 3.53948780453e-05 + + Energy Rydberg eV + E_KohnSham -34.2793831551 -466.394934834 + E_Harris -34.2793831604 -466.394934907 + E_Fermi -0.165061096051 -2.24577142442 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947551746932 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113427814586 + + Density error is 1.79715725644e-05 + + Energy Rydberg eV + E_KohnSham -34.279386975 -466.394986807 + E_Harris -34.2793869764 -466.394986826 + E_Fermi -0.165094177754 -2.24622152408 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947560977043 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113425057759 + + Density error is 3.22695782587e-06 + + Energy Rydberg eV + E_KohnSham -34.2793855875 -466.394967929 + E_Harris -34.2793855875 -466.39496793 + E_Fermi -0.165077819593 -2.24599895988 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00094755782389 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113423896998 + + Density error is 4.17066780686e-07 + + Energy Rydberg eV + E_KohnSham -34.2793858376 -466.394971332 + E_Harris -34.2793858376 -466.394971332 + E_Fermi -0.165074389556 -2.24595229183 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947558599427 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113423916451 + + Density error is 1.6792071639e-07 + + Energy Rydberg eV + E_KohnSham -34.2793858818 -466.394971933 + E_Harris -34.2793858818 -466.394971933 + E_Fermi -0.165074259672 -2.24595052468 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947558773776 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113423882582 + + Density error is 1.06997795085e-08 + + Energy Rydberg eV + E_KohnSham -34.2793858836 -466.394971957 + E_Harris -34.2793858836 -466.394971957 + E_band -7.94967933526 -108.160936232 + E_one_elec -69.1618824857 -940.995686212 + E_Hartree +35.9773244741 +489.496611642 + E_xc -8.19972106389 -111.562928479 + E_Ewald +7.22948264107 +98.3621575107 + E_demet -8.04190898464e-73 -1.09415784988e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194614479748 -2.64786583787 + E_Fermi -0.165074102913 -2.24594839185 + + charge density convergence is achieved + final etot is -466.394971957 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2494 2.00000 + 2 -12.9428 2.00000 + 3 -9.15343 2.00000 + 4 -6.73484 2.00000 + 5 1.21236 0.00000 + 6 4.33796 0.00000 + 7 11.0878 0.00000 + 8 11.3384 0.00000 + + EFERMI = -2.245948391852114 eV + OUT.ABACUS/ final etot is -466.3949719573173 eV + correction force for each atom along direction 1 is 1.36712e-05 + correction force for each atom along direction 2 is -5.20923e-05 + correction force for each atom along direction 3 is -4.00004e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.6496152 -0.44841810 +0.77427397 + H1 +0.41302604 +0.76533731 -0.70125521 + H2 +1.2365892 -0.31691921 -0.073018759 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3949719573173 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.3724 11 0.76 1.0e+02% + Run_lcao lcao_line 8.3627 1 8.4 1.e+02% + Potential init_pot 0.28928 2 0.14 3.5% + PW_Basis recip2real 0.30488 17 0.018 3.6% + PW_Basis gathers_scatterp 0.13280 17 0.0078 1.6% + Potential v_of_rho 1.0610 14 0.076 13.% + XC_Functional v_xc 0.30264 15 0.020 3.6% + H_Hartree_pw v_hartree 0.71304 14 0.051 8.5% + PW_Basis real2recip 0.71482 41 0.017 8.5% + PW_Basis gatherp_scatters 0.27839 41 0.0068 3.3% + ORB_control set_orb_tables 1.0979 1 1.1 13.% + ORB_gen_tables gen_tables 1.0979 1 1.1 13.% + ORB_table_phi init_Table 0.47647 1 0.48 5.7% + ORB_table_phi cal_ST_Phi12_R 0.47131 126 0.0037 5.6% + ORB_table_beta init_Table_Beta 0.18525 1 0.19 2.2% + ORB_table_beta VNL_PhiBeta_R 0.18369 56 0.0033 2.2% + ORB_table_alpha init_Table_Alpha 0.24871 1 0.25 3.0% + ORB_table_alpha S_PhiAlpha_R 0.24669 66 0.0037 2.9% + LOOP_ions opt_ions 6.7416 1 6.7 81.% + ESolver_KS_LCAO Run 6.1233 1 6.1 73.% + HSolverLCAO solve 3.6504 12 0.30 44.% + HamiltLCAO updateHk 1.8032 12 0.15 22.% + LCAO_Hamilt cal_Hgamma 1.7735 12 0.15 21.% + Gint_interface cal_gint 3.5195 25 0.14 42.% + Gint_Gamma distri_vl 3.1701 6 0.53 38.% + LCAO_Deepks cal_projected_DM 6.5516 14 0.47 78.% + LCAO_gen_fixedH add_v_delta 3.0229 6 0.50 36.% + LCAO_DESCRIPTOR add_v_delta 3.0229 6 0.50 36.% + ElecStateLCAO psiToRho 1.8304 12 0.15 22.% + Charge mix_rho 0.85693 11 0.078 10.% + LOOP_ions force_stress 0.61810 1 0.62 7.4% + Force_Stress_LCAO getForceStress 0.61807 1 0.62 7.4% + Force_LCAO_gamma ftable_gamma 0.40063 1 0.40 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.39274 1 0.39 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:29 2022 + Finish Time : Wed Sep 28 11:10:37 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..5895c76dfed1b2cea3acd78bf04ead5048454be3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123923 ima = 3.68261e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123233011523 + charge after normalized = 7.99999999999995 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011199460329 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112615101225 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112854450249 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112813466762 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112837738936 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112831210893 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112833918689 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011283312773 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112833007453 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112832994271 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112832985992 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/STRU new file mode 100644 index 0000000000000000000000000000000000000000..91796f8198bdff61ec887558a8aea45a789b705c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.116648665449 16.979478483170 2.679307174878 0 0 0 +H +0.0 +2 +-23.912548997340 15.732956862647 3.856631941409 0 0 0 +-21.393340726858 16.460855192452 2.634875710683 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/conv new file mode 100644 index 0000000000000000000000000000000000000000..a689e1f06a4fc77c223307259ea73c0e4c3c35b7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/conv @@ -0,0 +1 @@ +130 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..52b3f6d3ae332abb5898858130d6ede677dc63da --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750161958 0.01262809417 1.263908145 1.359346359 1.469155683 0.008632504721 0.01820162277 0.03906925091 +5.717293064e-19 0.001001122786 0.002594485551 0.01224832747 0.04471766702 -1.84229666e-19 2.010400345e-06 5.898032352e-06 +0.001623299399 0.005946330386 + +H atom_index 1 n_descriptor 18 +1.201340942 0.03596344023 0.09255331225 0.1287523927 0.3040757986 0.01999708533 0.02546114773 0.03932092466 +1.758704461e-17 4.074910296e-05 0.08847119743 0.1101716004 0.1133954113 8.887950992e-20 6.232974757e-06 0.01412080652 +0.02427921878 0.02835568339 + +H atom_index 2 n_descriptor 18 +1.272565581 0.03356982055 0.1164042263 0.1607989651 0.3280905735 0.02332044276 0.02961637583 0.0369196839 +-1.535563256e-17 4.722221692e-05 0.1056890287 0.1169856093 0.1379721172 2.661407792e-18 2.765877158e-06 0.01318150918 +0.02700725158 0.03173038935 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..1261d54c1b0fbad0612f4970e8c5af29ba47fd00 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:29 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0873559 SEC) : SETUP UNITCELL + DONE(0.0877228 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105868 SEC) : INIT PLANEWAVE + DONE(0.15533 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.440623 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651682e+02 0.000000e+00 2.144e-01 6.066e-01 + GE2 -4.663909e+02 -1.222647e+00 9.820e-02 5.669e-01 + GE3 -4.663959e+02 -5.003942e-03 6.314e-02 6.331e-01 + GE4 -4.663954e+02 4.957218e-04 1.978e-03 4.945e-01 + GE5 -4.663947e+02 7.338368e-04 9.219e-04 4.913e-01 + GE6 -4.663951e+02 -4.115957e-04 1.629e-04 4.904e-01 + GE7 -4.663949e+02 1.461913e-04 3.539e-05 4.762e-01 + GE8 -4.663950e+02 -5.197262e-05 1.797e-05 4.722e-01 + GE9 -4.663950e+02 1.887749e-05 3.227e-06 4.745e-01 + GE10 -4.663950e+02 -3.402529e-06 4.171e-07 4.758e-01 + GE11 -4.663950e+02 -6.014752e-07 1.679e-07 4.727e-01 + GE12 -4.663950e+02 -2.403671e-08 1.070e-08 4.068e-01 +E_delta_band = -7.00250306e-02 Ry = -9.52739419e-01 eV +E_delta_NN= -1.94614480e-01 Ry = -2.64786584e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.3724 11 0.76 1e+02 % + Run_lcao lcao_line 8.3627 1 8.4 1e+02 % + Potential init_pot 0.28928 2 0.14 3.5 % + PW_Basis recip2real 0.30488 17 0.018 3.6 % + PW_Basis gathers_scatterp 0.1328 17 0.0078 1.6 % + Potential v_of_rho 1.061 14 0.076 13 % + XC_Functional v_xc 0.30264 15 0.02 3.6 % + H_Hartree_pw v_hartree 0.71304 14 0.051 8.5 % + PW_Basis real2recip 0.71482 41 0.017 8.5 % + PW_Basis gatherp_scatters 0.27839 41 0.0068 3.3 % + ORB_control set_orb_tables 1.0979 1 1.1 13 % + ORB_gen_tables gen_tables 1.0979 1 1.1 13 % + ORB_table_phi init_Table 0.47647 1 0.48 5.7 % + ORB_table_phi cal_ST_Phi12_R 0.47131 126 0.0037 5.6 % + ORB_table_beta init_Table_Beta 0.18525 1 0.19 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.18369 56 0.0033 2.2 % + ORB_table_alpha init_Table_Alpha 0.24871 1 0.25 3 % + ORB_table_alpha S_PhiAlpha_R 0.24669 66 0.0037 2.9 % + LOOP_ions opt_ions 6.7416 1 6.7 81 % + ESolver_KS_LCAO Run 6.1233 1 6.1 73 % + HSolverLCAO solve 3.6504 12 0.3 44 % + HamiltLCAO updateHk 1.8032 12 0.15 22 % + LCAO_Hamilt cal_Hgamma 1.7735 12 0.15 21 % + Gint_interface cal_gint 3.5195 25 0.14 42 % + Gint_Gamma distri_vl 3.1701 6 0.53 38 % + LCAO_Deepks cal_projected_DM 6.5516 14 0.47 78 % + LCAO_gen_fixedH add_v_delta 3.0229 6 0.5 36 % + LCAO_DESCRIPTOR add_v_delta 3.0229 6 0.5 36 % + ElecStateLCAO psiToRho 1.8304 12 0.15 22 % + Charge mix_rho 0.85693 11 0.078 10 % + LOOP_ions force_stress 0.6181 1 0.62 7.4 % + Force_Stress_LCAO getForceStress 0.61807 1 0.62 7.4 % + Force_LCAO_gamma ftable_gamma 0.40063 1 0.4 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.39274 1 0.39 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:29 2022 + FINISH Time : Wed Sep 28 11:10:37 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/130/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5a95e3899abf81dee7a077c241beab3f1d709dd3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.17664 0.601645 0.0840978 +H 0.167779 0.589314 0.146062 +H 0.23272 0.567606 0.0662285 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..95c2ccd6c3995b0d8044a1c5642518bf871676b3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2058 2 + 2 -13.0696 2 + 3 -9.01786 2 + 4 -6.72212 2 + 5 1.19997 0 + 6 4.37201 0 + 7 11.0907 0 + 8 11.325 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..833fefa6fb0591bc41a9f91a685d78b575f3b8cb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:39 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.9459185767 16.8460682895 2.35473706008 0 0 0 0 + tauc_H1 4.69781930486 16.5007813045 4.08973274103 0 0 0 0 + tauc_H2 6.51614878535 15.8929735284 1.85439677891 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0730641292984 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0734363133054 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0891832263022 (SEC) + + DONE : INIT CHARGE Time : 0.130349103483 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374787 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000911 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00145 + + Density error is 0.215281506008 + + Energy Rydberg eV + E_KohnSham -34.186810335 -465.135417002 + E_Harris -34.3795317995 -467.757527045 + E_Fermi -0.402477700702 -5.47599004748 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116190797816 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131118484126 + + Density error is 0.0984585198012 + + Energy Rydberg eV + E_KohnSham -34.2775118393 -466.369474277 + E_Harris -34.2843656803 -466.462725568 + E_Fermi -0.210555163635 -2.86474996876 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110865407486 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122274750617 + + Density error is 0.0633339856993 + + Energy Rydberg eV + E_KohnSham -34.2778881034 -466.374593612 + E_Harris -34.2823041676 -466.434677249 + E_Fermi -0.200784197547 -2.731809155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103356644576 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106980919284 + + Density error is 0.00202621370344 + + Energy Rydberg eV + E_KohnSham -34.2778527604 -466.374112746 + E_Harris -34.2778549273 -466.374142229 + E_Fermi -0.165267800846 -2.24858378744 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103331588637 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106798789732 + + Density error is 0.000929691522997 + + Energy Rydberg eV + E_KohnSham -34.2777984632 -466.373373995 + E_Harris -34.2777991183 -466.373382908 + E_Fermi -0.164747647376 -2.24150673641 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103225648201 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106596254795 + + Density error is 0.000180647236726 + + Energy Rydberg eV + E_KohnSham -34.2778273034 -466.373766386 + E_Harris -34.2778273556 -466.373767096 + E_Fermi -0.164575077482 -2.23915880255 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010325531418 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106605123751 + + Density error is 3.85609586443e-05 + + Energy Rydberg eV + E_KohnSham -34.2778166433 -466.373621348 + E_Harris -34.2778166502 -466.373621441 + E_Fermi -0.164474161252 -2.2377857668 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103244995447 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106599409085 + + Density error is 1.6677939403e-05 + + Energy Rydberg eV + E_KohnSham -34.2778210701 -466.373681578 + E_Harris -34.2778210712 -466.373681593 + E_Fermi -0.164509033123 -2.23826022295 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103244816717 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106597417211 + + Density error is 2.93136262722e-06 + + Energy Rydberg eV + E_KohnSham -34.2778197004 -466.373662943 + E_Harris -34.2778197005 -466.373662943 + E_Fermi -0.16449299123 -2.23804196179 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103244904542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106597031555 + + Density error is 4.43302372719e-07 + + Energy Rydberg eV + E_KohnSham -34.2778198993 -466.373665648 + E_Harris -34.2778198993 -466.373665648 + E_Fermi -0.164490010158 -2.23800140223 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010324494085 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106597033648 + + Density error is 1.87863896314e-07 + + Energy Rydberg eV + E_KohnSham -34.2778199384 -466.373666181 + E_Harris -34.2778199384 -466.373666181 + E_Fermi -0.164489882909 -2.23799967091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103244952974 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106597016303 + + Density error is 1.09411615143e-08 + + Energy Rydberg eV + E_KohnSham -34.2778199391 -466.373666189 + E_Harris -34.2778199391 -466.373666189 + E_band -7.94010444674 -108.030663191 + E_one_elec -69.1575030266 -940.936100614 + E_Hartree +35.980313297 +489.537276665 + E_xc -8.20030604308 -111.57088753 + E_Ewald +7.22429070852 +98.2915176443 + E_demet -5.34708324944e-72 -7.27507998727e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19458303221 -2.64743797217 + E_Fermi -0.164489700312 -2.23799718655 + + charge density convergence is achieved + final etot is -466.373666189 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2058 2.00000 + 2 -13.0696 2.00000 + 3 -9.01786 2.00000 + 4 -6.72212 2.00000 + 5 1.19997 0.00000 + 6 4.37201 0.00000 + 7 11.0907 0.00000 + 8 11.3250 0.00000 + + EFERMI = -2.237997186554235 eV + OUT.ABACUS/ final etot is -466.3736661891172 eV + correction force for each atom along direction 1 is 0.000138090 + correction force for each atom along direction 2 is -3.69790e-05 + correction force for each atom along direction 3 is 0.000127975 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.3342280 -0.29928164 -2.1146477 + H1 -0.11829614 -0.39973154 +1.6042243 + H2 -1.2159319 +0.69901318 +0.51042341 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3736661891172 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7592 11 0.71 1.0e+02% + Run_lcao lcao_line 7.7516 1 7.8 1.e+02% + Potential init_pot 0.24382 2 0.12 3.1% + PW_Basis recip2real 0.28172 17 0.017 3.6% + PW_Basis gathers_scatterp 0.11239 17 0.0066 1.4% + Potential v_of_rho 0.99661 14 0.071 13.% + XC_Functional v_xc 0.29563 15 0.020 3.8% + H_Hartree_pw v_hartree 0.65944 14 0.047 8.5% + PW_Basis real2recip 0.64544 41 0.016 8.3% + PW_Basis gatherp_scatters 0.23780 41 0.0058 3.1% + ORB_control set_orb_tables 0.89539 1 0.90 12.% + ORB_gen_tables gen_tables 0.89539 1 0.90 12.% + ORB_table_phi init_Table 0.37579 1 0.38 4.8% + ORB_table_phi cal_ST_Phi12_R 0.37150 126 0.0029 4.8% + ORB_table_beta init_Table_Beta 0.15326 1 0.15 2.0% + ORB_table_beta VNL_PhiBeta_R 0.15199 56 0.0027 2.0% + ORB_table_alpha init_Table_Alpha 0.20822 1 0.21 2.7% + ORB_table_alpha S_PhiAlpha_R 0.20656 66 0.0031 2.7% + LOOP_ions opt_ions 6.4114 1 6.4 83.% + ESolver_KS_LCAO Run 5.8389 1 5.8 75.% + HSolverLCAO solve 3.4700 12 0.29 45.% + HamiltLCAO updateHk 1.7189 12 0.14 22.% + LCAO_Hamilt cal_Hgamma 1.6836 12 0.14 22.% + Gint_interface cal_gint 3.3667 25 0.13 43.% + Gint_Gamma distri_vl 3.0195 6 0.50 39.% + LCAO_Deepks cal_projected_DM 6.2403 14 0.45 80.% + LCAO_gen_fixedH add_v_delta 2.8913 6 0.48 37.% + LCAO_DESCRIPTOR add_v_delta 2.8912 6 0.48 37.% + ElecStateLCAO psiToRho 1.7337 12 0.14 22.% + Charge mix_rho 0.83320 11 0.076 11.% + LOOP_ions force_stress 0.57238 1 0.57 7.4% + Force_Stress_LCAO getForceStress 0.57235 1 0.57 7.4% + Force_LCAO_gamma ftable_gamma 0.37473 1 0.37 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.36743 1 0.37 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:39 2022 + Finish Time : Wed Sep 28 11:09:47 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c9e8186941b50d75729567ceea13a6fc8fb65c6b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123624 ima = 3.68593e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123546884529 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112348390929 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112961823653 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113202835885 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113164258861 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113187465291 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113179601105 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113182400883 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113181763938 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113181658254 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113181646876 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113181637329 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b7405542c21ad9a372a37a6ffc8eb5f359fd264e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.054081423292 16.846068289490 2.354737060074 0 0 0 +H +0.0 +2 +-23.302180695125 16.500781304469 4.089732741018 0 0 0 +-21.483851214671 15.892973528430 1.854396778905 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/conv new file mode 100644 index 0000000000000000000000000000000000000000..7417031591620f7ba167403bda72a83cdab95227 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/conv @@ -0,0 +1 @@ +131 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e66330375eebd97a1ed53851f66aeb1415dfd33c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747990938 0.01256166354 1.263019448 1.365536394 1.469023107 0.008271992114 0.01901626953 0.03901409457 +-1.328954705e-18 0.001049155527 0.002493772785 0.01200254012 0.04379650463 3.204417716e-19 1.721830004e-06 5.331476586e-06 +0.001663065023 0.005801731066 + +H atom_index 1 n_descriptor 18 +1.281464848 0.03300385145 0.1191863711 0.1657349174 0.3313967821 0.02338980316 0.03018601732 0.03654378545 +9.726115146e-18 4.503334911e-05 0.1067261096 0.1180822939 0.1421953119 -8.687936089e-18 2.521461152e-06 0.0131764508 +0.0271017285 0.03210564205 + +H atom_index 2 n_descriptor 18 +1.188331932 0.03612807263 0.0883423914 0.1240225054 0.3003234529 0.01917243036 0.02478144278 0.03961788843 +-1.355634172e-17 3.697679884e-05 0.08476449043 0.1060122946 0.1129298238 3.314148821e-18 6.626397988e-06 0.0143622042 +0.02354030449 0.02772193571 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9438aff54c97e068f74d2652da87e8d4258833af Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:39 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0730794 SEC) : SETUP UNITCELL + DONE(0.0734478 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0891965 SEC) : INIT PLANEWAVE + DONE(0.130451 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374829 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651354e+02 0.000000e+00 2.153e-01 5.589e-01 + GE2 -4.663695e+02 -1.234057e+00 9.846e-02 5.379e-01 + GE3 -4.663746e+02 -5.119335e-03 6.333e-02 6.017e-01 + GE4 -4.663741e+02 4.808663e-04 2.026e-03 4.756e-01 + GE5 -4.663734e+02 7.387511e-04 9.297e-04 4.730e-01 + GE6 -4.663738e+02 -3.923912e-04 1.806e-04 4.705e-01 + GE7 -4.663736e+02 1.450384e-04 3.856e-05 4.583e-01 + GE8 -4.663737e+02 -6.023040e-05 1.668e-05 4.543e-01 + GE9 -4.663737e+02 1.863547e-05 2.931e-06 4.519e-01 + GE10 -4.663737e+02 -2.705189e-06 4.433e-07 4.606e-01 + GE11 -4.663737e+02 -5.328123e-07 1.879e-07 4.544e-01 + GE12 -4.663737e+02 -8.574527e-09 1.094e-08 3.864e-01 +E_delta_band = -6.99681573e-02 Ry = -9.51965618e-01 eV +E_delta_NN= -1.94583032e-01 Ry = -2.64743797e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7592 11 0.71 1e+02 % + Run_lcao lcao_line 7.7516 1 7.8 1e+02 % + Potential init_pot 0.24382 2 0.12 3.1 % + PW_Basis recip2real 0.28172 17 0.017 3.6 % + PW_Basis gathers_scatterp 0.11239 17 0.0066 1.4 % + Potential v_of_rho 0.99661 14 0.071 13 % + XC_Functional v_xc 0.29563 15 0.02 3.8 % + H_Hartree_pw v_hartree 0.65944 14 0.047 8.5 % + PW_Basis real2recip 0.64544 41 0.016 8.3 % + PW_Basis gatherp_scatters 0.2378 41 0.0058 3.1 % + ORB_control set_orb_tables 0.89539 1 0.9 12 % + ORB_gen_tables gen_tables 0.89539 1 0.9 12 % + ORB_table_phi init_Table 0.37579 1 0.38 4.8 % + ORB_table_phi cal_ST_Phi12_R 0.3715 126 0.0029 4.8 % + ORB_table_beta init_Table_Beta 0.15326 1 0.15 2 % + ORB_table_beta VNL_PhiBeta_R 0.15199 56 0.0027 2 % + ORB_table_alpha init_Table_Alpha 0.20822 1 0.21 2.7 % + ORB_table_alpha S_PhiAlpha_R 0.20656 66 0.0031 2.7 % + LOOP_ions opt_ions 6.4114 1 6.4 83 % + ESolver_KS_LCAO Run 5.8389 1 5.8 75 % + HSolverLCAO solve 3.47 12 0.29 45 % + HamiltLCAO updateHk 1.7189 12 0.14 22 % + LCAO_Hamilt cal_Hgamma 1.6836 12 0.14 22 % + Gint_interface cal_gint 3.3667 25 0.13 43 % + Gint_Gamma distri_vl 3.0195 6 0.5 39 % + LCAO_Deepks cal_projected_DM 6.2403 14 0.45 80 % + LCAO_gen_fixedH add_v_delta 2.8913 6 0.48 37 % + LCAO_DESCRIPTOR add_v_delta 2.8912 6 0.48 37 % + ElecStateLCAO psiToRho 1.7337 12 0.14 22 % + Charge mix_rho 0.8332 11 0.076 11 % + LOOP_ions force_stress 0.57238 1 0.57 7.4 % + Force_Stress_LCAO getForceStress 0.57235 1 0.57 7.4 % + Force_LCAO_gamma ftable_gamma 0.37473 1 0.37 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.36743 1 0.37 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:39 2022 + FINISH Time : Wed Sep 28 11:09:47 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/131/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4f9781bc45442fbbcd7a26b2a5e4d500d54399cb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.184529 0.590195 0.0723728 +H 0.202856 0.606818 0.132772 +H 0.241093 0.582607 0.0438635 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8a9e24cf8185caeb6e956778952c9bb10a656707 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5197 2 + 2 -13.0383 2 + 3 -9.29189 2 + 4 -6.79535 2 + 5 1.41697 0 + 6 4.64968 0 + 7 11.0298 0 + 8 11.2939 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..90974a885293f509c34ad7ca1b0b329269b66468 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:25 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.16682011872 16.5254737025 2.0264379912 0 0 0 0 + tauc_H1 5.67997278253 16.990898937 3.71761157604 0 0 0 0 + tauc_H2 6.75060435037 16.3129975794 1.228177203 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0731608973633 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0734370562697 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0897454699423 (SEC) + + DONE : INIT CHARGE Time : 0.131262459984 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.37308 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000869 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00165 + + Density error is 0.216812280387 + + Energy Rydberg eV + E_KohnSham -34.1867898328 -465.135138055 + E_Harris -34.3832218474 -467.807732723 + E_Fermi -0.417365501881 -5.67854897422 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013279932884 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00135112357809 + + Density error is 0.0976329400248 + + Energy Rydberg eV + E_KohnSham -34.2786222525 -466.384582223 + E_Harris -34.2853583062 -466.476230936 + E_Fermi -0.223762844911 -3.04444969148 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127283657443 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124197402939 + + Density error is 0.0625512359007 + + Energy Rydberg eV + E_KohnSham -34.2789864372 -466.389537211 + E_Harris -34.2833354039 -466.448707938 + E_Fermi -0.211393674841 -2.876158499 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120262343269 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010570408569 + + Density error is 0.00200589696908 + + Energy Rydberg eV + E_KohnSham -34.2789993062 -466.389712303 + E_Harris -34.2790010006 -466.389735356 + E_Fermi -0.175435834064 -2.38692697665 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012079931987 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010568234923 + + Density error is 0.000990953373706 + + Energy Rydberg eV + E_KohnSham -34.2789210566 -466.388647662 + E_Harris -34.2789232388 -466.388677353 + E_Fermi -0.174520943137 -2.37447924699 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120608056922 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010547338764 + + Density error is 9.98968120074e-05 + + Energy Rydberg eV + E_KohnSham -34.2789715569 -466.389334753 + E_Harris -34.2789717255 -466.389337048 + E_Fermi -0.174651884599 -2.37626079698 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120583275076 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105441922756 + + Density error is 4.66891902627e-05 + + Energy Rydberg eV + E_KohnSham -34.2789558267 -466.389120733 + E_Harris -34.2789558394 -466.389120907 + E_Fermi -0.17452659242 -2.37455610944 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120578569678 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105448091554 + + Density error is 1.70462938352e-05 + + Energy Rydberg eV + E_KohnSham -34.2789583265 -466.389154745 + E_Harris -34.2789583278 -466.389154762 + E_Fermi -0.174588021588 -2.37539189614 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120580239241 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105446027036 + + Density error is 2.32134404804e-06 + + Energy Rydberg eV + E_KohnSham -34.2789567378 -466.38913313 + E_Harris -34.2789567378 -466.38913313 + E_Fermi -0.174570519929 -2.37515377386 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001205804452 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105445511243 + + Density error is 2.66606259483e-07 + + Energy Rydberg eV + E_KohnSham -34.2789569808 -466.389136436 + E_Harris -34.2789569808 -466.389136436 + E_Fermi -0.174568464602 -2.3751258097 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120580498536 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105445532838 + + Density error is 8.68448899771e-08 + + Energy Rydberg eV + E_KohnSham -34.2789570217 -466.389136993 + E_Harris -34.2789570217 -466.389136993 + E_band -8.03270221319 -109.290520437 + E_one_elec -69.6441016916 -947.556615097 + E_Hartree +36.2005824479 +492.53419221 + E_xc -8.23558660811 -112.050904243 + E_Ewald +7.52372864448 +102.365579771 + E_demet -5.24911733311e-87 -7.14179052009e-86 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195501666694 -2.65993663553 + E_Fermi -0.174568345817 -2.37512419355 + + charge density convergence is achieved + final etot is -466.389136993 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5197 2.00000 + 2 -13.0383 2.00000 + 3 -9.29189 2.00000 + 4 -6.79535 2.00000 + 5 1.41697 0.00000 + 6 4.64968 0.00000 + 7 11.0298 0.00000 + 8 11.2939 0.00000 + + EFERMI = -2.375124193545717 eV + OUT.ABACUS/ final etot is -466.3891369928041 eV + correction force for each atom along direction 1 is 0.000170485 + correction force for each atom along direction 2 is 5.94385e-05 + correction force for each atom along direction 3 is -2.22606e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.2615653 +0.13470342 +0.49912089 + H1 -0.14797417 +0.14673328 +0.54234996 + H2 +1.4095395 -0.28143670 -1.0414709 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3891369928041 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2543 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2467 1 7.2 1.e+02% + Potential init_pot 0.24044 2 0.12 3.3% + PW_Basis recip2real 0.26194 16 0.016 3.6% + PW_Basis gathers_scatterp 0.10577 16 0.0066 1.5% + Potential v_of_rho 0.91495 13 0.070 13.% + XC_Functional v_xc 0.27210 14 0.019 3.8% + H_Hartree_pw v_hartree 0.60561 13 0.047 8.3% + PW_Basis real2recip 0.59140 38 0.016 8.2% + PW_Basis gatherp_scatters 0.22000 38 0.0058 3.0% + ORB_control set_orb_tables 0.90320 1 0.90 12.% + ORB_gen_tables gen_tables 0.90319 1 0.90 12.% + ORB_table_phi init_Table 0.38043 1 0.38 5.2% + ORB_table_phi cal_ST_Phi12_R 0.37608 126 0.0030 5.2% + ORB_table_beta init_Table_Beta 0.15599 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15457 56 0.0028 2.1% + ORB_table_alpha init_Table_Alpha 0.20922 1 0.21 2.9% + ORB_table_alpha S_PhiAlpha_R 0.20750 66 0.0031 2.9% + LOOP_ions opt_ions 5.8997 1 5.9 81.% + ESolver_KS_LCAO Run 5.3330 1 5.3 74.% + HSolverLCAO solve 3.1734 11 0.29 44.% + HamiltLCAO updateHk 1.5865 11 0.14 22.% + LCAO_Hamilt cal_Hgamma 1.5534 11 0.14 21.% + Gint_interface cal_gint 3.0761 23 0.13 42.% + Gint_Gamma distri_vl 2.5574 6 0.43 35.% + LCAO_Deepks cal_projected_DM 5.7308 13 0.44 79.% + LCAO_gen_fixedH add_v_delta 2.4297 6 0.40 33.% + LCAO_DESCRIPTOR add_v_delta 2.4297 6 0.40 33.% + ElecStateLCAO psiToRho 1.5700 11 0.14 22.% + Charge mix_rho 0.75381 10 0.075 10.% + LOOP_ions force_stress 0.56659 1 0.57 7.8% + Force_Stress_LCAO getForceStress 0.56656 1 0.57 7.8% + Force_LCAO_gamma ftable_gamma 0.36808 1 0.37 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.36056 1 0.36 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:25 2022 + Finish Time : Wed Sep 28 11:12:32 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2a27d895bb3f4dc94a564519d46b145f0d1bb43b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124189 ima = 3.66836e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001228053322 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111628067769 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112153511118 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112446605316 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112373065454 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112412856324 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112409923646 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112413173147 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112412429876 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112412324175 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011241231428 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9008dad0f7655ff80c55b76fe4fb4e810921938c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.833179881260 16.525473702461 2.026437991227 0 0 0 +H +0.0 +2 +-22.320027217471 16.990898936990 3.717611576054 0 0 0 +-21.249395649617 16.312997579378 1.228177203002 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/conv new file mode 100644 index 0000000000000000000000000000000000000000..2eec36ee59699dffceec4e9b139e6facaff7ac43 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/conv @@ -0,0 +1 @@ +132 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..2538039901fa83b5bac2057337fe05fe7f905ea9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751605153 0.01283274606 1.285102227 1.369768576 1.470295073 0.009079427642 0.01802498802 0.03908570698 +-5.130531428e-19 0.00106444351 0.002830871016 0.0132332573 0.04790099393 2.548593098e-19 2.634437861e-06 7.061705231e-06 +0.001614347817 0.006077005596 + +H atom_index 1 n_descriptor 18 +1.252048535 0.03447023498 0.1104319174 0.1505321683 0.3206232254 0.02289401235 0.02837293484 0.03757265149 +2.586306514e-17 5.163341301e-05 0.1041837954 0.1151269475 0.1293069767 9.137406796e-19 3.67655134e-06 0.01330115155 +0.02705391681 0.03085576194 + +H atom_index 2 n_descriptor 18 +1.284586308 0.03339914721 0.1225036667 0.1664588633 0.3305908712 0.02445405428 0.03025561886 0.03682680966 +-2.772938518e-19 5.480977521e-05 0.1083333864 0.1203576503 0.142918176 3.651876137e-18 1.818943223e-06 0.01343768029 +0.02817465769 0.03221334977 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fcdedc47b1c0cf9b92e7233b5f69aa01ad66154e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:25 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0731763 SEC) : SETUP UNITCELL + DONE(0.0734461 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0897595 SEC) : INIT PLANEWAVE + DONE(0.131368 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.373125 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651351e+02 0.000000e+00 2.168e-01 5.576e-01 + GE2 -4.663846e+02 -1.249444e+00 9.763e-02 5.359e-01 + GE3 -4.663895e+02 -4.954987e-03 6.255e-02 5.924e-01 + GE4 -4.663897e+02 -1.750920e-04 2.006e-03 4.710e-01 + GE5 -4.663886e+02 1.064641e-03 9.910e-04 4.700e-01 + GE6 -4.663893e+02 -6.870913e-04 9.990e-05 4.536e-01 + GE7 -4.663891e+02 2.140198e-04 4.669e-05 4.647e-01 + GE8 -4.663892e+02 -3.401166e-05 1.705e-05 4.507e-01 + GE9 -4.663891e+02 2.161500e-05 2.321e-06 4.550e-01 + GE10 -4.663891e+02 -3.306305e-06 2.666e-07 4.476e-01 + GE11 -4.663891e+02 -5.565062e-07 8.684e-08 3.812e-01 +E_delta_band = -7.19218522e-02 Ry = -9.78547001e-01 eV +E_delta_NN= -1.95501667e-01 Ry = -2.65993664e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2543 11 0.66 1e+02 % + Run_lcao lcao_line 7.2467 1 7.2 1e+02 % + Potential init_pot 0.24044 2 0.12 3.3 % + PW_Basis recip2real 0.26194 16 0.016 3.6 % + PW_Basis gathers_scatterp 0.10577 16 0.0066 1.5 % + Potential v_of_rho 0.91495 13 0.07 13 % + XC_Functional v_xc 0.2721 14 0.019 3.8 % + H_Hartree_pw v_hartree 0.60561 13 0.047 8.3 % + PW_Basis real2recip 0.5914 38 0.016 8.2 % + PW_Basis gatherp_scatters 0.22 38 0.0058 3 % + ORB_control set_orb_tables 0.9032 1 0.9 12 % + ORB_gen_tables gen_tables 0.90319 1 0.9 12 % + ORB_table_phi init_Table 0.38043 1 0.38 5.2 % + ORB_table_phi cal_ST_Phi12_R 0.37608 126 0.003 5.2 % + ORB_table_beta init_Table_Beta 0.15599 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15457 56 0.0028 2.1 % + ORB_table_alpha init_Table_Alpha 0.20922 1 0.21 2.9 % + ORB_table_alpha S_PhiAlpha_R 0.2075 66 0.0031 2.9 % + LOOP_ions opt_ions 5.8997 1 5.9 81 % + ESolver_KS_LCAO Run 5.333 1 5.3 74 % + HSolverLCAO solve 3.1734 11 0.29 44 % + HamiltLCAO updateHk 1.5865 11 0.14 22 % + LCAO_Hamilt cal_Hgamma 1.5534 11 0.14 21 % + Gint_interface cal_gint 3.0761 23 0.13 42 % + Gint_Gamma distri_vl 2.5574 6 0.43 35 % + LCAO_Deepks cal_projected_DM 5.7308 13 0.44 79 % + LCAO_gen_fixedH add_v_delta 2.4297 6 0.4 33 % + LCAO_DESCRIPTOR add_v_delta 2.4297 6 0.4 33 % + ElecStateLCAO psiToRho 1.57 11 0.14 22 % + Charge mix_rho 0.75381 10 0.075 10 % + LOOP_ions force_stress 0.56659 1 0.57 7.8 % + Force_Stress_LCAO getForceStress 0.56656 1 0.57 7.8 % + Force_LCAO_gamma ftable_gamma 0.36808 1 0.37 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.36056 1 0.36 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:25 2022 + FINISH Time : Wed Sep 28 11:12:32 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/132/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..31fdc801a850941ced56c7d44e6d4d4ad3fc66e5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.188934 0.581497 0.0528637 +H 0.1554 0.622089 0.093036 +H 0.248048 0.610145 0.0410189 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ff829a37a4fd83c857f3d0532c092efd3fba6a55 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0641 2 + 2 -13.0402 2 + 3 -8.94209 2 + 4 -6.69239 2 + 5 1.16679 0 + 6 4.19805 0 + 7 11.121 0 + 8 11.3593 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4d5ae1d2decc8d7a124982e404b5f5bd45a5e1ae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:20 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.29016591341 16.2819059816 1.48018462971 0 0 0 0 + tauc_H1 4.35121059231 17.4184898136 2.60500671958 0 0 0 0 + tauc_H2 6.94535577101 17.0840708703 1.14853003257 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0738664048519 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0746714952593 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0905528227846 (SEC) + + DONE : INIT CHARGE Time : 0.13171815008 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374897 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00161 + + Density error is 0.213836295165 + + Energy Rydberg eV + E_KohnSham -34.1912756175 -465.196170287 + E_Harris -34.3801363118 -467.765751858 + E_Fermi -0.394342973092 -5.36531140031 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000949085447134 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00136067686549 + + Density error is 0.0985471460997 + + Energy Rydberg eV + E_KohnSham -34.2803540587 -466.408144656 + E_Harris -34.2872466752 -466.501923514 + E_Fermi -0.203740027702 -2.77202528743 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000907638556342 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125996997505 + + Density error is 0.0634531388252 + + Energy Rydberg eV + E_KohnSham -34.2807170663 -466.413083627 + E_Harris -34.2851509327 -466.473409475 + E_Fermi -0.194951120987 -2.65244607691 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00085494882534 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107285897666 + + Density error is 0.00203734296207 + + Energy Rydberg eV + E_KohnSham -34.2806639715 -466.412361235 + E_Harris -34.2806671685 -466.412404734 + E_Fermi -0.159755330485 -2.17358278046 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000855545678675 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107019144921 + + Density error is 0.000907388231571 + + Energy Rydberg eV + E_KohnSham -34.2806198055 -466.411760326 + E_Harris -34.2806202286 -466.411766083 + E_Fermi -0.159325539748 -2.1677351775 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000854819473589 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010676533613 + + Density error is 0.00019213826286 + + Energy Rydberg eV + E_KohnSham -34.2806431498 -466.412077942 + E_Harris -34.2806431818 -466.412078377 + E_Fermi -0.159081152343 -2.16441011627 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000855040732639 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010676016098 + + Density error is 3.32770546249e-05 + + Energy Rydberg eV + E_KohnSham -34.2806346993 -466.411962967 + E_Harris -34.2806347042 -466.411963034 + E_Fermi -0.158997752079 -2.16327539746 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000854985274804 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106756840739 + + Density error is 1.51674304078e-05 + + Energy Rydberg eV + E_KohnSham -34.2806386688 -466.412016975 + E_Harris -34.2806386698 -466.412016989 + E_Fermi -0.159026721009 -2.16366953998 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000854987046041 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106754139156 + + Density error is 1.89337502331e-06 + + Energy Rydberg eV + E_KohnSham -34.2806374366 -466.412000209 + E_Harris -34.2806374366 -466.412000209 + E_Fermi -0.159011303925 -2.16345977978 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000854986536606 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106753695173 + + Density error is 2.28627832573e-07 + + Energy Rydberg eV + E_KohnSham -34.2806376495 -466.412003106 + E_Harris -34.2806376495 -466.412003106 + E_Fermi -0.15900945993 -2.16343469095 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000854987044424 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106753738067 + + Density error is 4.97851040695e-08 + + Energy Rydberg eV + E_KohnSham -34.2806376755 -466.412003461 + E_Harris -34.2806376755 -466.412003461 + E_band -7.89945835686 -107.477644767 + E_one_elec -68.9342414268 -937.898470712 + E_Hartree +35.8778030946 +488.142553809 + E_xc -8.18332966923 -111.339912114 + E_Ewald +7.08422396852 +96.38581188 + E_demet -1.01204310856e-67 -1.37695528981e-66 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19408322183 -2.64063770309 + E_Fermi -0.15900937454 -2.16343352916 + + charge density convergence is achieved + final etot is -466.412003461 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0641 2.00000 + 2 -13.0402 2.00000 + 3 -8.94209 2.00000 + 4 -6.69239 2.00000 + 5 1.16679 0.00000 + 6 4.19805 0.00000 + 7 11.1210 0.00000 + 8 11.3593 0.00000 + + EFERMI = -2.163433529158689 eV + OUT.ABACUS/ final etot is -466.4120034608615 eV + correction force for each atom along direction 1 is -1.49663e-05 + correction force for each atom along direction 2 is 0.000104197 + correction force for each atom along direction 3 is 0.000140429 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.32532307 +0.17149149 -0.053266305 + H1 +0.36169617 -0.054394214 -0.20943578 + H2 -0.68701924 -0.11709728 +0.26270208 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4120034608615 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1787 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1711 1 7.2 1.e+02% + Potential init_pot 0.24049 2 0.12 3.4% + PW_Basis recip2real 0.26199 16 0.016 3.6% + PW_Basis gathers_scatterp 0.10493 16 0.0066 1.5% + Potential v_of_rho 0.93137 13 0.072 13.% + XC_Functional v_xc 0.28535 14 0.020 4.0% + H_Hartree_pw v_hartree 0.60842 13 0.047 8.5% + PW_Basis real2recip 0.59391 38 0.016 8.3% + PW_Basis gatherp_scatters 0.22026 38 0.0058 3.1% + ORB_control set_orb_tables 0.89552 1 0.90 12.% + ORB_gen_tables gen_tables 0.89551 1 0.90 12.% + ORB_table_phi init_Table 0.37222 1 0.37 5.2% + ORB_table_phi cal_ST_Phi12_R 0.36805 126 0.0029 5.1% + ORB_table_beta init_Table_Beta 0.15419 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15291 56 0.0027 2.1% + ORB_table_alpha init_Table_Alpha 0.21076 1 0.21 2.9% + ORB_table_alpha S_PhiAlpha_R 0.20912 66 0.0032 2.9% + LOOP_ions opt_ions 5.8319 1 5.8 81.% + ESolver_KS_LCAO Run 5.2701 1 5.3 73.% + HSolverLCAO solve 3.1026 11 0.28 43.% + HamiltLCAO updateHk 1.5540 11 0.14 22.% + LCAO_Hamilt cal_Hgamma 1.5225 11 0.14 21.% + Gint_interface cal_gint 3.0034 23 0.13 42.% + Gint_Gamma distri_vl 2.5193 6 0.42 35.% + LCAO_Deepks cal_projected_DM 5.6660 13 0.44 79.% + LCAO_gen_fixedH add_v_delta 2.3898 6 0.40 33.% + LCAO_DESCRIPTOR add_v_delta 2.3898 6 0.40 33.% + ElecStateLCAO psiToRho 1.5316 11 0.14 21.% + Charge mix_rho 0.75026 10 0.075 10.% + LOOP_ions force_stress 0.56167 1 0.56 7.8% + Force_Stress_LCAO getForceStress 0.56165 1 0.56 7.8% + Force_LCAO_gamma ftable_gamma 0.36266 1 0.36 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.35540 1 0.36 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:20 2022 + Finish Time : Wed Sep 28 11:03:27 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e19c39df6c3ceed6673deb85b7d41646cceac1c5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123541 ima = 3.65999e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123651346499 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112466295615 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113104019372 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113312483326 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113283495802 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113301781743 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113294854373 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113297337797 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011329669457 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113296621234 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113296609297 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d78f7580e58fcacd0cefcbc75ec1eb335b08956b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.709834086594 16.281905981591 1.480184629716 0 0 0 +H +0.0 +2 +-23.648789407698 17.418489813601 2.605006719589 0 0 0 +-21.054644228971 17.084070870291 1.148530032583 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/conv new file mode 100644 index 0000000000000000000000000000000000000000..7570bc72835420210b53a07f2702493638609ab2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/conv @@ -0,0 +1 @@ +133 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..50dc51226730b3816a74f3579d51dc9d48cc26d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746828985 0.01251081338 1.260619884 1.354294874 1.468320057 0.007969903333 0.01910776029 0.03896457313 +-1.086903677e-19 0.001018539434 0.002372448168 0.0117831226 0.04200384701 1.081988436e-19 1.547291857e-06 4.842371445e-06 +0.001697541613 0.005772280992 + +H atom_index 1 n_descriptor 18 +1.226518205 0.03479519955 0.09985289564 0.1402273913 0.3147943283 0.02077219946 0.02705920973 0.03801545201 +-1.83186036e-18 3.731847699e-05 0.09413476336 0.1144089835 0.1201766678 3.873613805e-20 5.132276913e-06 0.0133092419 +0.02488477209 0.02971408713 + +H atom_index 2 n_descriptor 18 +1.214889954 0.03519315616 0.09617997633 0.1352291051 0.310762961 0.02024826697 0.02638161737 0.03846669764 +-3.350963542e-17 3.636945347e-05 0.09104502899 0.1140965229 0.1158066814 8.881032146e-18 5.573894109e-06 0.01355219992 +0.02442157221 0.02913671415 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..541b06f0a74b53b7c84976f18ab97693b2895baf Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:20 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0738818 SEC) : SETUP UNITCELL + DONE(0.074681 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0905679 SEC) : INIT PLANEWAVE + DONE(0.131817 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374942 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651962e+02 0.000000e+00 2.138e-01 5.480e-01 + GE2 -4.664081e+02 -1.211974e+00 9.855e-02 5.276e-01 + GE3 -4.664131e+02 -4.938971e-03 6.345e-02 5.914e-01 + GE4 -4.664124e+02 7.223914e-04 2.037e-03 4.671e-01 + GE5 -4.664118e+02 6.009095e-04 9.074e-04 4.665e-01 + GE6 -4.664121e+02 -3.176156e-04 1.921e-04 4.610e-01 + GE7 -4.664120e+02 1.149743e-04 3.328e-05 4.446e-01 + GE8 -4.664120e+02 -5.400796e-05 1.517e-05 4.430e-01 + GE9 -4.664120e+02 1.676603e-05 1.893e-06 4.447e-01 + GE10 -4.664120e+02 -2.897066e-06 2.286e-07 4.441e-01 + GE11 -4.664120e+02 -3.545557e-07 4.979e-08 3.790e-01 +E_delta_band = -6.89895792e-02 Ry = -9.38651380e-01 eV +E_delta_NN= -1.94083222e-01 Ry = -2.64063770e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1787 11 0.65 1e+02 % + Run_lcao lcao_line 7.1711 1 7.2 1e+02 % + Potential init_pot 0.24049 2 0.12 3.4 % + PW_Basis recip2real 0.26199 16 0.016 3.6 % + PW_Basis gathers_scatterp 0.10493 16 0.0066 1.5 % + Potential v_of_rho 0.93137 13 0.072 13 % + XC_Functional v_xc 0.28535 14 0.02 4 % + H_Hartree_pw v_hartree 0.60842 13 0.047 8.5 % + PW_Basis real2recip 0.59391 38 0.016 8.3 % + PW_Basis gatherp_scatters 0.22026 38 0.0058 3.1 % + ORB_control set_orb_tables 0.89552 1 0.9 12 % + ORB_gen_tables gen_tables 0.89551 1 0.9 12 % + ORB_table_phi init_Table 0.37222 1 0.37 5.2 % + ORB_table_phi cal_ST_Phi12_R 0.36805 126 0.0029 5.1 % + ORB_table_beta init_Table_Beta 0.15419 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15291 56 0.0027 2.1 % + ORB_table_alpha init_Table_Alpha 0.21076 1 0.21 2.9 % + ORB_table_alpha S_PhiAlpha_R 0.20912 66 0.0032 2.9 % + LOOP_ions opt_ions 5.8319 1 5.8 81 % + ESolver_KS_LCAO Run 5.2701 1 5.3 73 % + HSolverLCAO solve 3.1026 11 0.28 43 % + HamiltLCAO updateHk 1.554 11 0.14 22 % + LCAO_Hamilt cal_Hgamma 1.5225 11 0.14 21 % + Gint_interface cal_gint 3.0034 23 0.13 42 % + Gint_Gamma distri_vl 2.5193 6 0.42 35 % + LCAO_Deepks cal_projected_DM 5.666 13 0.44 79 % + LCAO_gen_fixedH add_v_delta 2.3898 6 0.4 33 % + LCAO_DESCRIPTOR add_v_delta 2.3898 6 0.4 33 % + ElecStateLCAO psiToRho 1.5316 11 0.14 21 % + Charge mix_rho 0.75026 10 0.075 10 % + LOOP_ions force_stress 0.56167 1 0.56 7.8 % + Force_Stress_LCAO getForceStress 0.56165 1 0.56 7.8 % + Force_LCAO_gamma ftable_gamma 0.36266 1 0.36 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.3554 1 0.36 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:20 2022 + FINISH Time : Wed Sep 28 11:03:27 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/133/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3573d8ea21fc06d207fed20827f20fafc187923a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.202378 0.572659 0.0463012 +H 0.179739 0.552962 0.988911 +H 0.264809 0.578482 0.0341715 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..fbef7f1452d2c401478d43810acd35b61ff0ab90 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5489 2 + 2 -13.0889 2 + 3 -9.2789 2 + 4 -6.80195 2 + 5 1.45353 0 + 6 4.70281 0 + 7 11.0213 0 + 8 11.284 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..6210af28b0e4a08c875db738d82a9a79a1e6bc9a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:02 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.66657289312 16.0344531395 1.29643310489 0 0 0 0 + tauc_H1 5.03269104073 15.4829394239 27.6895058215 0 0 0 0 + tauc_H2 7.41466491995 16.1974993052 0.956803222551 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0859482841846 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0972793300665 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115513911326 (SEC) + + DONE : INIT CHARGE Time : 0.163838624567 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445767 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 100 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000845 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00194 + + Density error is 0.217369810936 + + Energy Rydberg eV + E_KohnSham -34.1863593817 -465.129281467 + E_Harris -34.3839214698 -467.817251573 + E_Fermi -0.419129619488 -5.70255102561 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00130671802559 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00153663609051 + + Density error is 0.0976071318566 + + Energy Rydberg eV + E_KohnSham -34.2785101028 -466.383056349 + E_Harris -34.2852205373 -466.474356494 + E_Fermi -0.225560514732 -3.06890824417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00125356424345 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00140126447812 + + Density error is 0.0625013840375 + + Energy Rydberg eV + E_KohnSham -34.2788797566 -466.388085747 + E_Harris -34.2832074559 -466.446967117 + E_Fermi -0.212718505483 -2.89418374461 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00118588586476 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116316144805 + + Density error is 0.00202083685408 + + Energy Rydberg eV + E_KohnSham -34.2789019873 -466.388388211 + E_Harris -34.2789039134 -466.388414417 + E_Fermi -0.176737905689 -2.40464256995 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0011913148043 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116101719486 + + Density error is 0.000999267671866 + + Energy Rydberg eV + E_KohnSham -34.278820205 -466.387275506 + E_Harris -34.278822829 -466.387311206 + E_Fermi -0.17573214433 -2.39095848465 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00118937877381 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011586643517 + + Density error is 9.91989258326e-05 + + Energy Rydberg eV + E_KohnSham -34.2788736873 -466.38800317 + E_Harris -34.2788736957 -466.388003284 + E_Fermi -0.175915623058 -2.39345484081 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00118911737151 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115819174625 + + Density error is 5.03303965339e-05 + + Energy Rydberg eV + E_KohnSham -34.2788570934 -466.387777398 + E_Harris -34.2788571075 -466.38777759 + E_Fermi -0.17578526295 -2.39168120054 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00118907419555 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115828483355 + + Density error is 1.52060996842e-05 + + Energy Rydberg eV + E_KohnSham -34.2788595232 -466.387810458 + E_Harris -34.2788595243 -466.387810471 + E_Fermi -0.175849643423 -2.39255714183 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00118909462033 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115825827385 + + Density error is 2.38012306079e-06 + + Energy Rydberg eV + E_KohnSham -34.2788579711 -466.38778934 + E_Harris -34.2788579711 -466.38778934 + E_Fermi -0.175834682063 -2.39235358208 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00118909658402 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115825253415 + + Density error is 3.0564305902e-07 + + Energy Rydberg eV + E_KohnSham -34.2788581853 -466.387792254 + E_Harris -34.2788581853 -466.387792254 + E_Fermi -0.175832521781 -2.39232418993 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00118909727487 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115825248715 + + Density error is 9.38883935479e-08 + + Energy Rydberg eV + E_KohnSham -34.2788582248 -466.387792792 + E_Harris -34.2788582248 -466.387792792 + E_band -8.04349226976 -109.437326688 + E_one_elec -69.7188633297 -948.573799367 + E_Hartree +36.2364007807 +493.021525629 + E_xc -8.24139511865 -112.129933083 + E_Ewald +7.56842437754 +102.973696417 + E_demet -1.29399642633e-88 -1.76057245897e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195635880935 -2.66176271397 + E_Fermi -0.175832365427 -2.39232206263 + + charge density convergence is achieved + final etot is -466.387792792 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5489 2.00000 + 2 -13.0889 2.00000 + 3 -9.27890 2.00000 + 4 -6.80195 2.00000 + 5 1.45353 0.00000 + 6 4.70281 0.00000 + 7 11.0213 0.00000 + 8 11.2840 0.00000 + + EFERMI = -2.392322062630267 eV + OUT.ABACUS/ final etot is -466.3877927917999 eV + correction force for each atom along direction 1 is 7.63846e-05 + correction force for each atom along direction 2 is -0.000176614 + correction force for each atom along direction 3 is -3.74390e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.1051736 +0.036791404 +0.73721044 + H1 -0.57344814 -0.27656784 -0.68754869 + H2 +1.6786218 +0.23977644 -0.049661748 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3877927917999 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5101 11 0.59 1.0e+02% + Run_lcao lcao_line 6.5004 1 6.5 1.e+02% + Potential init_pot 0.28875 2 0.14 4.4% + PW_Basis recip2real 0.26627 16 0.017 4.1% + PW_Basis gathers_scatterp 0.11414 16 0.0071 1.8% + Potential v_of_rho 0.86770 13 0.067 13.% + XC_Functional v_xc 0.23450 14 0.017 3.6% + H_Hartree_pw v_hartree 0.59482 13 0.046 9.1% + PW_Basis real2recip 0.55974 38 0.015 8.6% + PW_Basis gatherp_scatters 0.21883 38 0.0058 3.4% + ORB_control set_orb_tables 1.1163 1 1.1 17.% + ORB_gen_tables gen_tables 1.1163 1 1.1 17.% + ORB_table_phi init_Table 0.48876 1 0.49 7.5% + ORB_table_phi cal_ST_Phi12_R 0.48377 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.19102 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18955 56 0.0034 2.9% + ORB_table_alpha init_Table_Alpha 0.25812 1 0.26 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25619 66 0.0039 3.9% + LOOP_ions opt_ions 4.8601 1 4.9 75.% + ESolver_KS_LCAO Run 4.3059 1 4.3 66.% + HSolverLCAO solve 2.3516 11 0.21 36.% + HamiltLCAO updateHk 1.2244 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.1865 11 0.11 18.% + Gint_interface cal_gint 2.2243 23 0.097 34.% + Gint_Gamma distri_vl 2.0786 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.6911 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9462 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9462 6 0.32 30.% + ElecStateLCAO psiToRho 1.1105 11 0.10 17.% + Charge mix_rho 0.65146 10 0.065 10.% + LOOP_ions force_stress 0.55403 1 0.55 8.5% + Force_Stress_LCAO getForceStress 0.55400 1 0.55 8.5% + Force_LCAO_gamma ftable_gamma 0.33989 1 0.34 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.33325 1 0.33 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:02 2022 + Finish Time : Wed Sep 28 11:12:08 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2961a4c77dc2351f04a9f1ab3f1602ff11717c65 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123851 ima = 3.67211e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122814197999 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011167485768 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112177752688 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112476662956 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112399172798 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011244109763 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112438322392 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112441568722 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112440902749 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112440797585 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112440785352 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/STRU new file mode 100644 index 0000000000000000000000000000000000000000..aab7e95a7cc404c827010a1fe6c6e42849afb25d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.333427106873 16.034453139523 1.296433104909 0 0 0 +H +0.0 +2 +-22.967308959262 15.482939423933 -0.310494178527 0 0 0 +-20.585335080023 16.197499305192 0.956803222534 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/conv new file mode 100644 index 0000000000000000000000000000000000000000..ab6f860eaba64f2cf3631def5ab5836b65271f03 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/conv @@ -0,0 +1 @@ +134 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e4b5b1c35977d055444b36fc1ebd32b2dfccf8ab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751303239 0.01285004751 1.288883236 1.372270916 1.47045014 0.009050914744 0.01820087977 0.03907702788 +3.31183767e-19 0.001091100849 0.002839836308 0.01330316115 0.04818483564 -1.132218353e-18 2.647963959e-06 7.075995067e-06 +0.001619835957 0.006068793711 + +H atom_index 1 n_descriptor 18 +1.262992276 0.03406032586 0.1143168568 0.1557308605 0.3241036722 0.02340313977 0.02901157471 0.03721750728 +-5.527940111e-19 5.316648011e-05 0.1065442036 0.1161772622 0.1338171944 1.658744757e-17 3.09239637e-06 0.01326122911 +0.027499917 0.03134336411 + +H atom_index 2 n_descriptor 18 +1.282770118 0.03341486336 0.1217481255 0.1655302408 0.3300481319 0.02434700447 0.03015240992 0.03680869625 +3.872983395e-18 5.510680117e-05 0.108414757 0.1199955353 0.1421715248 -2.045456221e-18 1.96363784e-06 0.01340650266 +0.02816762996 0.03214809152 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a67a9ab7bee5ad5f554d7adf801d4deb3061cb5c Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..065e4fc9c4f652286628d19cb39a82bc97528389 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..4f5ca3a0ef3993055a60d149453adeefe8efb5b5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..aec7968c92c27d1d432fcdb601409267a6b07a70 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..4ef651eb593bc16ff4a2e5da999c076c7911b52f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:02 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0859735 SEC) : SETUP UNITCELL + DONE(0.0973022 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115533 SEC) : INIT PLANEWAVE + DONE(0.163967 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44583 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651293e+02 0.000000e+00 2.174e-01 5.132e-01 + GE2 -4.663831e+02 -1.253775e+00 9.761e-02 4.326e-01 + GE3 -4.663881e+02 -5.029398e-03 6.250e-02 4.901e-01 + GE4 -4.663884e+02 -3.024639e-04 2.021e-03 3.758e-01 + GE5 -4.663873e+02 1.112705e-03 9.993e-04 3.745e-01 + GE6 -4.663880e+02 -7.276643e-04 9.920e-05 3.511e-01 + GE7 -4.663878e+02 2.257722e-04 5.033e-05 3.586e-01 + GE8 -4.663878e+02 -3.305992e-05 1.521e-05 3.541e-01 + GE9 -4.663878e+02 2.111771e-05 2.380e-06 3.485e-01 + GE10 -4.663878e+02 -2.914024e-06 3.056e-07 3.515e-01 + GE11 -4.663878e+02 -5.377951e-07 9.389e-08 2.940e-01 +E_delta_band = -7.22109462e-02 Ry = -9.82480327e-01 eV +E_delta_NN= -1.95635881e-01 Ry = -2.66176271e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5101 11 0.59 1e+02 % + Run_lcao lcao_line 6.5004 1 6.5 1e+02 % + Potential init_pot 0.28875 2 0.14 4.4 % + PW_Basis recip2real 0.26627 16 0.017 4.1 % + PW_Basis gathers_scatterp 0.11414 16 0.0071 1.8 % + Potential v_of_rho 0.8677 13 0.067 13 % + XC_Functional v_xc 0.2345 14 0.017 3.6 % + H_Hartree_pw v_hartree 0.59482 13 0.046 9.1 % + PW_Basis real2recip 0.55974 38 0.015 8.6 % + PW_Basis gatherp_scatters 0.21883 38 0.0058 3.4 % + ORB_control set_orb_tables 1.1163 1 1.1 17 % + ORB_gen_tables gen_tables 1.1163 1 1.1 17 % + ORB_table_phi init_Table 0.48876 1 0.49 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.48377 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.19102 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18955 56 0.0034 2.9 % + ORB_table_alpha init_Table_Alpha 0.25812 1 0.26 4 % + ORB_table_alpha S_PhiAlpha_R 0.25619 66 0.0039 3.9 % + LOOP_ions opt_ions 4.8601 1 4.9 75 % + ESolver_KS_LCAO Run 4.3059 1 4.3 66 % + HSolverLCAO solve 2.3516 11 0.21 36 % + HamiltLCAO updateHk 1.2244 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.1865 11 0.11 18 % + Gint_interface cal_gint 2.2243 23 0.097 34 % + Gint_Gamma distri_vl 2.0786 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.6911 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9462 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9462 6 0.32 30 % + ElecStateLCAO psiToRho 1.1105 11 0.1 17 % + Charge mix_rho 0.65146 10 0.065 10 % + LOOP_ions force_stress 0.55403 1 0.55 8.5 % + Force_Stress_LCAO getForceStress 0.554 1 0.55 8.5 % + Force_LCAO_gamma ftable_gamma 0.33989 1 0.34 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.33325 1 0.33 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:02 2022 + FINISH Time : Wed Sep 28 11:12:08 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/134/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..08dcb25274b0a3d07e1a08b4d5698777d5fac567 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.22292 0.576868 0.0375759 +H 0.180496 0.530417 0.0575906 +H 0.279115 0.569423 0.0718097 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..337309950a67fae9d3e4969a730a6b49ffec3004 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1052 2 + 2 -13.1384 2 + 3 -8.90144 2 + 4 -6.70097 2 + 5 1.22233 0 + 6 4.29417 0 + 7 11.1083 0 + 8 11.3419 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9db8724e1eecf67ebc0b404668390bb2bfa45524 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:11 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.24176270687 16.1523040927 1.05212505963 0 0 0 0 + tauc_H1 5.05389995843 14.8516866458 1.61253750671 0 0 0 0 + tauc_H2 7.81522456845 15.9438425427 2.01067292078 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.100663775632 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101024958502 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119037461222 (SEC) + + DONE : INIT CHARGE Time : 0.162155389961 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.444346 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000612 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00156 + + Density error is 0.214761946813 + + Energy Rydberg eV + E_KohnSham -34.1906820109 -465.188093854 + E_Harris -34.3815305637 -467.784721627 + E_Fermi -0.39789700367 -5.41366646703 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000939429040085 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132584156728 + + Density error is 0.0985116861631 + + Energy Rydberg eV + E_KohnSham -34.2803974302 -466.408734755 + E_Harris -34.2872193969 -466.501552374 + E_Fermi -0.206535492855 -2.81005954206 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000907810056189 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122809767239 + + Density error is 0.0633546452467 + + Energy Rydberg eV + E_KohnSham -34.2807501708 -466.413534038 + E_Harris -34.2851387267 -466.473243404 + E_Fermi -0.196982204611 -2.68008038731 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000874630205636 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104746941615 + + Density error is 0.00206036337598 + + Energy Rydberg eV + E_KohnSham -34.2807122863 -466.413018592 + E_Harris -34.2807156625 -466.413064527 + E_Fermi -0.161754275712 -2.20077982554 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000875463898007 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104452321849 + + Density error is 0.000912690806451 + + Energy Rydberg eV + E_KohnSham -34.2806626353 -466.412343055 + E_Harris -34.280663185 -466.412350535 + E_Fermi -0.161202891917 -2.19327786415 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000874927410152 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104218814241 + + Density error is 0.000194528737797 + + Energy Rydberg eV + E_KohnSham -34.2806899208 -466.412714293 + E_Harris -34.2806899629 -466.412714867 + E_Fermi -0.161031354685 -2.19094398038 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0008751993435 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104208465848 + + Density error is 3.54158346719e-05 + + Energy Rydberg eV + E_KohnSham -34.2806798376 -466.412577105 + E_Harris -34.2806798436 -466.412577187 + E_Fermi -0.160922922636 -2.18946868666 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000875130579103 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010420590771 + + Density error is 1.64144678331e-05 + + Energy Rydberg eV + E_KohnSham -34.2806842133 -466.412636639 + E_Harris -34.2806842144 -466.412636655 + E_Fermi -0.16095735026 -2.18993709852 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000875136283783 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104203087391 + + Density error is 1.98673254732e-06 + + Energy Rydberg eV + E_KohnSham -34.280682879 -466.412618486 + E_Harris -34.280682879 -466.412618486 + E_Fermi -0.160940601298 -2.18970921719 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000875135895251 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010420262314 + + Density error is 3.79226044851e-07 + + Energy Rydberg eV + E_KohnSham -34.2806831195 -466.412621758 + E_Harris -34.2806831195 -466.412621758 + E_Fermi -0.160938762167 -2.18968419453 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000875136705751 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104202659477 + + Density error is 1.25218554666e-07 + + Energy Rydberg eV + E_KohnSham -34.2806831403 -466.412622041 + E_Harris -34.2806831403 -466.412622041 + E_Fermi -0.160938608743 -2.1896821071 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000875136920012 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104202645873 + + Density error is 1.00467582061e-08 + + Energy Rydberg eV + E_KohnSham -34.2806831437 -466.412622087 + E_Harris -34.2806831437 -466.412622087 + E_band -7.91521533238 -107.692029417 + E_one_elec -69.0555166327 -939.548504538 + E_Hartree +35.9367771917 +488.944937564 + E_xc -8.19274882912 -111.468066359 + E_Ewald +7.15565838222 +97.3577269396 + E_demet -5.89875376665e-71 -8.02566623255e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194273328195 -2.64322423288 + E_Fermi -0.160938491069 -2.18968050607 + + charge density convergence is achieved + final etot is -466.412622087 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1052 2.00000 + 2 -13.1384 2.00000 + 3 -8.90144 2.00000 + 4 -6.70097 2.00000 + 5 1.22233 0.00000 + 6 4.29417 0.00000 + 7 11.1083 0.00000 + 8 11.3419 0.00000 + + EFERMI = -2.189680506067222 eV + OUT.ABACUS/ final etot is -466.4126220866544 eV + correction force for each atom along direction 1 is 4.14705e-05 + correction force for each atom along direction 2 is 1.72133e-05 + correction force for each atom along direction 3 is 0.000166543 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.088878173 +0.14190115 -0.072923061 + H1 +0.34588395 +0.049738849 +0.12228798 + H2 -0.43476212 -0.19164000 -0.049364922 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4126220866544 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6280 11 0.69 1.0e+02% + Run_lcao lcao_line 7.6181 1 7.6 1.e+02% + Potential init_pot 0.28347 2 0.14 3.7% + PW_Basis recip2real 0.28568 17 0.017 3.7% + PW_Basis gathers_scatterp 0.13079 17 0.0077 1.7% + Potential v_of_rho 1.0401 14 0.074 14.% + XC_Functional v_xc 0.31747 15 0.021 4.2% + H_Hartree_pw v_hartree 0.67740 14 0.048 8.9% + PW_Basis real2recip 0.73649 41 0.018 9.7% + PW_Basis gatherp_scatters 0.28259 41 0.0069 3.7% + ORB_control set_orb_tables 1.0923 1 1.1 14.% + ORB_gen_tables gen_tables 1.0923 1 1.1 14.% + ORB_table_phi init_Table 0.47422 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46902 126 0.0037 6.1% + ORB_table_beta init_Table_Beta 0.18473 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18320 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24676 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24480 66 0.0037 3.2% + LOOP_ions opt_ions 5.9979 1 6.0 79.% + ESolver_KS_LCAO Run 5.4177 1 5.4 71.% + HSolverLCAO solve 2.7841 12 0.23 36.% + HamiltLCAO updateHk 1.4374 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4078 12 0.12 18.% + Gint_interface cal_gint 2.6076 25 0.10 34.% + Gint_Gamma distri_vl 2.8200 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.8329 14 0.42 76.% + LCAO_gen_fixedH add_v_delta 2.6720 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.6720 6 0.45 35.% + ElecStateLCAO psiToRho 1.3274 12 0.11 17.% + Charge mix_rho 0.98717 11 0.090 13.% + LOOP_ions force_stress 0.58003 1 0.58 7.6% + Force_Stress_LCAO getForceStress 0.58000 1 0.58 7.6% + Force_LCAO_gamma ftable_gamma 0.36657 1 0.37 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.35849 1 0.36 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:11 2022 + Finish Time : Wed Sep 28 11:08:19 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..41fed4fe466d4abdc0a15e1819ce6c997f1f5e6c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123538 ima = 3.66732e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123684368151 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112546080404 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113145183151 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113363723826 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113328677839 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113350186913 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113342478417 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113345158341 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113344457434 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113344393385 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113344378476 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113344372475 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/STRU new file mode 100644 index 0000000000000000000000000000000000000000..298b6e01af323dab5f8b45511ad3df76be2f9e39 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.758237293103 16.152304092687 1.052125059641 0 0 0 +H +0.0 +2 +-22.946100041590 14.851686645834 1.612537506701 0 0 0 +-20.184775431523 15.943842542712 2.010672920798 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/conv new file mode 100644 index 0000000000000000000000000000000000000000..5fd9bd3ed46a560051d6abf6011f3c2b5d3c17e4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/conv @@ -0,0 +1 @@ +135 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e6f9490405624e41ee4ba28ec5a7214e9c2e0f50 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745851736 0.01254381214 1.266373845 1.35986244 1.468505478 0.00785916398 0.01951031626 0.03892952366 +-5.964511332e-19 0.001060628881 0.002369515264 0.01194116909 0.0422110982 -5.276237712e-19 1.533084306e-06 4.818361509e-06 +0.001726192941 0.005735600074 + +H atom_index 1 n_descriptor 18 +1.23018463 0.03456293627 0.1012511995 0.1420330721 0.3163079989 0.02093210743 0.02730028953 0.03775941295 +-3.011319691e-17 3.737469006e-05 0.09563840153 0.1144170342 0.1217895489 -5.841233063e-18 5.005385676e-06 0.0131960702 +0.02511382596 0.02991825793 + +H atom_index 2 n_descriptor 18 +1.225592678 0.03472261308 0.0997673082 0.1400178093 0.3147520856 0.02072668763 0.02703291465 0.03792993553 +2.303856153e-17 3.700051074e-05 0.09441351904 0.1143012775 0.1200334603 7.472288371e-19 5.190920037e-06 0.01327661981 +0.02493380859 0.02969586372 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f7bfbaeeb33887ba33e485922ce3c9b3cd40f3f0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:11 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.100688 SEC) : SETUP UNITCELL + DONE(0.101041 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119057 SEC) : INIT PLANEWAVE + DONE(0.162289 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444414 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651881e+02 0.000000e+00 2.148e-01 5.485e-01 + GE2 -4.664087e+02 -1.220641e+00 9.851e-02 5.102e-01 + GE3 -4.664135e+02 -4.799283e-03 6.335e-02 5.827e-01 + GE4 -4.664130e+02 5.154458e-04 2.060e-03 4.383e-01 + GE5 -4.664123e+02 6.755366e-04 9.127e-04 4.368e-01 + GE6 -4.664127e+02 -3.712383e-04 1.945e-04 4.304e-01 + GE7 -4.664126e+02 1.371881e-04 3.542e-05 4.207e-01 + GE8 -4.664126e+02 -5.953356e-05 1.641e-05 4.126e-01 + GE9 -4.664126e+02 1.815333e-05 1.987e-06 4.109e-01 + GE10 -4.664126e+02 -3.272354e-06 3.792e-07 4.115e-01 + GE11 -4.664126e+02 -2.830764e-07 1.252e-07 4.122e-01 + GE12 -4.664126e+02 -4.564274e-08 1.005e-08 3.406e-01 +E_delta_band = -6.94200724e-02 Ry = -9.44508540e-01 eV +E_delta_NN= -1.94273328e-01 Ry = -2.64322423e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.628 11 0.69 1e+02 % + Run_lcao lcao_line 7.6181 1 7.6 1e+02 % + Potential init_pot 0.28347 2 0.14 3.7 % + PW_Basis recip2real 0.28568 17 0.017 3.7 % + PW_Basis gathers_scatterp 0.13079 17 0.0077 1.7 % + Potential v_of_rho 1.0401 14 0.074 14 % + XC_Functional v_xc 0.31747 15 0.021 4.2 % + H_Hartree_pw v_hartree 0.6774 14 0.048 8.9 % + PW_Basis real2recip 0.73649 41 0.018 9.7 % + PW_Basis gatherp_scatters 0.28259 41 0.0069 3.7 % + ORB_control set_orb_tables 1.0923 1 1.1 14 % + ORB_gen_tables gen_tables 1.0923 1 1.1 14 % + ORB_table_phi init_Table 0.47422 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.46902 126 0.0037 6.1 % + ORB_table_beta init_Table_Beta 0.18473 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.1832 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24676 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.2448 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9979 1 6 79 % + ESolver_KS_LCAO Run 5.4177 1 5.4 71 % + HSolverLCAO solve 2.7841 12 0.23 36 % + HamiltLCAO updateHk 1.4374 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.4078 12 0.12 18 % + Gint_interface cal_gint 2.6076 25 0.1 34 % + Gint_Gamma distri_vl 2.82 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.8329 14 0.42 76 % + LCAO_gen_fixedH add_v_delta 2.672 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.672 6 0.45 35 % + ElecStateLCAO psiToRho 1.3274 12 0.11 17 % + Charge mix_rho 0.98717 11 0.09 13 % + LOOP_ions force_stress 0.58003 1 0.58 7.6 % + Force_Stress_LCAO getForceStress 0.58 1 0.58 7.6 % + Force_LCAO_gamma ftable_gamma 0.36657 1 0.37 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.35849 1 0.36 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:11 2022 + FINISH Time : Wed Sep 28 11:08:19 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/135/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3ff2fb36b756c1ebd7f0aa51c6659e795a66f8cc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.221165 0.585827 0.0419392 +H 0.195715 0.635633 0.0720362 +H 0.258311 0.557296 0.0881791 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0542a163909ce74488c68389b3732a18d02fb67d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4509 2 + 2 -13.1333 2 + 3 -9.17205 2 + 4 -6.77978 2 + 5 1.40344 0 + 6 4.63113 0 + 7 11.0383 0 + 8 11.2891 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3ae2b9078daee2d6ae6ee49765a69644f5549929 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:20 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.19260732781 16.4031476565 1.17429721965 0 0 0 0 + tauc_H1 5.48001458967 17.7977315458 2.01701289789 0 0 0 0 + tauc_H2 7.23271864202 15.6042882651 2.46901424538 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105630611648 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105991149182 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124049892686 (SEC) + + DONE : INIT CHARGE Time : 0.167885255014 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450965 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000837 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118 + + Density error is 0.216138252023 + + Energy Rydberg eV + E_KohnSham -34.1888862186 -465.163660846 + E_Harris -34.3834757596 -467.811187375 + E_Fermi -0.414118878694 -5.63437639961 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108554870563 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130675783408 + + Density error is 0.0975752955707 + + Energy Rydberg eV + E_KohnSham -34.2789005741 -466.388368983 + E_Harris -34.2855633342 -466.479020485 + E_Fermi -0.222699856635 -3.02998699402 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103261329511 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123571777596 + + Density error is 0.0623954635391 + + Energy Rydberg eV + E_KohnSham -34.2791282172 -466.391466227 + E_Harris -34.2834140455 -466.449777912 + E_Fermi -0.209538839706 -2.85092217231 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000952578090449 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112581198341 + + Density error is 0.00201360314433 + + Energy Rydberg eV + E_KohnSham -34.2791504567 -466.391768811 + E_Harris -34.2791521585 -466.391791964 + E_Fermi -0.173827319535 -2.36504201374 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000953218606964 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112646233695 + + Density error is 0.000878257167681 + + Energy Rydberg eV + E_KohnSham -34.2790822157 -466.390840344 + E_Harris -34.2790840514 -466.39086532 + E_Fermi -0.172821026225 -2.35135069087 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000951977934442 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112494460976 + + Density error is 0.00012173782151 + + Energy Rydberg eV + E_KohnSham -34.2791286631 -466.391472293 + E_Harris -34.2791286922 -466.391472689 + E_Fermi -0.172995474278 -2.3537241784 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000951996741438 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112493823026 + + Density error is 4.43604445986e-05 + + Energy Rydberg eV + E_KohnSham -34.2791127738 -466.391256109 + E_Harris -34.279112785 -466.391256261 + E_Fermi -0.172855023725 -2.35181325059 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000951937989041 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112488153507 + + Density error is 1.29500094689e-05 + + Energy Rydberg eV + E_KohnSham -34.2791163883 -466.391305286 + E_Harris -34.279116389 -466.391305295 + E_Fermi -0.17290663309 -2.35251543203 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000951930223693 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112486745496 + + Density error is 1.59750282101e-06 + + Energy Rydberg eV + E_KohnSham -34.2791149833 -466.39128617 + E_Harris -34.2791149833 -466.391286171 + E_Fermi -0.172892473068 -2.35232277504 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000951932598616 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112486921923 + + Density error is 1.37736562417e-07 + + Energy Rydberg eV + E_KohnSham -34.2791151446 -466.391288365 + E_Harris -34.2791151446 -466.391288365 + E_Fermi -0.172891103848 -2.35230414584 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000951932983219 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112486965097 + + Density error is 5.70426889291e-08 + + Energy Rydberg eV + E_KohnSham -34.2791151758 -466.39128879 + E_Harris -34.2791151758 -466.39128879 + E_band -8.01664171477 -109.072006145 + E_one_elec -69.5872203997 -946.782705418 + E_Hartree +36.1778104995 +492.224363958 + E_xc -8.23200409563 -112.00216166 + E_Ewald +7.4860186848 +101.852509448 + E_demet -2.09122379464e-85 -2.84525594003e-84 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195382215071 -2.65831141283 + E_Fermi -0.172891145976 -2.35230471902 + + charge density convergence is achieved + final etot is -466.39128879 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4509 2.00000 + 2 -13.1333 2.00000 + 3 -9.17205 2.00000 + 4 -6.77978 2.00000 + 5 1.40344 0.00000 + 6 4.63113 0.00000 + 7 11.0383 0.00000 + 8 11.2891 0.00000 + + EFERMI = -2.352304719016584 eV + OUT.ABACUS/ final etot is -466.3912887896499 eV + correction force for each atom along direction 1 is -7.43512e-05 + correction force for each atom along direction 2 is 2.48048e-05 + correction force for each atom along direction 3 is 7.83653e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.79357909 -1.4769122 -0.77132044 + H1 -0.83241599 +1.5569524 +0.83188688 + H2 +0.038836899 -0.080040132 -0.060566436 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3912887896499 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4063 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3960 1 7.4 1.e+02% + Potential init_pot 0.28511 2 0.14 3.8% + PW_Basis recip2real 0.28471 16 0.018 3.8% + PW_Basis gathers_scatterp 0.12645 16 0.0079 1.7% + Potential v_of_rho 1.0200 13 0.078 14.% + XC_Functional v_xc 0.30073 14 0.021 4.1% + H_Hartree_pw v_hartree 0.67557 13 0.052 9.1% + PW_Basis real2recip 0.69985 38 0.018 9.4% + PW_Basis gatherp_scatters 0.26574 38 0.0070 3.6% + ORB_control set_orb_tables 1.1004 1 1.1 15.% + ORB_gen_tables gen_tables 1.1004 1 1.1 15.% + ORB_table_phi init_Table 0.47583 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47065 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18671 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18518 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24822 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24626 66 0.0037 3.3% + LOOP_ions opt_ions 5.7685 1 5.8 78.% + ESolver_KS_LCAO Run 5.1666 1 5.2 70.% + HSolverLCAO solve 2.6979 11 0.25 36.% + HamiltLCAO updateHk 1.3972 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.3696 11 0.12 18.% + Gint_interface cal_gint 2.5520 23 0.11 34.% + Gint_Gamma distri_vl 2.4873 6 0.41 34.% + LCAO_Deepks cal_projected_DM 5.5988 13 0.43 76.% + LCAO_gen_fixedH add_v_delta 2.3396 6 0.39 32.% + LCAO_DESCRIPTOR add_v_delta 2.3396 6 0.39 32.% + ElecStateLCAO psiToRho 1.2844 11 0.12 17.% + Charge mix_rho 0.90261 10 0.090 12.% + LOOP_ions force_stress 0.60171 1 0.60 8.1% + Force_Stress_LCAO getForceStress 0.60168 1 0.60 8.1% + Force_LCAO_gamma ftable_gamma 0.38239 1 0.38 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.37404 1 0.37 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:20 2022 + Finish Time : Wed Sep 28 11:04:27 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e4ad100414e5d471e7f378bb1d5a34a515b9746f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123925 ima = 3.67754e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012287258189 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111968761923 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011243145062 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112697664208 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112633134683 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112670031738 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112664073444 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011266710661 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112666619681 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112666544159 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112666540839 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/STRU new file mode 100644 index 0000000000000000000000000000000000000000..cc5c19d2540de25b6bf3206d5077f83159e9fb44 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.807392672177 16.403147656546 1.174297219677 0 0 0 +H +0.0 +2 +-22.519985410335 17.797731545782 2.017012897899 0 0 0 +-20.767281357967 15.604288265067 2.469014245395 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/conv new file mode 100644 index 0000000000000000000000000000000000000000..222ed3ee9c9234f2afe7a93bdfe2783fceaabb39 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/conv @@ -0,0 +1 @@ +136 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9bff25f8c5234e4a8fce451ebe6716ad09fe584f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749806182 0.01277075962 1.283040199 1.372356526 1.470068053 0.008722943478 0.01865404186 0.03904331676 +7.06770712e-18 0.001104988782 0.002717984897 0.01287122292 0.0468708402 1.376482306e-18 2.287328525e-06 6.423035158e-06 +0.001640577135 0.005977722294 + +H atom_index 1 n_descriptor 18 +1.289298235 0.03299424406 0.1233396027 0.1691290507 0.3324659367 0.0242741913 0.0305564535 0.03656548952 +-3.010092718e-17 5.253235993e-05 0.1081889445 0.1209397195 0.1452007767 6.430789355e-18 1.892063786e-06 0.01343759776 +0.02801132178 0.03239136822 + +H atom_index 2 n_descriptor 18 +1.238342467 0.03469442862 0.104837593 0.1445025362 0.3168068173 0.02190077507 0.02761259542 0.03779691205 +4.787522227e-18 4.765520109e-05 0.1000929525 0.114367458 0.1241083944 -1.93528603e-18 4.74892371e-06 0.01333491975 +0.02622682219 0.03023695771 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0eb0dd9c1bd7b91c8c69be5188d22fa5fc51df1e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:20 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105655 SEC) : SETUP UNITCELL + DONE(0.106006 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124071 SEC) : INIT PLANEWAVE + DONE(0.168019 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451033 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651637e+02 0.000000e+00 2.161e-01 5.678e-01 + GE2 -4.663884e+02 -1.224708e+00 9.758e-02 5.254e-01 + GE3 -4.663915e+02 -3.097244e-03 6.240e-02 5.954e-01 + GE4 -4.663918e+02 -3.025844e-04 2.014e-03 4.521e-01 + GE5 -4.663908e+02 9.284671e-04 8.783e-04 4.509e-01 + GE6 -4.663915e+02 -6.319493e-04 1.217e-04 4.357e-01 + GE7 -4.663913e+02 2.161844e-04 4.436e-05 4.355e-01 + GE8 -4.663913e+02 -4.917768e-05 1.295e-05 4.289e-01 + GE9 -4.663913e+02 1.911596e-05 1.598e-06 4.291e-01 + GE10 -4.663913e+02 -2.194321e-06 1.377e-07 4.294e-01 + GE11 -4.663913e+02 -4.248434e-07 5.704e-08 3.538e-01 +E_delta_band = -7.16623503e-02 Ry = -9.75016296e-01 eV +E_delta_NN= -1.95382215e-01 Ry = -2.65831141e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4063 11 0.67 1e+02 % + Run_lcao lcao_line 7.396 1 7.4 1e+02 % + Potential init_pot 0.28511 2 0.14 3.8 % + PW_Basis recip2real 0.28471 16 0.018 3.8 % + PW_Basis gathers_scatterp 0.12645 16 0.0079 1.7 % + Potential v_of_rho 1.02 13 0.078 14 % + XC_Functional v_xc 0.30073 14 0.021 4.1 % + H_Hartree_pw v_hartree 0.67557 13 0.052 9.1 % + PW_Basis real2recip 0.69985 38 0.018 9.4 % + PW_Basis gatherp_scatters 0.26574 38 0.007 3.6 % + ORB_control set_orb_tables 1.1004 1 1.1 15 % + ORB_gen_tables gen_tables 1.1004 1 1.1 15 % + ORB_table_phi init_Table 0.47583 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47065 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18671 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18518 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24822 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24626 66 0.0037 3.3 % + LOOP_ions opt_ions 5.7685 1 5.8 78 % + ESolver_KS_LCAO Run 5.1666 1 5.2 70 % + HSolverLCAO solve 2.6979 11 0.25 36 % + HamiltLCAO updateHk 1.3972 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.3696 11 0.12 18 % + Gint_interface cal_gint 2.552 23 0.11 34 % + Gint_Gamma distri_vl 2.4873 6 0.41 34 % + LCAO_Deepks cal_projected_DM 5.5988 13 0.43 76 % + LCAO_gen_fixedH add_v_delta 2.3396 6 0.39 32 % + LCAO_DESCRIPTOR add_v_delta 2.3396 6 0.39 32 % + ElecStateLCAO psiToRho 1.2844 11 0.12 17 % + Charge mix_rho 0.90261 10 0.09 12 % + LOOP_ions force_stress 0.60171 1 0.6 8.1 % + Force_Stress_LCAO getForceStress 0.60168 1 0.6 8.1 % + Force_LCAO_gamma ftable_gamma 0.38239 1 0.38 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.37404 1 0.37 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:20 2022 + FINISH Time : Wed Sep 28 11:04:27 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/136/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4ffb541ee30833f3f99e6b1a02ca8d50578d0f32 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.21436 0.590678 0.0381235 +H 0.245532 0.648344 0.0310544 +H 0.265187 0.55341 0.0429128 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ae2d8e4f006a96eaf66c82e119251fea58f07f6a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5864 2 + 2 -12.8755 2 + 3 -9.4449 2 + 4 -6.80896 2 + 5 1.37128 0 + 6 4.64294 0 + 7 11.025 0 + 8 11.3017 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..69b76a022701081d0863e6335cadf557f0d69a51 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:58 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.00208491751 16.5389759474 1.06745849339 0 0 0 0 + tauc_H1 6.87490614862 18.1536207313 0.869522756853 0 0 0 0 + tauc_H2 7.42522385541 15.4954892992 1.20155869259 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.104334009727 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.104746964097 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.122989466511 (SEC) + + DONE : INIT CHARGE Time : 0.167783563166 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.442841 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 100 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00146 + + Density error is 0.215205223106 + + Energy Rydberg eV + E_KohnSham -34.1867951138 -465.135209906 + E_Harris -34.3800058611 -467.763976985 + E_Fermi -0.417355971783 -5.67841931058 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00118562695384 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127045297915 + + Density error is 0.0971887465271 + + Energy Rydberg eV + E_KohnSham -34.276129741 -466.350669865 + E_Harris -34.2828639728 -466.442293789 + E_Fermi -0.226325439533 -3.07931558 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00110409533687 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117235632141 + + Density error is 0.0620847695725 + + Energy Rydberg eV + E_KohnSham -34.2763110149 -466.353136223 + E_Harris -34.2806475498 -466.412137807 + E_Fermi -0.212896816749 -2.89660979384 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000974620853974 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101389225193 + + Density error is 0.00199373466249 + + Energy Rydberg eV + E_KohnSham -34.2763348044 -466.353459896 + E_Harris -34.2763366448 -466.353484936 + E_Fermi -0.176910339319 -2.40698864986 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000976291812141 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101456516109 + + Density error is 0.000858483607844 + + Energy Rydberg eV + E_KohnSham -34.276269124 -466.352566267 + E_Harris -34.2762710941 -466.352593072 + E_Fermi -0.175982570506 -2.39436570757 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000974490227748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010127961965 + + Density error is 0.000120765088923 + + Energy Rydberg eV + E_KohnSham -34.2763164819 -466.353210606 + E_Harris -34.2763165198 -466.35321112 + E_Fermi -0.1761503913 -2.39664902661 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000974232220856 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101259794636 + + Density error is 4.10021383513e-05 + + Energy Rydberg eV + E_KohnSham -34.2763003705 -466.352991398 + E_Harris -34.2763003794 -466.35299152 + E_Fermi -0.176023764176 -2.3949261762 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000974215072517 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101262546032 + + Density error is 2.08533110187e-05 + + Energy Rydberg eV + E_KohnSham -34.2763036807 -466.353036436 + E_Harris -34.2763036824 -466.353036459 + E_Fermi -0.176075007208 -2.39562337341 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000974188953244 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101259094032 + + Density error is 1.94073634494e-06 + + Energy Rydberg eV + E_KohnSham -34.2763020839 -466.35301471 + E_Harris -34.2763020839 -466.35301471 + E_Fermi -0.17605095271 -2.39529609519 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000974192275409 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101258993044 + + Density error is 6.63927711305e-07 + + Energy Rydberg eV + E_KohnSham -34.2763023788 -466.353018722 + E_Harris -34.2763023788 -466.353018722 + E_Fermi -0.176050408597 -2.39528869215 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00097419259361 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101258967744 + + Density error is 1.64789134054e-07 + + Energy Rydberg eV + E_KohnSham -34.2763023941 -466.353018931 + E_Harris -34.2763023941 -466.353018931 + E_Fermi -0.176049950398 -2.39528245803 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000974192531204 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101258941644 + + Density error is 1.08959622724e-08 + + Energy Rydberg eV + E_KohnSham -34.276302402 -466.353019038 + E_Harris -34.276302402 -466.353019038 + E_band -8.04307528008 -109.431653252 + E_one_elec -69.6524317553 -947.669951429 + E_Hartree +36.19945243 +492.518817528 + E_xc -8.23542722826 -112.048735769 + E_Ewald +7.53566061895 +102.527922612 + E_demet -6.98003208707e-86 -9.4968208607e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195547464503 -2.6605597467 + E_Fermi -0.176049766176 -2.39527995157 + + charge density convergence is achieved + final etot is -466.353019038 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5864 2.00000 + 2 -12.8755 2.00000 + 3 -9.44490 2.00000 + 4 -6.80896 2.00000 + 5 1.37128 0.00000 + 6 4.64294 0.00000 + 7 11.0250 0.00000 + 8 11.3017 0.00000 + + EFERMI = -2.395279951567800 eV + OUT.ABACUS/ final etot is -466.3530190377945 eV + correction force for each atom along direction 1 is 0.000122515 + correction force for each atom along direction 2 is 6.22238e-05 + correction force for each atom along direction 3 is 0.000104777 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.1521918 +1.5322339 -0.18838402 + H1 -0.43632190 +0.33263125 -0.045508664 + H2 +1.5885137 -1.8648651 +0.23389268 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3530190377945 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4563 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4461 1 7.4 1.e+02% + Potential init_pot 0.27777 2 0.14 3.7% + PW_Basis recip2real 0.27879 17 0.016 3.7% + PW_Basis gathers_scatterp 0.12012 17 0.0071 1.6% + Potential v_of_rho 1.0458 14 0.075 14.% + XC_Functional v_xc 0.32177 15 0.021 4.3% + H_Hartree_pw v_hartree 0.67661 14 0.048 9.1% + PW_Basis real2recip 0.74544 41 0.018 10.% + PW_Basis gatherp_scatters 0.28181 41 0.0069 3.8% + ORB_control set_orb_tables 1.0908 1 1.1 15.% + ORB_gen_tables gen_tables 1.0908 1 1.1 15.% + ORB_table_phi init_Table 0.47261 1 0.47 6.3% + ORB_table_phi cal_ST_Phi12_R 0.46745 126 0.0037 6.3% + ORB_table_beta init_Table_Beta 0.18228 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18074 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24935 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24741 66 0.0037 3.3% + LOOP_ions opt_ions 5.8242 1 5.8 78.% + ESolver_KS_LCAO Run 5.2552 1 5.3 70.% + HSolverLCAO solve 2.6243 12 0.22 35.% + HamiltLCAO updateHk 1.3705 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.3408 12 0.11 18.% + Gint_interface cal_gint 2.4296 25 0.097 33.% + Gint_Gamma distri_vl 2.7443 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.6633 14 0.40 76.% + LCAO_gen_fixedH add_v_delta 2.5955 6 0.43 35.% + LCAO_DESCRIPTOR add_v_delta 2.5955 6 0.43 35.% + ElecStateLCAO psiToRho 1.2316 12 0.10 17.% + Charge mix_rho 0.98130 11 0.089 13.% + LOOP_ions force_stress 0.56880 1 0.57 7.6% + Force_Stress_LCAO getForceStress 0.56877 1 0.57 7.6% + Force_LCAO_gamma ftable_gamma 0.35638 1 0.36 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.34794 1 0.35 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:58 2022 + Finish Time : Wed Sep 28 11:02:05 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1a5832389e3241ca32aae3f17d57dce02af8f000 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124207 ima = 3.69891e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122372295024 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111460644953 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111940806421 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112221888639 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112153467463 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112192082545 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112187266715 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112190357403 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112189539211 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112189473851 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112189446621 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112189437947 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/STRU new file mode 100644 index 0000000000000000000000000000000000000000..369e791b7773e982569c5cd28b5306d4a5d7d1e4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.997915082477 16.538975947366 1.067458493381 0 0 0 +H +0.0 +2 +-21.125093851387 18.153620731321 0.869522756847 0 0 0 +-20.574776144595 15.495489299216 1.201558692587 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/conv new file mode 100644 index 0000000000000000000000000000000000000000..a875d5a1e76895b0cedda03ce3913ff19c2cd029 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/conv @@ -0,0 +1 @@ +137 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f6e231c74a615c21b92e37eae281170254bd3559 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753993101 0.01286591133 1.281414654 1.36766668 1.470536974 0.009586604256 0.01717917453 0.03916351764 +-1.640766388e-18 0.0009827107393 0.002963586502 0.01370638035 0.04875265036 -7.056890402e-20 3.043536327e-06 7.841584901e-06 +0.001589188858 0.006141552795 + +H atom_index 1 n_descriptor 18 +1.239224809 0.03523967359 0.107581542 0.1445189766 0.3156837186 0.02277678879 0.02759508516 0.03831876741 +-2.402282417e-17 5.206134253e-05 0.1021801387 0.1144745878 0.124035672 -1.726211772e-18 3.789941509e-06 0.01354897972 +0.02697150509 0.03025526611 + +H atom_index 2 n_descriptor 18 +1.299041229 0.03333076712 0.1301990491 0.1739681065 0.334211885 0.02574782065 0.03106340044 0.03700024077 +-3.783890308e-18 5.779085217e-05 0.1085095039 0.1254878074 0.1491640966 6.140399555e-18 6.711300611e-07 0.01384512239 +0.02901388773 0.032749614 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a0d2d0d8caf4d6dfcd36f58f1b335806d38bf244 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:58 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.104358 SEC) : SETUP UNITCELL + DONE(0.104764 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123009 SEC) : INIT PLANEWAVE + DONE(0.167917 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.442903 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651352e+02 0.000000e+00 2.152e-01 5.392e-01 + GE2 -4.663507e+02 -1.215460e+00 9.719e-02 4.933e-01 + GE3 -4.663531e+02 -2.466358e-03 6.208e-02 5.685e-01 + GE4 -4.663535e+02 -3.236733e-04 1.994e-03 4.209e-01 + GE5 -4.663526e+02 8.936288e-04 8.585e-04 4.181e-01 + GE6 -4.663532e+02 -6.443384e-04 1.208e-04 4.136e-01 + GE7 -4.663530e+02 2.192074e-04 4.100e-05 4.148e-01 + GE8 -4.663530e+02 -4.503816e-05 2.085e-05 3.996e-01 + GE9 -4.663530e+02 2.172622e-05 1.941e-06 3.982e-01 + GE10 -4.663530e+02 -4.012265e-06 6.639e-07 3.983e-01 + GE11 -4.663530e+02 -2.083575e-07 1.648e-07 3.987e-01 + GE12 -4.663530e+02 -1.070374e-07 1.090e-08 3.293e-01 +E_delta_band = -7.19909972e-02 Ry = -9.79487766e-01 eV +E_delta_NN= -1.95547465e-01 Ry = -2.66055975e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4563 11 0.68 1e+02 % + Run_lcao lcao_line 7.4461 1 7.4 1e+02 % + Potential init_pot 0.27777 2 0.14 3.7 % + PW_Basis recip2real 0.27879 17 0.016 3.7 % + PW_Basis gathers_scatterp 0.12012 17 0.0071 1.6 % + Potential v_of_rho 1.0458 14 0.075 14 % + XC_Functional v_xc 0.32177 15 0.021 4.3 % + H_Hartree_pw v_hartree 0.67661 14 0.048 9.1 % + PW_Basis real2recip 0.74544 41 0.018 10 % + PW_Basis gatherp_scatters 0.28181 41 0.0069 3.8 % + ORB_control set_orb_tables 1.0908 1 1.1 15 % + ORB_gen_tables gen_tables 1.0908 1 1.1 15 % + ORB_table_phi init_Table 0.47261 1 0.47 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.46745 126 0.0037 6.3 % + ORB_table_beta init_Table_Beta 0.18228 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18074 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24935 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24741 66 0.0037 3.3 % + LOOP_ions opt_ions 5.8242 1 5.8 78 % + ESolver_KS_LCAO Run 5.2552 1 5.3 70 % + HSolverLCAO solve 2.6243 12 0.22 35 % + HamiltLCAO updateHk 1.3705 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.3408 12 0.11 18 % + Gint_interface cal_gint 2.4296 25 0.097 33 % + Gint_Gamma distri_vl 2.7443 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.6633 14 0.4 76 % + LCAO_gen_fixedH add_v_delta 2.5955 6 0.43 35 % + LCAO_DESCRIPTOR add_v_delta 2.5955 6 0.43 35 % + ElecStateLCAO psiToRho 1.2316 12 0.1 17 % + Charge mix_rho 0.9813 11 0.089 13 % + LOOP_ions force_stress 0.5688 1 0.57 7.6 % + Force_Stress_LCAO getForceStress 0.56877 1 0.57 7.6 % + Force_LCAO_gamma ftable_gamma 0.35638 1 0.36 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.34794 1 0.35 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:58 2022 + FINISH Time : Wed Sep 28 11:02:05 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/137/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..da09ecabf3ea37e8c02b3aa50d1470549cfeacce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.222119 0.603968 0.0269135 +H 0.206622 0.660339 0.997856 +H 0.221311 0.554042 0.980415 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e0339c6bfeed8234d0f08a20d2f3666e0766fb3e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9933 2 + 2 -13.089 2 + 3 -8.8348 2 + 4 -6.67214 2 + 5 1.09842 0 + 6 4.16949 0 + 7 11.1342 0 + 8 11.359 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b82364620fb1264968dd32fc532f0102204da468 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:09 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.21933984501 16.9110928667 0.753578378419 0 0 0 0 + tauc_H1 5.78541515936 18.4894913 27.9399582715 0 0 0 0 + tauc_H2 6.19669672406 15.5131658597 27.451613506 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.113554693958 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.114129507504 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.142736080967 (SEC) + + DONE : INIT CHARGE Time : 0.185911023436 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.467729 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00111 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000793 + + Density error is 0.212886291657 + + Energy Rydberg eV + E_KohnSham -34.1907183139 -465.188587781 + E_Harris -34.3775312682 -467.730308421 + E_Fermi -0.391216888056 -5.32277883139 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00109748308402 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112979793836 + + Density error is 0.0986285866653 + + Energy Rydberg eV + E_KohnSham -34.277776731 -466.373078313 + E_Harris -34.2846122249 -466.466079979 + E_Fermi -0.202295106644 -2.75236612788 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00102564610966 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109592666462 + + Density error is 0.0633368824606 + + Energy Rydberg eV + E_KohnSham -34.277946365 -466.375386302 + E_Harris -34.2823379631 -466.43513706 + E_Fermi -0.192841812731 -2.62374746579 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000892522444289 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106243544269 + + Density error is 0.00208993089894 + + Energy Rydberg eV + E_KohnSham -34.2778976949 -466.374724111 + E_Harris -34.2779018753 -466.374780989 + E_Fermi -0.157860057057 -2.14779626258 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000888230158378 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106140728816 + + Density error is 0.000785571333669 + + Energy Rydberg eV + E_KohnSham -34.2778698122 -466.374344747 + E_Harris -34.2778699634 -466.374346806 + E_Fermi -0.157389750379 -2.14139741195 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000886501619159 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106109513336 + + Density error is 0.000185664589475 + + Energy Rydberg eV + E_KohnSham -34.277886942 -466.374577811 + E_Harris -34.2778869918 -466.374578488 + E_Fermi -0.157104036987 -2.13751008183 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000886610018323 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106140279786 + + Density error is 3.22450684175e-05 + + Energy Rydberg eV + E_KohnSham -34.2778806992 -466.374492874 + E_Harris -34.277880703 -466.374492924 + E_Fermi -0.157067429903 -2.13701201689 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000886563356296 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106129390728 + + Density error is 1.32330965736e-05 + + Energy Rydberg eV + E_KohnSham -34.2778843109 -466.374542013 + E_Harris -34.2778843117 -466.374542023 + E_Fermi -0.157087685328 -2.13728760609 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00088654445389 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106130045031 + + Density error is 1.56317844095e-06 + + Energy Rydberg eV + E_KohnSham -34.2778832108 -466.374527045 + E_Harris -34.2778832108 -466.374527045 + E_Fermi -0.157073532607 -2.13709504844 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000886543519545 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010613027468 + + Density error is 5.60182135325e-07 + + Energy Rydberg eV + E_KohnSham -34.2778834282 -466.374530003 + E_Harris -34.2778834282 -466.374530003 + E_Fermi -0.157072788471 -2.13708492395 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000886543713816 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106130360802 + + Density error is 1.7270813703e-07 + + Energy Rydberg eV + E_KohnSham -34.2778834302 -466.374530031 + E_Harris -34.2778834303 -466.374530031 + E_Fermi -0.157072495619 -2.1370809395 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000886543601338 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106130383696 + + Density error is 1.05282118192e-08 + + Energy Rydberg eV + E_KohnSham -34.2778834348 -466.374530093 + E_Harris -34.2778834348 -466.374530093 + E_band -7.87747586499 -107.178557621 + E_one_elec -68.8409088591 -936.628615983 + E_Hartree +35.8379088242 +487.599764413 + E_xc -8.17692559536 -111.252780219 + E_Ewald +7.02732467766 +95.6116573122 + E_demet -4.49547968355e-64 -6.11641389395e-63 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19389048731 -2.63801541541 + E_Fermi -0.157072324458 -2.13707861074 + + charge density convergence is achieved + final etot is -466.374530093 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9933 2.00000 + 2 -13.0890 2.00000 + 3 -8.83480 2.00000 + 4 -6.67214 2.00000 + 5 1.09842 0.00000 + 6 4.16949 0.00000 + 7 11.1342 0.00000 + 8 11.3590 0.00000 + + EFERMI = -2.137078610738123 eV + OUT.ABACUS/ final etot is -466.3745300927254 eV + correction force for each atom along direction 1 is -0.000101560 + correction force for each atom along direction 2 is -2.23542e-05 + correction force for each atom along direction 3 is -0.000167004 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.18983856 -1.5833839 -0.38624520 + H1 -0.11441437 +0.096408383 -0.49462898 + H2 -0.075424190 +1.4869756 +0.88087418 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3745300927254 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3616 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3518 1 7.4 1.e+02% + Potential init_pot 0.28146 2 0.14 3.8% + PW_Basis recip2real 0.30187 17 0.018 4.1% + PW_Basis gathers_scatterp 0.12983 17 0.0076 1.8% + Potential v_of_rho 1.0879 14 0.078 15.% + XC_Functional v_xc 0.30803 15 0.021 4.2% + H_Hartree_pw v_hartree 0.73175 14 0.052 9.9% + PW_Basis real2recip 0.75707 41 0.018 10.% + PW_Basis gatherp_scatters 0.28825 41 0.0070 3.9% + ORB_control set_orb_tables 1.0975 1 1.1 15.% + ORB_gen_tables gen_tables 1.0975 1 1.1 15.% + ORB_table_phi init_Table 0.47592 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47068 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18337 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18185 56 0.0032 2.5% + ORB_table_alpha init_Table_Alpha 0.24811 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24614 66 0.0037 3.3% + LOOP_ions opt_ions 5.7111 1 5.7 78.% + ESolver_KS_LCAO Run 5.0885 1 5.1 69.% + HSolverLCAO solve 2.4102 12 0.20 33.% + HamiltLCAO updateHk 1.2709 12 0.11 17.% + LCAO_Hamilt cal_Hgamma 1.2412 12 0.10 17.% + Gint_interface cal_gint 2.2048 25 0.088 30.% + Gint_Gamma distri_vl 2.6550 6 0.44 36.% + LCAO_Deepks cal_projected_DM 5.5586 14 0.40 76.% + LCAO_gen_fixedH add_v_delta 2.5060 6 0.42 34.% + LCAO_DESCRIPTOR add_v_delta 2.5061 6 0.42 34.% + ElecStateLCAO psiToRho 1.1219 12 0.093 15.% + Charge mix_rho 0.99066 11 0.090 13.% + LOOP_ions force_stress 0.62238 1 0.62 8.5% + Force_Stress_LCAO getForceStress 0.62235 1 0.62 8.5% + Force_LCAO_gamma ftable_gamma 0.33770 1 0.34 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.32944 1 0.33 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:09 2022 + Finish Time : Wed Sep 28 11:03:16 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..cd87e450138def8f3b50d6fcc15275175dd7584a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012372 ima = 3.68181e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123685810115 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112766558453 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113352766906 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011352763298 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011351018848 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113523491279 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113516803174 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113518996463 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113518403579 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011351838027 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113518359542 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113518350442 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/STRU new file mode 100644 index 0000000000000000000000000000000000000000..672c3fc7de3c507571a25c748d01bf33e7e28ac6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.780660154964 16.911092866682 0.753578378416 0 0 0 +H +0.0 +2 +-22.214584840611 18.489491300069 -0.060041728450 0 0 0 +-21.803303275931 15.513165859746 -0.548386493998 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/conv new file mode 100644 index 0000000000000000000000000000000000000000..8ba2e5ae5274b7bf9290bda4aeb6f3fd65f5d486 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/conv @@ -0,0 +1 @@ +138 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c521f3e23434a486787a1a8b93f04c87d90e8af3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745214297 0.01241553195 1.255174685 1.35704184 1.468017463 0.007713245261 0.01965467314 0.03892333952 +-8.147157865e-18 0.00102084655 0.002276742463 0.01156377819 0.04075375065 9.070664074e-19 1.330283129e-06 4.378465158e-06 +0.001732012878 0.005619812659 + +H atom_index 1 n_descriptor 18 +1.245563034 0.03395262571 0.1061827873 0.1493741501 0.3219773534 0.02146880651 0.02824684565 0.03720440563 +-1.811178705e-17 3.582131828e-05 0.09896520439 0.1149027413 0.1280768619 -1.073898222e-18 4.201029398e-06 0.01294490936 +0.025463797 0.03065943826 + +H atom_index 2 n_descriptor 18 +1.179918098 0.03615057427 0.08590197415 0.1216601706 0.2989720429 0.01856774272 0.02443665995 0.03976568709 +1.735183172e-17 3.084995469e-05 0.08172821669 0.1038062163 0.1128664574 -3.458957813e-18 6.253686545e-06 0.01442571884 +0.02282674601 0.02736253411 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..8f9503e6a2d6bbde5d8f2d99201eb542306cc015 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:09 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.113595 SEC) : SETUP UNITCELL + DONE(0.11415 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.142757 SEC) : INIT PLANEWAVE + DONE(0.186046 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.467793 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651886e+02 0.000000e+00 2.129e-01 5.220e-01 + GE2 -4.663731e+02 -1.184491e+00 9.863e-02 4.848e-01 + GE3 -4.663754e+02 -2.307989e-03 6.334e-02 5.542e-01 + GE4 -4.663747e+02 6.621907e-04 2.090e-03 4.091e-01 + GE5 -4.663743e+02 3.793639e-04 7.856e-04 4.082e-01 + GE6 -4.663746e+02 -2.330631e-04 1.857e-04 4.039e-01 + GE7 -4.663745e+02 8.493675e-05 3.225e-05 3.900e-01 + GE8 -4.663745e+02 -4.913927e-05 1.323e-05 3.852e-01 + GE9 -4.663745e+02 1.496772e-05 1.563e-06 3.846e-01 + GE10 -4.663745e+02 -2.957679e-06 5.602e-07 3.851e-01 + GE11 -4.663745e+02 -2.813976e-08 1.727e-07 3.888e-01 + GE12 -4.663745e+02 -6.155079e-08 1.053e-08 3.104e-01 +E_delta_band = -6.86080052e-02 Ry = -9.33459799e-01 eV +E_delta_NN= -1.93890487e-01 Ry = -2.63801542e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3616 11 0.67 1e+02 % + Run_lcao lcao_line 7.3518 1 7.4 1e+02 % + Potential init_pot 0.28146 2 0.14 3.8 % + PW_Basis recip2real 0.30187 17 0.018 4.1 % + PW_Basis gathers_scatterp 0.12983 17 0.0076 1.8 % + Potential v_of_rho 1.0879 14 0.078 15 % + XC_Functional v_xc 0.30803 15 0.021 4.2 % + H_Hartree_pw v_hartree 0.73175 14 0.052 9.9 % + PW_Basis real2recip 0.75707 41 0.018 10 % + PW_Basis gatherp_scatters 0.28825 41 0.007 3.9 % + ORB_control set_orb_tables 1.0975 1 1.1 15 % + ORB_gen_tables gen_tables 1.0975 1 1.1 15 % + ORB_table_phi init_Table 0.47592 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.47068 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18337 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18185 56 0.0032 2.5 % + ORB_table_alpha init_Table_Alpha 0.24811 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24614 66 0.0037 3.3 % + LOOP_ions opt_ions 5.7111 1 5.7 78 % + ESolver_KS_LCAO Run 5.0885 1 5.1 69 % + HSolverLCAO solve 2.4102 12 0.2 33 % + HamiltLCAO updateHk 1.2709 12 0.11 17 % + LCAO_Hamilt cal_Hgamma 1.2412 12 0.1 17 % + Gint_interface cal_gint 2.2048 25 0.088 30 % + Gint_Gamma distri_vl 2.655 6 0.44 36 % + LCAO_Deepks cal_projected_DM 5.5586 14 0.4 76 % + LCAO_gen_fixedH add_v_delta 2.506 6 0.42 34 % + LCAO_DESCRIPTOR add_v_delta 2.5061 6 0.42 34 % + ElecStateLCAO psiToRho 1.1219 12 0.093 15 % + Charge mix_rho 0.99066 11 0.09 13 % + LOOP_ions force_stress 0.62238 1 0.62 8.5 % + Force_Stress_LCAO getForceStress 0.62235 1 0.62 8.5 % + Force_LCAO_gamma ftable_gamma 0.3377 1 0.34 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.32944 1 0.33 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:09 2022 + FINISH Time : Wed Sep 28 11:03:16 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/138/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d2bb6d900a28b7db479d06375ea9584c7eed8f39 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.233089 0.620375 0.0206763 +H 0.197467 0.675519 0.00541559 +H 0.253779 0.598342 0.963354 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..00f2d62e7c5febd2168c0488943de486c9b0101b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1899 2 + 2 -12.9666 2 + 3 -9.0932 2 + 4 -6.72177 2 + 5 1.19898 0 + 6 4.28795 0 + 7 11.0985 0 + 8 11.3463 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7fb90247123e89580de05f4f7e6618b670c3189d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:35 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.52648920684 17.3705127897 0.578937492144 0 0 0 0 + tauc_H1 5.52906703307 18.9145181137 0.151636642026 0 0 0 0 + tauc_H2 7.10582337953 16.7535674628 26.9739181852 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0734373917081 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877919433675 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103620244504 (SEC) + + DONE : INIT CHARGE Time : 0.146334670431 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388087 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 0 9 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000798 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00099 + + Density error is 0.213561581797 + + Energy Rydberg eV + E_KohnSham -34.1914188528 -465.198119103 + E_Harris -34.3801750927 -467.766279498 + E_Fermi -0.399056562758 -5.42944307781 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00105915437501 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122581786733 + + Density error is 0.0982175862278 + + Energy Rydberg eV + E_KohnSham -34.279924306 -466.402297571 + E_Harris -34.2867487576 -466.495148997 + E_Fermi -0.209240343064 -2.84686091715 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00100871356889 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117045813899 + + Density error is 0.0630551092898 + + Energy Rydberg eV + E_KohnSham -34.2801967957 -466.406004983 + E_Harris -34.284602313 -466.46594512 + E_Fermi -0.199222444894 -2.71056042005 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00093535107732 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109400865047 + + Density error is 0.00198628829323 + + Energy Rydberg eV + E_KohnSham -34.2801601696 -466.405506659 + E_Harris -34.2801616611 -466.405526952 + E_Fermi -0.163814520937 -2.22881089989 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000935886337913 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109541533325 + + Density error is 0.000844345167518 + + Energy Rydberg eV + E_KohnSham -34.280114459 -466.404884735 + E_Harris -34.2801152324 -466.404895258 + E_Fermi -0.163310095587 -2.22194784091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000934871043697 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109424646303 + + Density error is 0.000170587838469 + + Energy Rydberg eV + E_KohnSham -34.2801417695 -466.405256312 + E_Harris -34.2801416582 -466.405254799 + E_Fermi -0.163144774492 -2.21969853202 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000935057641087 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109446638281 + + Density error is 3.38399136409e-05 + + Energy Rydberg eV + E_KohnSham -34.2801315658 -466.405117485 + E_Harris -34.2801315708 -466.405117553 + E_Fermi -0.163060065686 -2.21854600958 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000935003202705 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109440133801 + + Density error is 1.59209639909e-05 + + Energy Rydberg eV + E_KohnSham -34.2801355823 -466.405172132 + E_Harris -34.2801355834 -466.405172147 + E_Fermi -0.163090371852 -2.21895834612 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000935003076838 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010944031816 + + Density error is 2.67163094283e-06 + + Energy Rydberg eV + E_KohnSham -34.2801343017 -466.405154709 + E_Harris -34.2801343018 -466.405154709 + E_Fermi -0.163075022602 -2.21874950887 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000934999745038 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109439881575 + + Density error is 4.63541705571e-07 + + Energy Rydberg eV + E_KohnSham -34.2801345301 -466.405157816 + E_Harris -34.2801345301 -466.405157816 + E_Fermi -0.163072387852 -2.21871366126 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000935000564245 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109439976838 + + Density error is 1.74929093377e-07 + + Energy Rydberg eV + E_KohnSham -34.2801345588 -466.405158207 + E_Harris -34.2801345588 -466.405158207 + E_Fermi -0.163072211938 -2.21871126782 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000935000738792 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109439996357 + + Density error is 1.04956369882e-08 + + Energy Rydberg eV + E_KohnSham -34.2801345611 -466.405158238 + E_Harris -34.2801345611 -466.405158238 + E_band -7.93365774337 -107.942951292 + E_one_elec -69.085282705 -939.953492729 + E_Hartree +35.943362708 +489.03453811 + E_xc -8.19415285499 -111.487169111 + E_Ewald +7.18069300184 +97.6983404138 + E_demet -3.4942662242e-71 -4.7541930978e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19444283481 -2.64553048869 + E_Fermi -0.163072042571 -2.21870896346 + + charge density convergence is achieved + final etot is -466.405158238 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1899 2.00000 + 2 -12.9666 2.00000 + 3 -9.09320 2.00000 + 4 -6.72177 2.00000 + 5 1.19898 0.00000 + 6 4.28795 0.00000 + 7 11.0985 0.00000 + 8 11.3463 0.00000 + + EFERMI = -2.218708963459089 eV + OUT.ABACUS/ final etot is -466.4051582375853 eV + correction force for each atom along direction 1 is 7.00876e-05 + correction force for each atom along direction 2 is 1.71584e-05 + correction force for each atom along direction 3 is -7.49054e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.81658272 +1.1385348 +0.51709500 + H1 +0.56857846 -0.87909462 +0.21938692 + H2 +0.24800425 -0.25944022 -0.73648192 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4051582375853 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9129 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9051 1 6.9 1.e+02% + Potential init_pot 0.23897 2 0.12 3.5% + PW_Basis recip2real 0.25841 17 0.015 3.7% + PW_Basis gathers_scatterp 0.10682 17 0.0063 1.5% + Potential v_of_rho 0.96599 14 0.069 14.% + XC_Functional v_xc 0.28598 15 0.019 4.1% + H_Hartree_pw v_hartree 0.63670 14 0.045 9.2% + PW_Basis real2recip 0.64620 41 0.016 9.3% + PW_Basis gatherp_scatters 0.24257 41 0.0059 3.5% + ORB_control set_orb_tables 0.89133 1 0.89 13.% + ORB_gen_tables gen_tables 0.89133 1 0.89 13.% + ORB_table_phi init_Table 0.37256 1 0.37 5.4% + ORB_table_phi cal_ST_Phi12_R 0.36832 126 0.0029 5.3% + ORB_table_beta init_Table_Beta 0.15215 1 0.15 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15084 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20926 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20754 66 0.0031 3.0% + LOOP_ions opt_ions 5.5562 1 5.6 80.% + ESolver_KS_LCAO Run 5.0503 1 5.1 73.% + HSolverLCAO solve 2.7131 12 0.23 39.% + HamiltLCAO updateHk 1.3709 12 0.11 20.% + LCAO_Hamilt cal_Hgamma 1.3419 12 0.11 19.% + Gint_interface cal_gint 2.5559 25 0.10 37.% + Gint_Gamma distri_vl 2.6204 6 0.44 38.% + LCAO_Deepks cal_projected_DM 5.4089 14 0.39 78.% + LCAO_gen_fixedH add_v_delta 2.4925 6 0.42 36.% + LCAO_DESCRIPTOR add_v_delta 2.4925 6 0.42 36.% + ElecStateLCAO psiToRho 1.3258 12 0.11 19.% + Charge mix_rho 0.81831 11 0.074 12.% + LOOP_ions force_stress 0.50574 1 0.51 7.3% + Force_Stress_LCAO getForceStress 0.50572 1 0.51 7.3% + Force_LCAO_gamma ftable_gamma 0.31029 1 0.31 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.30305 1 0.30 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:35 2022 + Finish Time : Wed Sep 28 11:02:42 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..38cde0d0bf9f82e3190866c1c8397cfc456ab714 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123793 ima = 3.681e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123222212233 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112163460943 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112758510797 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112979683145 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112945395043 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112967349414 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112960055763 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112962589074 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112961900883 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112961817964 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011296180299 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112961794041 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/STRU new file mode 100644 index 0000000000000000000000000000000000000000..cd87b6e80e1b1ae3edf5e7c79bc21807fb77d3ed --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.473510793188 17.370512789693 0.578937492163 0 0 0 +H +0.0 +2 +-22.470932966911 18.914518113693 0.151636642025 0 0 0 +-20.894176620489 16.753567462754 -1.026081814740 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/conv new file mode 100644 index 0000000000000000000000000000000000000000..bc6820cefd89789030ebe1ce39df17228c7aea2c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/conv @@ -0,0 +1 @@ +139 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d1ce2289e525c381a00d3aff983dfc6210a06c62 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749241373 0.01259459486 1.262814051 1.357146354 1.468894965 0.008434302299 0.01843748342 0.03904125424 +6.911788274e-19 0.001005960436 0.002526678416 0.01207797554 0.04391210999 -1.424074143e-20 1.863329877e-06 5.573038267e-06 +0.001641733608 0.00590530699 + +H atom_index 1 n_descriptor 18 +1.202980671 0.03581890509 0.09279408498 0.1296213129 0.3051735665 0.0199472174 0.0255888067 0.03916814451 +2.967611303e-17 3.932019063e-05 0.08848566548 0.1109218601 0.1135450868 -1.061647343e-17 6.154350604e-06 0.0140143706 +0.02420007852 0.02846029762 + +H atom_index 2 n_descriptor 18 +1.260520666 0.03386937046 0.1116941117 0.1551301495 0.3247865545 0.02260439016 0.0289471142 0.03712187608 +3.234179699e-18 4.441639882e-05 0.1031566859 0.1156995563 0.1331106986 4.878661682e-18 3.50678548e-06 0.01309829372 +0.02643637306 0.03123429195 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a482843ebed0a1870cb7771678b185a28b0d32c0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:35 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0734525 SEC) : SETUP UNITCELL + DONE(0.087806 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103634 SEC) : INIT PLANEWAVE + DONE(0.146442 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.388132 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651981e+02 0.000000e+00 2.136e-01 4.927e-01 + GE2 -4.664023e+02 -1.204178e+00 9.822e-02 4.734e-01 + GE3 -4.664060e+02 -3.707412e-03 6.306e-02 5.338e-01 + GE4 -4.664055e+02 4.983246e-04 1.986e-03 4.083e-01 + GE5 -4.664049e+02 6.219239e-04 8.443e-04 4.088e-01 + GE6 -4.664053e+02 -3.715777e-04 1.706e-04 4.059e-01 + GE7 -4.664051e+02 1.388276e-04 3.384e-05 3.934e-01 + GE8 -4.664052e+02 -5.464750e-05 1.592e-05 3.876e-01 + GE9 -4.664052e+02 1.742353e-05 2.672e-06 3.871e-01 + GE10 -4.664052e+02 -3.106957e-06 4.635e-07 3.901e-01 + GE11 -4.664052e+02 -3.908764e-07 1.749e-07 3.908e-01 + GE12 -4.664052e+02 -3.089372e-08 1.050e-08 3.244e-01 +E_delta_band = -6.96881239e-02 Ry = -9.48155568e-01 eV +E_delta_NN= -1.94442835e-01 Ry = -2.64553049e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9129 11 0.63 1e+02 % + Run_lcao lcao_line 6.9051 1 6.9 1e+02 % + Potential init_pot 0.23897 2 0.12 3.5 % + PW_Basis recip2real 0.25841 17 0.015 3.7 % + PW_Basis gathers_scatterp 0.10682 17 0.0063 1.5 % + Potential v_of_rho 0.96599 14 0.069 14 % + XC_Functional v_xc 0.28598 15 0.019 4.1 % + H_Hartree_pw v_hartree 0.6367 14 0.045 9.2 % + PW_Basis real2recip 0.6462 41 0.016 9.3 % + PW_Basis gatherp_scatters 0.24257 41 0.0059 3.5 % + ORB_control set_orb_tables 0.89133 1 0.89 13 % + ORB_gen_tables gen_tables 0.89133 1 0.89 13 % + ORB_table_phi init_Table 0.37256 1 0.37 5.4 % + ORB_table_phi cal_ST_Phi12_R 0.36832 126 0.0029 5.3 % + ORB_table_beta init_Table_Beta 0.15215 1 0.15 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15084 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20926 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20754 66 0.0031 3 % + LOOP_ions opt_ions 5.5562 1 5.6 80 % + ESolver_KS_LCAO Run 5.0503 1 5.1 73 % + HSolverLCAO solve 2.7131 12 0.23 39 % + HamiltLCAO updateHk 1.3709 12 0.11 20 % + LCAO_Hamilt cal_Hgamma 1.3419 12 0.11 19 % + Gint_interface cal_gint 2.5559 25 0.1 37 % + Gint_Gamma distri_vl 2.6204 6 0.44 38 % + LCAO_Deepks cal_projected_DM 5.4089 14 0.39 78 % + LCAO_gen_fixedH add_v_delta 2.4925 6 0.42 36 % + LCAO_DESCRIPTOR add_v_delta 2.4925 6 0.42 36 % + ElecStateLCAO psiToRho 1.3258 12 0.11 19 % + Charge mix_rho 0.81831 11 0.074 12 % + LOOP_ions force_stress 0.50574 1 0.51 7.3 % + Force_Stress_LCAO getForceStress 0.50572 1 0.51 7.3 % + Force_LCAO_gamma ftable_gamma 0.31029 1 0.31 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.30305 1 0.3 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:35 2022 + FINISH Time : Wed Sep 28 11:02:42 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/139/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..262f17537b11d906acf0789dba246d0e9a461c8d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.582156 0.257408 0.372219 +H 0.62941 0.239952 0.413794 +H 0.595491 0.318113 0.355833 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..243e35c3cba06b8bf9ff134edd3c014d3bbdea76 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3839 2 + 2 -13.2063 2 + 3 -9.07386 2 + 4 -6.76537 2 + 5 1.4064 0 + 6 4.59977 0 + 7 11.0482 0 + 8 11.2924 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1b61024701c99e832e12a1eecd5d19fadd7d0ec6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:24 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.3003808164 7.20741109914 10.4221263444 0 0 0 0 + tauc_H1 17.6234728071 6.71865494892 11.5862436079 0 0 0 0 + tauc_H2 16.6737455963 8.90715394606 9.96332725768 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0878451298449 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0913692814245 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.110160077949 (SEC) + + DONE : INIT CHARGE Time : 0.15883651321 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.461123 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00164 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000744 + + Density error is 0.215999211619 + + Energy Rydberg eV + E_KohnSham -34.1906284181 -465.187364687 + E_Harris -34.3845104013 -467.825264398 + E_Fermi -0.412193523367 -5.60818059649 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00149858886653 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00096898572001 + + Density error is 0.097604166738 + + Energy Rydberg eV + E_KohnSham -34.2801996969 -466.406044455 + E_Harris -34.2868308005 -466.496265248 + E_Fermi -0.22050477069 -3.00012131757 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00137443692206 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000934689417236 + + Density error is 0.0624560167057 + + Energy Rydberg eV + E_KohnSham -34.2804007559 -466.408780003 + E_Harris -34.2846630299 -466.466771217 + E_Fermi -0.207395134933 -2.82175557257 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115797944208 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000893754115763 + + Density error is 0.00202756285141 + + Energy Rydberg eV + E_KohnSham -34.2804227407 -466.409079122 + E_Harris -34.2804243115 -466.409100495 + E_Fermi -0.171862605177 -2.33831070354 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115481992913 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000895249202478 + + Density error is 0.000865350727996 + + Energy Rydberg eV + E_KohnSham -34.2803574682 -466.408191045 + E_Harris -34.2803592573 -466.408215386 + E_Fermi -0.170848972739 -2.3245195267 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115300011923 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000894462050213 + + Density error is 0.000146949299306 + + Energy Rydberg eV + E_KohnSham -34.280401775 -466.40879387 + E_Harris -34.2804018155 -466.40879442 + E_Fermi -0.17101680455 -2.32680299564 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115274932689 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000894709815353 + + Density error is 4.22692882492e-05 + + Energy Rydberg eV + E_KohnSham -34.2803860963 -466.40858055 + E_Harris -34.2803861063 -466.408580686 + E_Fermi -0.170866133784 -2.32475301469 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115276622748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000894634181264 + + Density error is 1.57419588917e-05 + + Energy Rydberg eV + E_KohnSham -34.2803902057 -466.408636461 + E_Harris -34.2803902068 -466.408636476 + E_Fermi -0.17091578229 -2.32542851727 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115272839601 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000894634368583 + + Density error is 1.78464948854e-06 + + Energy Rydberg eV + E_KohnSham -34.2803887242 -466.408616305 + E_Harris -34.2803887242 -466.408616305 + E_Fermi -0.170899092562 -2.32520144188 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115272369909 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00089463590563 + + Density error is 2.23349455931e-07 + + Energy Rydberg eV + E_KohnSham -34.2803889548 -466.408619441 + E_Harris -34.2803889548 -466.408619441 + E_Fermi -0.170897358602 -2.32517785014 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115272399818 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000894636230885 + + Density error is 1.00102695744e-07 + + Energy Rydberg eV + E_KohnSham -34.28038898 -466.408619784 + E_Harris -34.28038898 -466.408619784 + E_Fermi -0.170897346958 -2.32517769171 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115272378181 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000894636312905 + + Density error is 9.85250034643e-09 + + Energy Rydberg eV + E_KohnSham -34.2803889809 -466.408619796 + E_Harris -34.2803889809 -466.408619796 + E_band -8.00098388077 -108.858970385 + E_one_elec -69.5284186762 -945.982666926 + E_Hartree +36.1535551025 +491.894352351 + E_xc -8.22793632346 -111.94681678 + E_Ewald +7.44625746308 +101.311530273 + E_demet -2.40663132252e-84 -3.27438989715e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195222764298 -2.65614197377 + E_Fermi -0.170897261813 -2.32517653325 + + charge density convergence is achieved + final etot is -466.408619796 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3839 2.00000 + 2 -13.2063 2.00000 + 3 -9.07386 2.00000 + 4 -6.76537 2.00000 + 5 1.40640 0.00000 + 6 4.59977 0.00000 + 7 11.0482 0.00000 + 8 11.2924 0.00000 + + EFERMI = -2.325176533254828 eV + OUT.ABACUS/ final etot is -466.4086197960390 eV + correction force for each atom along direction 1 is 0.000137034 + correction force for each atom along direction 2 is 6.84055e-05 + correction force for each atom along direction 3 is 0.000125735 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.55320458 -1.0879961 +0.069873490 + H1 +0.26812965 -0.053935191 +0.21520155 + H2 +0.28507492 +1.1419313 -0.28507504 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4086197960390 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8915 11 0.63 1.0e+02% + Run_lcao lcao_line 6.8816 1 6.9 1.e+02% + Potential init_pot 0.30964 2 0.15 4.5% + PW_Basis recip2real 0.30982 17 0.018 4.5% + PW_Basis gathers_scatterp 0.15715 17 0.0092 2.3% + Potential v_of_rho 0.92538 14 0.066 13.% + XC_Functional v_xc 0.26080 15 0.017 3.8% + H_Hartree_pw v_hartree 0.62805 14 0.045 9.1% + PW_Basis real2recip 0.60655 41 0.015 8.8% + PW_Basis gatherp_scatters 0.24605 41 0.0060 3.6% + ORB_control set_orb_tables 1.1123 1 1.1 16.% + ORB_gen_tables gen_tables 1.1123 1 1.1 16.% + ORB_table_phi init_Table 0.48984 1 0.49 7.1% + ORB_table_phi cal_ST_Phi12_R 0.48480 126 0.0038 7.0% + ORB_table_beta init_Table_Beta 0.18888 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18739 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25228 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25046 66 0.0038 3.6% + LOOP_ions opt_ions 5.2323 1 5.2 76.% + ESolver_KS_LCAO Run 4.6507 1 4.7 67.% + HSolverLCAO solve 2.5131 12 0.21 36.% + HamiltLCAO updateHk 1.2925 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2616 12 0.11 18.% + Gint_interface cal_gint 0.43002 25 0.017 6.2% + Gint_Gamma distri_vl_value 0.72400 12 0.060 11.% + Gint_Gamma distri_vl 2.4177 6 0.40 35.% + LCAO_Deepks cal_projected_DM 4.8322 14 0.35 70.% + LCAO_gen_fixedH add_v_delta 2.2864 6 0.38 33.% + LCAO_DESCRIPTOR add_v_delta 2.2864 6 0.38 33.% + ElecStateLCAO psiToRho 1.2020 12 0.10 17.% + Charge mix_rho 0.71761 11 0.065 10.% + LOOP_ions force_stress 0.58141 1 0.58 8.4% + Force_Stress_LCAO getForceStress 0.58138 1 0.58 8.4% + Force_LCAO_gamma ftable_gamma 0.36914 1 0.37 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.12703 1 0.13 1.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:24 2022 + Finish Time : Wed Sep 28 11:04:31 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..438684248826a0bc4057ca8743fa6ee8c049f3a9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123919 ima = 3.64994e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122995907856 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112172505822 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112622141065 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112877692069 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112817401053 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112852481837 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112845479491 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112848531639 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112847876358 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112847811791 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112847804818 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112847800565 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a88843d3ff8fb4fc7fc551f0a23c786bec7e6b52 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.699619183593 7.207411099146 10.422126344428 0 0 0 +H +0.0 +2 +-10.376527192948 6.718654948914 11.586243607960 0 0 0 +-11.326254403662 8.907153946039 9.963327257676 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/conv new file mode 100644 index 0000000000000000000000000000000000000000..e91895e442de4cfa64340864891a3c55947c44d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/conv @@ -0,0 +1 @@ +14 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5c5e06d3c54966ddc551df0543222b117803f5a4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748165598 0.01274153101 1.283672905 1.371560742 1.469783209 0.008405919504 0.01913346816 0.03899079401 +-2.381003682e-18 0.001130465058 0.002619029968 0.01268595224 0.04582169597 -5.054432884e-20 2.049306996e-06 5.947999491e-06 +0.001677446663 0.005907997036 + +H atom_index 1 n_descriptor 18 +1.248033448 0.03416700429 0.1077676064 0.1492378286 0.3206330422 0.02213296412 0.02822227811 0.03729861356 +2.030599859e-17 4.601716961e-05 0.1020692493 0.1147660089 0.1282064808 1.23354438e-18 4.338705088e-06 0.01313907812 +0.0263925971 0.03070775442 + +H atom_index 2 n_descriptor 18 +1.271105451 0.03337610678 0.115995645 0.160249741 0.3277660851 0.02318618721 0.02955635923 0.03668842466 +-1.698751961e-17 4.816179405e-05 0.1066306523 0.1168418898 0.1376627393 -1.237353854e-17 3.059892991e-06 0.01312063035 +0.02721522117 0.03170057281 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..6d8540c9b3e226441390fbdc19c6a3da0596388d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:24 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0878675 SEC) : SETUP UNITCELL + DONE(0.0913854 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.110183 SEC) : INIT PLANEWAVE + DONE(0.158983 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.461188 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651874e+02 0.000000e+00 2.160e-01 5.040e-01 + GE2 -4.664060e+02 -1.218680e+00 9.760e-02 4.262e-01 + GE3 -4.664088e+02 -2.735548e-03 6.246e-02 4.824e-01 + GE4 -4.664091e+02 -2.991191e-04 2.028e-03 3.748e-01 + GE5 -4.664082e+02 8.880777e-04 8.654e-04 3.737e-01 + GE6 -4.664088e+02 -6.028254e-04 1.469e-04 3.694e-01 + GE7 -4.664086e+02 2.133202e-04 4.227e-05 3.601e-01 + GE8 -4.664086e+02 -5.591164e-05 1.574e-05 3.515e-01 + GE9 -4.664086e+02 2.015687e-05 1.785e-06 3.534e-01 + GE10 -4.664086e+02 -3.136346e-06 2.233e-07 3.515e-01 + GE11 -4.664086e+02 -3.430300e-07 1.001e-07 3.492e-01 + GE12 -4.664086e+02 -1.214007e-08 9.853e-09 2.934e-01 +E_delta_band = -7.13762175e-02 Ry = -9.71123260e-01 eV +E_delta_NN= -1.95222764e-01 Ry = -2.65614197e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8915 11 0.63 1e+02 % + Run_lcao lcao_line 6.8816 1 6.9 1e+02 % + Potential init_pot 0.30964 2 0.15 4.5 % + PW_Basis recip2real 0.30982 17 0.018 4.5 % + PW_Basis gathers_scatterp 0.15715 17 0.0092 2.3 % + Potential v_of_rho 0.92538 14 0.066 13 % + XC_Functional v_xc 0.2608 15 0.017 3.8 % + H_Hartree_pw v_hartree 0.62805 14 0.045 9.1 % + PW_Basis real2recip 0.60655 41 0.015 8.8 % + PW_Basis gatherp_scatters 0.24605 41 0.006 3.6 % + ORB_control set_orb_tables 1.1123 1 1.1 16 % + ORB_gen_tables gen_tables 1.1123 1 1.1 16 % + ORB_table_phi init_Table 0.48984 1 0.49 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.4848 126 0.0038 7 % + ORB_table_beta init_Table_Beta 0.18888 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18739 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.25228 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25046 66 0.0038 3.6 % + LOOP_ions opt_ions 5.2323 1 5.2 76 % + ESolver_KS_LCAO Run 4.6507 1 4.7 67 % + HSolverLCAO solve 2.5131 12 0.21 36 % + HamiltLCAO updateHk 1.2925 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.2616 12 0.11 18 % + Gint_interface cal_gint 0.43002 25 0.017 6.2 % + Gint_Gamma distri_vl_value 0.724 12 0.06 11 % + Gint_Gamma distri_vl 2.4177 6 0.4 35 % + LCAO_Deepks cal_projected_DM 4.8322 14 0.35 70 % + LCAO_gen_fixedH add_v_delta 2.2864 6 0.38 33 % + LCAO_DESCRIPTOR add_v_delta 2.2864 6 0.38 33 % + ElecStateLCAO psiToRho 1.202 12 0.1 17 % + Charge mix_rho 0.71761 11 0.065 10 % + LOOP_ions force_stress 0.58141 1 0.58 8.4 % + Force_Stress_LCAO getForceStress 0.58138 1 0.58 8.4 % + Force_LCAO_gamma ftable_gamma 0.36914 1 0.37 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.12703 1 0.13 1.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:24 2022 + FINISH Time : Wed Sep 28 11:04:31 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/14/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..76c106ca3db1cdd482e46ec79dfcfd7acac256d4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.224946 0.632394 0.0298752 +H 0.176388 0.659713 0.997482 +H 0.275827 0.656538 0.993526 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..60f14af820b9ff03da58d89b3b33d6ca201d516b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3734 2 + 2 -12.7246 2 + 3 -9.40598 2 + 4 -6.76463 2 + 5 1.21646 0 + 6 4.3471 0 + 7 11.0736 0 + 8 11.3507 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..dc9f902107955537323107c864eb9c5cc6a2b605 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:23 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.29848695744 17.7070346877 0.836506818996 0 0 0 0 + tauc_H1 4.93885237519 18.47197314 27.929508227 0 0 0 0 + tauc_H2 7.72316227839 18.383073478 27.8187256061 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101007344558 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101377643543 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119412019999 (SEC) + + DONE : INIT CHARGE Time : 0.162491988693 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.444066 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000811 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133 + + Density error is 0.213963444472 + + Energy Rydberg eV + E_KohnSham -34.1878181317 -465.14912878 + E_Harris -34.3784550102 -467.742876575 + E_Fermi -0.404641527712 -5.50543042431 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0011437423259 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121786578768 + + Density error is 0.0978808601568 + + Energy Rydberg eV + E_KohnSham -34.2781784212 -466.378543589 + E_Harris -34.2851283265 -466.473101901 + E_Fermi -0.214007410224 -2.91172019327 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00109310840499 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113287686377 + + Density error is 0.062990351183 + + Energy Rydberg eV + E_KohnSham -34.2786104136 -466.384421147 + E_Harris -34.2831061714 -466.445589069 + E_Fermi -0.204446317142 -2.78163484825 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00103185361733 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000981841001326 + + Density error is 0.00192665616809 + + Energy Rydberg eV + E_KohnSham -34.2785696977 -466.383867178 + E_Harris -34.2785697666 -466.383868116 + E_Fermi -0.168551119788 -2.29325563339 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00103422010617 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098152370889 + + Density error is 0.00101972538703 + + Energy Rydberg eV + E_KohnSham -34.2785059029 -466.382999206 + E_Harris -34.2785078642 -466.383025891 + E_Fermi -0.168157066857 -2.28789426822 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00103292156735 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000979293545317 + + Density error is 9.81181292539e-05 + + Energy Rydberg eV + E_KohnSham -34.2785437236 -466.383513783 + E_Harris -34.2785437294 -466.383513862 + E_Fermi -0.168001084231 -2.28577201572 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00103299239054 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000979094601577 + + Density error is 3.71326044836e-05 + + Energy Rydberg eV + E_KohnSham -34.278532076 -466.383355309 + E_Harris -34.2785320835 -466.383355411 + E_Fermi -0.167904236096 -2.28445432924 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00103289989371 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000979075199987 + + Density error is 1.43420695859e-05 + + Energy Rydberg eV + E_KohnSham -34.2785343288 -466.38338596 + E_Harris -34.2785343296 -466.383385972 + E_Fermi -0.167944495098 -2.28500208106 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00103290431663 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00097906291989 + + Density error is 2.70731229442e-06 + + Energy Rydberg eV + E_KohnSham -34.2785330032 -466.383367925 + E_Harris -34.2785330032 -466.383367925 + E_Fermi -0.167930964974 -2.28481799429 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00103290777163 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00097906129063 + + Density error is 1.44857836117e-07 + + Energy Rydberg eV + E_KohnSham -34.2785331709 -466.383370206 + E_Harris -34.2785331709 -466.383370206 + E_Fermi -0.167928161598 -2.2847798524 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00103290791974 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00097906140581 + + Density error is 4.26947605065e-08 + + Energy Rydberg eV + E_KohnSham -34.2785332267 -466.383370966 + E_Harris -34.2785332267 -466.383370966 + E_band -7.97733919033 -108.537267867 + E_one_elec -69.2406875428 -942.06788402 + E_Hartree +36.0058338465 +489.884501554 + E_xc -8.20418138798 -111.623614302 + E_Ewald +7.28490032754 +99.1161538166 + E_demet -1.42152598506e-74 -1.93408532519e-73 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194784914805 -2.65018472579 + E_Fermi -0.16792815267 -2.28477973092 + + charge density convergence is achieved + final etot is -466.383370966 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3734 2.00000 + 2 -12.7246 2.00000 + 3 -9.40598 2.00000 + 4 -6.76463 2.00000 + 5 1.21646 0.00000 + 6 4.34710 0.00000 + 7 11.0736 0.00000 + 8 11.3507 0.00000 + + EFERMI = -2.284779730924211 eV + OUT.ABACUS/ final etot is -466.3833709657336 eV + correction force for each atom along direction 1 is 5.13895e-05 + correction force for each atom along direction 2 is 7.89327e-05 + correction force for each atom along direction 3 is 1.31733e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.4812726 +0.12511887 -0.28211167 + H1 -1.2704289 +0.33559349 -0.34564826 + H2 -0.21084370 -0.46071235 +0.62775992 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3833709657336 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7844 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7751 1 6.8 1.e+02% + Potential init_pot 0.28142 2 0.14 4.1% + PW_Basis recip2real 0.27187 16 0.017 4.0% + PW_Basis gathers_scatterp 0.12448 16 0.0078 1.8% + Potential v_of_rho 0.97637 13 0.075 14.% + XC_Functional v_xc 0.29729 14 0.021 4.4% + H_Hartree_pw v_hartree 0.63523 13 0.049 9.4% + PW_Basis real2recip 0.67846 38 0.018 10.% + PW_Basis gatherp_scatters 0.25898 38 0.0068 3.8% + ORB_control set_orb_tables 1.0870 1 1.1 16.% + ORB_gen_tables gen_tables 1.0870 1 1.1 16.% + ORB_table_phi init_Table 0.47132 1 0.47 6.9% + ORB_table_phi cal_ST_Phi12_R 0.46613 126 0.0037 6.9% + ORB_table_beta init_Table_Beta 0.18278 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18123 56 0.0032 2.7% + ORB_table_alpha init_Table_Alpha 0.24626 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24430 66 0.0037 3.6% + LOOP_ions opt_ions 5.1627 1 5.2 76.% + ESolver_KS_LCAO Run 4.6182 1 4.6 68.% + HSolverLCAO solve 2.1975 11 0.20 32.% + HamiltLCAO updateHk 1.1732 11 0.11 17.% + LCAO_Hamilt cal_Hgamma 1.1458 11 0.10 17.% + Gint_interface cal_gint 2.0059 23 0.087 30.% + Gint_Gamma distri_vl 2.2268 6 0.37 33.% + LCAO_Deepks cal_projected_DM 5.0109 13 0.39 74.% + LCAO_gen_fixedH add_v_delta 2.0797 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.0798 6 0.35 31.% + ElecStateLCAO psiToRho 1.0082 11 0.092 15.% + Charge mix_rho 0.90060 10 0.090 13.% + LOOP_ions force_stress 0.54435 1 0.54 8.0% + Force_Stress_LCAO getForceStress 0.54431 1 0.54 8.0% + Force_LCAO_gamma ftable_gamma 0.33247 1 0.33 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.32437 1 0.32 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:23 2022 + Finish Time : Wed Sep 28 11:14:30 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8952d63fe49565d70b3fc4af6385a9657ec27e1a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123606 ima = 3.67632e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122865688798 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111479566948 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112145127986 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112410815315 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011235614385 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112386137297 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112383176215 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112385947497 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112385355007 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112385216797 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112385211494 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b93468b9a0d244288227504280d0f89bf219a3ea --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.701513042549 17.707034687699 0.836506819011 0 0 0 +H +0.0 +2 +-23.061147624789 18.471973139973 -0.070491772945 0 0 0 +-20.276837721612 18.383073477952 -0.181274393947 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/conv new file mode 100644 index 0000000000000000000000000000000000000000..ced64abdc5b5f4a581e786d42a39a2cd5f234fc4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/conv @@ -0,0 +1 @@ +140 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b6fb66fe18430d3fb21816ea7cea4f7d807fc9d5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753896463 0.01275023295 1.265925382 1.353124286 1.46960711 0.009403320521 0.01684927806 0.0391730242 +-7.784788961e-18 0.0009044822223 0.002807248998 0.01305295301 0.04641531815 -1.41866571e-18 2.647797406e-06 7.162087683e-06 +0.001584408839 0.006118001943 + +H atom_index 1 n_descriptor 18 +1.272040253 0.03410346911 0.1187418133 0.1601494994 0.3268154222 0.02415618705 0.02952410008 0.03736347043 +-2.622993026e-17 5.117804933e-05 0.1064356197 0.117828441 0.1373372518 7.34715926e-18 1.994738117e-06 0.01335196611 +0.02761660707 0.03169911746 + +H atom_index 2 n_descriptor 18 +1.215268439 0.03598435666 0.09893519786 0.1340906999 0.3076149501 0.02135877359 0.02619373088 0.03921098449 +-3.038965741e-17 4.586394862e-05 0.09380543876 0.1137784185 0.114800492 -6.137022417e-18 5.028325971e-06 0.01397398047 +0.02547449115 0.02903557573 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4a481f25f9e2330a32085fd3c759fbf073745a23 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:23 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101031 SEC) : SETUP UNITCELL + DONE(0.101392 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119433 SEC) : INIT PLANEWAVE + DONE(0.162627 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444132 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651491e+02 0.000000e+00 2.140e-01 5.157e-01 + GE2 -4.663785e+02 -1.229415e+00 9.788e-02 4.750e-01 + GE3 -4.663844e+02 -5.877557e-03 6.299e-02 5.443e-01 + GE4 -4.663839e+02 5.539686e-04 1.927e-03 4.006e-01 + GE5 -4.663830e+02 8.679721e-04 1.020e-03 4.020e-01 + GE6 -4.663835e+02 -5.145771e-04 9.812e-05 3.957e-01 + GE7 -4.663834e+02 1.584745e-04 3.713e-05 3.833e-01 + GE8 -4.663834e+02 -3.065143e-05 1.434e-05 3.778e-01 + GE9 -4.663834e+02 1.803558e-05 2.707e-06 3.762e-01 + GE10 -4.663834e+02 -2.281227e-06 1.449e-07 3.771e-01 + GE11 -4.663834e+02 -7.597378e-07 4.269e-08 3.074e-01 +E_delta_band = -7.03864448e-02 Ry = -9.57656711e-01 eV +E_delta_NN= -1.94784915e-01 Ry = -2.65018473e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7844 11 0.62 1e+02 % + Run_lcao lcao_line 6.7751 1 6.8 1e+02 % + Potential init_pot 0.28142 2 0.14 4.1 % + PW_Basis recip2real 0.27187 16 0.017 4 % + PW_Basis gathers_scatterp 0.12448 16 0.0078 1.8 % + Potential v_of_rho 0.97637 13 0.075 14 % + XC_Functional v_xc 0.29729 14 0.021 4.4 % + H_Hartree_pw v_hartree 0.63523 13 0.049 9.4 % + PW_Basis real2recip 0.67846 38 0.018 10 % + PW_Basis gatherp_scatters 0.25898 38 0.0068 3.8 % + ORB_control set_orb_tables 1.087 1 1.1 16 % + ORB_gen_tables gen_tables 1.087 1 1.1 16 % + ORB_table_phi init_Table 0.47132 1 0.47 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.46613 126 0.0037 6.9 % + ORB_table_beta init_Table_Beta 0.18278 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18123 56 0.0032 2.7 % + ORB_table_alpha init_Table_Alpha 0.24626 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.2443 66 0.0037 3.6 % + LOOP_ions opt_ions 5.1627 1 5.2 76 % + ESolver_KS_LCAO Run 4.6182 1 4.6 68 % + HSolverLCAO solve 2.1975 11 0.2 32 % + HamiltLCAO updateHk 1.1732 11 0.11 17 % + LCAO_Hamilt cal_Hgamma 1.1458 11 0.1 17 % + Gint_interface cal_gint 2.0059 23 0.087 30 % + Gint_Gamma distri_vl 2.2268 6 0.37 33 % + LCAO_Deepks cal_projected_DM 5.0109 13 0.39 74 % + LCAO_gen_fixedH add_v_delta 2.0797 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.0798 6 0.35 31 % + ElecStateLCAO psiToRho 1.0082 11 0.092 15 % + Charge mix_rho 0.9006 10 0.09 13 % + LOOP_ions force_stress 0.54435 1 0.54 8 % + Force_Stress_LCAO getForceStress 0.54431 1 0.54 8 % + Force_LCAO_gamma ftable_gamma 0.33247 1 0.33 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.32437 1 0.32 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:23 2022 + FINISH Time : Wed Sep 28 11:14:30 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/140/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..804386a64412201eee7d4f968fe522850a63b3f6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.207049 0.643611 0.0427952 +H 0.14424 0.662552 0.0331261 +H 0.238304 0.69804 0.0639908 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8fa5963ac93dd9378a5a11969b5a5393650fe8d7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1381 2 + 2 -12.9759 2 + 3 -9.052 2 + 4 -6.71073 2 + 5 1.19582 0 + 6 4.23319 0 + 7 11.109 0 + 8 11.3566 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4f4445c6ad8a7f4808d7473c4b66cfbd757fa0d9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:21 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.79737509829 18.0211110146 1.19826634633 0 0 0 0 + tauc_H1 4.03871633484 18.5514607485 0.927530709676 0 0 0 0 + tauc_H2 6.67251539349 19.5451082648 1.79174252145 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0740938965654 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0744963173803 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0903053806943 (SEC) + + DONE : INIT CHARGE Time : 0.131680127404 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.377528 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000881 + + Density error is 0.213571575819 + + Energy Rydberg eV + E_KohnSham -34.1922717718 -465.209723661 + E_Harris -34.3807301247 -467.773831096 + E_Fermi -0.396741764217 -5.39794862792 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121608216173 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000966239661173 + + Density error is 0.0983519720066 + + Energy Rydberg eV + E_KohnSham -34.2810327137 -466.417378231 + E_Harris -34.2878960589 -466.510758833 + E_Fermi -0.2065619866 -2.81042000796 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113125485377 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000915624528247 + + Density error is 0.0632789313408 + + Energy Rydberg eV + E_KohnSham -34.2813643762 -466.421890731 + E_Harris -34.2857941648 -466.482161096 + E_Fermi -0.197226781035 -2.68340802027 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000985417824011 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000833177848213 + + Density error is 0.00199653101397 + + Energy Rydberg eV + E_KohnSham -34.2813190283 -466.42127374 + E_Harris -34.281321163 -466.421302785 + E_Fermi -0.161897013681 -2.20272187525 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000984443156653 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000831569629762 + + Density error is 0.000894960707249 + + Energy Rydberg eV + E_KohnSham -34.2812729031 -466.420646175 + E_Harris -34.281273419 -466.420653194 + E_Fermi -0.161458997223 -2.1967623556 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000982652575215 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830531127926 + + Density error is 0.000175522173629 + + Energy Rydberg eV + E_KohnSham -34.2812980393 -466.420988171 + E_Harris -34.2812980604 -466.420988458 + E_Fermi -0.161250127405 -2.19392053593 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000982699151854 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830636318373 + + Density error is 3.28094867722e-05 + + Energy Rydberg eV + E_KohnSham -34.2812893343 -466.420869733 + E_Harris -34.281289339 -466.420869797 + E_Fermi -0.161159458861 -2.19268692711 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000982659076976 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830580978787 + + Density error is 1.6007150672e-05 + + Energy Rydberg eV + E_KohnSham -34.2812929999 -466.420919606 + E_Harris -34.2812930011 -466.420919622 + E_Fermi -0.16118968951 -2.19309823619 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000982646419051 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00083057541381 + + Density error is 2.28200583605e-06 + + Energy Rydberg eV + E_KohnSham -34.2812917134 -466.420902103 + E_Harris -34.2812917135 -466.420902103 + E_Fermi -0.161174130054 -2.19288653892 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000982642929609 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830574620208 + + Density error is 4.72366848216e-07 + + Energy Rydberg eV + E_KohnSham -34.2812919667 -466.420905549 + E_Harris -34.2812919667 -466.420905549 + E_Fermi -0.161172018276 -2.19285780672 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000982642812451 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830575158917 + + Density error is 1.59968315776e-07 + + Energy Rydberg eV + E_KohnSham -34.2812919859 -466.42090581 + E_Harris -34.2812919859 -466.42090581 + E_Fermi -0.16117180852 -2.19285495284 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00098264257865 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830575232046 + + Density error is 1.06362628555e-08 + + Energy Rydberg eV + E_KohnSham -34.2812919898 -466.420905864 + E_Harris -34.2812919898 -466.420905864 + E_band -7.9197320796 -107.753482916 + E_one_elec -69.0150651906 -938.998134433 + E_Hartree +35.9117285382 +488.604133148 + E_xc -8.18886525715 -111.415227651 + E_Ewald +7.1358200565 +97.0878126711 + E_demet -5.03127373776e-70 -6.84539910313e-69 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194276005493 -2.64326065939 + E_Fermi -0.161171655177 -2.1928528665 + + charge density convergence is achieved + final etot is -466.420905864 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1381 2.00000 + 2 -12.9759 2.00000 + 3 -9.05200 2.00000 + 4 -6.71073 2.00000 + 5 1.19582 0.00000 + 6 4.23319 0.00000 + 7 11.1090 0.00000 + 8 11.3566 0.00000 + + EFERMI = -2.192852866496300 eV + OUT.ABACUS/ final etot is -466.4209058635909 eV + correction force for each atom along direction 1 is -5.46123e-05 + correction force for each atom along direction 2 is 8.64847e-05 + correction force for each atom along direction 3 is 6.04166e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.13869551 +0.23154814 +0.027094499 + H1 +0.35685136 -0.022375975 +0.076765841 + H2 -0.21815586 -0.20917216 -0.10386034 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4209058635909 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4163 11 0.67 1.0e+02% + Run_lcao lcao_line 7.4078 1 7.4 1.e+02% + Potential init_pot 0.24378 2 0.12 3.3% + PW_Basis recip2real 0.26832 17 0.016 3.6% + PW_Basis gathers_scatterp 0.11230 17 0.0066 1.5% + Potential v_of_rho 0.96642 14 0.069 13.% + XC_Functional v_xc 0.28578 15 0.019 3.9% + H_Hartree_pw v_hartree 0.64005 14 0.046 8.6% + PW_Basis real2recip 0.64066 41 0.016 8.6% + PW_Basis gatherp_scatters 0.23848 41 0.0058 3.2% + ORB_control set_orb_tables 0.89339 1 0.89 12.% + ORB_gen_tables gen_tables 0.89339 1 0.89 12.% + ORB_table_phi init_Table 0.37729 1 0.38 5.1% + ORB_table_phi cal_ST_Phi12_R 0.37295 126 0.0030 5.0% + ORB_table_beta init_Table_Beta 0.15311 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15181 56 0.0027 2.0% + ORB_table_alpha init_Table_Alpha 0.20499 1 0.20 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20329 66 0.0031 2.7% + LOOP_ions opt_ions 6.0684 1 6.1 82.% + ESolver_KS_LCAO Run 5.5299 1 5.5 75.% + HSolverLCAO solve 3.2060 12 0.27 43.% + HamiltLCAO updateHk 1.5952 12 0.13 22.% + LCAO_Hamilt cal_Hgamma 1.5681 12 0.13 21.% + Gint_interface cal_gint 3.0864 25 0.12 42.% + Gint_Gamma distri_vl 2.8675 6 0.48 39.% + LCAO_Deepks cal_projected_DM 5.9059 14 0.42 80.% + LCAO_gen_fixedH add_v_delta 2.7388 6 0.46 37.% + LCAO_DESCRIPTOR add_v_delta 2.7387 6 0.46 37.% + ElecStateLCAO psiToRho 1.5925 12 0.13 21.% + Charge mix_rho 0.82750 11 0.075 11.% + LOOP_ions force_stress 0.53834 1 0.54 7.3% + Force_Stress_LCAO getForceStress 0.53832 1 0.54 7.3% + Force_LCAO_gamma ftable_gamma 0.34838 1 0.35 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.34117 1 0.34 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:21 2022 + Finish Time : Wed Sep 28 11:11:28 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6ea97d1d4eaf14cc6ec6ee0c6f7c53144c844303 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123942 ima = 3.66952e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123343674739 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112161969034 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112784956181 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113001046589 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011296850485 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112988009547 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112981783962 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112984321365 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112983583904 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112983519585 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112983501066 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112983493083 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c896f65ac0c86b262061eb9ec6bc8b62673e94c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.202624901729 18.021111014627 1.198266346349 0 0 0 +H +0.0 +2 +-23.961283665175 18.551460748532 0.927530709697 0 0 0 +-21.327484606487 19.545108264807 1.791742521473 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/conv new file mode 100644 index 0000000000000000000000000000000000000000..e7fdd36d05e24e18ecddacb83395b083f87b7561 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/conv @@ -0,0 +1 @@ +141 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ed6d2a663ba2eb09a2f064dc535c1741125354cb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748572368 0.01257658699 1.262869791 1.353571674 1.468633987 0.008280188168 0.01856600769 0.03901314221 +-1.107455616e-18 0.001004392624 0.002473733864 0.01198334151 0.04322261499 -2.506305382e-19 1.772576079e-06 5.342842484e-06 +0.001658817605 0.005886801544 + +H atom_index 1 n_descriptor 18 +1.226487184 0.03497915789 0.1000075734 0.1397252849 0.3139102989 0.02095098746 0.02698703228 0.03818292917 +1.591455893e-17 4.014623918e-05 0.09441821838 0.114372941 0.1197567373 4.420613444e-18 5.196589026e-06 0.01341850552 +0.02505553415 0.02966863362 + +H atom_index 2 n_descriptor 18 +1.227939118 0.03492967718 0.1004764372 0.1403603591 0.3144114807 0.02101777615 0.02707190059 0.03812861487 +-7.645792233e-19 4.027286199e-05 0.09480219169 0.1144145429 0.1203107554 -3.633964426e-18 5.132805481e-06 0.0133914947 +0.02511285064 0.0297398396 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..42971378f3da5fcaeb0a4cb2c0f33575a79f5223 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:21 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.074113 SEC) : SETUP UNITCELL + DONE(0.0745057 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0903184 SEC) : INIT PLANEWAVE + DONE(0.131786 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.377574 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652097e+02 0.000000e+00 2.136e-01 5.323e-01 + GE2 -4.664174e+02 -1.207655e+00 9.835e-02 5.105e-01 + GE3 -4.664219e+02 -4.512500e-03 6.328e-02 5.703e-01 + GE4 -4.664213e+02 6.169907e-04 1.997e-03 4.501e-01 + GE5 -4.664206e+02 6.275646e-04 8.950e-04 4.495e-01 + GE6 -4.664210e+02 -3.419953e-04 1.755e-04 4.427e-01 + GE7 -4.664209e+02 1.184382e-04 3.281e-05 4.362e-01 + GE8 -4.664209e+02 -4.987363e-05 1.601e-05 4.257e-01 + GE9 -4.664209e+02 1.750317e-05 2.282e-06 4.305e-01 + GE10 -4.664209e+02 -3.446228e-06 4.724e-07 4.311e-01 + GE11 -4.664209e+02 -2.602539e-07 1.600e-07 4.331e-01 + GE12 -4.664209e+02 -5.402227e-08 1.064e-08 3.626e-01 +E_delta_band = -6.93658687e-02 Ry = -9.43771061e-01 eV +E_delta_NN= -1.94276005e-01 Ry = -2.64326066e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4163 11 0.67 1e+02 % + Run_lcao lcao_line 7.4078 1 7.4 1e+02 % + Potential init_pot 0.24378 2 0.12 3.3 % + PW_Basis recip2real 0.26832 17 0.016 3.6 % + PW_Basis gathers_scatterp 0.1123 17 0.0066 1.5 % + Potential v_of_rho 0.96642 14 0.069 13 % + XC_Functional v_xc 0.28578 15 0.019 3.9 % + H_Hartree_pw v_hartree 0.64005 14 0.046 8.6 % + PW_Basis real2recip 0.64066 41 0.016 8.6 % + PW_Basis gatherp_scatters 0.23848 41 0.0058 3.2 % + ORB_control set_orb_tables 0.89339 1 0.89 12 % + ORB_gen_tables gen_tables 0.89339 1 0.89 12 % + ORB_table_phi init_Table 0.37729 1 0.38 5.1 % + ORB_table_phi cal_ST_Phi12_R 0.37295 126 0.003 5 % + ORB_table_beta init_Table_Beta 0.15311 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15181 56 0.0027 2 % + ORB_table_alpha init_Table_Alpha 0.20499 1 0.2 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20329 66 0.0031 2.7 % + LOOP_ions opt_ions 6.0684 1 6.1 82 % + ESolver_KS_LCAO Run 5.5299 1 5.5 75 % + HSolverLCAO solve 3.206 12 0.27 43 % + HamiltLCAO updateHk 1.5952 12 0.13 22 % + LCAO_Hamilt cal_Hgamma 1.5681 12 0.13 21 % + Gint_interface cal_gint 3.0864 25 0.12 42 % + Gint_Gamma distri_vl 2.8675 6 0.48 39 % + LCAO_Deepks cal_projected_DM 5.9059 14 0.42 80 % + LCAO_gen_fixedH add_v_delta 2.7388 6 0.46 37 % + LCAO_DESCRIPTOR add_v_delta 2.7387 6 0.46 37 % + ElecStateLCAO psiToRho 1.5925 12 0.13 21 % + Charge mix_rho 0.8275 11 0.075 11 % + LOOP_ions force_stress 0.53834 1 0.54 7.3 % + Force_Stress_LCAO getForceStress 0.53832 1 0.54 7.3 % + Force_LCAO_gamma ftable_gamma 0.34838 1 0.35 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.34117 1 0.34 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:21 2022 + FINISH Time : Wed Sep 28 11:11:28 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/141/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ad43f734330f5e1b1bf5db5872492fc0928bb893 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.184474 0.655932 0.0761611 +H 0.143932 0.628422 0.118735 +H 0.209141 0.706717 0.111266 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..42e0da8585d56832b1d28ebc7522d391e8b367e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2984 2 + 2 -12.9161 2 + 3 -9.21796 2 + 4 -6.74762 2 + 5 1.26072 0 + 6 4.3648 0 + 7 11.0792 0 + 8 11.3404 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fa77f7cd15cd6366b1213f062cabbdda8d9d6562 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:25 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.16528571177 18.3660950773 2.13251182291 0 0 0 0 + tauc_H1 4.03008326445 17.5958183288 3.3245738144 0 0 0 0 + tauc_H2 5.85594017677 19.7880692456 3.11545771089 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.087926796112 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0885307206952 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106681810618 (SEC) + + DONE : INIT CHARGE Time : 0.150198964283 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.432742 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000919 + + Density error is 0.213756181088 + + Energy Rydberg eV + E_KohnSham -34.191794933 -465.203235937 + E_Harris -34.3813165879 -467.781810337 + E_Fermi -0.403381737258 -5.48829009585 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00134830450489 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114319749733 + + Density error is 0.0978751427806 + + Energy Rydberg eV + E_KohnSham -34.280567646 -466.41105066 + E_Harris -34.2873631773 -466.503508606 + E_Fermi -0.21339672598 -2.90341140787 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125827486105 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109265756735 + + Density error is 0.0628353459409 + + Energy Rydberg eV + E_KohnSham -34.2808410854 -466.414770994 + E_Harris -34.2852371604 -466.474582663 + E_Fermi -0.202664457188 -2.75739139983 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110302764806 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102310577622 + + Density error is 0.00195645079287 + + Energy Rydberg eV + E_KohnSham -34.2808180081 -466.414457011 + E_Harris -34.2808186084 -466.414465178 + E_Fermi -0.167082116442 -2.27326881751 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110162818233 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010234362299 + + Density error is 0.000866429330977 + + Energy Rydberg eV + E_KohnSham -34.2807635143 -466.413715585 + E_Harris -34.2807646119 -466.413730518 + E_Fermi -0.166480959658 -2.26508965985 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010998156538 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010223738014 + + Density error is 0.000136753226659 + + Energy Rydberg eV + E_KohnSham -34.2807986404 -466.4141935 + E_Harris -34.2807986698 -466.414193901 + E_Fermi -0.166417338044 -2.26422404339 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109983861709 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102255927474 + + Density error is 3.53449934196e-05 + + Energy Rydberg eV + E_KohnSham -34.2807862202 -466.414024515 + E_Harris -34.2807862265 -466.414024601 + E_Fermi -0.166316164081 -2.26284750101 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109979138556 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102247108944 + + Density error is 1.57628922543e-05 + + Energy Rydberg eV + E_KohnSham -34.2807897237 -466.414072182 + E_Harris -34.2807897247 -466.414072196 + E_Fermi -0.166352955632 -2.26334807573 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010997728376 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102247031625 + + Density error is 2.59046531453e-06 + + Energy Rydberg eV + E_KohnSham -34.2807883844 -466.41405396 + E_Harris -34.2807883845 -466.414053961 + E_Fermi -0.166337516049 -2.26313800943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109976935869 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102247142968 + + Density error is 3.080737461e-07 + + Energy Rydberg eV + E_KohnSham -34.2807885961 -466.414056841 + E_Harris -34.2807885961 -466.414056841 + E_Fermi -0.166334812129 -2.26310122072 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109976971943 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102247196461 + + Density error is 1.23922232874e-07 + + Energy Rydberg eV + E_KohnSham -34.2807886367 -466.414057392 + E_Harris -34.2807886367 -466.414057392 + E_Fermi -0.16633473508 -2.2631001724 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109976966163 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102247211708 + + Density error is 1.05456284062e-08 + + Energy Rydberg eV + E_KohnSham -34.2807886385 -466.414057417 + E_Harris -34.2807886385 -466.414057417 + E_band -7.96432891387 -108.360253975 + E_one_elec -69.2326953291 -941.959144374 + E_Hartree +36.0086260277 +489.922491127 + E_xc -8.20460790102 -111.62941731 + E_Ewald +7.27232574985 +98.94506791 + E_demet -1.66970467247e-75 -2.27174975228e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194727925731 -2.64940934967 + E_Fermi -0.166334629353 -2.26309873392 + + charge density convergence is achieved + final etot is -466.414057417 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2984 2.00000 + 2 -12.9161 2.00000 + 3 -9.21796 2.00000 + 4 -6.74762 2.00000 + 5 1.26072 0.00000 + 6 4.36480 0.00000 + 7 11.0792 0.00000 + 8 11.3404 0.00000 + + EFERMI = -2.263098733916172 eV + OUT.ABACUS/ final etot is -466.4140574167905 eV + correction force for each atom along direction 1 is 3.49781e-05 + correction force for each atom along direction 2 is 3.58413e-05 + correction force for each atom along direction 3 is 0.000184938 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.59155611 +0.71584086 -0.047515290 + H1 -0.53267668 -0.44984202 +0.39520570 + H2 -0.058879435 -0.26599884 -0.34769041 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4140574167905 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.2704 11 0.75 1.0e+02% + Run_lcao lcao_line 8.2604 1 8.3 1.e+02% + Potential init_pot 0.28437 2 0.14 3.4% + PW_Basis recip2real 0.30179 17 0.018 3.6% + PW_Basis gathers_scatterp 0.13145 17 0.0077 1.6% + Potential v_of_rho 1.1063 14 0.079 13.% + XC_Functional v_xc 0.32761 15 0.022 4.0% + H_Hartree_pw v_hartree 0.73187 14 0.052 8.8% + PW_Basis real2recip 0.74836 41 0.018 9.0% + PW_Basis gatherp_scatters 0.28158 41 0.0069 3.4% + ORB_control set_orb_tables 1.0925 1 1.1 13.% + ORB_gen_tables gen_tables 1.0925 1 1.1 13.% + ORB_table_phi init_Table 0.47300 1 0.47 5.7% + ORB_table_phi cal_ST_Phi12_R 0.46784 126 0.0037 5.7% + ORB_table_beta init_Table_Beta 0.18293 1 0.18 2.2% + ORB_table_beta VNL_PhiBeta_R 0.18145 56 0.0032 2.2% + ORB_table_alpha init_Table_Alpha 0.24538 1 0.25 3.0% + ORB_table_alpha S_PhiAlpha_R 0.24343 66 0.0037 2.9% + LOOP_ions opt_ions 6.6556 1 6.7 80.% + ESolver_KS_LCAO Run 6.0417 1 6.0 73.% + HSolverLCAO solve 3.3534 12 0.28 41.% + HamiltLCAO updateHk 1.6873 12 0.14 20.% + LCAO_Hamilt cal_Hgamma 1.6577 12 0.14 20.% + Gint_interface cal_gint 3.2015 25 0.13 39.% + Gint_Gamma distri_vl 3.1352 6 0.52 38.% + LCAO_Deepks cal_projected_DM 6.4743 14 0.46 78.% + LCAO_gen_fixedH add_v_delta 2.9864 6 0.50 36.% + LCAO_DESCRIPTOR add_v_delta 2.9864 6 0.50 36.% + ElecStateLCAO psiToRho 1.6482 12 0.14 20.% + Charge mix_rho 0.98533 11 0.090 12.% + LOOP_ions force_stress 0.61369 1 0.61 7.4% + Force_Stress_LCAO getForceStress 0.61366 1 0.61 7.4% + Force_LCAO_gamma ftable_gamma 0.39229 1 0.39 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.38413 1 0.38 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:25 2022 + Finish Time : Wed Sep 28 11:10:34 2022 + Total Time : 0 h 0 mins 9 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..73dd349cc938959487701f11a7cc59daee5b0963 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012366 ima = 3.67521e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122926049822 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011185017777 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112425244968 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112664444427 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112617699078 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011264589088 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011263987144 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112642578728 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011264191143 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112641804816 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112641794087 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112641788438 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a336d79da6ec6a556976121af5cf16ebea5e6c23 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.834714288229 18.366095077305 2.132511822907 0 0 0 +H +0.0 +2 +-23.969916735544 17.595818328820 3.324573814396 0 0 0 +-22.144059823225 19.788069245641 3.115457710913 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/conv new file mode 100644 index 0000000000000000000000000000000000000000..ae3bd8eccc3db5dacb0bc2fd4f6b13b043121265 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/conv @@ -0,0 +1 @@ +142 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8444b5247b94a057598bb30f547e3599de549933 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750961438 0.01269787692 1.269117996 1.357154676 1.469319827 0.008795588595 0.01789379724 0.03907976071 +-4.423960961e-19 0.0009934723307 0.002658469305 0.01252786259 0.04540547033 -2.523254171e-19 2.215166346e-06 6.272322273e-06 +0.001617367709 0.006025669388 + +H atom_index 1 n_descriptor 18 +1.259754229 0.03411761735 0.1122684939 0.1543850619 0.3237589013 0.02293135981 0.02885041748 0.03731622059 +-1.667943536e-17 4.780430387e-05 0.103810373 0.1157927161 0.1324892221 -7.918710407e-18 3.33117364e-06 0.01319884122 +0.02676248256 0.03118397085 + +H atom_index 2 n_descriptor 18 +1.22494937 0.03530198656 0.1003908661 0.138515717 0.3121343445 0.02128180995 0.0268156692 0.0384767449 +2.187636823e-17 4.455461843e-05 0.09527012105 0.1141769559 0.118744615 8.348885942e-18 5.178102502e-06 0.01360126568 +0.02544289923 0.02955380011 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d6fd77a4977d18fbc7d9f0f7b4ee9af9edfb0fc0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:25 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0879521 SEC) : SETUP UNITCELL + DONE(0.0885462 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106704 SEC) : INIT PLANEWAVE + DONE(0.150335 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.432806 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652032e+02 0.000000e+00 2.138e-01 5.970e-01 + GE2 -4.664111e+02 -1.207815e+00 9.788e-02 5.611e-01 + GE3 -4.664148e+02 -3.720334e-03 6.284e-02 6.331e-01 + GE4 -4.664145e+02 3.139827e-04 1.956e-03 4.942e-01 + GE5 -4.664137e+02 7.414259e-04 8.664e-04 4.870e-01 + GE6 -4.664142e+02 -4.779148e-04 1.368e-04 4.831e-01 + GE7 -4.664140e+02 1.689848e-04 3.534e-05 4.724e-01 + GE8 -4.664141e+02 -4.766701e-05 1.576e-05 4.684e-01 + GE9 -4.664141e+02 1.822170e-05 2.590e-06 4.663e-01 + GE10 -4.664141e+02 -2.880381e-06 3.081e-07 4.631e-01 + GE11 -4.664141e+02 -5.512427e-07 1.239e-07 4.650e-01 + GE12 -4.664141e+02 -2.467234e-08 1.055e-08 3.889e-01 +E_delta_band = -7.02907399e-02 Ry = -9.56354579e-01 eV +E_delta_NN= -1.94727926e-01 Ry = -2.64940935e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.2704 11 0.75 1e+02 % + Run_lcao lcao_line 8.2604 1 8.3 1e+02 % + Potential init_pot 0.28437 2 0.14 3.4 % + PW_Basis recip2real 0.30179 17 0.018 3.6 % + PW_Basis gathers_scatterp 0.13145 17 0.0077 1.6 % + Potential v_of_rho 1.1063 14 0.079 13 % + XC_Functional v_xc 0.32761 15 0.022 4 % + H_Hartree_pw v_hartree 0.73187 14 0.052 8.8 % + PW_Basis real2recip 0.74836 41 0.018 9 % + PW_Basis gatherp_scatters 0.28158 41 0.0069 3.4 % + ORB_control set_orb_tables 1.0925 1 1.1 13 % + ORB_gen_tables gen_tables 1.0925 1 1.1 13 % + ORB_table_phi init_Table 0.473 1 0.47 5.7 % + ORB_table_phi cal_ST_Phi12_R 0.46784 126 0.0037 5.7 % + ORB_table_beta init_Table_Beta 0.18293 1 0.18 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.18145 56 0.0032 2.2 % + ORB_table_alpha init_Table_Alpha 0.24538 1 0.25 3 % + ORB_table_alpha S_PhiAlpha_R 0.24343 66 0.0037 2.9 % + LOOP_ions opt_ions 6.6556 1 6.7 80 % + ESolver_KS_LCAO Run 6.0417 1 6 73 % + HSolverLCAO solve 3.3534 12 0.28 41 % + HamiltLCAO updateHk 1.6873 12 0.14 20 % + LCAO_Hamilt cal_Hgamma 1.6577 12 0.14 20 % + Gint_interface cal_gint 3.2015 25 0.13 39 % + Gint_Gamma distri_vl 3.1352 6 0.52 38 % + LCAO_Deepks cal_projected_DM 6.4743 14 0.46 78 % + LCAO_gen_fixedH add_v_delta 2.9864 6 0.5 36 % + LCAO_DESCRIPTOR add_v_delta 2.9864 6 0.5 36 % + ElecStateLCAO psiToRho 1.6482 12 0.14 20 % + Charge mix_rho 0.98533 11 0.09 12 % + LOOP_ions force_stress 0.61369 1 0.61 7.4 % + Force_Stress_LCAO getForceStress 0.61366 1 0.61 7.4 % + Force_LCAO_gamma ftable_gamma 0.39229 1 0.39 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.38413 1 0.38 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:25 2022 + FINISH Time : Wed Sep 28 11:10:34 2022 + TOTAL Time : 9 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/142/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..41480cf3b996404b096cb22c910b89d1670a0669 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.159286 0.661765 0.113578 +H 0.202916 0.618033 0.137499 +H 0.199079 0.711476 0.1117 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..99446b29a3d2a1828102e0c477a8ee6fe5c56f70 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5512 2 + 2 -12.7287 2 + 3 -9.52335 2 + 4 -6.80157 2 + 5 1.30307 0 + 6 4.53491 0 + 7 11.0398 0 + 8 11.327 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3ecc30dd49f4f4d0330bdc85e1796702c5d1a83b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:03 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.45999836398 18.529423809 3.18019354497 0 0 0 0 + tauc_H1 5.68164548663 17.3049252287 3.84996847569 0 0 0 0 + tauc_H2 5.57421145844 19.9213186769 3.12759013889 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0886709667534 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0980662220464 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116429825761 (SEC) + + DONE : INIT CHARGE Time : 0.166582133566 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450044 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00139 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113 + + Density error is 0.214028589377 + + Energy Rydberg eV + E_KohnSham -34.1870348729 -465.138471996 + E_Harris -34.3781535942 -467.7387756 + E_Fermi -0.413161210556 -5.62134665614 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00138478162784 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112335524019 + + Density error is 0.0972594886827 + + Energy Rydberg eV + E_KohnSham -34.2760032529 -466.348948906 + E_Harris -34.2828030644 -466.441465087 + E_Fermi -0.222982554322 -3.03383329338 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127585400867 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105277749907 + + Density error is 0.0622767605347 + + Energy Rydberg eV + E_KohnSham -34.2762214691 -466.351917889 + E_Harris -34.2806165718 -466.41171633 + E_Fermi -0.210684305065 -2.86650702806 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109206668346 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946421396912 + + Density error is 0.00196547848024 + + Energy Rydberg eV + E_KohnSham -34.276222887 -466.351937181 + E_Harris -34.2762240476 -466.351952972 + E_Fermi -0.174662981532 -2.3764117785 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109265611654 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000948402834631 + + Density error is 0.000853257349048 + + Energy Rydberg eV + E_KohnSham -34.2761628445 -466.351120261 + E_Harris -34.2761643606 -466.351140888 + E_Fermi -0.173967266429 -2.36694608892 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010904056917 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946926950229 + + Density error is 0.000108502840861 + + Energy Rydberg eV + E_KohnSham -34.2762045189 -466.35168727 + E_Harris -34.2762045406 -466.351687565 + E_Fermi -0.17400077152 -2.36740194907 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109003446766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946810385434 + + Density error is 3.77867983341e-05 + + Energy Rydberg eV + E_KohnSham -34.2761913898 -466.35150864 + E_Harris -34.2761913974 -466.351508744 + E_Fermi -0.173893321232 -2.3659400129 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109004307917 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946797631713 + + Density error is 2.1006918899e-05 + + Energy Rydberg eV + E_KohnSham -34.2761938959 -466.351542737 + E_Harris -34.2761938978 -466.351542762 + E_Fermi -0.173941379688 -2.36659388174 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109000432465 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946787261975 + + Density error is 1.77322531262e-06 + + Energy Rydberg eV + E_KohnSham -34.2761923102 -466.351521162 + E_Harris -34.2761923102 -466.351521163 + E_Fermi -0.173917609908 -2.36627047729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109000513982 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946786594379 + + Density error is 3.23870498386e-07 + + Energy Rydberg eV + E_KohnSham -34.2761926332 -466.351525557 + E_Harris -34.2761926332 -466.351525557 + E_Fermi -0.173916655897 -2.3662574973 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109000540795 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946787019729 + + Density error is 1.2015945284e-07 + + Energy Rydberg eV + E_KohnSham -34.2761926617 -466.351525944 + E_Harris -34.2761926617 -466.351525944 + E_Fermi -0.173916543488 -2.3662559679 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109000525741 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946787011466 + + Density error is 1.14213063172e-08 + + Energy Rydberg eV + E_KohnSham -34.2761926636 -466.351525971 + E_Harris -34.2761926636 -466.351525971 + E_band -8.02676375221 -109.20972353 + E_one_elec -69.5183225433 -945.845301991 + E_Hartree +36.1333996139 +491.62012286 + E_xc -8.22458941068 -111.901279696 + E_Ewald +7.4571376523 +101.459562842 + E_demet -1.21320129469e-81 -1.65064504287e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195289114849 -2.65704471932 + E_Fermi -0.173916413183 -2.36625419501 + + charge density convergence is achieved + final etot is -466.351525971 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5512 2.00000 + 2 -12.7287 2.00000 + 3 -9.52335 2.00000 + 4 -6.80157 2.00000 + 5 1.30307 0.00000 + 6 4.53491 0.00000 + 7 11.0398 0.00000 + 8 11.3270 0.00000 + + EFERMI = -2.366254195013228 eV + OUT.ABACUS/ final etot is -466.3515259712953 eV + correction force for each atom along direction 1 is 0.000100769 + correction force for each atom along direction 2 is 5.51192e-05 + correction force for each atom along direction 3 is 7.66285e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.21186808 -1.5183945 +0.34461169 + H1 -0.51756058 -0.42365609 -0.035843498 + H2 +0.72942866 +1.9420506 -0.30876819 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3515259712953 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.4304 11 0.77 1.0e+02% + Run_lcao lcao_line 8.4197 1 8.4 1.e+02% + Potential init_pot 0.28604 2 0.14 3.4% + PW_Basis recip2real 0.30260 17 0.018 3.6% + PW_Basis gathers_scatterp 0.13074 17 0.0077 1.6% + Potential v_of_rho 1.0673 14 0.076 13.% + XC_Functional v_xc 0.31076 15 0.021 3.7% + H_Hartree_pw v_hartree 0.71112 14 0.051 8.4% + PW_Basis real2recip 0.70441 41 0.017 8.4% + PW_Basis gatherp_scatters 0.26757 41 0.0065 3.2% + ORB_control set_orb_tables 1.1005 1 1.1 13.% + ORB_gen_tables gen_tables 1.1005 1 1.1 13.% + ORB_table_phi init_Table 0.47605 1 0.48 5.6% + ORB_table_phi cal_ST_Phi12_R 0.47082 126 0.0037 5.6% + ORB_table_beta init_Table_Beta 0.18681 1 0.19 2.2% + ORB_table_beta VNL_PhiBeta_R 0.18525 56 0.0033 2.2% + ORB_table_alpha init_Table_Alpha 0.25235 1 0.25 3.0% + ORB_table_alpha S_PhiAlpha_R 0.25037 66 0.0038 3.0% + LOOP_ions opt_ions 6.7876 1 6.8 81.% + ESolver_KS_LCAO Run 6.1689 1 6.2 73.% + HSolverLCAO solve 3.6836 12 0.31 44.% + HamiltLCAO updateHk 1.8337 12 0.15 22.% + LCAO_Hamilt cal_Hgamma 1.8040 12 0.15 21.% + Gint_interface cal_gint 3.5583 25 0.14 42.% + Gint_Gamma distri_vl 3.2008 6 0.53 38.% + LCAO_Deepks cal_projected_DM 6.5944 14 0.47 78.% + LCAO_gen_fixedH add_v_delta 3.0541 6 0.51 36.% + LCAO_DESCRIPTOR add_v_delta 3.0541 6 0.51 36.% + ElecStateLCAO psiToRho 1.8331 12 0.15 22.% + Charge mix_rho 0.86522 11 0.079 10.% + LOOP_ions force_stress 0.61855 1 0.62 7.3% + Force_Stress_LCAO getForceStress 0.61852 1 0.62 7.3% + Force_LCAO_gamma ftable_gamma 0.40257 1 0.40 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.39470 1 0.39 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:03 2022 + Finish Time : Wed Sep 28 11:08:11 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e826541acf196be8845184e1a36996abd88fc1b8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124248 ima = 3.65637e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122321773653 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111276060903 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111817527577 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001120908165 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112029331718 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112062584664 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112059629841 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112062619764 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112061710439 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112061632365 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112061621686 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112061615537 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9f36ce3512bc35f9e94778a748e9f4c0cd75409d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.540001636018 18.529423808998 3.180193544945 0 0 0 +H +0.0 +2 +-22.318354513353 17.304925228695 3.849968475698 0 0 0 +-22.425788541552 19.921318676918 3.127590138892 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/conv new file mode 100644 index 0000000000000000000000000000000000000000..49d5116bb5e2dc0147187894755cd72642d2d1d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/conv @@ -0,0 +1 @@ +143 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b43243341691f1939f39b8ed800c876ce24724dd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755244105 0.01286711429 1.275907759 1.359879392 1.470288178 0.00981789331 0.01654972765 0.03919214716 +4.521902692e-18 0.0009068381761 0.002985239857 0.01387310455 0.04832393469 3.877558014e-19 3.165940132e-06 8.130244194e-06 +0.001589042785 0.006174869549 + +H atom_index 1 n_descriptor 18 +1.233315619 0.03562092443 0.1066228227 0.1419148849 0.3134474254 0.02275793444 0.02724452849 0.03872084843 +-4.774729632e-17 5.050174312e-05 0.1007604891 0.1143363522 0.1216610687 -4.272916276e-19 3.635348395e-06 0.01368773652 +0.02684363083 0.02996332686 + +H atom_index 2 n_descriptor 18 +1.289002696 0.03381795262 0.1273797259 0.168768613 0.3313293513 0.02557645181 0.0304951704 0.03726547316 +-1.715159822e-17 5.566154815e-05 0.1084612943 0.1228892457 0.144668558 -2.330670039e-18 7.770727028e-07 0.01364603185 +0.02881060763 0.03239240649 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a77c4c30ce7696417398cd98049c44a3cd7dcbfb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/e_base.npy new file mode 100644 index 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TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:03 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0886924 SEC) : SETUP UNITCELL + DONE(0.098087 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116453 SEC) : INIT PLANEWAVE + DONE(0.166711 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.45011 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651385e+02 0.000000e+00 2.140e-01 6.136e-01 + GE2 -4.663489e+02 -1.210477e+00 9.726e-02 5.721e-01 + GE3 -4.663519e+02 -2.968983e-03 6.228e-02 6.339e-01 + GE4 -4.663519e+02 -1.929144e-05 1.965e-03 4.968e-01 + GE5 -4.663511e+02 8.169192e-04 8.533e-04 4.991e-01 + GE6 -4.663517e+02 -5.670091e-04 1.085e-04 4.952e-01 + GE7 -4.663515e+02 1.786306e-04 3.779e-05 4.856e-01 + GE8 -4.663515e+02 -3.409753e-05 2.101e-05 4.754e-01 + GE9 -4.663515e+02 2.157500e-05 1.773e-06 4.776e-01 + GE10 -4.663515e+02 -4.394116e-06 3.239e-07 4.718e-01 + GE11 -4.663515e+02 -3.879886e-07 1.202e-07 4.784e-01 + GE12 -4.663515e+02 -2.679541e-08 1.142e-08 4.067e-01 +E_delta_band = -7.14711390e-02 Ry = -9.72414733e-01 eV +E_delta_NN= -1.95289115e-01 Ry = -2.65704472e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.4304 11 0.77 1e+02 % + Run_lcao lcao_line 8.4197 1 8.4 1e+02 % + Potential init_pot 0.28604 2 0.14 3.4 % + PW_Basis recip2real 0.3026 17 0.018 3.6 % + PW_Basis gathers_scatterp 0.13074 17 0.0077 1.6 % + Potential v_of_rho 1.0673 14 0.076 13 % + XC_Functional v_xc 0.31076 15 0.021 3.7 % + H_Hartree_pw v_hartree 0.71112 14 0.051 8.4 % + PW_Basis real2recip 0.70441 41 0.017 8.4 % + PW_Basis gatherp_scatters 0.26757 41 0.0065 3.2 % + ORB_control set_orb_tables 1.1005 1 1.1 13 % + ORB_gen_tables gen_tables 1.1005 1 1.1 13 % + ORB_table_phi init_Table 0.47605 1 0.48 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.47082 126 0.0037 5.6 % + ORB_table_beta init_Table_Beta 0.18681 1 0.19 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.18525 56 0.0033 2.2 % + ORB_table_alpha init_Table_Alpha 0.25235 1 0.25 3 % + ORB_table_alpha S_PhiAlpha_R 0.25037 66 0.0038 3 % + LOOP_ions opt_ions 6.7876 1 6.8 81 % + ESolver_KS_LCAO Run 6.1689 1 6.2 73 % + HSolverLCAO solve 3.6836 12 0.31 44 % + HamiltLCAO updateHk 1.8337 12 0.15 22 % + LCAO_Hamilt cal_Hgamma 1.804 12 0.15 21 % + Gint_interface cal_gint 3.5583 25 0.14 42 % + Gint_Gamma distri_vl 3.2008 6 0.53 38 % + LCAO_Deepks cal_projected_DM 6.5944 14 0.47 78 % + LCAO_gen_fixedH add_v_delta 3.0541 6 0.51 36 % + LCAO_DESCRIPTOR add_v_delta 3.0541 6 0.51 36 % + ElecStateLCAO psiToRho 1.8331 12 0.15 22 % + Charge mix_rho 0.86522 11 0.079 10 % + LOOP_ions force_stress 0.61855 1 0.62 7.3 % + Force_Stress_LCAO getForceStress 0.61852 1 0.62 7.3 % + Force_LCAO_gamma ftable_gamma 0.40257 1 0.4 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.3947 1 0.39 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:03 2022 + FINISH Time : Wed Sep 28 11:08:11 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/143/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4ce3c2d91a0c2c585a88e9795d28504153a29f23 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.137429 0.670954 0.135393 +H 0.167427 0.622643 0.166444 +H 0.152665 0.729461 0.161716 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..cecd995f9049f555959923874b01b7e22a4de359 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1685 2 + 2 -13.3962 2 + 3 -8.75696 2 + 4 -6.7128 2 + 5 1.32777 0 + 6 4.49921 0 + 7 11.084 0 + 8 11.2999 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0d7d55389e6e7e523a756c8c0a37daa2bc9c28ae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:52 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.84800608424 18.7867120538 3.79101276057 0 0 0 0 + tauc_H1 4.68796538051 17.4340090167 4.6604430333 0 0 0 0 + tauc_H2 4.27462251622 20.4249002133 4.52805208683 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0862244332325 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0983349533427 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11649488568 (SEC) + + DONE : INIT CHARGE Time : 0.165791428975 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443774 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00145 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00081 + + Density error is 0.215508920827 + + Energy Rydberg eV + E_KohnSham -34.1903590912 -465.183700307 + E_Harris -34.3829094799 -467.803482745 + E_Fermi -0.404383063339 -5.50191383611 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00132662846227 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106728368368 + + Density error is 0.0980760291982 + + Energy Rydberg eV + E_KohnSham -34.278751284 -466.386337787 + E_Harris -34.2853458043 -466.476060839 + E_Fermi -0.213296747321 -2.90205112843 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012201507624 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103333654837 + + Density error is 0.0627322833463 + + Energy Rydberg eV + E_KohnSham -34.2788727387 -466.387990263 + E_Harris -34.2830912173 -466.445385609 + E_Fermi -0.200689514098 -2.73052092058 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102895783163 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991550275728 + + Density error is 0.00212343418609 + + Energy Rydberg eV + E_KohnSham -34.2788845936 -466.388151558 + E_Harris -34.2788888665 -466.388209694 + E_Fermi -0.165656277934 -2.25386928937 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102369985274 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991677843272 + + Density error is 0.000809832378541 + + Energy Rydberg eV + E_KohnSham -34.2788349601 -466.387476259 + E_Harris -34.2788358386 -466.387488211 + E_Fermi -0.164688508738 -2.24070211395 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102191398035 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000990989337618 + + Density error is 0.000228693592367 + + Energy Rydberg eV + E_KohnSham -34.2788706197 -466.387961433 + E_Harris -34.2788708064 -466.387963973 + E_Fermi -0.164778696777 -2.24192918517 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102173418133 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991392287666 + + Density error is 3.77635658592e-05 + + Energy Rydberg eV + E_KohnSham -34.278854855 -466.387746942 + E_Harris -34.2788548625 -466.387747045 + E_Fermi -0.164591314335 -2.23937971626 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010217520783 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991304313613 + + Density error is 1.75610480611e-05 + + Energy Rydberg eV + E_KohnSham -34.2788611229 -466.387832222 + E_Harris -34.278861124 -466.387832237 + E_Fermi -0.164636312596 -2.23999194902 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102170653223 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991302576973 + + Density error is 1.9294443658e-06 + + Energy Rydberg eV + E_KohnSham -34.2788597531 -466.387813586 + E_Harris -34.2788597531 -466.387813586 + E_Fermi -0.164617366531 -2.23973417457 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102170280575 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991304671327 + + Density error is 4.41480344474e-07 + + Energy Rydberg eV + E_KohnSham -34.2788599822 -466.387816702 + E_Harris -34.2788599822 -466.387816702 + E_Fermi -0.164615696948 -2.23971145874 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102170282027 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991305136402 + + Density error is 1.51089372379e-07 + + Energy Rydberg eV + E_KohnSham -34.2788600012 -466.38781696 + E_Harris -34.2788600012 -466.38781696 + E_Fermi -0.164615499986 -2.23970877893 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102170258134 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991305265166 + + Density error is 9.47752136489e-09 + + Energy Rydberg eV + E_KohnSham -34.278860004 -466.387816999 + E_Harris -34.278860004 -466.387816999 + E_band -7.9429220105 -108.068998112 + E_one_elec -69.3005474419 -942.882319729 + E_Hartree +36.0581701961 +490.596574121 + E_xc -8.21203902775 -111.730522976 + E_Ewald +7.29993144701 +99.3206626888 + E_demet -2.55033726381e-77 -3.46991186095e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194626470543 -2.64802898101 + E_Fermi -0.164615354227 -2.23970679578 + + charge density convergence is achieved + final etot is -466.387816999 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1685 2.00000 + 2 -13.3962 2.00000 + 3 -8.75696 2.00000 + 4 -6.71280 2.00000 + 5 1.32777 0.00000 + 6 4.49921 0.00000 + 7 11.0840 0.00000 + 8 11.2999 0.00000 + + EFERMI = -2.239706795779483 eV + OUT.ABACUS/ final etot is -466.3878169992919 eV + correction force for each atom along direction 1 is 0.000161384 + correction force for each atom along direction 2 is 3.83880e-05 + correction force for each atom along direction 3 is 1.98639e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.72979250 +0.60618945 -0.83697506 + H1 +0.50614415 -0.14362354 +0.61373193 + H2 +0.22364835 -0.46256591 +0.22324313 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3878169992919 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.1191 11 0.74 1.0e+02% + Run_lcao lcao_line 8.1103 1 8.1 1.e+02% + Potential init_pot 0.28135 2 0.14 3.5% + PW_Basis recip2real 0.30023 17 0.018 3.7% + PW_Basis gathers_scatterp 0.13158 17 0.0077 1.6% + Potential v_of_rho 1.0558 14 0.075 13.% + XC_Functional v_xc 0.30307 15 0.020 3.7% + H_Hartree_pw v_hartree 0.70855 14 0.051 8.7% + PW_Basis real2recip 0.70243 41 0.017 8.7% + PW_Basis gatherp_scatters 0.26724 41 0.0065 3.3% + ORB_control set_orb_tables 1.0850 1 1.1 13.% + ORB_gen_tables gen_tables 1.0850 1 1.1 13.% + ORB_table_phi init_Table 0.47327 1 0.47 5.8% + ORB_table_phi cal_ST_Phi12_R 0.46808 126 0.0037 5.8% + ORB_table_beta init_Table_Beta 0.18249 1 0.18 2.2% + ORB_table_beta VNL_PhiBeta_R 0.18092 56 0.0032 2.2% + ORB_table_alpha init_Table_Alpha 0.24455 1 0.24 3.0% + ORB_table_alpha S_PhiAlpha_R 0.24261 66 0.0037 3.0% + LOOP_ions opt_ions 6.4914 1 6.5 80.% + ESolver_KS_LCAO Run 5.8824 1 5.9 72.% + HSolverLCAO solve 3.4289 12 0.29 42.% + HamiltLCAO updateHk 1.7183 12 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.6886 12 0.14 21.% + Gint_interface cal_gint 3.2919 25 0.13 41.% + Gint_Gamma distri_vl 3.0588 6 0.51 38.% + LCAO_Deepks cal_projected_DM 6.3059 14 0.45 78.% + LCAO_gen_fixedH add_v_delta 2.9113 6 0.49 36.% + LCAO_DESCRIPTOR add_v_delta 2.9113 6 0.49 36.% + ElecStateLCAO psiToRho 1.6930 12 0.14 21.% + Charge mix_rho 0.85290 11 0.078 11.% + LOOP_ions force_stress 0.60883 1 0.61 7.5% + Force_Stress_LCAO getForceStress 0.60880 1 0.61 7.5% + Force_LCAO_gamma ftable_gamma 0.39315 1 0.39 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.38529 1 0.39 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:52 2022 + Finish Time : Wed Sep 28 11:09:01 2022 + Total Time : 0 h 0 mins 9 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6acb31a2ce83d5642b8ccbddaff4400092bfb80e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123683 ima = 3.68143e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123589789381 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112926324846 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113354356884 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011356339568 + charge after normalized = 7.99999999999996 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113519432535 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113549971036 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113537426192 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113540196772 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113539545636 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113539486351 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113539471384 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113539463934 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7b1240877122bddea03cefffb7543adee6ee66f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.151993915762 18.786712053825 3.791012760569 0 0 0 +H +0.0 +2 +-23.312034619467 17.434009016678 4.660443033275 0 0 0 +-23.725377483797 20.424900213312 4.528052086813 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/conv new file mode 100644 index 0000000000000000000000000000000000000000..fa45dcae78b4f1f96cdf911de30fddd4dd8b505a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/conv @@ -0,0 +1 @@ +144 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..02a6900041e65f617da5c46b212db11d9cbea387 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742738023 0.01257841554 1.278729326 1.373128548 1.46883292 0.007508042852 0.02072620688 0.03883005232 +7.714749782e-18 0.001153768295 0.002307895232 0.01234036828 0.0418665219 9.518532745e-19 1.39941936e-06 4.529312931e-06 +0.001819886751 0.005547473451 + +H atom_index 1 n_descriptor 18 +1.253906994 0.03337060785 0.1102096633 0.1537031557 0.3249384701 0.0219402676 0.02878277863 0.03662509285 +1.687688466e-17 3.684362417e-05 0.1030112231 0.1150421562 0.1319579486 5.176058438e-18 3.871064587e-06 0.01280093582 +0.02618339769 0.03108809128 + +H atom_index 2 n_descriptor 18 +1.228134886 0.03429093946 0.1015498046 0.1419993572 0.3168063711 0.02083291695 0.02729819105 0.03746298662 +-3.228678072e-17 3.485759234e-05 0.09643740702 0.1142098245 0.1218263479 1.32007449e-17 4.94485832e-06 0.01305115789 +0.02521503988 0.0299193233 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..39cb385678ed7199724f99e5d9adf603a1cf9bea Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:52 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0862467 SEC) : SETUP UNITCELL + DONE(0.098353 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116514 SEC) : INIT PLANEWAVE + DONE(0.165915 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443969 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651837e+02 0.000000e+00 2.155e-01 5.911e-01 + GE2 -4.663863e+02 -1.202637e+00 9.808e-02 5.449e-01 + GE3 -4.663880e+02 -1.652477e-03 6.273e-02 6.134e-01 + GE4 -4.663882e+02 -1.612945e-04 2.123e-03 4.765e-01 + GE5 -4.663875e+02 6.752986e-04 8.098e-04 4.736e-01 + GE6 -4.663880e+02 -4.851733e-04 2.287e-04 4.645e-01 + GE7 -4.663877e+02 2.144902e-04 3.776e-05 4.623e-01 + GE8 -4.663878e+02 -8.527907e-05 1.756e-05 4.520e-01 + GE9 -4.663878e+02 1.863605e-05 1.929e-06 4.528e-01 + GE10 -4.663878e+02 -3.116956e-06 4.415e-07 4.508e-01 + GE11 -4.663878e+02 -2.577383e-07 1.511e-07 4.543e-01 + GE12 -4.663878e+02 -3.909567e-08 9.478e-09 3.837e-01 +E_delta_band = -7.02512930e-02 Ry = -9.55817876e-01 eV +E_delta_NN= -1.94626471e-01 Ry = -2.64802898e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.1191 11 0.74 1e+02 % + Run_lcao lcao_line 8.1103 1 8.1 1e+02 % + Potential init_pot 0.28135 2 0.14 3.5 % + PW_Basis recip2real 0.30023 17 0.018 3.7 % + PW_Basis gathers_scatterp 0.13158 17 0.0077 1.6 % + Potential v_of_rho 1.0558 14 0.075 13 % + XC_Functional v_xc 0.30307 15 0.02 3.7 % + H_Hartree_pw v_hartree 0.70855 14 0.051 8.7 % + PW_Basis real2recip 0.70243 41 0.017 8.7 % + PW_Basis gatherp_scatters 0.26724 41 0.0065 3.3 % + ORB_control set_orb_tables 1.085 1 1.1 13 % + ORB_gen_tables gen_tables 1.085 1 1.1 13 % + ORB_table_phi init_Table 0.47327 1 0.47 5.8 % + ORB_table_phi cal_ST_Phi12_R 0.46808 126 0.0037 5.8 % + ORB_table_beta init_Table_Beta 0.18249 1 0.18 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.18092 56 0.0032 2.2 % + ORB_table_alpha init_Table_Alpha 0.24455 1 0.24 3 % + ORB_table_alpha S_PhiAlpha_R 0.24261 66 0.0037 3 % + LOOP_ions opt_ions 6.4914 1 6.5 80 % + ESolver_KS_LCAO Run 5.8824 1 5.9 72 % + HSolverLCAO solve 3.4289 12 0.29 42 % + HamiltLCAO updateHk 1.7183 12 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.6886 12 0.14 21 % + Gint_interface cal_gint 3.2919 25 0.13 41 % + Gint_Gamma distri_vl 3.0588 6 0.51 38 % + LCAO_Deepks cal_projected_DM 6.3059 14 0.45 78 % + LCAO_gen_fixedH add_v_delta 2.9113 6 0.49 36 % + LCAO_DESCRIPTOR add_v_delta 2.9113 6 0.49 36 % + ElecStateLCAO psiToRho 1.693 12 0.14 21 % + Charge mix_rho 0.8529 11 0.078 11 % + LOOP_ions force_stress 0.60883 1 0.61 7.5 % + Force_Stress_LCAO getForceStress 0.6088 1 0.61 7.5 % + Force_LCAO_gamma ftable_gamma 0.39315 1 0.39 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.38529 1 0.39 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:52 2022 + FINISH Time : Wed Sep 28 11:09:01 2022 + TOTAL Time : 9 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/144/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..873126a18c5d37019db69375cd36fe27b64ccd2b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.134415 0.670751 0.149396 +H 0.143027 0.623124 0.194201 +H 0.11592 0.718673 0.191722 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ae23cc3b3c27e112e18a63a465b7cebfd9c4fdf2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.305 2 + 2 -12.5872 2 + 3 -9.46228 2 + 4 -6.75195 2 + 5 1.15401 0 + 6 4.19619 0 + 7 11.0935 0 + 8 11.3814 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..70c6c130370932eefd03f2bd054fb326f3b26135 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:10 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.7636064068 18.7810173222 4.18308368621 0 0 0 0 + tauc_H1 4.0047645443 17.4474825532 5.43763939154 0 0 0 0 + tauc_H2 3.24575528047 20.1228536569 5.36822448297 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0872420421375 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101230087117 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11932699686 (SEC) + + DONE : INIT CHARGE Time : 0.167851865991 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448634 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000965 + + Density error is 0.211153367883 + + Energy Rydberg eV + E_KohnSham -34.1920113391 -465.206180292 + E_Harris -34.3767007827 -467.719009086 + E_Fermi -0.397972015403 -5.41468705402 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00123934861119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012839033685 + + Density error is 0.0975956578393 + + Energy Rydberg eV + E_KohnSham -34.2789046282 -466.388424142 + E_Harris -34.2858149768 -466.482444258 + E_Fermi -0.210517008481 -2.86423084126 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115463240481 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123000062001 + + Density error is 0.062725700154 + + Energy Rydberg eV + E_KohnSham -34.2791488529 -466.39174699 + E_Harris -34.2836264047 -466.452667207 + E_Fermi -0.200823782502 -2.73234773594 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100871396189 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116596712381 + + Density error is 0.00188930242158 + + Energy Rydberg eV + E_KohnSham -34.2790985203 -466.391062179 + E_Harris -34.2790981373 -466.391056969 + E_Fermi -0.165197541511 -2.24762786014 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100825604997 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116839247465 + + Density error is 0.000796986624092 + + Energy Rydberg eV + E_KohnSham -34.2790572578 -466.390500774 + E_Harris -34.2790580719 -466.39051185 + E_Fermi -0.164895007649 -2.24351167579 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100646924716 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116715035856 + + Density error is 8.95763671405e-05 + + Energy Rydberg eV + E_KohnSham -34.2790850297 -466.39087863 + E_Harris -34.2790850309 -466.390878647 + E_Fermi -0.164692256349 -2.24075310282 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100630021686 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116711081618 + + Density error is 2.63827260092e-05 + + Energy Rydberg eV + E_KohnSham -34.2790768688 -466.390767596 + E_Harris -34.2790768727 -466.390767649 + E_Fermi -0.164613822337 -2.23968595334 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100628406407 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116704576686 + + Density error is 8.93228529829e-06 + + Energy Rydberg eV + E_KohnSham -34.2790783807 -466.390788166 + E_Harris -34.2790783811 -466.390788171 + E_Fermi -0.164642889509 -2.24008143251 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100627677025 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116705143673 + + Density error is 8.15565613295e-07 + + Energy Rydberg eV + E_KohnSham -34.2790774221 -466.390775124 + E_Harris -34.2790774221 -466.390775124 + E_Fermi -0.164633533847 -2.23995414219 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100627723821 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116705330156 + + Density error is 1.08487590376e-07 + + Energy Rydberg eV + E_KohnSham -34.2790775921 -466.390777436 + E_Harris -34.2790775921 -466.390777436 + E_Fermi -0.164633023772 -2.23994720227 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100627751078 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116705369559 + + Density error is 3.31008914605e-08 + + Energy Rydberg eV + E_KohnSham -34.2790776047 -466.390777608 + E_Harris -34.2790776047 -466.390777608 + E_band -7.95349964 -108.212914145 + E_one_elec -69.0645398674 -939.671271945 + E_Hartree +35.9204895566 +488.72333292 + E_xc -8.19025582917 -111.434147354 + E_Ewald +7.17997627496 +97.6885888443 + E_demet -3.10092045113e-70 -4.21901871801e-69 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194446063086 -2.64557441164 + E_Fermi -0.164633011283 -2.23994703234 + + charge density convergence is achieved + final etot is -466.390777608 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3050 2.00000 + 2 -12.5872 2.00000 + 3 -9.46228 2.00000 + 4 -6.75195 2.00000 + 5 1.15401 0.00000 + 6 4.19619 0.00000 + 7 11.0935 0.00000 + 8 11.3814 0.00000 + + EFERMI = -2.239947032341718 eV + OUT.ABACUS/ final etot is -466.3907776080234 eV + correction force for each atom along direction 1 is -0.000162308 + correction force for each atom along direction 2 is 4.20667e-05 + correction force for each atom along direction 3 is 4.48439e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.20044687 +0.31293365 +0.92008726 + H1 +0.16479924 -0.43928959 -0.31239518 + H2 +0.035647630 +0.12635594 -0.60769208 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3907776080234 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6421 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6324 1 6.6 1.e+02% + Potential init_pot 0.28318 2 0.14 4.3% + PW_Basis recip2real 0.26263 16 0.016 4.0% + PW_Basis gathers_scatterp 0.11106 16 0.0069 1.7% + Potential v_of_rho 0.86145 13 0.066 13.% + XC_Functional v_xc 0.23928 14 0.017 3.6% + H_Hartree_pw v_hartree 0.58626 13 0.045 8.8% + PW_Basis real2recip 0.55125 38 0.015 8.3% + PW_Basis gatherp_scatters 0.21103 38 0.0056 3.2% + ORB_control set_orb_tables 1.1119 1 1.1 17.% + ORB_gen_tables gen_tables 1.1119 1 1.1 17.% + ORB_table_phi init_Table 0.48734 1 0.49 7.3% + ORB_table_phi cal_ST_Phi12_R 0.48236 126 0.0038 7.3% + ORB_table_beta init_Table_Beta 0.18802 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18649 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25734 1 0.26 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25543 66 0.0039 3.8% + LOOP_ions opt_ions 4.9946 1 5.0 75.% + ESolver_KS_LCAO Run 4.4196 1 4.4 67.% + HSolverLCAO solve 2.4669 11 0.22 37.% + HamiltLCAO updateHk 1.2704 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2322 11 0.11 19.% + Gint_interface cal_gint 2.3631 23 0.10 36.% + Gint_Gamma distri_vl 2.1205 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.8213 13 0.37 73.% + LCAO_gen_fixedH add_v_delta 1.9888 6 0.33 30.% + LCAO_DESCRIPTOR add_v_delta 1.9888 6 0.33 30.% + ElecStateLCAO psiToRho 1.1798 11 0.11 18.% + Charge mix_rho 0.65618 10 0.066 9.9% + LOOP_ions force_stress 0.57484 1 0.57 8.7% + Force_Stress_LCAO getForceStress 0.57482 1 0.57 8.7% + Force_LCAO_gamma ftable_gamma 0.36013 1 0.36 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.35346 1 0.35 5.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:10 2022 + Finish Time : Wed Sep 28 11:04:16 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..93f386db4a6637fd482b89db51ed2fb29b76e9a8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123533 ima = 3.70705e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122557538187 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111468677761 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112110094578 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112334664622 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298208923 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318858301 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112316807475 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318780716 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318322214 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318288521 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318283215 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0b7b4cd832eac82b291c8b44eb971fbb647c5ae1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.236393593183 18.781017322196 4.183083686184 0 0 0 +H +0.0 +2 +-23.995235455670 17.447482553242 5.437639391533 0 0 0 +-24.754244719507 20.122853656882 5.368224482988 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/conv new file mode 100644 index 0000000000000000000000000000000000000000..a5cce89f27a90c2efb4005f56ec30655e60e3493 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/conv @@ -0,0 +1 @@ +145 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9092890afc403be3195b631dcff3b7bf462f7e79 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754894783 0.0127336798 1.261432085 1.341853791 1.469282044 0.009553994478 0.01628933241 0.03920537308 +5.698652993e-19 0.0008373427285 0.002791262794 0.01308431821 0.04562384248 1.395659547e-18 2.675027445e-06 7.234431306e-06 +0.001583004156 0.006143296961 + +H atom_index 1 n_descriptor 18 +1.239730465 0.03531208782 0.1078045328 0.1448463146 0.3162008744 0.02274406846 0.02762973104 0.03843699003 +2.504021379e-18 4.693940843e-05 0.09968823223 0.1150356517 0.1240770782 2.627637886e-20 3.398956802e-06 0.01353055809 +0.0264360159 0.0302441798 + +H atom_index 2 n_descriptor 18 +1.22645785 0.03575074268 0.1032870696 0.138922745 0.3115262916 0.022082352 0.02684663293 0.03891841673 +-1.111866874e-17 4.572798069e-05 0.09638152754 0.1144005531 0.1189275261 -1.15382449e-17 4.089158879e-06 0.013759078 +0.02591705344 0.02959237611 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d6f4653848a8ae683e1eaa0eac11fe0aef6434ba Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:10 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872651 SEC) : SETUP UNITCELL + DONE(0.101247 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119346 SEC) : INIT PLANEWAVE + DONE(0.167984 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448703 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652062e+02 0.000000e+00 2.112e-01 5.201e-01 + GE2 -4.663884e+02 -1.182244e+00 9.760e-02 4.459e-01 + GE3 -4.663917e+02 -3.322848e-03 6.273e-02 4.969e-01 + GE4 -4.663911e+02 6.848112e-04 1.889e-03 3.889e-01 + GE5 -4.663905e+02 5.614051e-04 7.970e-04 3.858e-01 + GE6 -4.663909e+02 -3.778564e-04 8.958e-05 3.711e-01 + GE7 -4.663908e+02 1.110339e-04 2.638e-05 3.632e-01 + GE8 -4.663908e+02 -2.056983e-05 8.932e-06 3.570e-01 + GE9 -4.663908e+02 1.304229e-05 8.156e-07 3.612e-01 + GE10 -4.663908e+02 -2.312348e-06 1.085e-07 3.618e-01 + GE11 -4.663908e+02 -1.718121e-07 3.310e-08 3.065e-01 +E_delta_band = -6.96983234e-02 Ry = -9.48294339e-01 eV +E_delta_NN= -1.94446063e-01 Ry = -2.64557441e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6421 11 0.6 1e+02 % + Run_lcao lcao_line 6.6324 1 6.6 1e+02 % + Potential init_pot 0.28318 2 0.14 4.3 % + PW_Basis recip2real 0.26263 16 0.016 4 % + PW_Basis gathers_scatterp 0.11106 16 0.0069 1.7 % + Potential v_of_rho 0.86145 13 0.066 13 % + XC_Functional v_xc 0.23928 14 0.017 3.6 % + H_Hartree_pw v_hartree 0.58626 13 0.045 8.8 % + PW_Basis real2recip 0.55125 38 0.015 8.3 % + PW_Basis gatherp_scatters 0.21103 38 0.0056 3.2 % + ORB_control set_orb_tables 1.1119 1 1.1 17 % + ORB_gen_tables gen_tables 1.1119 1 1.1 17 % + ORB_table_phi init_Table 0.48734 1 0.49 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.48236 126 0.0038 7.3 % + ORB_table_beta init_Table_Beta 0.18802 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18649 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25734 1 0.26 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25543 66 0.0039 3.8 % + LOOP_ions opt_ions 4.9946 1 5 75 % + ESolver_KS_LCAO Run 4.4196 1 4.4 67 % + HSolverLCAO solve 2.4669 11 0.22 37 % + HamiltLCAO updateHk 1.2704 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2322 11 0.11 19 % + Gint_interface cal_gint 2.3631 23 0.1 36 % + Gint_Gamma distri_vl 2.1205 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.8213 13 0.37 73 % + LCAO_gen_fixedH add_v_delta 1.9888 6 0.33 30 % + LCAO_DESCRIPTOR add_v_delta 1.9888 6 0.33 30 % + ElecStateLCAO psiToRho 1.1798 11 0.11 18 % + Charge mix_rho 0.65618 10 0.066 9.9 % + LOOP_ions force_stress 0.57484 1 0.57 8.7 % + Force_Stress_LCAO getForceStress 0.57482 1 0.57 8.7 % + Force_LCAO_gamma ftable_gamma 0.36013 1 0.36 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.35346 1 0.35 5.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:10 2022 + FINISH Time : Wed Sep 28 11:04:16 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/145/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..891dfd885f5b76ce143fa945ef0a48a7d8f524ec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.143229 0.66371 0.162615 +H 0.164862 0.603594 0.172494 +H 0.0814753 0.667678 0.183947 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..54f17c06c83ae9d6ffa57a888e85152586e165a3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.269 2 + 2 -13.3314 2 + 3 -8.89149 2 + 4 -6.73813 2 + 5 1.37822 0 + 6 4.5564 0 + 7 11.0657 0 + 8 11.2931 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a0da1d94967c2859a9604e3fc3461b7288d44344 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:47 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.0104137309 18.5838772452 4.55320806582 0 0 0 0 + tauc_H1 4.6161384743 16.9006372847 4.82983738201 0 0 0 0 + tauc_H2 2.28130820935 18.6949768825 5.15050697092 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0734633506896 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0866280131044 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.102250821225 (SEC) + + DONE : INIT CHARGE Time : 0.1435536474 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.387357 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000516 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00178 + + Density error is 0.216451842162 + + Energy Rydberg eV + E_KohnSham -34.1898161342 -465.176312998 + E_Harris -34.3843432373 -467.822990014 + E_Fermi -0.408597849884 -5.55925894896 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000800504436178 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0014513999349 + + Density error is 0.0979794466366 + + Energy Rydberg eV + E_KohnSham -34.2798547363 -466.401351026 + E_Harris -34.2864791807 -466.491481215 + E_Fermi -0.216432516624 -2.94471545856 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000774076161327 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133404445892 + + Density error is 0.0627404849434 + + Energy Rydberg eV + E_KohnSham -34.2800993109 -466.404678635 + E_Harris -34.2843537891 -466.462563779 + E_Fermi -0.204017691111 -2.77580309192 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000742927074433 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112822130548 + + Density error is 0.00208530362262 + + Energy Rydberg eV + E_KohnSham -34.2801110971 -466.404838994 + E_Harris -34.2801141911 -466.40488109 + E_Fermi -0.168686579542 -2.29509865791 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000743757434405 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112513834617 + + Density error is 0.000874187847171 + + Energy Rydberg eV + E_KohnSham -34.2800506432 -466.404016476 + E_Harris -34.2800517541 -466.404031591 + E_Fermi -0.167755225997 -2.28242694284 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000743149473301 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112308298625 + + Density error is 0.000195194157303 + + Energy Rydberg eV + E_KohnSham -34.2800890758 -466.404539378 + E_Harris -34.2800891519 -466.404540414 + E_Fermi -0.167836682124 -2.2835352103 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000743378194314 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112279253386 + + Density error is 4.2914726698e-05 + + Energy Rydberg eV + E_KohnSham -34.2800743643 -466.404339219 + E_Harris -34.2800743744 -466.404339356 + E_Fermi -0.167666394928 -2.28121833414 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000743313929079 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011228017126 + + Density error is 1.83515916789e-05 + + Energy Rydberg eV + E_KohnSham -34.2800796073 -466.404410553 + E_Harris -34.2800796088 -466.404410573 + E_Fermi -0.167715223932 -2.28188268682 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000743319874901 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011227669491 + + Density error is 1.96804019754e-06 + + Energy Rydberg eV + E_KohnSham -34.2800780232 -466.404389 + E_Harris -34.2800780232 -466.404389 + E_Fermi -0.167696055834 -2.28162189146 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000743319905577 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112276035019 + + Density error is 4.02862429012e-07 + + Energy Rydberg eV + E_KohnSham -34.2800783033 -466.404392811 + E_Harris -34.2800783033 -466.404392811 + E_Fermi -0.167694258091 -2.28159743192 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000743320647199 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112276063897 + + Density error is 1.42662539062e-07 + + Energy Rydberg eV + E_KohnSham -34.2800783212 -466.404393055 + E_Harris -34.2800783212 -466.404393055 + E_Fermi -0.167694096582 -2.28159523448 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000743320869608 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011227603961 + + Density error is 1.02232572478e-08 + + Energy Rydberg eV + E_KohnSham -34.2800783244 -466.404393098 + E_Harris -34.2800783244 -466.404393098 + E_band -7.97166190155 -108.460024391 + E_one_elec -69.4211304724 -944.522936026 + E_Hartree +36.1097753353 +491.29869806 + E_xc -8.22065902368 -111.847804037 + E_Ewald +7.37603529793 +100.356108701 + E_demet -3.10911967965e-81 -4.23017434072e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19493325715 -2.65220302694 + E_Fermi -0.167693961225 -2.28159339285 + + charge density convergence is achieved + final etot is -466.404393098 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2690 2.00000 + 2 -13.3314 2.00000 + 3 -8.89149 2.00000 + 4 -6.73813 2.00000 + 5 1.37822 0.00000 + 6 4.55640 0.00000 + 7 11.0657 0.00000 + 8 11.2931 0.00000 + + EFERMI = -2.281593392854920 eV + OUT.ABACUS/ final etot is -466.4043930981699 eV + correction force for each atom along direction 1 is -0.000127732 + correction force for each atom along direction 2 is -3.95236e-05 + correction force for each atom along direction 3 is 0.000170220 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.13720170 +1.1193768 -0.37506381 + H1 -0.0046150290 -0.83032988 +0.24416281 + H2 -0.13258667 -0.28904696 +0.13090100 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4043930981699 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3904 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3832 1 7.4 1.e+02% + Potential init_pot 0.24190 2 0.12 3.3% + PW_Basis recip2real 0.28011 17 0.016 3.8% + PW_Basis gathers_scatterp 0.11258 17 0.0066 1.5% + Potential v_of_rho 0.99609 14 0.071 13.% + XC_Functional v_xc 0.29740 15 0.020 4.0% + H_Hartree_pw v_hartree 0.65772 14 0.047 8.9% + PW_Basis real2recip 0.64614 41 0.016 8.7% + PW_Basis gatherp_scatters 0.24073 41 0.0059 3.3% + ORB_control set_orb_tables 0.89176 1 0.89 12.% + ORB_gen_tables gen_tables 0.89175 1 0.89 12.% + ORB_table_phi init_Table 0.37356 1 0.37 5.1% + ORB_table_phi cal_ST_Phi12_R 0.36933 126 0.0029 5.0% + ORB_table_beta init_Table_Beta 0.15280 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15147 56 0.0027 2.0% + ORB_table_alpha init_Table_Alpha 0.20689 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20520 66 0.0031 2.8% + LOOP_ions opt_ions 6.0287 1 6.0 82.% + ESolver_KS_LCAO Run 5.4632 1 5.5 74.% + HSolverLCAO solve 3.0969 12 0.26 42.% + HamiltLCAO updateHk 1.5562 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.5215 12 0.13 21.% + Gint_interface cal_gint 2.9779 25 0.12 40.% + Gint_Gamma distri_vl 2.8405 6 0.47 38.% + LCAO_Deepks cal_projected_DM 5.8679 14 0.42 79.% + LCAO_gen_fixedH add_v_delta 2.7121 6 0.45 37.% + LCAO_DESCRIPTOR add_v_delta 2.7120 6 0.45 37.% + ElecStateLCAO psiToRho 1.5151 12 0.13 21.% + Charge mix_rho 0.82722 11 0.075 11.% + LOOP_ions force_stress 0.56537 1 0.57 7.7% + Force_Stress_LCAO getForceStress 0.56535 1 0.57 7.6% + Force_LCAO_gamma ftable_gamma 0.36595 1 0.37 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.35869 1 0.36 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:47 2022 + Finish Time : Wed Sep 28 11:08:54 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..afb94e3dfdc436ff234de3768704ab7b0d049704 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.01236 ima = 3.69926e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123450191698 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112626557481 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011308876532 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113330172247 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113279284622 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113309828055 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113300517017 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113303708592 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113302929585 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113302873502 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113302858348 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113302851669 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/STRU new file mode 100644 index 0000000000000000000000000000000000000000..08afe2b1a266d797046fb54133f2804fbd38ebfb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.989586269087 18.583877245210 4.553208065803 0 0 0 +H +0.0 +2 +-23.383861525682 16.900637284722 4.829837381993 0 0 0 +-25.718691790674 18.694976882509 5.150506970929 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/conv new file mode 100644 index 0000000000000000000000000000000000000000..c47c8a2060312e45c28cb8e5709ed40f8d08211b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/conv @@ -0,0 +1 @@ +146 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ec54daa1b0d66752555682f2284d2bb98c330f89 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745068535 0.01265854986 1.282018297 1.373018226 1.469310892 0.007877326388 0.02007532579 0.03890309044 +-2.021165106e-18 0.001158654736 0.002443089209 0.01245482425 0.04372902646 3.337945762e-19 1.652552143e-06 5.117707955e-06 +0.001754934732 0.00571669278 + +H atom_index 1 n_descriptor 18 +1.259714419 0.03340833964 0.1118003891 0.1555910648 0.3255998862 0.02234306242 0.02900932205 0.03666280388 +1.981908598e-17 4.16947485e-05 0.1043467341 0.1154257061 0.1336458576 2.821371744e-18 3.745403948e-06 0.01292186239 +0.02654166819 0.03127888524 + +H atom_index 2 n_descriptor 18 +1.241716786 0.03404199695 0.1055770596 0.147205029 0.3199923774 0.02155177235 0.02797055157 0.0371934716 +8.894819076e-18 4.016676007e-05 0.1000884662 0.1145118664 0.1264150612 -5.591504056e-18 4.626722638e-06 0.01301564267 +0.02588225236 0.03048434114 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..89fc310c7d6eab7bc36a4d10d9984efa07df2622 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:47 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0734789 SEC) : SETUP UNITCELL + DONE(0.0866397 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.102264 SEC) : INIT PLANEWAVE + DONE(0.143661 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.387405 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651763e+02 0.000000e+00 2.165e-01 5.371e-01 + GE2 -4.664014e+02 -1.225038e+00 9.798e-02 5.096e-01 + GE3 -4.664047e+02 -3.327608e-03 6.274e-02 5.659e-01 + GE4 -4.664048e+02 -1.603594e-04 2.085e-03 4.425e-01 + GE5 -4.664040e+02 8.225177e-04 8.742e-04 4.446e-01 + GE6 -4.664045e+02 -5.229021e-04 1.952e-04 4.337e-01 + GE7 -4.664043e+02 2.001598e-04 4.291e-05 4.324e-01 + GE8 -4.664044e+02 -7.133450e-05 1.835e-05 4.252e-01 + GE9 -4.664044e+02 2.155287e-05 1.968e-06 4.240e-01 + GE10 -4.664044e+02 -3.810993e-06 4.029e-07 4.248e-01 + GE11 -4.664044e+02 -2.440539e-07 1.427e-07 4.174e-01 + GE12 -4.664044e+02 -4.296602e-08 1.022e-08 3.519e-01 +E_delta_band = -7.08337955e-02 Ry = -9.63743230e-01 eV +E_delta_NN= -1.94933257e-01 Ry = -2.65220303e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3904 11 0.67 1e+02 % + Run_lcao lcao_line 7.3832 1 7.4 1e+02 % + Potential init_pot 0.2419 2 0.12 3.3 % + PW_Basis recip2real 0.28011 17 0.016 3.8 % + PW_Basis gathers_scatterp 0.11258 17 0.0066 1.5 % + Potential v_of_rho 0.99609 14 0.071 13 % + XC_Functional v_xc 0.2974 15 0.02 4 % + H_Hartree_pw v_hartree 0.65772 14 0.047 8.9 % + PW_Basis real2recip 0.64614 41 0.016 8.7 % + PW_Basis gatherp_scatters 0.24073 41 0.0059 3.3 % + ORB_control set_orb_tables 0.89176 1 0.89 12 % + ORB_gen_tables gen_tables 0.89175 1 0.89 12 % + ORB_table_phi init_Table 0.37356 1 0.37 5.1 % + ORB_table_phi cal_ST_Phi12_R 0.36933 126 0.0029 5 % + ORB_table_beta init_Table_Beta 0.1528 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15147 56 0.0027 2 % + ORB_table_alpha init_Table_Alpha 0.20689 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.2052 66 0.0031 2.8 % + LOOP_ions opt_ions 6.0287 1 6 82 % + ESolver_KS_LCAO Run 5.4632 1 5.5 74 % + HSolverLCAO solve 3.0969 12 0.26 42 % + HamiltLCAO updateHk 1.5562 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.5215 12 0.13 21 % + Gint_interface cal_gint 2.9779 25 0.12 40 % + Gint_Gamma distri_vl 2.8405 6 0.47 38 % + LCAO_Deepks cal_projected_DM 5.8679 14 0.42 79 % + LCAO_gen_fixedH add_v_delta 2.7121 6 0.45 37 % + LCAO_DESCRIPTOR add_v_delta 2.712 6 0.45 37 % + ElecStateLCAO psiToRho 1.5151 12 0.13 21 % + Charge mix_rho 0.82722 11 0.075 11 % + LOOP_ions force_stress 0.56537 1 0.57 7.7 % + Force_Stress_LCAO getForceStress 0.56535 1 0.57 7.6 % + Force_LCAO_gamma ftable_gamma 0.36595 1 0.37 5 % + Force_LCAO_gamma cal_fvl_dphi 0.35869 1 0.36 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:47 2022 + FINISH Time : Wed Sep 28 11:08:54 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/146/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..2d361ad0300a7bf94a9c3c989c879c7fa267d7c5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.151015 0.640733 0.178258 +H 0.173354 0.586598 0.143382 +H 0.101156 0.66297 0.140075 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..4cd2d1a5022df65020c0d0772020c6aa055f5664 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0079 2 + 2 -12.7061 2 + 3 -9.15145 2 + 4 -6.68399 2 + 5 1.02063 0 + 6 3.95006 0 + 7 11.146 0 + 8 11.4018 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..6e81e8891cf97ba68ce26c0de07f727953703aae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:39 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.22841233217 17.9405127829 4.99122639674 0 0 0 0 + tauc_H1 4.85391367251 16.4247543508 4.01468857284 0 0 0 0 + tauc_H2 2.83237224589 18.5631630085 3.92210430885 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0737197237983 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0740055518972 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.089852029521 (SEC) + + DONE : INIT CHARGE Time : 0.131236749491 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374579 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00142 + + Density error is 0.211012293954 + + Energy Rydberg eV + E_KohnSham -34.1916698585 -465.201534211 + E_Harris -34.3751712411 -467.698198605 + E_Fermi -0.386517202292 -5.25883632618 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103223252074 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134549409961 + + Density error is 0.0986241345219 + + Energy Rydberg eV + E_KohnSham -34.279088272 -466.390922744 + E_Harris -34.2862005695 -466.487690517 + E_Fermi -0.198119720086 -2.69555707933 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000985290352851 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012588450816 + + Density error is 0.0636493850726 + + Energy Rydberg eV + E_KohnSham -34.279466949 -466.39607491 + E_Harris -34.2840264976 -466.45811075 + E_Fermi -0.191225084033 -2.60175074337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000920690478047 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011077063416 + + Density error is 0.0019566232969 + + Energy Rydberg eV + E_KohnSham -34.2793710612 -466.394770289 + E_Harris -34.2793731731 -466.394799022 + E_Fermi -0.156025784396 -2.1228397027 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000920578669086 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110721065202 + + Density error is 0.000885980620816 + + Energy Rydberg eV + E_KohnSham -34.2793419521 -466.394374239 + E_Harris -34.2793422201 -466.394377886 + E_Fermi -0.155957131664 -2.12190563437 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000919777557052 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110503651936 + + Density error is 0.000173022330742 + + Energy Rydberg eV + E_KohnSham -34.2793540924 -466.394539416 + E_Harris -34.279354096 -466.394539465 + E_Fermi -0.155522910702 -2.1159977551 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000919921871747 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110512137035 + + Density error is 2.57722150128e-05 + + Energy Rydberg eV + E_KohnSham -34.2793510181 -466.394497588 + E_Harris -34.2793510196 -466.394497608 + E_Fermi -0.155506515913 -2.11577469254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000919873641679 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110507326817 + + Density error is 1.09612948897e-05 + + Energy Rydberg eV + E_KohnSham -34.2793531367 -466.394526413 + E_Harris -34.2793531372 -466.39452642 + E_Fermi -0.155518295416 -2.11593496091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000919875226141 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110506561803 + + Density error is 2.4057034826e-06 + + Energy Rydberg eV + E_KohnSham -34.2793522939 -466.394514947 + E_Harris -34.2793522939 -466.394514947 + E_Fermi -0.155508308235 -2.11579907834 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000919871218427 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110505759267 + + Density error is 5.33464759613e-07 + + Energy Rydberg eV + E_KohnSham -34.2793524755 -466.394517417 + E_Harris -34.2793524755 -466.394517417 + E_Fermi -0.155506365926 -2.11577265187 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000919872017096 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110505796178 + + Density error is 1.92891796322e-07 + + Energy Rydberg eV + E_KohnSham -34.2793524811 -466.394517494 + E_Harris -34.2793524811 -466.394517493 + E_Fermi -0.155506113054 -2.11576921136 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000919872233885 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110505785288 + + Density error is 1.09640123263e-08 + + Energy Rydberg eV + E_KohnSham -34.2793524847 -466.394517542 + E_Harris -34.2793524847 -466.394517542 + E_band -7.8716195298 -107.098878093 + E_one_elec -68.6541638651 -934.087819992 + E_Hartree +35.7369749967 +486.226489238 + E_xc -8.16103722695 -111.036607877 + E_Ewald +6.92448433677 +94.2124426918 + E_demet -2.27222382091e-60 -3.09151910958e-59 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193700390621 -2.63542901727 + E_Fermi -0.155505927998 -2.11576669355 + + charge density convergence is achieved + final etot is -466.394517542 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0079 2.00000 + 2 -12.7061 2.00000 + 3 -9.15145 2.00000 + 4 -6.68399 2.00000 + 5 1.02063 0.00000 + 6 3.95006 0.00000 + 7 11.1460 0.00000 + 8 11.4018 0.00000 + + EFERMI = -2.115766693552303 eV + OUT.ABACUS/ final etot is -466.3945175417052 eV + correction force for each atom along direction 1 is -0.000123236 + correction force for each atom along direction 2 is -3.96139e-05 + correction force for each atom along direction 3 is -7.37431e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.086913535 -1.0303187 -1.0904335 + H1 -0.44310223 +1.1546301 +0.78173956 + H2 +0.35618869 -0.12431139 +0.30869395 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3945175417052 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5712 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5637 1 7.6 1.e+02% + Potential init_pot 0.24326 2 0.12 3.2% + PW_Basis recip2real 0.27897 17 0.016 3.7% + PW_Basis gathers_scatterp 0.11359 17 0.0067 1.5% + Potential v_of_rho 0.97241 14 0.069 13.% + XC_Functional v_xc 0.28848 15 0.019 3.8% + H_Hartree_pw v_hartree 0.64269 14 0.046 8.5% + PW_Basis real2recip 0.64349 41 0.016 8.5% + PW_Basis gatherp_scatters 0.23661 41 0.0058 3.1% + ORB_control set_orb_tables 0.90210 1 0.90 12.% + ORB_gen_tables gen_tables 0.90208 1 0.90 12.% + ORB_table_phi init_Table 0.37932 1 0.38 5.0% + ORB_table_phi cal_ST_Phi12_R 0.37511 126 0.0030 5.0% + ORB_table_beta init_Table_Beta 0.15597 1 0.16 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15459 56 0.0028 2.0% + ORB_table_alpha init_Table_Alpha 0.20914 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20744 66 0.0031 2.7% + LOOP_ions opt_ions 6.2170 1 6.2 82.% + ESolver_KS_LCAO Run 5.6502 1 5.7 75.% + HSolverLCAO solve 3.3150 12 0.28 44.% + HamiltLCAO updateHk 1.6205 12 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.5850 12 0.13 21.% + Gint_interface cal_gint 3.2087 25 0.13 42.% + Gint_Gamma distri_vl 2.9281 6 0.49 39.% + LCAO_Deepks cal_projected_DM 6.0516 14 0.43 80.% + LCAO_gen_fixedH add_v_delta 2.8006 6 0.47 37.% + LCAO_DESCRIPTOR add_v_delta 2.8007 6 0.47 37.% + ElecStateLCAO psiToRho 1.6770 12 0.14 22.% + Charge mix_rho 0.82746 11 0.075 11.% + LOOP_ions force_stress 0.56663 1 0.57 7.5% + Force_Stress_LCAO getForceStress 0.56661 1 0.57 7.5% + Force_LCAO_gamma ftable_gamma 0.37021 1 0.37 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.36298 1 0.36 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:39 2022 + Finish Time : Wed Sep 28 11:08:46 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..cb892e43b9ade9c36141cf0f8be486dbae91bd6f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123371 ima = 3.67358e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123422955227 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112104814498 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112856497193 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011304809922 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113035575551 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113043888232 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113040573252 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113042184633 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113041669001 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113041638932 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113041619565 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113041609608 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e3eddca286839103684c013bbd2a19d2d6da5d4a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.771587667825 17.940512782844 4.991226396745 0 0 0 +H +0.0 +2 +-23.146086327500 16.424754350795 4.014688572863 0 0 0 +-25.167627754124 18.563163008516 3.922104308860 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/conv new file mode 100644 index 0000000000000000000000000000000000000000..020a79f56ff2eeba490f7e7109f7e691b4ddf06e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/conv @@ -0,0 +1 @@ +147 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4cf7c1f413a7f29e0133f2346d39f180c7b9e148 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751002449 0.01245840693 1.246126579 1.337626979 1.468136702 0.008595044487 0.01756437349 0.03911962333 +1.714970984e-18 0.0008794278363 0.00245157694 0.01163983182 0.04209453422 -6.619740375e-19 1.755730336e-06 5.303334805e-06 +0.001597692773 0.005912079963 + +H atom_index 1 n_descriptor 18 +1.18795889 0.03645322446 0.08822123316 0.1234329147 0.2992170273 0.01924214828 0.02468234718 0.04001737599 +-1.587462828e-17 3.628070907e-05 0.08316784935 0.1053131715 0.1131002356 -5.316746281e-18 6.278649709e-06 0.01453933081 +0.02326502966 0.02760700727 + +H atom_index 2 n_descriptor 18 +1.221888597 0.0353811355 0.09855296698 0.1374497633 0.3118331846 0.02082274324 0.02667151135 0.03864781871 +2.789687138e-17 3.914088609e-05 0.09191961338 0.1145014286 0.1176397444 -3.515395614e-18 5.094813213e-06 0.01361381332 +0.0246645802 0.02938976273 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e9733f2ba79a505cfe2b43b61eb8d760ca7da9a7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:39 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0737338 SEC) : SETUP UNITCELL + DONE(0.0740145 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0898654 SEC) : INIT PLANEWAVE + DONE(0.131344 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374625 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652015e+02 0.000000e+00 2.110e-01 5.506e-01 + GE2 -4.663909e+02 -1.189389e+00 9.862e-02 5.226e-01 + GE3 -4.663961e+02 -5.152165e-03 6.365e-02 5.825e-01 + GE4 -4.663948e+02 1.304621e-03 1.957e-03 4.573e-01 + GE5 -4.663944e+02 3.960503e-04 8.860e-04 4.591e-01 + GE6 -4.663945e+02 -1.651770e-04 1.730e-04 4.530e-01 + GE7 -4.663945e+02 4.182718e-05 2.577e-05 4.377e-01 + GE8 -4.663945e+02 -2.882422e-05 1.096e-05 4.433e-01 + GE9 -4.663945e+02 1.146568e-05 2.406e-06 4.445e-01 + GE10 -4.663945e+02 -2.469762e-06 5.335e-07 4.396e-01 + GE11 -4.663945e+02 -7.671782e-08 1.929e-07 4.310e-01 + GE12 -4.663945e+02 -4.820113e-08 1.096e-08 3.754e-01 +E_delta_band = -6.80896646e-02 Ry = -9.26407414e-01 eV +E_delta_NN= -1.93700391e-01 Ry = -2.63542902e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5712 11 0.69 1e+02 % + Run_lcao lcao_line 7.5637 1 7.6 1e+02 % + Potential init_pot 0.24326 2 0.12 3.2 % + PW_Basis recip2real 0.27897 17 0.016 3.7 % + PW_Basis gathers_scatterp 0.11359 17 0.0067 1.5 % + Potential v_of_rho 0.97241 14 0.069 13 % + XC_Functional v_xc 0.28848 15 0.019 3.8 % + H_Hartree_pw v_hartree 0.64269 14 0.046 8.5 % + PW_Basis real2recip 0.64349 41 0.016 8.5 % + PW_Basis gatherp_scatters 0.23661 41 0.0058 3.1 % + ORB_control set_orb_tables 0.9021 1 0.9 12 % + ORB_gen_tables gen_tables 0.90208 1 0.9 12 % + ORB_table_phi init_Table 0.37932 1 0.38 5 % + ORB_table_phi cal_ST_Phi12_R 0.37511 126 0.003 5 % + ORB_table_beta init_Table_Beta 0.15597 1 0.16 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15459 56 0.0028 2 % + ORB_table_alpha init_Table_Alpha 0.20914 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20744 66 0.0031 2.7 % + LOOP_ions opt_ions 6.217 1 6.2 82 % + ESolver_KS_LCAO Run 5.6502 1 5.7 75 % + HSolverLCAO solve 3.315 12 0.28 44 % + HamiltLCAO updateHk 1.6205 12 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.585 12 0.13 21 % + Gint_interface cal_gint 3.2087 25 0.13 42 % + Gint_Gamma distri_vl 2.9281 6 0.49 39 % + LCAO_Deepks cal_projected_DM 6.0516 14 0.43 80 % + LCAO_gen_fixedH add_v_delta 2.8006 6 0.47 37 % + LCAO_DESCRIPTOR add_v_delta 2.8007 6 0.47 37 % + ElecStateLCAO psiToRho 1.677 12 0.14 22 % + Charge mix_rho 0.82746 11 0.075 11 % + LOOP_ions force_stress 0.56663 1 0.57 7.5 % + Force_Stress_LCAO getForceStress 0.56661 1 0.57 7.5 % + Force_LCAO_gamma ftable_gamma 0.37021 1 0.37 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.36298 1 0.36 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:39 2022 + FINISH Time : Wed Sep 28 11:08:46 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/147/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ef84b8b15e07b6d1f799012753ff84c52fc8a10b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.16191 0.632535 0.178405 +H 0.183706 0.593765 0.225089 +H 0.213887 0.66532 0.154555 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..734086aac3e9bca080196abf6460730f00471335 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.279 2 + 2 -13.2318 2 + 3 -8.97197 2 + 4 -6.74096 2 + 5 1.3506 0 + 6 4.51369 0 + 7 11.0682 0 + 8 11.3039 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..bd7ff5268b23d83376eba111a90fff5828646a18 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:53 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.53347004756 17.7109755654 4.99533752861 0 0 0 0 + tauc_H1 5.14375410313 16.6254226392 6.30248833107 0 0 0 0 + tauc_H2 5.98884139519 18.6289499269 4.3275525222 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.100993931001 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101336784248 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119296298167 (SEC) + + DONE : INIT CHARGE Time : 0.162278677319 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445177 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000974 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132 + + Density error is 0.215961321597 + + Energy Rydberg eV + E_KohnSham -34.1899893504 -465.178669724 + E_Harris -34.3838801119 -467.816688871 + E_Fermi -0.408216532631 -5.55407086158 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00120639416067 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116614031729 + + Density error is 0.0980361852969 + + Energy Rydberg eV + E_KohnSham -34.2802061613 -466.406132408 + E_Harris -34.2868814469 -466.496954328 + E_Fermi -0.21562701578 -2.93375605735 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00114564212382 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108517418773 + + Density error is 0.0628277270607 + + Energy Rydberg eV + E_KohnSham -34.2804805031 -466.40986502 + E_Harris -34.2847806065 -466.468370929 + E_Fermi -0.203835347248 -2.77332217639 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00105038153113 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000952687024516 + + Density error is 0.00204488418743 + + Energy Rydberg eV + E_KohnSham -34.2804812504 -466.409875188 + E_Harris -34.2804832882 -466.409902913 + E_Fermi -0.168397471109 -2.29116513587 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0010499824076 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000952127091367 + + Density error is 0.000894396601572 + + Energy Rydberg eV + E_KohnSham -34.2804197205 -466.409038031 + E_Harris -34.2804208892 -466.409053932 + E_Fermi -0.167562242737 -2.27980127088 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104867657831 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950585890943 + + Density error is 0.000181998421383 + + Energy Rydberg eV + E_KohnSham -34.280458236 -466.409562061 + E_Harris -34.2804583171 -466.409563164 + E_Fermi -0.167601040417 -2.2803291404 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104883835809 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00095062242439 + + Density error is 4.09878401108e-05 + + Energy Rydberg eV + E_KohnSham -34.2804434311 -466.409360629 + E_Harris -34.2804434403 -466.409360754 + E_Fermi -0.167449691726 -2.27826993582 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104877012103 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950604337906 + + Density error is 1.76859657138e-05 + + Energy Rydberg eV + E_KohnSham -34.2804484858 -466.409429402 + E_Harris -34.2804484871 -466.40942942 + E_Fermi -0.167496756472 -2.27891028453 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104875598491 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950583595939 + + Density error is 1.42568885454e-06 + + Energy Rydberg eV + E_KohnSham -34.2804469762 -466.409408863 + E_Harris -34.2804469762 -466.409408864 + E_Fermi -0.167477013175 -2.27864166319 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104875755776 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950582497103 + + Density error is 2.39872020286e-07 + + Energy Rydberg eV + E_KohnSham -34.2804472363 -466.409412402 + E_Harris -34.2804472363 -466.409412402 + E_Fermi -0.167476047437 -2.27862852366 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104875808116 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950582624345 + + Density error is 5.79884740172e-08 + + Energy Rydberg eV + E_KohnSham -34.2804472546 -466.409412651 + E_Harris -34.2804472546 -466.409412651 + E_band -7.97073666036 -108.447435838 + E_one_elec -69.3790538086 -943.950453646 + E_Hartree +36.0868528623 +490.986821814 + E_xc -8.21710205468 -111.799408991 + E_Ewald +7.35302937358 +100.043097042 + E_demet -6.31154958142e-80 -8.58730375168e-79 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194904285434 -2.65180884652 + E_Fermi -0.167475971284 -2.27862748755 + + charge density convergence is achieved + final etot is -466.409412651 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2790 2.00000 + 2 -13.2318 2.00000 + 3 -8.97197 2.00000 + 4 -6.74096 2.00000 + 5 1.35060 0.00000 + 6 4.51369 0.00000 + 7 11.0682 0.00000 + 8 11.3039 0.00000 + + EFERMI = -2.278627487550387 eV + OUT.ABACUS/ final etot is -466.4094126507142 eV + correction force for each atom along direction 1 is 0.000195090 + correction force for each atom along direction 2 is 1.66540e-05 + correction force for each atom along direction 3 is 0.000109505 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.51266902 +0.70284075 -0.86818639 + H1 +0.51920379 -0.53408548 +0.68968836 + H2 -0.0065347732 -0.16875528 +0.17849802 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4094126507142 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5701 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5605 1 7.6 1.e+02% + Potential init_pot 0.28536 2 0.14 3.8% + PW_Basis recip2real 0.28109 16 0.018 3.7% + PW_Basis gathers_scatterp 0.12292 16 0.0077 1.6% + Potential v_of_rho 1.0200 13 0.078 13.% + XC_Functional v_xc 0.30855 14 0.022 4.1% + H_Hartree_pw v_hartree 0.66945 13 0.051 8.8% + PW_Basis real2recip 0.70584 38 0.019 9.3% + PW_Basis gatherp_scatters 0.27373 38 0.0072 3.6% + ORB_control set_orb_tables 1.1053 1 1.1 15.% + ORB_gen_tables gen_tables 1.1053 1 1.1 15.% + ORB_table_phi init_Table 0.47773 1 0.48 6.3% + ORB_table_phi cal_ST_Phi12_R 0.47250 126 0.0038 6.2% + ORB_table_beta init_Table_Beta 0.18924 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18771 56 0.0034 2.5% + ORB_table_alpha init_Table_Alpha 0.24819 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24621 66 0.0037 3.3% + LOOP_ions opt_ions 5.9344 1 5.9 78.% + ESolver_KS_LCAO Run 5.3368 1 5.3 70.% + HSolverLCAO solve 2.8494 11 0.26 38.% + HamiltLCAO updateHk 1.4689 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.4414 11 0.13 19.% + Gint_interface cal_gint 2.6955 23 0.12 36.% + Gint_Gamma distri_vl 2.5626 6 0.43 34.% + LCAO_Deepks cal_projected_DM 5.7615 13 0.44 76.% + LCAO_gen_fixedH add_v_delta 2.4154 6 0.40 32.% + LCAO_DESCRIPTOR add_v_delta 2.4153 6 0.40 32.% + ElecStateLCAO psiToRho 1.3631 11 0.12 18.% + Charge mix_rho 0.91568 10 0.092 12.% + LOOP_ions force_stress 0.59744 1 0.60 7.9% + Force_Stress_LCAO getForceStress 0.59741 1 0.60 7.9% + Force_LCAO_gamma ftable_gamma 0.37750 1 0.38 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.36941 1 0.37 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:53 2022 + Finish Time : Wed Sep 28 11:06:01 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..770c376d82db62e8d055896ccc486ae181987610 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123476 ima = 3.68573e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123366777426 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240730895 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112909188371 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113152814214 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113101661807 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113132908001 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113123675978 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113126728537 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113126009484 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113125958303 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113125947561 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/STRU new file mode 100644 index 0000000000000000000000000000000000000000..f54b0eb0c256365e5b046695884cd40b4af56478 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.466529952435 17.710975565455 4.995337528622 0 0 0 +H +0.0 +2 +-22.856245896856 16.625422639241 6.302488331086 0 0 0 +-22.011158604789 18.628949926928 4.327552522186 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/conv new file mode 100644 index 0000000000000000000000000000000000000000..3ed10051583757b4fd2429413cce146093fc6f19 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/conv @@ -0,0 +1 @@ +148 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d95b9e1a6661743f19c321da84eaf0a772c98e4e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746603468 0.01266651163 1.278475569 1.369687207 1.469326764 0.0080988874 0.01953419682 0.03894912671 +2.10772147e-18 0.001124982116 0.002500637285 0.01239738069 0.04429727147 -2.036274917e-19 1.777175722e-06 5.388857268e-06 +0.001712169211 0.005806407911 + +H atom_index 1 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:53 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101017 SEC) : SETUP UNITCELL + DONE(0.101352 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119314 SEC) : INIT PLANEWAVE + DONE(0.16241 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445241 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651787e+02 0.000000e+00 2.160e-01 5.800e-01 + GE2 -4.664061e+02 -1.227463e+00 9.804e-02 5.403e-01 + GE3 -4.664099e+02 -3.732611e-03 6.283e-02 6.068e-01 + GE4 -4.664099e+02 -1.016804e-05 2.045e-03 4.676e-01 + GE5 -4.664090e+02 8.371565e-04 8.944e-04 4.661e-01 + GE6 -4.664096e+02 -5.240302e-04 1.820e-04 4.584e-01 + GE7 -4.664094e+02 2.014322e-04 4.099e-05 4.505e-01 + GE8 -4.664094e+02 -6.877304e-05 1.769e-05 4.454e-01 + GE9 -4.664094e+02 2.053867e-05 1.426e-06 4.449e-01 + GE10 -4.664094e+02 -3.538880e-06 2.399e-07 4.434e-01 + GE11 -4.664094e+02 -2.484077e-07 5.799e-08 3.707e-01 +E_delta_band = -7.07306583e-02 Ry = -9.62339976e-01 eV +E_delta_NN= -1.94904285e-01 Ry = -2.65180885e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5701 11 0.69 1e+02 % + Run_lcao lcao_line 7.5605 1 7.6 1e+02 % + Potential init_pot 0.28536 2 0.14 3.8 % + PW_Basis recip2real 0.28109 16 0.018 3.7 % + PW_Basis gathers_scatterp 0.12292 16 0.0077 1.6 % + Potential v_of_rho 1.02 13 0.078 13 % + XC_Functional v_xc 0.30855 14 0.022 4.1 % + H_Hartree_pw v_hartree 0.66945 13 0.051 8.8 % + PW_Basis real2recip 0.70584 38 0.019 9.3 % + PW_Basis gatherp_scatters 0.27373 38 0.0072 3.6 % + ORB_control set_orb_tables 1.1053 1 1.1 15 % + ORB_gen_tables gen_tables 1.1053 1 1.1 15 % + ORB_table_phi init_Table 0.47773 1 0.48 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.4725 126 0.0038 6.2 % + ORB_table_beta init_Table_Beta 0.18924 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18771 56 0.0034 2.5 % + ORB_table_alpha init_Table_Alpha 0.24819 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24621 66 0.0037 3.3 % + LOOP_ions opt_ions 5.9344 1 5.9 78 % + ESolver_KS_LCAO Run 5.3368 1 5.3 70 % + HSolverLCAO solve 2.8494 11 0.26 38 % + HamiltLCAO updateHk 1.4689 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.4414 11 0.13 19 % + Gint_interface cal_gint 2.6955 23 0.12 36 % + Gint_Gamma distri_vl 2.5626 6 0.43 34 % + LCAO_Deepks cal_projected_DM 5.7615 13 0.44 76 % + LCAO_gen_fixedH add_v_delta 2.4154 6 0.4 32 % + LCAO_DESCRIPTOR add_v_delta 2.4153 6 0.4 32 % + ElecStateLCAO psiToRho 1.3631 11 0.12 18 % + Charge mix_rho 0.91568 10 0.092 12 % + LOOP_ions force_stress 0.59744 1 0.6 7.9 % + Force_Stress_LCAO getForceStress 0.59741 1 0.6 7.9 % + Force_LCAO_gamma ftable_gamma 0.3775 1 0.38 5 % + Force_LCAO_gamma cal_fvl_dphi 0.36941 1 0.37 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:53 2022 + FINISH Time : Wed Sep 28 11:06:01 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/148/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..04fb93ddef60a1b2ee57cfc43f8469d0aa141eb5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.185807 0.615689 0.191029 +H 0.128214 0.632442 0.220694 +H 0.208913 0.674944 0.177463 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..dce88a9457b20449771aa7bf9b44c986464f3da6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3001 2 + 2 -12.763 2 + 3 -9.32931 2 + 4 -6.74882 2 + 5 1.2044 0 + 6 4.28684 0 + 7 11.0863 0 + 8 11.3578 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..00630d3a3d5702cff91dc56a5a51bdedce1f717c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:42 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.20260930524 17.2392786678 5.34881792579 0 0 0 0 + tauc_H1 3.58998147945 17.7083630231 6.179443912 0 0 0 0 + tauc_H2 5.84956545009 18.8984416599 4.9689636257 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.073152304634 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0739668573318 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0898264119897 (SEC) + + DONE : INIT CHARGE Time : 0.132132146276 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374391 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00149 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000866 + + Density error is 0.212929482608 + + Energy Rydberg eV + E_KohnSham -34.1911105332 -465.193924199 + E_Harris -34.3791248215 -467.751989825 + E_Fermi -0.401031498418 -5.45631345596 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00134313414265 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104894676356 + + Density error is 0.0979479925978 + + Energy Rydberg eV + E_KohnSham -34.2796756473 -466.398914396 + E_Harris -34.2865606287 -466.492589372 + E_Fermi -0.211789956474 -2.88155018722 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00123602698241 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998292229141 + + Density error is 0.0628921601734 + + Energy Rydberg eV + E_KohnSham -34.2799884033 -466.403169659 + E_Harris -34.2844500376 -466.463873308 + E_Fermi -0.201899917638 -2.74698930561 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104582153527 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926721526963 + + Density error is 0.00192696531424 + + Energy Rydberg eV + E_KohnSham -34.2799491785 -466.402635977 + E_Harris -34.2799493041 -466.402637686 + E_Fermi -0.166223008541 -2.26158005486 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0010450737636 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092752922017 + + Density error is 0.000894141884074 + + Energy Rydberg eV + E_KohnSham -34.2798977961 -466.401936884 + E_Harris -34.2798991236 -466.401954946 + E_Fermi -0.165824894861 -2.25616344036 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104283820542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926503966216 + + Density error is 0.000110329510875 + + Energy Rydberg eV + E_KohnSham -34.2799278435 -466.4023457 + E_Harris -34.2799278449 -466.402345719 + E_Fermi -0.165651611823 -2.25380580367 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104272032659 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926553239357 + + Density error is 3.27233220663e-05 + + Energy Rydberg eV + E_KohnSham -34.2799190365 -466.402225875 + E_Harris -34.2799190421 -466.402225951 + E_Fermi -0.1655621008 -2.25258794373 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104270535932 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926489309819 + + Density error is 1.29691024242e-05 + + Energy Rydberg eV + E_KohnSham -34.2799212485 -466.402255971 + E_Harris -34.2799212493 -466.402255981 + E_Fermi -0.165595258894 -2.25303908275 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104268730993 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926488234361 + + Density error is 1.76277710544e-06 + + Energy Rydberg eV + E_KohnSham -34.2799200193 -466.402239247 + E_Harris -34.2799200193 -466.402239247 + E_Fermi -0.165582618456 -2.25286710076 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104268316014 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926489341689 + + Density error is 2.2755019891e-07 + + Energy Rydberg eV + E_KohnSham -34.2799202302 -466.402242116 + E_Harris -34.2799202302 -466.402242116 + E_Fermi -0.165580956751 -2.2528444921 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104268334558 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926489845403 + + Density error is 7.29562912514e-08 + + Energy Rydberg eV + E_KohnSham -34.2799202542 -466.402242443 + E_Harris -34.2799202542 -466.402242443 + E_band -7.95859967017 -108.282303615 + E_one_elec -69.1495704147 -940.828171892 + E_Hartree +35.9653124652 +489.333179876 + E_xc -8.19761323598 -111.53425001 + E_Ewald +7.22654373377 +98.3221716255 + E_demet -8.88343810809e-73 -1.208653761e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194602698615 -2.64770554735 + E_Fermi -0.165580889307 -2.25284357448 + + charge density convergence is achieved + final etot is -466.402242443 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3001 2.00000 + 2 -12.7630 2.00000 + 3 -9.32931 2.00000 + 4 -6.74882 2.00000 + 5 1.20440 0.00000 + 6 4.28684 0.00000 + 7 11.0863 0.00000 + 8 11.3578 0.00000 + + EFERMI = -2.252843574476180 eV + OUT.ABACUS/ final etot is -466.4022424426483 eV + correction force for each atom along direction 1 is 1.39047e-05 + correction force for each atom along direction 2 is 0.000148899 + correction force for each atom along direction 3 is -9.79239e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0143898 -0.058635585 +0.53139148 + H1 +0.47030902 -0.48238878 -0.23326868 + H2 +0.54408081 +0.54102436 -0.29812279 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4022424426483 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9820 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9745 1 7.0 1.e+02% + Potential init_pot 0.23888 2 0.12 3.4% + PW_Basis recip2real 0.25996 16 0.016 3.7% + PW_Basis gathers_scatterp 0.10343 16 0.0065 1.5% + Potential v_of_rho 0.92214 13 0.071 13.% + XC_Functional v_xc 0.27837 14 0.020 4.0% + H_Hartree_pw v_hartree 0.60600 13 0.047 8.7% + PW_Basis real2recip 0.60125 38 0.016 8.6% + PW_Basis gatherp_scatters 0.22225 38 0.0058 3.2% + ORB_control set_orb_tables 0.89315 1 0.89 13.% + ORB_gen_tables gen_tables 0.89315 1 0.89 13.% + ORB_table_phi init_Table 0.37274 1 0.37 5.3% + ORB_table_phi cal_ST_Phi12_R 0.36851 126 0.0029 5.3% + ORB_table_beta init_Table_Beta 0.15287 1 0.15 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15156 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20948 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20784 66 0.0031 3.0% + LOOP_ions opt_ions 5.6383 1 5.6 81.% + ESolver_KS_LCAO Run 5.0882 1 5.1 73.% + HSolverLCAO solve 2.9142 11 0.26 42.% + HamiltLCAO updateHk 1.4683 11 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.4370 11 0.13 21.% + Gint_interface cal_gint 2.8085 23 0.12 40.% + Gint_Gamma distri_vl 2.4326 6 0.41 35.% + LCAO_Deepks cal_projected_DM 5.4775 13 0.42 78.% + LCAO_gen_fixedH add_v_delta 2.3057 6 0.38 33.% + LCAO_DESCRIPTOR add_v_delta 2.3057 6 0.38 33.% + ElecStateLCAO psiToRho 1.4302 11 0.13 20.% + Charge mix_rho 0.75794 10 0.076 11.% + LOOP_ions force_stress 0.54993 1 0.55 7.9% + Force_Stress_LCAO getForceStress 0.54991 1 0.55 7.9% + Force_LCAO_gamma ftable_gamma 0.35271 1 0.35 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.34524 1 0.35 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:42 2022 + Finish Time : Wed Sep 28 11:04:49 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..05bbb22c255686718b6fd42d329426349e6224e5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123759 ima = 3.6694e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122824454785 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111624647598 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112253762228 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112493103353 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011245119324 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112473842091 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112470683493 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112473202034 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112472586817 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112472520065 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112472509434 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7493b7e9e8c366163bde5286532033df9fafbc96 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.797390694747 17.239278667802 5.348817925812 0 0 0 +H +0.0 +2 +-24.410018520531 17.708363023057 6.179443912021 0 0 0 +-22.150434549934 18.898441659862 4.968963625679 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/conv new file mode 100644 index 0000000000000000000000000000000000000000..b7432db675dea8b4521d5c6a9f2422f945463c4b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/conv @@ -0,0 +1 @@ +149 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..cb5ccf1de042ea73764aa842723487910e9950f5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752840142 0.01270461575 1.264275578 1.350922788 1.469292771 0.009138932892 0.01715597051 0.03913918582 +-1.667048192e-18 0.0009214451657 0.002720151012 0.01270543152 0.04557686785 -1.892557305e-20 2.413755408e-06 6.684343354e-06 +0.001591475672 0.006085009501 + +H atom_index 1 n_descriptor 18 +1.217016751 0.03578937796 0.09865881839 0.1349194844 0.3087054753 0.02118231438 0.02631495404 0.03901484025 +-5.09136581e-17 4.465025036e-05 0.09337756648 0.1139441538 0.115527202 -1.732530254e-18 5.191837356e-06 0.01387047119 +0.02527114212 0.02912760949 + +H atom_index 2 n_descriptor 18 +1.25850884 0.03439949587 0.1127665519 0.1536379841 0.3229268019 0.02319459406 0.02875067296 0.03757604912 +8.215440488e-19 4.851606961e-05 0.1035697703 0.1159512112 0.131768533 -4.443662732e-18 3.011494852e-06 0.01328038805 +0.02686707207 0.03111594879 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..2bea93077a35ccb7e86e5ebeb35996e17db07206 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:42 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0731669 SEC) : SETUP UNITCELL + DONE(0.0739768 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0898384 SEC) : INIT PLANEWAVE + DONE(0.132238 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374439 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651939e+02 0.000000e+00 2.129e-01 5.310e-01 + GE2 -4.663989e+02 -1.204990e+00 9.795e-02 5.099e-01 + GE3 -4.664032e+02 -4.255263e-03 6.289e-02 5.701e-01 + GE4 -4.664026e+02 5.336814e-04 1.927e-03 4.490e-01 + GE5 -4.664019e+02 6.990930e-04 8.941e-04 4.487e-01 + GE6 -4.664023e+02 -4.088156e-04 1.103e-04 4.431e-01 + GE7 -4.664022e+02 1.198247e-04 3.272e-05 4.285e-01 + GE8 -4.664023e+02 -3.009549e-05 1.297e-05 4.281e-01 + GE9 -4.664022e+02 1.672380e-05 1.763e-06 4.323e-01 + GE10 -4.664022e+02 -2.868532e-06 2.276e-07 4.311e-01 + GE11 -4.664022e+02 -3.270934e-07 7.296e-08 3.631e-01 +E_delta_band = -7.00098961e-02 Ry = -9.52533504e-01 eV +E_delta_NN= -1.94602699e-01 Ry = -2.64770555e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.982 11 0.63 1e+02 % + Run_lcao lcao_line 6.9745 1 7 1e+02 % + Potential init_pot 0.23888 2 0.12 3.4 % + PW_Basis recip2real 0.25996 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.10343 16 0.0065 1.5 % + Potential v_of_rho 0.92214 13 0.071 13 % + XC_Functional v_xc 0.27837 14 0.02 4 % + H_Hartree_pw v_hartree 0.606 13 0.047 8.7 % + PW_Basis real2recip 0.60125 38 0.016 8.6 % + PW_Basis gatherp_scatters 0.22225 38 0.0058 3.2 % + ORB_control set_orb_tables 0.89315 1 0.89 13 % + ORB_gen_tables gen_tables 0.89315 1 0.89 13 % + ORB_table_phi init_Table 0.37274 1 0.37 5.3 % + ORB_table_phi cal_ST_Phi12_R 0.36851 126 0.0029 5.3 % + ORB_table_beta init_Table_Beta 0.15287 1 0.15 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15156 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20948 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20784 66 0.0031 3 % + LOOP_ions opt_ions 5.6383 1 5.6 81 % + ESolver_KS_LCAO Run 5.0882 1 5.1 73 % + HSolverLCAO solve 2.9142 11 0.26 42 % + HamiltLCAO updateHk 1.4683 11 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.437 11 0.13 21 % + Gint_interface cal_gint 2.8085 23 0.12 40 % + Gint_Gamma distri_vl 2.4326 6 0.41 35 % + LCAO_Deepks cal_projected_DM 5.4775 13 0.42 78 % + LCAO_gen_fixedH add_v_delta 2.3057 6 0.38 33 % + LCAO_DESCRIPTOR add_v_delta 2.3057 6 0.38 33 % + ElecStateLCAO psiToRho 1.4302 11 0.13 20 % + Charge mix_rho 0.75794 10 0.076 11 % + LOOP_ions force_stress 0.54993 1 0.55 7.9 % + Force_Stress_LCAO getForceStress 0.54991 1 0.55 7.9 % + Force_LCAO_gamma ftable_gamma 0.35271 1 0.35 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.34524 1 0.35 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:42 2022 + FINISH Time : Wed Sep 28 11:04:49 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/149/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..29c281aad0d1330f5f90c52371084f57ad07b649 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.585452 0.275478 0.387907 +H 0.603699 0.29673 0.447109 +H 0.594514 0.324797 0.348394 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..7e8c188491725015244ed2d4c50c3e61c3c3ded7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4025 2 + 2 -13.2386 2 + 3 -9.06304 2 + 4 -6.76931 2 + 5 1.42037 0 + 6 4.63546 0 + 7 11.0428 0 + 8 11.2843 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..151aafaa2cc11059b9600a69404145f3621b1647 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:42 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.3926589641 7.7133895821 10.8614069404 0 0 0 0 + tauc_H1 16.9035802035 8.30842832493 12.5190468676 0 0 0 0 + tauc_H2 16.6463814075 9.09430738173 9.75503138904 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0988644530489 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.112583489001 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.130619735031 (SEC) + + DONE : INIT CHARGE Time : 0.173879161688 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.456424 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000947 + + Density error is 0.216487499657 + + Energy Rydberg eV + E_KohnSham -34.1896270565 -465.173740463 + E_Harris -34.3845297338 -467.82552743 + E_Fermi -0.413283283434 -5.62300754286 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125702524593 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126846207447 + + Density error is 0.0976518344797 + + Energy Rydberg eV + E_KohnSham -34.2795525719 -466.397239868 + E_Harris -34.2861764418 -466.487362243 + E_Fermi -0.221638608185 -3.01554796811 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116943120136 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122150216993 + + Density error is 0.0624124233565 + + Energy Rydberg eV + E_KohnSham -34.2797782262 -466.400310053 + E_Harris -34.2840313302 -466.458176501 + E_Fermi -0.208322997124 -2.83437978533 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102764986846 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116063169163 + + Density error is 0.00203617291926 + + Energy Rydberg eV + E_KohnSham -34.2798041706 -466.400663044 + E_Harris -34.2798061757 -466.400690326 + E_Fermi -0.172770907443 -2.35066878986 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102719249791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116324784695 + + Density error is 0.000867652421327 + + Energy Rydberg eV + E_KohnSham -34.2797372974 -466.399753188 + E_Harris -34.2797390437 -466.399776948 + E_Fermi -0.171711927012 -2.33626062192 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102575100379 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116200403015 + + Density error is 0.000160324452892 + + Energy Rydberg eV + E_KohnSham -34.2797831214 -466.400376655 + E_Harris -34.2797831901 -466.400377591 + E_Fermi -0.171913417608 -2.33900204212 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010257106326 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116226485835 + + Density error is 4.36327934967e-05 + + Energy Rydberg eV + E_KohnSham -34.2797660638 -466.400144575 + E_Harris -34.2797660742 -466.400144716 + E_Fermi -0.171748512535 -2.3367583935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102570560827 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116217871394 + + Density error is 1.50581263719e-05 + + Energy Rydberg eV + E_KohnSham -34.2797707247 -466.40020799 + E_Harris -34.2797707256 -466.400208002 + E_Fermi -0.171798396706 -2.33743710247 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010256858366 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011621744055 + + Density error is 1.6735497821e-06 + + Energy Rydberg eV + E_KohnSham -34.2797693 -466.400188606 + E_Harris -34.2797693 -466.400188606 + E_Fermi -0.171782118725 -2.33721562917 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102568270753 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116217505792 + + Density error is 1.35155848345e-07 + + Energy Rydberg eV + E_KohnSham -34.2797694852 -466.400191125 + E_Harris -34.2797694852 -466.400191125 + E_Fermi -0.171780552223 -2.33719431582 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102568308572 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116217573377 + + Density error is 4.2493386712e-08 + + Energy Rydberg eV + E_KohnSham -34.2797695163 -466.400191549 + E_Harris -34.2797695163 -466.400191549 + E_band -8.00744144132 -108.946830003 + E_one_elec -69.5737044452 -946.598811423 + E_Hartree +36.1753319146 +492.19064108 + E_xc -8.23151399783 -111.995493537 + E_Ewald +7.47387567213 +101.687295284 + E_demet -1.73896319996e-85 -2.36598081318e-84 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195310298768 -2.65733294133 + E_Fermi -0.1717805959 -2.33719491008 + + charge density convergence is achieved + final etot is -466.400191549 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4025 2.00000 + 2 -13.2386 2.00000 + 3 -9.06304 2.00000 + 4 -6.76931 2.00000 + 5 1.42037 0.00000 + 6 4.63546 0.00000 + 7 11.0428 0.00000 + 8 11.2843 0.00000 + + EFERMI = -2.337194910079417 eV + OUT.ABACUS/ final etot is -466.4001915490365 eV + correction force for each atom along direction 1 is 7.26639e-05 + correction force for each atom along direction 2 is 2.38508e-05 + correction force for each atom along direction 3 is 7.45295e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.31158634 -1.3805288 +0.78361375 + H1 +0.067339318 +0.11816470 +0.15476084 + H2 +0.24424702 +1.2623641 -0.93837459 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4001915490365 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9328 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9244 1 6.9 1.e+02% + Potential init_pot 0.28432 2 0.14 4.1% + PW_Basis recip2real 0.25764 16 0.016 3.7% + PW_Basis gathers_scatterp 0.11866 16 0.0074 1.7% + Potential v_of_rho 0.83266 13 0.064 12.% + XC_Functional v_xc 0.23367 14 0.017 3.4% + H_Hartree_pw v_hartree 0.56267 13 0.043 8.1% + PW_Basis real2recip 0.65079 38 0.017 9.4% + PW_Basis gatherp_scatters 0.26997 38 0.0071 3.9% + ORB_control set_orb_tables 1.1034 1 1.1 16.% + ORB_gen_tables gen_tables 1.1034 1 1.1 16.% + ORB_table_phi init_Table 0.47787 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47258 126 0.0038 6.8% + ORB_table_beta init_Table_Beta 0.18614 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18459 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24982 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24780 66 0.0038 3.6% + LOOP_ions opt_ions 5.2880 1 5.3 76.% + ESolver_KS_LCAO Run 4.7132 1 4.7 68.% + HSolverLCAO solve 2.5165 11 0.23 36.% + HamiltLCAO updateHk 1.2858 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2584 11 0.11 18.% + Gint_interface cal_gint 0.39182 23 0.017 5.7% + Gint_Gamma distri_vl_value 0.68865 11 0.063 9.9% + Gint_Gamma distri_vl 2.2845 6 0.38 33.% + LCAO_Deepks cal_projected_DM 4.8733 13 0.37 70.% + LCAO_gen_fixedH add_v_delta 2.1440 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1441 6 0.36 31.% + ElecStateLCAO psiToRho 1.1743 11 0.11 17.% + Charge mix_rho 0.81001 10 0.081 12.% + LOOP_ions force_stress 0.57465 1 0.57 8.3% + Force_Stress_LCAO getForceStress 0.57462 1 0.57 8.3% + Force_LCAO_gamma ftable_gamma 0.38231 1 0.38 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.12245 1 0.12 1.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:42 2022 + Finish Time : Wed Sep 28 11:12:49 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..01678b96e2ab30a3a8b4af092f1ff65b79569e34 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123829 ima = 3.68723e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123040474454 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112225581958 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112665601551 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112923509141 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112861829597 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112898895212 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112890478065 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112893497752 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112892944651 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011289286931 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112892865949 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7d473d4aa64739c095de1bc3106fc88310217759 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.607341035948 7.713389582109 10.861406940423 0 0 0 +H +0.0 +2 +-11.096419796482 8.308428324901 12.519046867650 0 0 0 +-11.353618592446 9.094307381705 9.755031389060 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/conv new file mode 100644 index 0000000000000000000000000000000000000000..9fdd7f3e706826e95f82ff6b01411d493a76afce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/conv @@ -0,0 +1 @@ +15 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..697dd4172062b95f09112c4c971782f8fe3faf83 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747951824 0.01274367275 1.285052949 1.374036459 1.469909859 0.008390422164 0.01926910542 0.03899220594 +-2.964566645e-19 0.001146251482 0.002622038058 0.01272180732 0.04595721881 7.102535514e-20 2.040439842e-06 5.938409458e-06 +0.001681628371 0.005888636067 + +H atom_index 1 n_descriptor 18 +1.24380321 0.03428216178 0.1063374933 0.1473277767 0.3193116706 0.02192970597 0.0279807365 0.03739915637 +2.162150248e-17 4.567942152e-05 0.1011813396 0.1145482563 0.1265771407 -6.592789986e-18 4.590353879e-06 0.01316692757 +0.02625902073 0.03052094609 + +H atom_index 2 n_descriptor 18 +1.280494306 0.03303428006 0.1195147561 0.1649581759 0.3305092842 0.02359562488 0.03009649311 0.03648658932 +-2.816204484e-17 4.908997438e-05 0.1076860675 0.118576875 0.141694613 -1.148997275e-18 2.566567257e-06 0.0132097506 +0.02755265004 0.0320753061 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a0a8156bbad1a2d3c0694a2341b6da9f6d84fbb0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:42 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0988903 SEC) : SETUP UNITCELL + DONE(0.1126 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.130641 SEC) : INIT PLANEWAVE + DONE(0.174014 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.456487 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651737e+02 0.000000e+00 2.165e-01 5.555e-01 + GE2 -4.663972e+02 -1.223499e+00 9.765e-02 4.756e-01 + GE3 -4.664003e+02 -3.070184e-03 6.241e-02 5.430e-01 + GE4 -4.664007e+02 -3.529912e-04 2.036e-03 4.036e-01 + GE5 -4.663998e+02 9.098564e-04 8.677e-04 4.040e-01 + GE6 -4.664004e+02 -6.234672e-04 1.603e-04 3.933e-01 + GE7 -4.664001e+02 2.320800e-04 4.363e-05 3.898e-01 + GE8 -4.664002e+02 -6.341504e-05 1.506e-05 3.858e-01 + GE9 -4.664002e+02 1.938410e-05 1.674e-06 3.851e-01 + GE10 -4.664002e+02 -2.519460e-06 1.352e-07 3.842e-01 + GE11 -4.664002e+02 -4.237388e-07 4.249e-08 3.267e-01 +E_delta_band = -7.15516387e-02 Ry = -9.73509988e-01 eV +E_delta_NN= -1.95310299e-01 Ry = -2.65733294e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9328 11 0.63 1e+02 % + Run_lcao lcao_line 6.9244 1 6.9 1e+02 % + Potential init_pot 0.28432 2 0.14 4.1 % + PW_Basis recip2real 0.25764 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.11866 16 0.0074 1.7 % + Potential v_of_rho 0.83266 13 0.064 12 % + XC_Functional v_xc 0.23367 14 0.017 3.4 % + H_Hartree_pw v_hartree 0.56267 13 0.043 8.1 % + PW_Basis real2recip 0.65079 38 0.017 9.4 % + PW_Basis gatherp_scatters 0.26997 38 0.0071 3.9 % + ORB_control set_orb_tables 1.1034 1 1.1 16 % + ORB_gen_tables gen_tables 1.1034 1 1.1 16 % + ORB_table_phi init_Table 0.47787 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47258 126 0.0038 6.8 % + ORB_table_beta init_Table_Beta 0.18614 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18459 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24982 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.2478 66 0.0038 3.6 % + LOOP_ions opt_ions 5.288 1 5.3 76 % + ESolver_KS_LCAO Run 4.7132 1 4.7 68 % + HSolverLCAO solve 2.5165 11 0.23 36 % + HamiltLCAO updateHk 1.2858 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2584 11 0.11 18 % + Gint_interface cal_gint 0.39182 23 0.017 5.7 % + Gint_Gamma distri_vl_value 0.68865 11 0.063 9.9 % + Gint_Gamma distri_vl 2.2845 6 0.38 33 % + LCAO_Deepks cal_projected_DM 4.8733 13 0.37 70 % + LCAO_gen_fixedH add_v_delta 2.144 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1441 6 0.36 31 % + ElecStateLCAO psiToRho 1.1743 11 0.11 17 % + Charge mix_rho 0.81001 10 0.081 12 % + LOOP_ions force_stress 0.57465 1 0.57 8.3 % + Force_Stress_LCAO getForceStress 0.57462 1 0.57 8.3 % + Force_LCAO_gamma ftable_gamma 0.38231 1 0.38 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.12245 1 0.12 1.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:42 2022 + FINISH Time : Wed Sep 28 11:12:49 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/15/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d5a2978c48f8e6b83d3cab133e64a540ad79f3d6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.204862 0.604295 0.197488 +H 0.139904 0.597475 0.206298 +H 0.209602 0.64784 0.144148 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..906a2e81f48e41c477eb9129b1aa8d36908191e3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9829 2 + 2 -12.7493 2 + 3 -9.09092 2 + 4 -6.67591 2 + 5 0.98963 0 + 6 3.9608 0 + 7 11.1494 0 + 8 11.3958 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..2673e165fb8aaaae0376bac9efc7f53dc2fa0a07 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:07 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.73613841173 16.920268245 5.52965160556 0 0 0 0 + tauc_H1 3.91730592491 16.7292918841 5.77635186403 0 0 0 0 + tauc_H2 5.86884551334 18.1395212854 4.03614817633 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105753147796 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.106149225012 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124142997973 (SEC) + + DONE : INIT CHARGE Time : 0.167400225192 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450121 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000512 + + Density error is 0.211840382422 + + Energy Rydberg eV + E_KohnSham -34.1889349425 -465.164323769 + E_Harris -34.3742414717 -467.685548442 + E_Fermi -0.386962538818 -5.26489544046 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122452247091 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000713256841955 + + Density error is 0.0989983603787 + + Energy Rydberg eV + E_KohnSham -34.2775920976 -466.370566247 + E_Harris -34.2847832437 -466.46840681 + E_Fermi -0.197104394123 -2.68174286091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116060451094 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000690573182714 + + Density error is 0.0638755202372 + + Energy Rydberg eV + E_KohnSham -34.2780572459 -466.376894915 + E_Harris -34.2826425415 -466.439281061 + E_Fermi -0.1908175703 -2.59620623459 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105929612082 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000673669716934 + + Density error is 0.00198561782363 + + Energy Rydberg eV + E_KohnSham -34.2779556259 -466.375512303 + E_Harris -34.2779583834 -466.375549821 + E_Fermi -0.15562363426 -2.1173681694 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105763976337 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000672245308114 + + Density error is 0.00095237245567 + + Energy Rydberg eV + E_KohnSham -34.2779212775 -466.375044969 + E_Harris -34.2779215825 -466.375049119 + E_Fermi -0.155557092547 -2.11646282296 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105626358415 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000672153084002 + + Density error is 0.000188027856243 + + Energy Rydberg eV + E_KohnSham -34.2779347166 -466.375227818 + E_Harris -34.2779347191 -466.375227852 + E_Fermi -0.155119366811 -2.11050725878 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105644494721 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000672327791792 + + Density error is 2.80898931569e-05 + + Energy Rydberg eV + E_KohnSham -34.2779309996 -466.375177245 + E_Harris -34.2779310012 -466.375177267 + E_Fermi -0.155091766449 -2.11013173659 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105636409309 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000672275079898 + + Density error is 1.21621875046e-05 + + Energy Rydberg eV + E_KohnSham -34.2779334114 -466.37521006 + E_Harris -34.277933412 -466.375210068 + E_Fermi -0.155106218025 -2.11032836037 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010563651781 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000672282931129 + + Density error is 2.94364737472e-06 + + Energy Rydberg eV + E_KohnSham -34.2779325164 -466.375197882 + E_Harris -34.2779325164 -466.375197882 + E_Fermi -0.155095612574 -2.1101840658 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105636168981 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000672283708856 + + Density error is 5.88663935892e-07 + + Energy Rydberg eV + E_KohnSham -34.277932709 -466.375200503 + E_Harris -34.277932709 -466.375200503 + E_Fermi -0.155093065956 -2.1101494173 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105636195038 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000672284327813 + + Density error is 2.09872149615e-07 + + Energy Rydberg eV + E_KohnSham -34.2779327159 -466.375200597 + E_Harris -34.2779327159 -466.375200597 + E_Fermi -0.155092778622 -2.11014550792 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105636196024 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000672284609192 + + Density error is 1.09497810255e-08 + + Energy Rydberg eV + E_KohnSham -34.2779327198 -466.37520065 + E_Harris -34.2779327198 -466.37520065 + E_band -7.8642041117 -106.997986154 + E_one_elec -68.6304214908 -933.764788416 + E_Hartree +35.727946577 +486.103651287 + E_xc -8.15972147401 -111.01870614 + E_Ewald +6.9099182642 +94.0142611074 + E_demet -4.96782517826e-59 -6.75907290922e-58 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193666962462 -2.63497420384 + E_Fermi -0.155092575242 -2.11014274079 + + charge density convergence is achieved + final etot is -466.37520065 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9829 2.00000 + 2 -12.7493 2.00000 + 3 -9.09092 2.00000 + 4 -6.67591 2.00000 + 5 0.989630 0.00000 + 6 3.96080 0.00000 + 7 11.1494 0.00000 + 8 11.3958 0.00000 + + EFERMI = -2.110142740790637 eV + OUT.ABACUS/ final etot is -466.3752006504732 eV + correction force for each atom along direction 1 is -0.000135852 + correction force for each atom along direction 2 is -1.77598e-05 + correction force for each atom along direction 3 is -0.000141532 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.17514971 +1.2165087 -1.4988498 + H1 -0.0034750604 +0.026269838 -0.028089914 + H2 -0.17167465 -1.2427786 +1.5269397 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3752006504732 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9896 11 0.73 1.0e+02% + Run_lcao lcao_line 7.9798 1 8.0 1.e+02% + Potential init_pot 0.28423 2 0.14 3.6% + PW_Basis recip2real 0.30440 17 0.018 3.8% + PW_Basis gathers_scatterp 0.13088 17 0.0077 1.6% + Potential v_of_rho 1.0924 14 0.078 14.% + XC_Functional v_xc 0.31452 15 0.021 3.9% + H_Hartree_pw v_hartree 0.73061 14 0.052 9.1% + PW_Basis real2recip 0.75226 41 0.018 9.4% + PW_Basis gatherp_scatters 0.28574 41 0.0070 3.6% + ORB_control set_orb_tables 1.0909 1 1.1 14.% + ORB_gen_tables gen_tables 1.0909 1 1.1 14.% + ORB_table_phi init_Table 0.47444 1 0.47 5.9% + ORB_table_phi cal_ST_Phi12_R 0.46915 126 0.0037 5.9% + ORB_table_beta init_Table_Beta 0.18320 1 0.18 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18167 56 0.0032 2.3% + ORB_table_alpha init_Table_Alpha 0.24425 1 0.24 3.1% + ORB_table_alpha S_PhiAlpha_R 0.24229 66 0.0037 3.0% + LOOP_ions opt_ions 6.3607 1 6.4 80.% + ESolver_KS_LCAO Run 5.7644 1 5.8 72.% + HSolverLCAO solve 3.0883 12 0.26 39.% + HamiltLCAO updateHk 1.5751 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.5454 12 0.13 19.% + Gint_interface cal_gint 2.9220 25 0.12 37.% + Gint_Gamma distri_vl 2.9927 6 0.50 37.% + LCAO_Deepks cal_projected_DM 6.1868 14 0.44 77.% + LCAO_gen_fixedH add_v_delta 2.8440 6 0.47 36.% + LCAO_DESCRIPTOR add_v_delta 2.8441 6 0.47 36.% + ElecStateLCAO psiToRho 1.4958 12 0.12 19.% + Charge mix_rho 0.98450 11 0.090 12.% + LOOP_ions force_stress 0.59615 1 0.60 7.5% + Force_Stress_LCAO getForceStress 0.59612 1 0.60 7.5% + Force_LCAO_gamma ftable_gamma 0.37654 1 0.38 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.36832 1 0.37 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:07 2022 + Finish Time : Wed Sep 28 11:07:15 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..74906ea1aac61096c229c9afbb32eb517e11fa78 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123543 ima = 3.68985e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012364129054 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112149290062 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112936541728 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113136799745 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113121441126 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113131319529 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113127547286 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113129251678 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113128696536 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113128660127 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113128638705 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113128627716 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e9b5b73a1c223472be9d12dbd10f9e6f7036d40b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.263861588290 16.920268244986 5.529651605580 0 0 0 +H +0.0 +2 +-24.082694075098 16.729291884110 5.776351864030 0 0 0 +-22.131154486678 18.139521285340 4.036148176311 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/conv new file mode 100644 index 0000000000000000000000000000000000000000..55530ec4c656a7823387dd56d55660772647c881 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/conv @@ -0,0 +1 @@ +150 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ff488bab9452af2b052876ec8523aaa8434722b8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75017764 0.01240824998 1.243029123 1.341278769 1.468054293 0.008448197001 0.01790557998 0.03910133434 +-1.070650037e-18 0.0008944707201 0.002407980946 0.0114521194 0.04168749623 -1.905188505e-19 1.620043722e-06 5.045592965e-06 +0.001606051379 0.005840924257 + +H atom_index 1 n_descriptor 18 +1.236779088 0.03477381045 0.1030486692 0.1442141817 0.3174244139 0.02136938352 0.02757471842 0.03800611437 +1.088712165e-17 3.921470548e-05 0.09556001264 0.1149530268 0.1235367459 -1.15555617e-18 4.50666325e-06 0.01329163227 +0.02512770684 0.03013843029 + +H atom_index 2 n_descriptor 18 +1.168184241 0.03691215311 0.08235111711 0.1160157244 0.2919147918 0.018213514 0.02356472385 0.04073392004 +1.062265839e-17 3.357372026e-05 0.07797820783 0.0987375673 0.1120145812 -6.130534256e-18 6.713964066e-06 0.015146045 +0.02230406588 0.02653676676 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..caabf2487ec4cb0ff32b592a9624325306e979e7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:07 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105775 SEC) : SETUP UNITCELL + DONE(0.106165 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124164 SEC) : INIT PLANEWAVE + DONE(0.167524 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.45019 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651643e+02 0.000000e+00 2.118e-01 5.749e-01 + GE2 -4.663706e+02 -1.206242e+00 9.900e-02 5.376e-01 + GE3 -4.663769e+02 -6.328667e-03 6.388e-02 6.088e-01 + GE4 -4.663755e+02 1.382612e-03 1.986e-03 4.661e-01 + GE5 -4.663750e+02 4.673338e-04 9.524e-04 4.660e-01 + GE6 -4.663752e+02 -1.828492e-04 1.880e-04 4.627e-01 + GE7 -4.663752e+02 5.057292e-05 2.809e-05 4.443e-01 + GE8 -4.663752e+02 -3.281431e-05 1.216e-05 4.443e-01 + GE9 -4.663752e+02 1.217773e-05 2.944e-06 4.429e-01 + GE10 -4.663752e+02 -2.620711e-06 5.887e-07 4.420e-01 + GE11 -4.663752e+02 -9.452030e-08 2.099e-07 4.436e-01 + GE12 -4.663752e+02 -5.335319e-08 1.095e-08 3.683e-01 +E_delta_band = -6.80123662e-02 Ry = -9.25355714e-01 eV +E_delta_NN= -1.93666962e-01 Ry = -2.63497420e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9896 11 0.73 1e+02 % + Run_lcao lcao_line 7.9798 1 8 1e+02 % + Potential init_pot 0.28423 2 0.14 3.6 % + PW_Basis recip2real 0.3044 17 0.018 3.8 % + PW_Basis gathers_scatterp 0.13088 17 0.0077 1.6 % + Potential v_of_rho 1.0924 14 0.078 14 % + XC_Functional v_xc 0.31452 15 0.021 3.9 % + H_Hartree_pw v_hartree 0.73061 14 0.052 9.1 % + PW_Basis real2recip 0.75226 41 0.018 9.4 % + PW_Basis gatherp_scatters 0.28574 41 0.007 3.6 % + ORB_control set_orb_tables 1.0909 1 1.1 14 % + ORB_gen_tables gen_tables 1.0909 1 1.1 14 % + ORB_table_phi init_Table 0.47444 1 0.47 5.9 % + ORB_table_phi cal_ST_Phi12_R 0.46915 126 0.0037 5.9 % + ORB_table_beta init_Table_Beta 0.1832 1 0.18 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.18167 56 0.0032 2.3 % + ORB_table_alpha init_Table_Alpha 0.24425 1 0.24 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.24229 66 0.0037 3 % + LOOP_ions opt_ions 6.3607 1 6.4 80 % + ESolver_KS_LCAO Run 5.7644 1 5.8 72 % + HSolverLCAO solve 3.0883 12 0.26 39 % + HamiltLCAO updateHk 1.5751 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.5454 12 0.13 19 % + Gint_interface cal_gint 2.922 25 0.12 37 % + Gint_Gamma distri_vl 2.9927 6 0.5 37 % + LCAO_Deepks cal_projected_DM 6.1868 14 0.44 77 % + LCAO_gen_fixedH add_v_delta 2.844 6 0.47 36 % + LCAO_DESCRIPTOR add_v_delta 2.8441 6 0.47 36 % + ElecStateLCAO psiToRho 1.4958 12 0.12 19 % + Charge mix_rho 0.9845 11 0.09 12 % + LOOP_ions force_stress 0.59615 1 0.6 7.5 % + Force_Stress_LCAO getForceStress 0.59612 1 0.6 7.5 % + Force_LCAO_gamma ftable_gamma 0.37654 1 0.38 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.36832 1 0.37 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:07 2022 + FINISH Time : Wed Sep 28 11:07:15 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/150/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..75f216cec305cb09aeda75bddb3face5568eae5e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.216018 0.588294 0.204518 +H 0.160898 0.596775 0.237901 +H 0.19326 0.592404 0.145682 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3dd840f4f0557f7257bb3eeeda0ec96b5cfbe329 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6382 2 + 2 -13.005 2 + 3 -9.39542 2 + 4 -6.82026 2 + 5 1.45668 0 + 6 4.75331 0 + 7 11.0084 0 + 8 11.2807 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3db1775e7d8bcf1a503cee4474af2e4deae1b1b3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:46 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.04849636796 16.4722187309 5.72650757679 0 0 0 0 + tauc_H1 4.50515029608 16.709699143 6.66122438315 0 0 0 0 + tauc_H2 5.41126736028 16.5872985402 4.0790936077 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0728517409288 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0874054121748 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103744124157 (SEC) + + DONE : INIT CHARGE Time : 0.145272398638 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.390407 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000888 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000777 + + Density error is 0.217412864316 + + Energy Rydberg eV + E_KohnSham -34.1838740594 -465.095466923 + E_Harris -34.3821650446 -467.793354183 + E_Fermi -0.422705508109 -5.75120348627 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00136826778475 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092879512856 + + Density error is 0.0974028125893 + + Energy Rydberg eV + E_KohnSham -34.2763035701 -466.353034932 + E_Harris -34.2830435378 -466.444736897 + E_Fermi -0.228681253124 -3.11136806827 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00131161467008 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00088508157987 + + Density error is 0.0623405619718 + + Energy Rydberg eV + E_KohnSham -34.2766617318 -466.357907971 + E_Harris -34.2810058205 -466.41701233 + E_Fermi -0.215492949081 -2.93193198632 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00123959326312 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830165554279 + + Density error is 0.00203276606275 + + Energy Rydberg eV + E_KohnSham -34.2766896548 -466.358287883 + E_Harris -34.2766919909 -466.358319667 + E_Fermi -0.17933803702 -2.44001917161 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00124549608496 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000833531411663 + + Density error is 0.000993276580142 + + Energy Rydberg eV + E_KohnSham -34.2766081088 -466.357178392 + E_Harris -34.2766105685 -466.357211858 + E_Fermi -0.178364246294 -2.42677006908 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00124357415614 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000832311319194 + + Density error is 0.000110095321821 + + Energy Rydberg eV + E_KohnSham -34.2766605355 -466.357891694 + E_Harris -34.2766605568 -466.357891985 + E_Fermi -0.178531294803 -2.42904288064 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00124332450487 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000832228744155 + + Density error is 4.78603038155e-05 + + Energy Rydberg eV + E_KohnSham -34.2766443948 -466.357672089 + E_Harris -34.2766444086 -466.357672277 + E_Fermi -0.178402006188 -2.42728381878 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00124325503502 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000832188978003 + + Density error is 2.61047098242e-05 + + Energy Rydberg eV + E_KohnSham -34.2766471653 -466.357709783 + E_Harris -34.2766471682 -466.357709823 + E_Fermi -0.178471442399 -2.42822854691 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00124326257433 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000832198105556 + + Density error is 1.79232824141e-06 + + Energy Rydberg eV + E_KohnSham -34.2766452292 -466.357683442 + E_Harris -34.2766452293 -466.357683442 + E_Fermi -0.178442226991 -2.42783105089 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0012432637355 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00083219847422 + + Density error is 2.19097237959e-07 + + Energy Rydberg eV + E_KohnSham -34.2766456295 -466.357688888 + E_Harris -34.2766456295 -466.357688888 + E_Fermi -0.178440803696 -2.42781168596 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00124326483642 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000832199090377 + + Density error is 7.66179301125e-08 + + Energy Rydberg eV + E_KohnSham -34.2766456605 -466.35768931 + E_Harris -34.2766456605 -466.35768931 + E_band -8.06410336638 -109.717755044 + E_one_elec -69.8067283966 -949.769264932 + E_Hartree +36.2740324016 +493.533530099 + E_xc -8.24746772181 -112.212555088 + E_Ewald +7.62675612362 +103.767340538 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195823767999 -2.66431904862 + E_Fermi -0.178440808639 -2.42781175322 + + charge density convergence is achieved + final etot is -466.35768931 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6382 2.00000 + 2 -13.0050 2.00000 + 3 -9.39542 2.00000 + 4 -6.82026 2.00000 + 5 1.45668 0.00000 + 6 4.75331 0.00000 + 7 11.0084 0.00000 + 8 11.2807 0.00000 + + EFERMI = -2.427811753219580 eV + OUT.ABACUS/ final etot is -466.3576893096757 eV + correction force for each atom along direction 1 is -7.65044e-05 + correction force for each atom along direction 2 is -0.000129744 + correction force for each atom along direction 3 is -7.57165e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.80720799 -0.14851708 +1.5554745 + H1 -0.41134302 +0.062273397 +0.80110292 + H2 -0.39586497 +0.086243679 -2.3565774 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3576893096757 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9848 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9772 1 7.0 1.e+02% + Potential init_pot 0.24447 2 0.12 3.5% + PW_Basis recip2real 0.26621 16 0.017 3.8% + PW_Basis gathers_scatterp 0.10708 16 0.0067 1.5% + Potential v_of_rho 0.93772 13 0.072 13.% + XC_Functional v_xc 0.28612 14 0.020 4.1% + H_Hartree_pw v_hartree 0.61372 13 0.047 8.8% + PW_Basis real2recip 0.59922 38 0.016 8.6% + PW_Basis gatherp_scatters 0.22276 38 0.0059 3.2% + ORB_control set_orb_tables 0.90272 1 0.90 13.% + ORB_gen_tables gen_tables 0.90271 1 0.90 13.% + ORB_table_phi init_Table 0.37814 1 0.38 5.4% + ORB_table_phi cal_ST_Phi12_R 0.37380 126 0.0030 5.4% + ORB_table_beta init_Table_Beta 0.15574 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15443 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.21100 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20934 66 0.0032 3.0% + LOOP_ions opt_ions 5.6143 1 5.6 80.% + ESolver_KS_LCAO Run 5.0666 1 5.1 73.% + HSolverLCAO solve 2.8785 11 0.26 41.% + HamiltLCAO updateHk 1.4546 11 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.4251 11 0.13 20.% + Gint_interface cal_gint 2.7683 23 0.12 40.% + Gint_Gamma distri_vl 2.4269 6 0.40 35.% + LCAO_Deepks cal_projected_DM 5.4542 13 0.42 78.% + LCAO_gen_fixedH add_v_delta 2.2994 6 0.38 33.% + LCAO_DESCRIPTOR add_v_delta 2.2994 6 0.38 33.% + ElecStateLCAO psiToRho 1.4070 11 0.13 20.% + Charge mix_rho 0.76316 10 0.076 11.% + LOOP_ions force_stress 0.54758 1 0.55 7.8% + Force_Stress_LCAO getForceStress 0.54756 1 0.55 7.8% + Force_LCAO_gamma ftable_gamma 0.35185 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.34394 1 0.34 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:46 2022 + Finish Time : Wed Sep 28 11:07:53 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..aebebdb534f8a14d4b0328525b03f12e7f49025e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124165 ima = 3.70421e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122618340636 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111433612114 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111937424649 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112247537511 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112168806667 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112210086794 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112207216055 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112210890916 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112209772053 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112209694403 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112209687398 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4f5b1129e4492bb46f31531a211e2e1981c71d16 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.951503632034 16.472218730934 5.726507576794 0 0 0 +H +0.0 +2 +-23.494849703911 16.709699142990 6.661224383173 0 0 0 +-22.588732639711 16.587298540199 4.079093607692 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/conv new file mode 100644 index 0000000000000000000000000000000000000000..abf9488208b3771be9d19ebfb0f59f2da562a9d1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/conv @@ -0,0 +1 @@ +151 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5c0e588feed3d64e3e8e2c01b9b9970673164c99 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753060712 0.01289473932 1.289951448 1.373022092 1.470790038 0.009445732991 0.01766137233 0.03912665361 +-6.104863099e-19 0.001051052111 0.002965191305 0.01374466199 0.0492946621 -2.186006748e-19 3.023800226e-06 7.755692931e-06 +0.00159825492 0.006125790356 + +H atom_index 1 n_descriptor 18 +1.25907089 0.03444629455 0.1141166495 0.153725921 0.3223229973 0.02362327686 0.02876088501 0.03755313681 +-2.290686137e-17 5.512119256e-05 0.1067793576 0.1159824846 0.1320770912 -8.355097498e-18 2.904724449e-06 0.01335678796 +0.02774556496 0.0311758794 + +H atom_index 2 n_descriptor 18 +1.298120949 0.03322062556 0.1292206966 0.1734306778 0.3339321611 0.02553775708 0.03100998049 0.03687278732 +-9.396778653e-18 5.893240118e-05 0.1087068454 0.1253092953 0.1488101106 -5.357121892e-18 8.629968662e-07 0.01380658221 +0.02902306779 0.03271932943 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..52e7677540833bbe97510c8d35bfe10f5dd762e1 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:46 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0728674 SEC) : SETUP UNITCELL + DONE(0.0874185 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103757 SEC) : INIT PLANEWAVE + DONE(0.145373 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.390451 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650955e+02 0.000000e+00 2.174e-01 5.289e-01 + GE2 -4.663530e+02 -1.257568e+00 9.740e-02 5.085e-01 + GE3 -4.663579e+02 -4.873039e-03 6.234e-02 5.688e-01 + GE4 -4.663583e+02 -3.799121e-04 2.033e-03 4.465e-01 + GE5 -4.663572e+02 1.109490e-03 9.933e-04 4.466e-01 + GE6 -4.663579e+02 -7.133019e-04 1.101e-04 4.376e-01 + GE7 -4.663577e+02 2.196056e-04 4.786e-05 4.423e-01 + GE8 -4.663577e+02 -3.769448e-05 2.610e-05 4.230e-01 + GE9 -4.663577e+02 2.634086e-05 1.792e-06 4.260e-01 + GE10 -4.663577e+02 -5.445698e-06 2.191e-07 4.247e-01 + GE11 -4.663577e+02 -4.217694e-07 7.662e-08 3.601e-01 +E_delta_band = -7.25857007e-02 Ry = -9.87579122e-01 eV +E_delta_NN= -1.95823768e-01 Ry = -2.66431905e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9848 11 0.63 1e+02 % + Run_lcao lcao_line 6.9772 1 7 1e+02 % + Potential init_pot 0.24447 2 0.12 3.5 % + PW_Basis recip2real 0.26621 16 0.017 3.8 % + PW_Basis gathers_scatterp 0.10708 16 0.0067 1.5 % + Potential v_of_rho 0.93772 13 0.072 13 % + XC_Functional v_xc 0.28612 14 0.02 4.1 % + H_Hartree_pw v_hartree 0.61372 13 0.047 8.8 % + PW_Basis real2recip 0.59922 38 0.016 8.6 % + PW_Basis gatherp_scatters 0.22276 38 0.0059 3.2 % + ORB_control set_orb_tables 0.90272 1 0.9 13 % + ORB_gen_tables gen_tables 0.90271 1 0.9 13 % + ORB_table_phi init_Table 0.37814 1 0.38 5.4 % + ORB_table_phi cal_ST_Phi12_R 0.3738 126 0.003 5.4 % + ORB_table_beta init_Table_Beta 0.15574 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15443 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.211 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20934 66 0.0032 3 % + LOOP_ions opt_ions 5.6143 1 5.6 80 % + ESolver_KS_LCAO Run 5.0666 1 5.1 73 % + HSolverLCAO solve 2.8785 11 0.26 41 % + HamiltLCAO updateHk 1.4546 11 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.4251 11 0.13 20 % + Gint_interface cal_gint 2.7683 23 0.12 40 % + Gint_Gamma distri_vl 2.4269 6 0.4 35 % + LCAO_Deepks cal_projected_DM 5.4542 13 0.42 78 % + LCAO_gen_fixedH add_v_delta 2.2994 6 0.38 33 % + LCAO_DESCRIPTOR add_v_delta 2.2994 6 0.38 33 % + ElecStateLCAO psiToRho 1.407 11 0.13 20 % + Charge mix_rho 0.76316 10 0.076 11 % + LOOP_ions force_stress 0.54758 1 0.55 7.8 % + Force_Stress_LCAO getForceStress 0.54756 1 0.55 7.8 % + Force_LCAO_gamma ftable_gamma 0.35185 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.34394 1 0.34 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:46 2022 + FINISH Time : Wed Sep 28 11:07:53 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/151/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fa03ec5e607923064e5b25dbc69d22a6e6401b1f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.220961 0.581886 0.202051 +H 0.180249 0.544028 0.240121 +H 0.220394 0.548548 0.142974 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d34a4cd554f36e053fe5aa869f19fc0dd33a226d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9779 2 + 2 -12.6596 2 + 3 -9.16552 2 + 4 -6.67816 2 + 5 0.994908 0 + 6 3.88795 0 + 7 11.1539 0 + 8 11.4117 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..aa9af36453cc5aabeff1b044cf93ded4e00ca56b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:05 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.18690988445 16.2928052633 5.65741693071 0 0 0 0 + tauc_H1 5.04696591659 15.23277316 6.72340164615 0 0 0 0 + tauc_H2 6.1710284471 15.3593551984 4.0032654615 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.074045728605 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0787946192382 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0946483654845 (SEC) + + DONE : INIT CHARGE Time : 0.13676371775 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.379022 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000822 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000734 + + Density error is 0.210685626565 + + Energy Rydberg eV + E_KohnSham -34.1915648795 -465.200105898 + E_Harris -34.3742835464 -467.686120899 + E_Fermi -0.384340330019 -5.22921845946 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00100648482156 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102640208022 + + Density error is 0.0987682884938 + + Energy Rydberg eV + E_KohnSham -34.278890881 -466.388237102 + E_Harris -34.2860698363 -466.4859118 + E_Fermi -0.19614061278 -2.66862994302 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000958275391827 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989758871531 + + Density error is 0.0637608705229 + + Energy Rydberg eV + E_KohnSham -34.2793158627 -466.394019275 + E_Harris -34.2839037 -466.456440003 + E_Fermi -0.189862309684 -2.58320924714 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000894390015942 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957641521435 + + Density error is 0.00194938413424 + + Energy Rydberg eV + E_KohnSham -34.2792093209 -466.392569699 + E_Harris -34.2792113195 -466.392596892 + E_Fermi -0.154710546418 -2.10494497198 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000894398028011 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957333640718 + + Density error is 0.000900601140097 + + Energy Rydberg eV + E_KohnSham -34.2791819234 -466.392196937 + E_Harris -34.2791821905 -466.39220057 + E_Fermi -0.154706958064 -2.10489614991 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000893645580606 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957102342731 + + Density error is 0.000184109334409 + + Energy Rydberg eV + E_KohnSham -34.2791924729 -466.392340471 + E_Harris -34.2791924822 -466.392340597 + E_Fermi -0.154225298999 -2.09834284214 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000893855884894 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957324497946 + + Density error is 2.70769405106e-05 + + Energy Rydberg eV + E_KohnSham -34.2791898908 -466.392305339 + E_Harris -34.2791898925 -466.392305362 + E_Fermi -0.154230623491 -2.09841528556 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00089379840123 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957250369645 + + Density error is 1.05346758575e-05 + + Energy Rydberg eV + E_KohnSham -34.2791920137 -466.392334223 + E_Harris -34.2791920142 -466.392334229 + E_Fermi -0.154239538895 -2.09853658586 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000893799062268 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00095725454286 + + Density error is 1.89552299302e-06 + + Energy Rydberg eV + E_KohnSham -34.2791911808 -466.39232289 + E_Harris -34.2791911808 -466.39232289 + E_Fermi -0.154229413336 -2.09839882056 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00089379922567 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957256472433 + + Density error is 2.93459179905e-07 + + Energy Rydberg eV + E_KohnSham -34.2791913244 -466.392324843 + E_Harris -34.2791913244 -466.392324843 + E_Fermi -0.154227698784 -2.09837549289 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000893799492239 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957256993445 + + Density error is 6.61484242457e-08 + + Energy Rydberg eV + E_KohnSham -34.2791913458 -466.392325135 + E_Harris -34.2791913458 -466.392325135 + E_band -7.86159250348 -106.962453401 + E_one_elec -68.5817959052 -933.103203383 + E_Hartree +35.7021042156 +485.752047921 + E_xc -8.15542952765 -110.960311213 + E_Ewald +6.88168311143 +93.6301021459 + E_demet -8.54983706742e-59 -1.16326501089e-57 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193575832497 -2.63373431705 + E_Fermi -0.154227547343 -2.09837343243 + + charge density convergence is achieved + final etot is -466.392325135 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9779 2.00000 + 2 -12.6596 2.00000 + 3 -9.16552 2.00000 + 4 -6.67816 2.00000 + 5 0.994908 0.00000 + 6 3.88795 0.00000 + 7 11.1539 0.00000 + 8 11.4117 0.00000 + + EFERMI = -2.098373432431537 eV + OUT.ABACUS/ final etot is -466.3923251354333 eV + correction force for each atom along direction 1 is -0.000166413 + correction force for each atom along direction 2 is -0.000153329 + correction force for each atom along direction 3 is 1.19048e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.65610465 -1.2565131 -0.56859047 + H1 +0.60034930 +0.59110658 -0.49824231 + H2 +0.055755358 +0.66540648 +1.0668328 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3923251354333 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0693 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0609 1 7.1 1.e+02% + Potential init_pot 0.24135 2 0.12 3.4% + PW_Basis recip2real 0.26182 16 0.016 3.7% + PW_Basis gathers_scatterp 0.10608 16 0.0066 1.5% + Potential v_of_rho 0.92363 13 0.071 13.% + XC_Functional v_xc 0.27792 14 0.020 3.9% + H_Hartree_pw v_hartree 0.60818 13 0.047 8.6% + PW_Basis real2recip 0.60514 38 0.016 8.6% + PW_Basis gatherp_scatters 0.22941 38 0.0060 3.2% + ORB_control set_orb_tables 0.90510 1 0.91 13.% + ORB_gen_tables gen_tables 0.90510 1 0.91 13.% + ORB_table_phi init_Table 0.37643 1 0.38 5.3% + ORB_table_phi cal_ST_Phi12_R 0.37228 126 0.0030 5.3% + ORB_table_beta init_Table_Beta 0.15964 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15832 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.21099 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20930 66 0.0032 3.0% + LOOP_ions opt_ions 5.7082 1 5.7 81.% + ESolver_KS_LCAO Run 5.1546 1 5.2 73.% + HSolverLCAO solve 2.9731 11 0.27 42.% + HamiltLCAO updateHk 1.4944 11 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.4627 11 0.13 21.% + Gint_interface cal_gint 2.8592 23 0.12 40.% + Gint_Gamma distri_vl 2.4639 6 0.41 35.% + LCAO_Deepks cal_projected_DM 5.5456 13 0.43 78.% + LCAO_gen_fixedH add_v_delta 2.3327 6 0.39 33.% + LCAO_DESCRIPTOR add_v_delta 2.3327 6 0.39 33.% + ElecStateLCAO psiToRho 1.4622 11 0.13 21.% + Charge mix_rho 0.76362 10 0.076 11.% + LOOP_ions force_stress 0.55338 1 0.55 7.8% + Force_Stress_LCAO getForceStress 0.55335 1 0.55 7.8% + Force_LCAO_gamma ftable_gamma 0.35275 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.34539 1 0.35 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:05 2022 + Finish Time : Wed Sep 28 11:06:12 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..70a6ce388c040947e7299a257830e0cb09a7ccf4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012352 ima = 3.70289e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123426193143 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011201581471 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112802583607 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112991660755 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112981979049 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011298915526 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011298583137 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112987488382 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112987031673 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112986966701 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112986951923 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b081e25e8223dfd1eb4f262002a153718beb46ee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.813090115563 16.292805263308 5.657416930701 0 0 0 +H +0.0 +2 +-22.953034083390 15.232773160027 6.723401646141 0 0 0 +-21.828971552870 15.359355198364 4.003265461521 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/conv new file mode 100644 index 0000000000000000000000000000000000000000..2dabb372f0cd190e41ea4c81893ad6378576f85e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/conv @@ -0,0 +1 @@ +152 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..221684ffc35eb8364737662b1864b7580b773714 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751368077 0.01243729205 1.24389338 1.33357326 1.468021747 0.008634957101 0.01739537169 0.03913626173 +1.827263755e-18 0.0008577642722 0.002439944363 0.01158791167 0.04178121743 -3.464712067e-19 1.74425697e-06 5.265707591e-06 +0.001590397882 0.005913979991 + +H atom_index 1 n_descriptor 18 +1.205469051 0.03595248162 0.09345838045 0.1304764672 0.3057961789 0.02006850312 0.02570132051 0.03934407286 +-1.301577872e-17 3.749090866e-05 0.08742392357 0.1115013645 0.1139489932 -4.307268054e-18 5.658401908e-06 0.01403179349 +0.02395796348 0.02853660972 + +H atom_index 2 n_descriptor 18 +1.195436278 0.03626426837 0.09044155096 0.1263819078 0.3020163913 0.01960055214 0.02511305896 0.03975390231 +3.453645793e-17 3.665265889e-05 0.08485153576 0.1078940597 0.1135080938 -3.451833239e-18 5.989318133e-06 0.01432175536 +0.02354082112 0.02800287672 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e2a9a2a0cb7bea53ac7f40f0718a2427f6296369 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..7435d9133db42a2a9ca49d581773f7f8fb0c0a38 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:05 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0740619 SEC) : SETUP UNITCELL + DONE(0.0788047 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0946597 SEC) : INIT PLANEWAVE + DONE(0.136867 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.379068 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652001e+02 0.000000e+00 2.107e-01 5.397e-01 + GE2 -4.663882e+02 -1.188131e+00 9.877e-02 5.221e-01 + GE3 -4.663940e+02 -5.782173e-03 6.376e-02 5.839e-01 + GE4 -4.663926e+02 1.449576e-03 1.949e-03 4.543e-01 + GE5 -4.663922e+02 3.727619e-04 9.006e-04 4.535e-01 + GE6 -4.663923e+02 -1.435335e-04 1.841e-04 4.493e-01 + GE7 -4.663923e+02 3.513197e-05 2.708e-05 4.362e-01 + GE8 -4.663923e+02 -2.888405e-05 1.053e-05 4.309e-01 + GE9 -4.663923e+02 1.133266e-05 1.896e-06 4.319e-01 + GE10 -4.663923e+02 -1.953416e-06 2.935e-07 4.366e-01 + GE11 -4.663923e+02 -2.920164e-07 6.615e-08 3.626e-01 +E_delta_band = -6.78225925e-02 Ry = -9.22773711e-01 eV +E_delta_NN= -1.93575832e-01 Ry = -2.63373432e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0693 11 0.64 1e+02 % + Run_lcao lcao_line 7.0609 1 7.1 1e+02 % + Potential init_pot 0.24135 2 0.12 3.4 % + PW_Basis recip2real 0.26182 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.10608 16 0.0066 1.5 % + Potential v_of_rho 0.92363 13 0.071 13 % + XC_Functional v_xc 0.27792 14 0.02 3.9 % + H_Hartree_pw v_hartree 0.60818 13 0.047 8.6 % + PW_Basis real2recip 0.60514 38 0.016 8.6 % + PW_Basis gatherp_scatters 0.22941 38 0.006 3.2 % + ORB_control set_orb_tables 0.9051 1 0.91 13 % + ORB_gen_tables gen_tables 0.9051 1 0.91 13 % + ORB_table_phi init_Table 0.37643 1 0.38 5.3 % + ORB_table_phi cal_ST_Phi12_R 0.37228 126 0.003 5.3 % + ORB_table_beta init_Table_Beta 0.15964 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15832 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.21099 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.2093 66 0.0032 3 % + LOOP_ions opt_ions 5.7082 1 5.7 81 % + ESolver_KS_LCAO Run 5.1546 1 5.2 73 % + HSolverLCAO solve 2.9731 11 0.27 42 % + HamiltLCAO updateHk 1.4944 11 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.4627 11 0.13 21 % + Gint_interface cal_gint 2.8592 23 0.12 40 % + Gint_Gamma distri_vl 2.4639 6 0.41 35 % + LCAO_Deepks cal_projected_DM 5.5456 13 0.43 78 % + LCAO_gen_fixedH add_v_delta 2.3327 6 0.39 33 % + LCAO_DESCRIPTOR add_v_delta 2.3327 6 0.39 33 % + ElecStateLCAO psiToRho 1.4622 11 0.13 21 % + Charge mix_rho 0.76362 10 0.076 11 % + LOOP_ions force_stress 0.55338 1 0.55 7.8 % + Force_Stress_LCAO getForceStress 0.55335 1 0.55 7.8 % + Force_LCAO_gamma ftable_gamma 0.35275 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.34539 1 0.35 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:05 2022 + FINISH Time : Wed Sep 28 11:06:12 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/152/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..665994222299e2e877e6562c9d17d93f6a2294c8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.214642 0.576605 0.211526 +H 0.212453 0.540477 0.26568 +H 0.256121 0.548534 0.167696 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bb4688006bc4052b1573067773d5647258a14d2d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1235 2 + 2 -13.2465 2 + 3 -8.83187 2 + 4 -6.70339 2 + 5 1.25606 0 + 6 4.37483 0 + 7 11.1 0 + 8 11.3252 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ff64c015923932aadde2ee391538e0f657c8e2cb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:45 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.0099688241 16.1449446867 5.92272054169 0 0 0 0 + tauc_H1 5.94867804945 15.1333606517 7.43904196506 0 0 0 0 + tauc_H2 7.17139299773 15.3589599932 4.69548973016 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0893852051171 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0959025919381 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.114384603193 (SEC) + + DONE : INIT CHARGE Time : 0.164224518263 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441152 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000751 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121 + + Density error is 0.215396904852 + + Energy Rydberg eV + E_KohnSham -34.1898498685 -465.176771977 + E_Harris -34.3819316518 -467.790178712 + E_Fermi -0.400396998863 -5.44768064664 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000972293812258 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127772004306 + + Density error is 0.0984300091154 + + Energy Rydberg eV + E_KohnSham -34.2794858017 -466.396331414 + E_Harris -34.2862230104 -466.48799584 + E_Fermi -0.208770078961 -2.84046264578 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000932064639801 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120902334857 + + Density error is 0.0631575071107 + + Energy Rydberg eV + E_KohnSham -34.2797844971 -466.400395372 + E_Harris -34.2841145181 -466.45930833 + E_Fermi -0.198281946544 -2.69776428353 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000879938936023 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110241917547 + + Density error is 0.0020934317505 + + Energy Rydberg eV + E_KohnSham -34.2797622109 -466.400092153 + E_Harris -34.2797660438 -466.400144302 + E_Fermi -0.163111528896 -2.21924620248 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000880293750556 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110164347716 + + Density error is 0.000873748389682 + + Energy Rydberg eV + E_KohnSham -34.2797125476 -466.399416449 + E_Harris -34.2797131465 -466.399424598 + E_Fermi -0.162420533903 -2.20984473328 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00087956314517 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110026122408 + + Density error is 0.000202183055677 + + Energy Rydberg eV + E_KohnSham -34.2797420334 -466.399817624 + E_Harris -34.2797421037 -466.399818581 + E_Fermi -0.162322446592 -2.20851018696 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000879827250165 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110044107455 + + Density error is 3.69721651312e-05 + + Energy Rydberg eV + E_KohnSham -34.2797304793 -466.399660423 + E_Harris -34.2797304861 -466.399660515 + E_Fermi -0.16219422225 -2.20676560527 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00087976071764 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011003746609 + + Density error is 1.60796722474e-05 + + Energy Rydberg eV + E_KohnSham -34.2797353783 -466.399727077 + E_Harris -34.2797353793 -466.399727091 + E_Fermi -0.162231485632 -2.2072725996 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000879759052042 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001100360311 + + Density error is 1.73354867449e-06 + + Energy Rydberg eV + E_KohnSham -34.2797340582 -466.399709116 + E_Harris -34.2797340582 -466.399709116 + E_Fermi -0.162214457714 -2.20704092288 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000879760345858 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110036036178 + + Density error is 2.36701175968e-07 + + Energy Rydberg eV + E_KohnSham -34.2797342689 -466.399711983 + E_Harris -34.2797342689 -466.399711983 + E_Fermi -0.162212869903 -2.20701931961 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000879760528301 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110036059274 + + Density error is 8.57724949104e-08 + + Energy Rydberg eV + E_KohnSham -34.2797342951 -466.399712339 + E_Harris -34.2797342951 -466.399712339 + E_band -7.92391823791 -107.810438522 + E_one_elec -69.1436026598 -940.746976422 + E_Hartree +35.9811171389 +489.548213495 + E_xc -8.19979024472 -111.563869733 + E_Ewald +7.20722592776 +98.0593393908 + E_demet -5.1481054967e-73 -7.00435686602e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194395883585 -2.6448916845 + E_Fermi -0.162212832363 -2.20701880886 + + charge density convergence is achieved + final etot is -466.399712339 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1235 2.00000 + 2 -13.2465 2.00000 + 3 -8.83187 2.00000 + 4 -6.70339 2.00000 + 5 1.25606 0.00000 + 6 4.37483 0.00000 + 7 11.1000 0.00000 + 8 11.3252 0.00000 + + EFERMI = -2.207018808859760 eV + OUT.ABACUS/ final etot is -466.3997123388988 eV + correction force for each atom along direction 1 is 6.77796e-05 + correction force for each atom along direction 2 is 4.75306e-07 + correction force for each atom along direction 3 is -7.87349e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.090702916 +0.50071263 -0.86458897 + H1 +0.24414395 -0.48650358 +0.18111600 + H2 -0.33484687 -0.014209050 +0.68347297 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3997123388988 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5026 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4919 1 6.5 1.e+02% + Potential init_pot 0.28082 2 0.14 4.3% + PW_Basis recip2real 0.27045 16 0.017 4.2% + PW_Basis gathers_scatterp 0.11836 16 0.0074 1.8% + Potential v_of_rho 0.87994 13 0.068 14.% + XC_Functional v_xc 0.24846 14 0.018 3.8% + H_Hartree_pw v_hartree 0.59276 13 0.046 9.1% + PW_Basis real2recip 0.55662 38 0.015 8.6% + PW_Basis gatherp_scatters 0.21432 38 0.0056 3.3% + ORB_control set_orb_tables 1.1108 1 1.1 17.% + ORB_gen_tables gen_tables 1.1108 1 1.1 17.% + ORB_table_phi init_Table 0.49111 1 0.49 7.6% + ORB_table_phi cal_ST_Phi12_R 0.48620 126 0.0039 7.5% + ORB_table_beta init_Table_Beta 0.19103 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18957 56 0.0034 2.9% + ORB_table_alpha init_Table_Alpha 0.24873 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24690 66 0.0037 3.8% + LOOP_ions opt_ions 4.8644 1 4.9 75.% + ESolver_KS_LCAO Run 4.3226 1 4.3 66.% + HSolverLCAO solve 2.3529 11 0.21 36.% + HamiltLCAO updateHk 1.2191 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.1856 11 0.11 18.% + Gint_interface cal_gint 2.2292 23 0.097 34.% + Gint_Gamma distri_vl 2.0803 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.6957 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9492 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9492 6 0.32 30.% + ElecStateLCAO psiToRho 1.1198 11 0.10 17.% + Charge mix_rho 0.65430 10 0.065 10.% + LOOP_ions force_stress 0.54153 1 0.54 8.3% + Force_Stress_LCAO getForceStress 0.54150 1 0.54 8.3% + Force_LCAO_gamma ftable_gamma 0.33111 1 0.33 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.32438 1 0.32 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:45 2022 + Finish Time : Wed Sep 28 11:05:51 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..97d8ddb77608ce7ae3e9b9a91097dfc7543f2037 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123577 ima = 3.69571e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123728836011 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756019445 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113299679688 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113514673821 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113477560657 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113501171091 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113492194245 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011349489862 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113494273174 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113494204939 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113494198219 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7ca6f0d2f775bf1932b30aa9be1c60ed78f12726 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.990031175888 16.144944686765 5.922720541671 0 0 0 +H +0.0 +2 +-22.051321950567 15.133360651675 7.439041965084 0 0 0 +-20.828607002251 15.358959993137 4.695489730142 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/conv new file mode 100644 index 0000000000000000000000000000000000000000..bbc2a8dd88f5bfd2ea6c3e59b691ab4da5486286 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/conv @@ -0,0 +1 @@ +153 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7243cb14de97c78ba3897f106d63faed8cd603cd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.744445515 0.01254697147 1.270470469 1.365734926 1.468594324 0.007689249066 0.02005149081 0.03888354723 +-7.865572357e-19 0.001099365354 0.0023362106 0.01205613946 0.04197985258 1.178759103e-18 1.454372693e-06 4.653886794e-06 +0.001765894236 0.005647980173 + +H atom_index 1 n_descriptor 18 +1.248195019 0.03377034397 0.1075835848 0.1505664683 0.3226682889 0.02169057451 0.02839594248 0.03699165064 +-4.092825586e-18 3.758521137e-05 0.1008106561 0.1148512509 0.1292095431 -6.385765444e-18 4.18282929e-06 0.01290870758 +0.02584408785 0.03079191685 + +H atom_index 2 n_descriptor 18 +1.216457715 0.03488741147 0.09720038722 0.1364803875 0.3122148233 0.02029571104 0.02655704264 0.0381206236 +4.960558348e-17 3.507163081e-05 0.09244558561 0.1140236239 0.1169639931 1.32617564e-18 5.460721583e-06 0.01337647537 +0.02461918393 0.02929168049 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9f1fb1c8c74d38f9a29e5825fb09568d1524ee42 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:45 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0894082 SEC) : SETUP UNITCELL + DONE(0.0959219 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.114411 SEC) : INIT PLANEWAVE + DONE(0.164349 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.441225 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651768e+02 0.000000e+00 2.154e-01 5.073e-01 + GE2 -4.663963e+02 -1.219559e+00 9.843e-02 4.318e-01 + GE3 -4.664004e+02 -4.063959e-03 6.316e-02 4.883e-01 + GE4 -4.664001e+02 3.032194e-04 2.093e-03 3.748e-01 + GE5 -4.663994e+02 6.757033e-04 8.737e-04 3.754e-01 + GE6 -4.663998e+02 -4.011744e-04 2.022e-04 3.679e-01 + GE7 -4.663997e+02 1.572007e-04 3.697e-05 3.624e-01 + GE8 -4.663997e+02 -6.665409e-05 1.608e-05 3.521e-01 + GE9 -4.663997e+02 1.796141e-05 1.734e-06 3.529e-01 + GE10 -4.663997e+02 -2.867249e-06 2.367e-07 3.516e-01 + GE11 -4.663997e+02 -3.558754e-07 8.577e-08 2.970e-01 +E_delta_band = -6.97114264e-02 Ry = -9.48472615e-01 eV +E_delta_NN= -1.94395884e-01 Ry = -2.64489168e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5026 11 0.59 1e+02 % + Run_lcao lcao_line 6.4919 1 6.5 1e+02 % + Potential init_pot 0.28082 2 0.14 4.3 % + PW_Basis recip2real 0.27045 16 0.017 4.2 % + PW_Basis gathers_scatterp 0.11836 16 0.0074 1.8 % + Potential v_of_rho 0.87994 13 0.068 14 % + XC_Functional v_xc 0.24846 14 0.018 3.8 % + H_Hartree_pw v_hartree 0.59276 13 0.046 9.1 % + PW_Basis real2recip 0.55662 38 0.015 8.6 % + PW_Basis gatherp_scatters 0.21432 38 0.0056 3.3 % + ORB_control set_orb_tables 1.1108 1 1.1 17 % + ORB_gen_tables gen_tables 1.1108 1 1.1 17 % + ORB_table_phi init_Table 0.49111 1 0.49 7.6 % + ORB_table_phi cal_ST_Phi12_R 0.4862 126 0.0039 7.5 % + ORB_table_beta init_Table_Beta 0.19103 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18957 56 0.0034 2.9 % + ORB_table_alpha init_Table_Alpha 0.24873 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.2469 66 0.0037 3.8 % + LOOP_ions opt_ions 4.8644 1 4.9 75 % + ESolver_KS_LCAO Run 4.3226 1 4.3 66 % + HSolverLCAO solve 2.3529 11 0.21 36 % + HamiltLCAO updateHk 1.2191 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.1856 11 0.11 18 % + Gint_interface cal_gint 2.2292 23 0.097 34 % + Gint_Gamma distri_vl 2.0803 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.6957 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9492 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9492 6 0.32 30 % + ElecStateLCAO psiToRho 1.1198 11 0.1 17 % + Charge mix_rho 0.6543 10 0.065 10 % + LOOP_ions force_stress 0.54153 1 0.54 8.3 % + Force_Stress_LCAO getForceStress 0.5415 1 0.54 8.3 % + Force_LCAO_gamma ftable_gamma 0.33111 1 0.33 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.32438 1 0.32 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:45 2022 + FINISH Time : Wed Sep 28 11:05:51 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/153/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ab1344b72032d04849c522b6a2569d3528b67916 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.207398 0.567987 0.220387 +H 0.231542 0.535345 0.272147 +H 0.242914 0.539383 0.176505 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..db3ea18b839d9ee7eae2b1bddf1d4d1e0a9a60ce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6294 2 + 2 -12.7915 2 + 3 -9.53151 2 + 4 -6.81766 2 + 5 1.36256 0 + 6 4.64606 0 + 7 11.0214 0 + 8 11.3086 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..8542cb7c924b6b0ba36658e83b1b4d1680a107de --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.80715631372 15.9036356253 6.17084167179 0 0 0 0 + tauc_H1 6.48316671122 14.9896640923 7.62011435164 0 0 0 0 + tauc_H2 6.80160399427 15.1027278012 4.94212618201 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0877462881864 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.096167294511 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.114484740089 (SEC) + + DONE : INIT CHARGE Time : 0.164356539723 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.452947 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000977 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122 + + Density error is 0.21556754871 + + Energy Rydberg eV + E_KohnSham -34.1843560778 -465.102025119 + E_Harris -34.3788005751 -467.747578227 + E_Fermi -0.418009474733 -5.68731067436 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00124758161799 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132600739932 + + Density error is 0.0972197916872 + + Energy Rydberg eV + E_KohnSham -34.2749392555 -466.334472479 + E_Harris -34.2817372526 -466.426963974 + E_Fermi -0.226602596066 -3.08308648809 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00118206891585 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124748588711 + + Density error is 0.0622187887891 + + Energy Rydberg eV + E_KohnSham -34.2752352359 -466.338499499 + E_Harris -34.2796276199 -466.398260948 + E_Fermi -0.213897258969 -2.91022150856 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109040022745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113267268377 + + Density error is 0.00199801824092 + + Energy Rydberg eV + E_KohnSham -34.2752492505 -466.338690177 + E_Harris -34.2752510389 -466.338714509 + E_Fermi -0.177720615362 -2.41801302099 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109481690554 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113641115685 + + Density error is 0.00092748326276 + + Energy Rydberg eV + E_KohnSham -34.2751795126 -466.337741344 + E_Harris -34.2751816485 -466.337770405 + E_Fermi -0.176930274036 -2.40725987559 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109294224128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113439075408 + + Density error is 0.000126451767833 + + Energy Rydberg eV + E_KohnSham -34.2752266239 -466.338382327 + E_Harris -34.2752266634 -466.338382864 + E_Fermi -0.177022012124 -2.40850803631 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109281349435 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113423016024 + + Density error is 4.13127544654e-05 + + Energy Rydberg eV + E_KohnSham -34.2752108183 -466.33816728 + E_Harris -34.2752108266 -466.338167393 + E_Fermi -0.176898210077 -2.40682362305 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109276774997 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113419500073 + + Density error is 2.17401510935e-05 + + Energy Rydberg eV + E_KohnSham -34.2752140468 -466.338211206 + E_Harris -34.2752140486 -466.338211231 + E_Fermi -0.176947048376 -2.4074881022 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109275703466 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113417628789 + + Density error is 1.931348853e-06 + + Energy Rydberg eV + E_KohnSham -34.2752124679 -466.338189724 + E_Harris -34.2752124679 -466.338189724 + E_Fermi -0.176922724439 -2.40715715806 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109275725322 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113417588081 + + Density error is 4.44495753602e-07 + + Energy Rydberg eV + E_KohnSham -34.2752127532 -466.338193605 + E_Harris -34.2752127532 -466.338193605 + E_Fermi -0.176921597747 -2.40714182862 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109275796782 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113417645718 + + Density error is 1.56531758012e-07 + + Energy Rydberg eV + E_KohnSham -34.2752127799 -466.338193968 + E_Harris -34.2752127799 -466.338193968 + E_Fermi -0.176921405257 -2.40713920966 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109275803368 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113417645268 + + Density error is 1.13042080964e-08 + + Energy Rydberg eV + E_KohnSham -34.2752127824 -466.338194002 + E_Harris -34.2752127824 -466.338194002 + E_band -8.05106009821 -109.540292276 + E_one_elec -69.6730285511 -947.950185212 + E_Hartree +36.2063924249 +492.613241003 + E_xc -8.23639227559 -112.061865911 + E_Ewald +7.55131723586 +102.740941813 + E_demet -5.07257840084e-86 -6.90159698032e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195576302379 -2.66095210613 + E_Fermi -0.176921232151 -2.40713685443 + + charge density convergence is achieved + final etot is -466.338194002 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6294 2.00000 + 2 -12.7915 2.00000 + 3 -9.53151 2.00000 + 4 -6.81766 2.00000 + 5 1.36256 0.00000 + 6 4.64606 0.00000 + 7 11.0214 0.00000 + 8 11.3086 0.00000 + + EFERMI = -2.407136854427962 eV + OUT.ABACUS/ final etot is -466.3381940024378 eV + correction force for each atom along direction 1 is 0.000143382 + correction force for each atom along direction 2 is -5.03206e-06 + correction force for each atom along direction 3 is -3.55840e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.68834526 +0.45105048 +1.5306343 + H1 -0.32726020 +0.22513991 +0.62057052 + H2 +1.0156055 -0.67619039 -2.1512048 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3381940024378 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7472 11 0.70 1.0e+02% + Run_lcao lcao_line 7.7372 1 7.7 1.e+02% + Potential init_pot 0.29106 2 0.15 3.8% + PW_Basis recip2real 0.31380 17 0.018 4.1% + PW_Basis gathers_scatterp 0.13623 17 0.0080 1.8% + Potential v_of_rho 1.0884 14 0.078 14.% + XC_Functional v_xc 0.30859 15 0.021 4.0% + H_Hartree_pw v_hartree 0.73262 14 0.052 9.5% + PW_Basis real2recip 0.72264 41 0.018 9.3% + PW_Basis gatherp_scatters 0.28718 41 0.0070 3.7% + ORB_control set_orb_tables 1.1100 1 1.1 14.% + ORB_gen_tables gen_tables 1.1100 1 1.1 14.% + ORB_table_phi init_Table 0.48504 1 0.49 6.3% + ORB_table_phi cal_ST_Phi12_R 0.47986 126 0.0038 6.2% + ORB_table_beta init_Table_Beta 0.18730 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18575 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.25117 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24916 66 0.0038 3.2% + LOOP_ions opt_ions 6.0966 1 6.1 79.% + ESolver_KS_LCAO Run 5.5172 1 5.5 71.% + HSolverLCAO solve 3.0091 12 0.25 39.% + HamiltLCAO updateHk 1.5357 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4999 12 0.12 19.% + Gint_interface cal_gint 2.8322 25 0.11 37.% + Gint_Gamma distri_vl 2.8731 6 0.48 37.% + LCAO_Deepks cal_projected_DM 5.9260 14 0.42 76.% + LCAO_gen_fixedH add_v_delta 2.7282 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.7283 6 0.45 35.% + ElecStateLCAO psiToRho 1.4563 12 0.12 19.% + Charge mix_rho 0.85560 11 0.078 11.% + LOOP_ions force_stress 0.57919 1 0.58 7.5% + Force_Stress_LCAO getForceStress 0.57916 1 0.58 7.5% + Force_LCAO_gamma ftable_gamma 0.35500 1 0.36 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.34713 1 0.35 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:17 2022 + Finish Time : Wed Sep 28 11:12:24 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..faee5d88b66f080c42e2e281321b91e34625f655 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124207 ima = 3.71747e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122371347272 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111235056436 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111768017203 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112064275355 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111994106442 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112032814698 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112028244527 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112031320919 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112030498082 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112030421144 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112030407499 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112030399291 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a6285fee9579560b5d972703841707db8bfa6edd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.192843686300 15.903635625330 6.170841671777 0 0 0 +H +0.0 +2 +-21.516833288804 14.989664092317 7.620114351655 0 0 0 +-21.198396005749 15.102727801157 4.942126181990 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/conv new file mode 100644 index 0000000000000000000000000000000000000000..5014ab9d8af22b57f8aeaac4944544cd5380967e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/conv @@ -0,0 +1 @@ +154 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..70424e20c7076cad3a691d95e601ac8e1dff3f3b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755203405 0.01290448294 1.281923885 1.365364063 1.470632053 0.009871214045 0.01671214459 0.03918642228 +6.644440987e-18 0.0009386200657 0.003040880233 0.01410357216 0.04918068467 -7.983285528e-20 3.315162724e-06 8.358838512e-06 +0.001589999065 0.006178382743 + +H atom_index 1 n_descriptor 18 +1.243285319 0.03530035105 0.1102781733 0.1464061475 0.316765318 0.02333010768 0.02783063299 0.03837051805 +5.352926632e-17 5.295266017e-05 0.1039908754 0.1148156571 0.1256163317 -2.335686395e-19 3.095281115e-06 0.01355644303 +0.02742851758 0.03045495378 + +H atom_index 2 n_descriptor 18 +1.297965579 0.03357103167 0.1312675633 0.1734727457 0.3337235477 0.02610184994 0.03100501085 0.03718740518 +-3.397398294e-17 5.803286444e-05 0.1086302505 0.1260610276 0.1486847335 1.110834677e-17 4.496211632e-07 0.01386773017 +0.02927918729 0.03272603766 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5a23287ad4a9b7bd88949aa779d3ac808797b974 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/e_base.npy new file mode 100644 index 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TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0877693 SEC) : SETUP UNITCELL + DONE(0.0961883 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11451 SEC) : INIT PLANEWAVE + DONE(0.164493 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.453009 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651020e+02 0.000000e+00 2.156e-01 5.598e-01 + GE2 -4.663345e+02 -1.232447e+00 9.722e-02 5.135e-01 + GE3 -4.663385e+02 -4.027021e-03 6.222e-02 5.773e-01 + GE4 -4.663387e+02 -1.906780e-04 1.998e-03 4.412e-01 + GE5 -4.663377e+02 9.488336e-04 9.275e-04 4.434e-01 + GE6 -4.663384e+02 -6.409831e-04 1.265e-04 4.384e-01 + GE7 -4.663382e+02 2.150472e-04 4.131e-05 4.344e-01 + GE8 -4.663382e+02 -4.392655e-05 2.174e-05 4.221e-01 + GE9 -4.663382e+02 2.148214e-05 1.931e-06 4.201e-01 + GE10 -4.663382e+02 -3.881247e-06 4.445e-07 4.231e-01 + GE11 -4.663382e+02 -3.632229e-07 1.565e-07 4.247e-01 + GE12 -4.663382e+02 -3.396874e-08 1.130e-08 3.568e-01 +E_delta_band = -7.20746860e-02 Ry = -9.80626411e-01 eV +E_delta_NN= -1.95576302e-01 Ry = -2.66095211e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7472 11 0.7 1e+02 % + Run_lcao lcao_line 7.7372 1 7.7 1e+02 % + Potential init_pot 0.29106 2 0.15 3.8 % + PW_Basis recip2real 0.3138 17 0.018 4.1 % + PW_Basis gathers_scatterp 0.13623 17 0.008 1.8 % + Potential v_of_rho 1.0884 14 0.078 14 % + XC_Functional v_xc 0.30859 15 0.021 4 % + H_Hartree_pw v_hartree 0.73262 14 0.052 9.5 % + PW_Basis real2recip 0.72264 41 0.018 9.3 % + PW_Basis gatherp_scatters 0.28718 41 0.007 3.7 % + ORB_control set_orb_tables 1.11 1 1.1 14 % + ORB_gen_tables gen_tables 1.11 1 1.1 14 % + ORB_table_phi init_Table 0.48504 1 0.49 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.47986 126 0.0038 6.2 % + ORB_table_beta init_Table_Beta 0.1873 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18575 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.25117 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24916 66 0.0038 3.2 % + LOOP_ions opt_ions 6.0966 1 6.1 79 % + ESolver_KS_LCAO Run 5.5172 1 5.5 71 % + HSolverLCAO solve 3.0091 12 0.25 39 % + HamiltLCAO updateHk 1.5357 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4999 12 0.12 19 % + Gint_interface cal_gint 2.8322 25 0.11 37 % + Gint_Gamma distri_vl 2.8731 6 0.48 37 % + LCAO_Deepks cal_projected_DM 5.926 14 0.42 76 % + LCAO_gen_fixedH add_v_delta 2.7282 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.7283 6 0.45 35 % + ElecStateLCAO psiToRho 1.4563 12 0.12 19 % + Charge mix_rho 0.8556 11 0.078 11 % + LOOP_ions force_stress 0.57919 1 0.58 7.5 % + Force_Stress_LCAO getForceStress 0.57916 1 0.58 7.5 % + Force_LCAO_gamma ftable_gamma 0.355 1 0.36 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.34713 1 0.35 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:17 2022 + FINISH Time : Wed Sep 28 11:12:24 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/154/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..92522a8693056de682ff81b8ab0dc27b2aaf24b6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.205333 0.562535 0.227261 +H 0.248278 0.551641 0.274283 +H 0.209831 0.51579 0.178562 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ba31c329e06adf9efa98a4ba1aeea674092cd074 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0521 2 + 2 -13.28 2 + 3 -8.73573 2 + 4 -6.68356 2 + 5 1.18755 0 + 6 4.33726 0 + 7 11.1136 0 + 8 11.3277 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b8b724db733365ea9e0598b1406d40c0f969a6e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:10 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.74931075898 15.7509873568 6.36330566305 0 0 0 0 + tauc_H1 6.95179718487 15.4459591614 7.67993069642 0 0 0 0 + tauc_H2 5.87526986558 14.4421331202 4.99972339703 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0865519292729 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0869504229725 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105104824337 (SEC) + + DONE : INIT CHARGE Time : 0.152909869369 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.442182 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00108 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000653 + + Density error is 0.215368392985 + + Energy Rydberg eV + E_KohnSham -34.1872182753 -465.140967313 + E_Harris -34.3794612398 -467.756567031 + E_Fermi -0.398021408713 -5.41535908449 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0011629181678 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000913932810199 + + Density error is 0.0986278808975 + + Energy Rydberg eV + E_KohnSham -34.2769066709 -466.361240539 + E_Harris -34.2836838745 -466.453449125 + E_Fermi -0.206039645572 -2.80331319368 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109889263028 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000888886538164 + + Density error is 0.0633349708211 + + Energy Rydberg eV + E_KohnSham -34.2772015458 -466.365252518 + E_Harris -34.2815430469 -466.42432167 + E_Fermi -0.196077346132 -2.66776915611 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000995823234274 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865126082158 + + Density error is 0.00215219973743 + + Energy Rydberg eV + E_KohnSham -34.2771701466 -466.36482531 + E_Harris -34.2771755568 -466.364898919 + E_Fermi -0.161033837967 -2.19097776715 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000993930481531 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000863836110934 + + Density error is 0.000864712562883 + + Energy Rydberg eV + E_KohnSham -34.2771266522 -466.364233537 + E_Harris -34.277127206 -466.364241073 + E_Fermi -0.160383978427 -2.18213597452 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000992724651334 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000863533152135 + + Density error is 0.000205306373616 + + Energy Rydberg eV + E_KohnSham -34.2771518363 -466.364576184 + E_Harris -34.2771518873 -466.364576878 + E_Fermi -0.160225065169 -2.17997384872 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000992877108602 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000863833456673 + + Density error is 3.35361411754e-05 + + Energy Rydberg eV + E_KohnSham -34.2771422758 -466.364446107 + E_Harris -34.2771422806 -466.364446172 + E_Fermi -0.160115003213 -2.17847637898 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000992805867658 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000863739988386 + + Density error is 1.72404317906e-05 + + Energy Rydberg eV + E_KohnSham -34.277146731 -466.364506724 + E_Harris -34.2771467323 -466.364506742 + E_Fermi -0.160147294207 -2.17891572049 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000992801060254 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000863750164654 + + Density error is 2.8270594668e-06 + + Energy Rydberg eV + E_KohnSham -34.2771454453 -466.36448923 + E_Harris -34.2771454453 -466.364489231 + E_Fermi -0.160130701047 -2.17868995897 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000992798746426 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000863751574303 + + Density error is 4.65040062403e-07 + + Energy Rydberg eV + E_KohnSham -34.2771457107 -466.364492842 + E_Harris -34.2771457107 -466.364492841 + E_Fermi -0.160127983795 -2.17865298886 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000992798680939 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000863752024593 + + Density error is 1.9209108549e-07 + + Energy Rydberg eV + E_KohnSham -34.2771457303 -466.364493108 + E_Harris -34.2771457303 -466.364493108 + E_Fermi -0.160127828011 -2.17865086931 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000992798638604 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000863752280814 + + Density error is 9.76297338448e-09 + + Energy Rydberg eV + E_KohnSham -34.2771457309 -466.364493117 + E_Harris -34.2771457309 -466.364493117 + E_band -7.90130968978 -107.502833444 + E_one_elec -69.0443728663 -939.396885819 + E_Hartree +35.9382347911 +488.96476922 + E_xc -8.19285508795 -111.469512084 + E_Ewald +7.14674250989 +97.2364202733 + E_demet -3.90946462674e-69 -5.31909950532e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194179478223 -2.64194733851 + E_Fermi -0.160127637953 -2.17864828345 + + charge density convergence is achieved + final etot is -466.364493117 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0521 2.00000 + 2 -13.2800 2.00000 + 3 -8.73573 2.00000 + 4 -6.68356 2.00000 + 5 1.18755 0.00000 + 6 4.33726 0.00000 + 7 11.1136 0.00000 + 8 11.3277 0.00000 + + EFERMI = -2.178648283445016 eV + OUT.ABACUS/ final etot is -466.3644931169424 eV + correction force for each atom along direction 1 is -3.10271e-05 + correction force for each atom along direction 2 is -5.29661e-05 + correction force for each atom along direction 3 is -3.03842e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0077037 -0.17583444 -1.6064406 + H1 +0.72213874 -0.56942090 +0.33390340 + H2 +0.28556494 +0.74525534 +1.2725373 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3644931169424 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7766 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7669 1 6.8 1.e+02% + Potential init_pot 0.29543 2 0.15 4.4% + PW_Basis recip2real 0.28280 17 0.017 4.2% + PW_Basis gathers_scatterp 0.12062 17 0.0071 1.8% + Charge atomic_rho 0.10300 1 0.10 1.5% + Potential v_of_rho 0.94456 14 0.067 14.% + XC_Functional v_xc 0.26235 15 0.017 3.9% + H_Hartree_pw v_hartree 0.64030 14 0.046 9.4% + PW_Basis real2recip 0.60448 41 0.015 8.9% + PW_Basis gatherp_scatters 0.23548 41 0.0057 3.5% + ORB_control set_orb_tables 1.1105 1 1.1 16.% + ORB_gen_tables gen_tables 1.1104 1 1.1 16.% + ORB_table_phi init_Table 0.48788 1 0.49 7.2% + ORB_table_phi cal_ST_Phi12_R 0.48296 126 0.0038 7.1% + ORB_table_beta init_Table_Beta 0.18537 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18393 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25753 1 0.26 3.8% + ORB_table_alpha S_PhiAlpha_R 0.25565 66 0.0039 3.8% + LOOP_ions opt_ions 5.1388 1 5.1 76.% + ESolver_KS_LCAO Run 4.5970 1 4.6 68.% + HSolverLCAO solve 2.4524 12 0.20 36.% + HamiltLCAO updateHk 1.2798 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2380 12 0.10 18.% + Gint_interface cal_gint 2.2999 25 0.092 34.% + Gint_Gamma distri_vl 2.3812 6 0.40 35.% + LCAO_Deepks cal_projected_DM 4.9729 14 0.36 73.% + LCAO_gen_fixedH add_v_delta 2.2476 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2477 6 0.37 33.% + ElecStateLCAO psiToRho 1.1571 12 0.096 17.% + Charge mix_rho 0.71929 11 0.065 11.% + LOOP_ions force_stress 0.54158 1 0.54 8.0% + Force_Stress_LCAO getForceStress 0.54155 1 0.54 8.0% + Force_LCAO_gamma ftable_gamma 0.32749 1 0.33 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.32083 1 0.32 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:09 2022 + Finish Time : Wed Sep 28 11:07:16 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3a89c34581aa810bd5a1ce9332da8697e2b3328a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123343 ima = 3.69369e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124007899453 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113036026001 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113595694466 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011379782245 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011376718477 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113786921174 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113778963374 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011378144143 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113780684233 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113780625425 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113780613778 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113780604002 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/STRU new file mode 100644 index 0000000000000000000000000000000000000000..2f58fa764580e96cab6966e2b79e3299699b9e3d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.250689241000 15.750987356786 6.363305663042 0 0 0 +H +0.0 +2 +-21.048202815151 15.445959161374 7.679930696438 0 0 0 +-22.124730134439 14.442133120233 4.999723397008 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/conv new file mode 100644 index 0000000000000000000000000000000000000000..f0c676a570bfb860a2bfb9b1c501283ba542bd06 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/conv @@ -0,0 +1 @@ +155 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e431eb1c423d93c5b4615386d1c09c44fe5bb859 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742911472 0.01246008629 1.265270616 1.36744985 1.468284527 0.007463454067 0.02052575165 0.03884620077 +7.301688315e-19 0.001090565014 0.002244852839 0.01189859774 0.04068459611 1.508768506e-19 1.269442016e-06 4.238310214e-06 +0.001802764184 0.005500283531 + +H atom_index 1 n_descriptor 18 +1.258158289 0.03325660303 0.1113522601 0.1558971356 0.3265214912 0.02201135013 0.0290501486 0.0365900487 +1.871767601e-17 3.530995011e-05 0.1031327777 0.1153009568 0.1337471464 4.026586209e-18 3.593060591e-06 0.01278522893 +0.02609285459 0.03126906199 + +H atom_index 2 n_descriptor 18 +1.189870505 0.03562730176 0.08950656963 0.1261893499 0.30376951 0.01905954659 0.02510753149 0.03908335021 +3.391685161e-17 3.03107869e-05 0.08532567478 0.1078616794 0.113286944 5.143266788e-18 5.893992468e-06 0.01395856726 +0.02342263357 0.02799106191 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..7ed0057ceee66f7b89f06de2a1e58ba28e795c52 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/e_base.npy 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0000000000000000000000000000000000000000..7eb044ed549e1ee3a9484ea2afbee5750dd02737 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..5d40674fbedac343efa3890f440d89cbaed80705 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..de633caa44bd440a792757d47d64b4804926f02b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:09 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0865759 SEC) : SETUP UNITCELL + DONE(0.0869672 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105127 SEC) : INIT PLANEWAVE + DONE(0.15304 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.442247 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651410e+02 0.000000e+00 2.154e-01 4.985e-01 + GE2 -4.663612e+02 -1.220273e+00 9.863e-02 4.287e-01 + GE3 -4.663653e+02 -4.011979e-03 6.333e-02 4.806e-01 + GE4 -4.663648e+02 4.272081e-04 2.152e-03 3.693e-01 + GE5 -4.663642e+02 5.917728e-04 8.647e-04 3.695e-01 + GE6 -4.663646e+02 -3.426474e-04 2.053e-04 3.664e-01 + GE7 -4.663644e+02 1.300771e-04 3.354e-05 3.542e-01 + GE8 -4.663645e+02 -6.061704e-05 1.724e-05 3.473e-01 + GE9 -4.663645e+02 1.749387e-05 2.827e-06 3.402e-01 + GE10 -4.663645e+02 -3.611089e-06 4.650e-07 3.442e-01 + GE11 -4.663645e+02 -2.664767e-07 1.921e-07 3.471e-01 + GE12 -4.663645e+02 -8.945660e-09 9.763e-09 2.889e-01 +E_delta_band = -6.92844006e-02 Ry = -9.42662631e-01 eV +E_delta_NN= -1.94179478e-01 Ry = -2.64194734e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7766 11 0.62 1e+02 % + Run_lcao lcao_line 6.7669 1 6.8 1e+02 % + Potential init_pot 0.29543 2 0.15 4.4 % + PW_Basis recip2real 0.2828 17 0.017 4.2 % + PW_Basis gathers_scatterp 0.12062 17 0.0071 1.8 % + Charge atomic_rho 0.103 1 0.1 1.5 % + Potential v_of_rho 0.94456 14 0.067 14 % + XC_Functional v_xc 0.26235 15 0.017 3.9 % + H_Hartree_pw v_hartree 0.6403 14 0.046 9.4 % + PW_Basis real2recip 0.60448 41 0.015 8.9 % + PW_Basis gatherp_scatters 0.23548 41 0.0057 3.5 % + ORB_control set_orb_tables 1.1105 1 1.1 16 % + ORB_gen_tables gen_tables 1.1104 1 1.1 16 % + ORB_table_phi init_Table 0.48788 1 0.49 7.2 % + ORB_table_phi cal_ST_Phi12_R 0.48296 126 0.0038 7.1 % + ORB_table_beta init_Table_Beta 0.18537 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18393 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.25753 1 0.26 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.25565 66 0.0039 3.8 % + LOOP_ions opt_ions 5.1388 1 5.1 76 % + ESolver_KS_LCAO Run 4.597 1 4.6 68 % + HSolverLCAO solve 2.4524 12 0.2 36 % + HamiltLCAO updateHk 1.2798 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.238 12 0.1 18 % + Gint_interface cal_gint 2.2999 25 0.092 34 % + Gint_Gamma distri_vl 2.3812 6 0.4 35 % + LCAO_Deepks cal_projected_DM 4.9729 14 0.36 73 % + LCAO_gen_fixedH add_v_delta 2.2476 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2477 6 0.37 33 % + ElecStateLCAO psiToRho 1.1571 12 0.096 17 % + Charge mix_rho 0.71929 11 0.065 11 % + LOOP_ions force_stress 0.54158 1 0.54 8 % + Force_Stress_LCAO getForceStress 0.54155 1 0.54 8 % + Force_LCAO_gamma ftable_gamma 0.32749 1 0.33 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.32083 1 0.32 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:09 2022 + FINISH Time : Wed Sep 28 11:07:16 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/155/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5b9471bae7e297abd64bb833a24cd93540361996 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.223187 0.547234 0.214962 +H 0.248521 0.557577 0.273495 +H 0.270455 0.514548 0.187904 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..4699cb41e17405e1f75f058b3d6266b6134c051e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6266 2 + 2 -13.0485 2 + 3 -9.35982 2 + 4 -6.81859 2 + 5 1.47429 0 + 6 4.76152 0 + 7 11.0079 0 + 8 11.2782 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e23d72308e5d4cb272b8808ff924f599a11b4e6e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:16 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.24922476028 15.3225588268 6.01893138966 0 0 0 0 + tauc_H1 6.9586015958 15.6121427798 7.65786086812 0 0 0 0 + tauc_H2 7.57273264449 14.4073462002 5.26131523494 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0730713714702 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0733934108496 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0891419935809 (SEC) + + DONE : INIT CHARGE Time : 0.131540189599 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374959 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00114 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138 + + Density error is 0.217289299808 + + Energy Rydberg eV + E_KohnSham -34.1854555107 -465.116983671 + E_Harris -34.3830426453 -467.805294552 + E_Fermi -0.422349554813 -5.74636049322 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00141674966075 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128206641127 + + Density error is 0.0972875451294 + + Energy Rydberg eV + E_KohnSham -34.2770898689 -466.363733075 + E_Harris -34.2837898152 -466.454890522 + E_Fermi -0.228937227228 -3.11485077462 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00133897397168 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119115508591 + + Density error is 0.0622062772604 + + Energy Rydberg eV + E_KohnSham -34.2773901601 -466.367818747 + E_Harris -34.2817007718 -466.426467627 + E_Fermi -0.215222557141 -2.92825311524 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122148325737 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104726237735 + + Density error is 0.00203221989645 + + Energy Rydberg eV + E_KohnSham -34.277425869 -466.368304591 + E_Harris -34.2774277356 -466.368329988 + E_Fermi -0.179172497111 -2.4377668856 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122502814705 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104813555406 + + Density error is 0.00095659232225 + + Energy Rydberg eV + E_KohnSham -34.2773452012 -466.367207049 + E_Harris -34.2773480826 -466.367246252 + E_Fermi -0.178078362076 -2.42288041474 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0012229837065 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104644204238 + + Density error is 0.000104785944995 + + Energy Rydberg eV + E_KohnSham -34.2773999657 -466.367952159 + E_Harris -34.2773999824 -466.367952386 + E_Fermi -0.178321726557 -2.42619155837 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122265350017 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104620620018 + + Density error is 4.80239038142e-05 + + Energy Rydberg eV + E_KohnSham -34.2773829455 -466.367720587 + E_Harris -34.2773829587 -466.367720767 + E_Fermi -0.178192156622 -2.42442866897 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122265032661 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104624041834 + + Density error is 2.1387586297e-05 + + Energy Rydberg eV + E_KohnSham -34.2773853821 -466.367753739 + E_Harris -34.277385384 -466.367753765 + E_Fermi -0.178260856116 -2.42536337353 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122264209736 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104621918592 + + Density error is 1.83364727001e-06 + + Energy Rydberg eV + E_KohnSham -34.277383692 -466.367730743 + E_Harris -34.277383692 -466.367730744 + E_Fermi -0.178237003155 -2.42503883736 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122264165248 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104621621229 + + Density error is 1.61447808303e-07 + + Energy Rydberg eV + E_KohnSham -34.2773840033 -466.367734978 + E_Harris -34.2773840033 -466.367734978 + E_Fermi -0.178235355463 -2.42501641935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122264255869 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104621685974 + + Density error is 6.49246686429e-08 + + Energy Rydberg eV + E_KohnSham -34.2773840381 -466.367735452 + E_Harris -34.2773840381 -466.367735452 + E_band -8.06331797481 -109.707069243 + E_one_elec -69.8153628244 -949.88674235 + E_Hartree +36.2793068949 +493.605293261 + E_xc -8.24832209326 -112.224179408 + E_Ewald +7.63021380524 +103.814384709 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195831171996 -2.66441978517 + E_Fermi -0.178235428228 -2.42501740938 + + charge density convergence is achieved + final etot is -466.367735452 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6266 2.00000 + 2 -13.0485 2.00000 + 3 -9.35982 2.00000 + 4 -6.81859 2.00000 + 5 1.47429 0.00000 + 6 4.76152 0.00000 + 7 11.0079 0.00000 + 8 11.2782 0.00000 + + EFERMI = -2.425017409377622 eV + OUT.ABACUS/ final etot is -466.3677354522583 eV + correction force for each atom along direction 1 is 0.000172875 + correction force for each atom along direction 2 is -4.70648e-05 + correction force for each atom along direction 3 is 6.34574e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.3521732 +0.69855863 +0.15312295 + H1 +0.068051628 +0.37614598 +1.0711651 + H2 +1.2841216 -1.0747046 -1.2242880 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3677354522583 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8212 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8137 1 6.8 1.e+02% + Potential init_pot 0.24117 2 0.12 3.5% + PW_Basis recip2real 0.26280 16 0.016 3.9% + PW_Basis gathers_scatterp 0.10549 16 0.0066 1.5% + Potential v_of_rho 0.92644 13 0.071 14.% + XC_Functional v_xc 0.27801 14 0.020 4.1% + H_Hartree_pw v_hartree 0.60943 13 0.047 8.9% + PW_Basis real2recip 0.60298 38 0.016 8.8% + PW_Basis gatherp_scatters 0.22714 38 0.0060 3.3% + ORB_control set_orb_tables 0.89850 1 0.90 13.% + ORB_gen_tables gen_tables 0.89849 1 0.90 13.% + ORB_table_phi init_Table 0.37859 1 0.38 5.6% + ORB_table_phi cal_ST_Phi12_R 0.37436 126 0.0030 5.5% + ORB_table_beta init_Table_Beta 0.15348 1 0.15 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15216 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20882 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20717 66 0.0031 3.0% + LOOP_ions opt_ions 5.4696 1 5.5 80.% + ESolver_KS_LCAO Run 4.9363 1 4.9 72.% + HSolverLCAO solve 2.7470 11 0.25 40.% + HamiltLCAO updateHk 1.3905 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3590 11 0.12 20.% + Gint_interface cal_gint 2.6185 23 0.11 38.% + Gint_Gamma distri_vl 2.3772 6 0.40 35.% + LCAO_Deepks cal_projected_DM 5.3134 13 0.41 78.% + LCAO_gen_fixedH add_v_delta 2.2471 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2470 6 0.37 33.% + ElecStateLCAO psiToRho 1.3402 11 0.12 20.% + Charge mix_rho 0.76553 10 0.077 11.% + LOOP_ions force_stress 0.53309 1 0.53 7.8% + Force_Stress_LCAO getForceStress 0.53305 1 0.53 7.8% + Force_LCAO_gamma ftable_gamma 0.33438 1 0.33 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.32709 1 0.33 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:16 2022 + Finish Time : Wed Sep 28 11:08:23 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3971aa57cc9de739bcfa16eddeefda01997a1083 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012423 ima = 3.70406e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122587866542 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011155523872 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112024950569 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112328941229 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112248890748 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112291975281 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011228949082 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112292772877 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112291878722 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112291795905 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112291792322 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0f26619d2bcf734214d59c8c0d59281abfc492a9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.750775239715 15.322558826755 6.018931389662 0 0 0 +H +0.0 +2 +-21.041398404217 15.612142779801 7.657860868110 0 0 0 +-20.427267355499 14.407346200236 5.261315234947 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/conv new file mode 100644 index 0000000000000000000000000000000000000000..fa769cc8976e5881c50396cd7334e6f9d080744c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/conv @@ -0,0 +1 @@ +156 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b361651524dc8257465cac0444a483ee045dd1ff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752482397 0.01289314146 1.291595253 1.37353907 1.470773368 0.009326019761 0.01786978459 0.03911209083 +-2.179489793e-19 0.001073795192 0.00293604737 0.01365174595 0.04914093361 7.737202387e-21 2.932176573e-06 7.581092196e-06 +0.001605176192 0.0061128026 + +H atom_index 1 n_descriptor 18 +1.267094846 0.03409554803 0.1166787238 0.1576047827 0.3249579508 0.02389456941 0.02923135101 0.03726359563 +1.255036371e-20 5.561780172e-05 0.1077632669 0.1170970626 0.1354299192 2.339925207e-18 2.580605951e-06 0.01333415296 +0.02794483825 0.0315213033 + +H atom_index 2 n_descriptor 18 +1.291140259 0.03333574279 0.1259588965 0.1697463362 0.332073302 0.02506365094 0.03061561826 0.03684689839 +-4.141430424e-17 5.798510896e-05 0.1088116542 0.1229699164 0.1457417523 8.55062308e-18 1.285190117e-06 0.01361737772 +0.02873105017 0.03246881871 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f25ae0080c089ac23e16ee75b5fbdbfb3aad970b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:16 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0730862 SEC) : SETUP UNITCELL + DONE(0.0734032 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0891557 SEC) : INIT PLANEWAVE + DONE(0.131671 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.375003 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651170e+02 0.000000e+00 2.173e-01 5.210e-01 + GE2 -4.663637e+02 -1.246749e+00 9.729e-02 4.964e-01 + GE3 -4.663678e+02 -4.085671e-03 6.221e-02 5.622e-01 + GE4 -4.663683e+02 -4.858448e-04 2.032e-03 4.377e-01 + GE5 -4.663672e+02 1.097542e-03 9.566e-04 4.356e-01 + GE6 -4.663680e+02 -7.451098e-04 1.048e-04 4.193e-01 + GE7 -4.663677e+02 2.315717e-04 4.802e-05 4.286e-01 + GE8 -4.663678e+02 -3.315127e-05 2.139e-05 4.098e-01 + GE9 -4.663677e+02 2.299523e-05 1.834e-06 4.150e-01 + GE10 -4.663677e+02 -4.234899e-06 1.614e-07 4.106e-01 + GE11 -4.663677e+02 -4.739436e-07 6.492e-08 3.450e-01 +E_delta_band = -7.26113515e-02 Ry = -9.87928120e-01 eV +E_delta_NN= -1.95831172e-01 Ry = -2.66441979e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8212 11 0.62 1e+02 % + Run_lcao lcao_line 6.8137 1 6.8 1e+02 % + Potential init_pot 0.24117 2 0.12 3.5 % + PW_Basis recip2real 0.2628 16 0.016 3.9 % + PW_Basis gathers_scatterp 0.10549 16 0.0066 1.5 % + Potential v_of_rho 0.92644 13 0.071 14 % + XC_Functional v_xc 0.27801 14 0.02 4.1 % + H_Hartree_pw v_hartree 0.60943 13 0.047 8.9 % + PW_Basis real2recip 0.60298 38 0.016 8.8 % + PW_Basis gatherp_scatters 0.22714 38 0.006 3.3 % + ORB_control set_orb_tables 0.8985 1 0.9 13 % + ORB_gen_tables gen_tables 0.89849 1 0.9 13 % + ORB_table_phi init_Table 0.37859 1 0.38 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.37436 126 0.003 5.5 % + ORB_table_beta init_Table_Beta 0.15348 1 0.15 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15216 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20882 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20717 66 0.0031 3 % + LOOP_ions opt_ions 5.4696 1 5.5 80 % + ESolver_KS_LCAO Run 4.9363 1 4.9 72 % + HSolverLCAO solve 2.747 11 0.25 40 % + HamiltLCAO updateHk 1.3905 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.359 11 0.12 20 % + Gint_interface cal_gint 2.6185 23 0.11 38 % + Gint_Gamma distri_vl 2.3772 6 0.4 35 % + LCAO_Deepks cal_projected_DM 5.3134 13 0.41 78 % + LCAO_gen_fixedH add_v_delta 2.2471 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.247 6 0.37 33 % + ElecStateLCAO psiToRho 1.3402 11 0.12 20 % + Charge mix_rho 0.76553 10 0.077 11 % + LOOP_ions force_stress 0.53309 1 0.53 7.8 % + Force_Stress_LCAO getForceStress 0.53305 1 0.53 7.8 % + Force_LCAO_gamma ftable_gamma 0.33438 1 0.33 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.32709 1 0.33 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:16 2022 + FINISH Time : Wed Sep 28 11:08:23 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/156/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a335856908f842bfde8aac83e407454f741e90ab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.230794 0.539734 0.208814 +H 0.214751 0.486533 0.242811 +H 0.285558 0.527911 0.174736 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..439a65e50aafe5234286f6e2007a9917e7037ce2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2079 2 + 2 -13.3056 2 + 3 -8.86043 2 + 4 -6.7237 2 + 5 1.33452 0 + 6 4.48516 0 + 7 11.0796 0 + 8 11.3059 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..69f1c28240d04be936593bb1cf4cf089e908d443 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:43 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.4622281253 15.112546048 5.8467874522 0 0 0 0 + tauc_H1 6.01303060295 13.6229253122 6.79870981093 0 0 0 0 + tauc_H2 7.99561482174 14.7815144299 4.89259683009 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0739505657248 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0742629086189 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0900631629166 (SEC) + + DONE : INIT CHARGE Time : 0.132072539363 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.376334 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000549 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00158 + + Density error is 0.215987138051 + + Energy Rydberg eV + E_KohnSham -34.1901348097 -465.1806488 + E_Harris -34.3836506853 -467.813567361 + E_Fermi -0.405263131194 -5.51388777356 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000821204623096 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00140064514239 + + Density error is 0.0981145334262 + + Energy Rydberg eV + E_KohnSham -34.2799806273 -466.403063861 + E_Harris -34.2866391891 -466.493658242 + E_Fermi -0.213311784263 -2.90225571652 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000794019412124 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130104042583 + + Density error is 0.0629016934424 + + Energy Rydberg eV + E_KohnSham -34.2802482999 -466.406705733 + E_Harris -34.2845277198 -466.464930229 + E_Fermi -0.201637617314 -2.74342052661 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000764775403686 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113089560945 + + Density error is 0.00209039020312 + + Energy Rydberg eV + E_KohnSham -34.2802470433 -466.406688636 + E_Harris -34.2802506165 -466.406737252 + E_Fermi -0.166381765848 -2.26374005883 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000765955723265 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112907106778 + + Density error is 0.000873406679183 + + Energy Rydberg eV + E_KohnSham -34.2801909002 -466.405924771 + E_Harris -34.2801917742 -466.405936662 + E_Fermi -0.165544870894 -2.25235351884 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000765398477165 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112714333396 + + Density error is 0.000200968643744 + + Energy Rydberg eV + E_KohnSham -34.280225693 -466.40639815 + E_Harris -34.2802257685 -466.406399178 + E_Fermi -0.165555749551 -2.25250153055 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000765659513612 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112703413386 + + Density error is 3.99000388484e-05 + + Energy Rydberg eV + E_KohnSham -34.2802122026 -466.406214605 + E_Harris -34.280212211 -466.406214718 + E_Fermi -0.165398241885 -2.25035852882 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000765600286346 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112701521411 + + Density error is 1.75696918481e-05 + + Energy Rydberg eV + E_KohnSham -34.2802173565 -466.406284727 + E_Harris -34.2802173578 -466.406284745 + E_Fermi -0.165442082564 -2.25095501185 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000765607051865 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112698989466 + + Density error is 1.99431858097e-06 + + Energy Rydberg eV + E_KohnSham -34.2802158899 -466.406264773 + E_Harris -34.2802158899 -466.406264773 + E_Fermi -0.16542382153 -2.25070655774 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00076560650762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112698434008 + + Density error is 3.68919572398e-07 + + Energy Rydberg eV + E_KohnSham -34.2802161453 -466.406268248 + E_Harris -34.2802161453 -466.406268248 + E_Fermi -0.165421951393 -2.25068111323 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000765607179244 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112698477075 + + Density error is 1.41500511133e-07 + + Energy Rydberg eV + E_KohnSham -34.2802161663 -466.406268534 + E_Harris -34.2802161663 -466.406268534 + E_Fermi -0.165421828913 -2.2506794468 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000765607385988 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112698464732 + + Density error is 9.95453526552e-09 + + Energy Rydberg eV + E_KohnSham -34.2802161683 -466.406268561 + E_Harris -34.2802161683 -466.406268561 + E_band -7.9521999901 -108.195231501 + E_one_elec -69.3115413281 -943.031899225 + E_Hartree +36.0592761435 +490.611621307 + E_xc -8.21241873463 -111.735689153 + E_Ewald +7.30879989864 +99.4413241634 + E_demet -4.60765207127e-78 -6.26903225708e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194711128891 -2.64918081693 + E_Fermi -0.165421693638 -2.25067760629 + + charge density convergence is achieved + final etot is -466.406268561 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2079 2.00000 + 2 -13.3056 2.00000 + 3 -8.86043 2.00000 + 4 -6.72370 2.00000 + 5 1.33452 0.00000 + 6 4.48516 0.00000 + 7 11.0796 0.00000 + 8 11.3059 0.00000 + + EFERMI = -2.250677606286837 eV + OUT.ABACUS/ final etot is -466.4062685610626 eV + correction force for each atom along direction 1 is 9.44739e-05 + correction force for each atom along direction 2 is -0.000105698 + correction force for each atom along direction 3 is 9.39396e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.24273513 +0.83200662 -0.17370677 + H1 +0.18501425 -0.49418811 +0.074515730 + H2 +0.057720878 -0.33781851 +0.099191039 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4062685610626 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4164 11 0.67 1.0e+02% + Run_lcao lcao_line 7.4088 1 7.4 1.e+02% + Potential init_pot 0.24431 2 0.12 3.3% + PW_Basis recip2real 0.28713 17 0.017 3.9% + PW_Basis gathers_scatterp 0.11412 17 0.0067 1.5% + Potential v_of_rho 0.99920 14 0.071 13.% + XC_Functional v_xc 0.29052 15 0.019 3.9% + H_Hartree_pw v_hartree 0.66686 14 0.048 9.0% + PW_Basis real2recip 0.65200 41 0.016 8.8% + PW_Basis gatherp_scatters 0.24216 41 0.0059 3.3% + ORB_control set_orb_tables 0.89545 1 0.90 12.% + ORB_gen_tables gen_tables 0.89545 1 0.90 12.% + ORB_table_phi init_Table 0.37168 1 0.37 5.0% + ORB_table_phi cal_ST_Phi12_R 0.36738 126 0.0029 5.0% + ORB_table_beta init_Table_Beta 0.15616 1 0.16 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15485 56 0.0028 2.1% + ORB_table_alpha init_Table_Alpha 0.21038 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20868 66 0.0032 2.8% + LOOP_ions opt_ions 6.0676 1 6.1 82.% + ESolver_KS_LCAO Run 5.5187 1 5.5 74.% + HSolverLCAO solve 3.1509 12 0.26 42.% + HamiltLCAO updateHk 1.5811 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.5459 12 0.13 21.% + Gint_interface cal_gint 3.0220 25 0.12 41.% + Gint_Gamma distri_vl 2.8646 6 0.48 39.% + LCAO_Deepks cal_projected_DM 5.9072 14 0.42 80.% + LCAO_gen_fixedH add_v_delta 2.7353 6 0.46 37.% + LCAO_DESCRIPTOR add_v_delta 2.7352 6 0.46 37.% + ElecStateLCAO psiToRho 1.5520 12 0.13 21.% + Charge mix_rho 0.82758 11 0.075 11.% + LOOP_ions force_stress 0.54883 1 0.55 7.4% + Force_Stress_LCAO getForceStress 0.54881 1 0.55 7.4% + Force_LCAO_gamma ftable_gamma 0.35012 1 0.35 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.34294 1 0.34 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:43 2022 + Finish Time : Wed Sep 28 11:05:50 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e4c59a5caa9cca35b44834c64276775226a0a88a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123637 ima = 3.68752e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123553303185 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112670452503 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113162258362 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113392284927 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113346941285 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113374699954 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113365388833 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113368353254 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113367625564 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113367564172 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113367551891 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113367545131 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/STRU new file mode 100644 index 0000000000000000000000000000000000000000..455874fd0e0eef13c45016425b00e7c70ea2ab31 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.537771874728 15.112546048036 5.846787452205 0 0 0 +H +0.0 +2 +-21.986969397023 13.622925312235 6.798709810926 0 0 0 +-20.004385178258 14.781514429922 4.892596830084 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/conv new file mode 100644 index 0000000000000000000000000000000000000000..4e93332ba8758868e3974ac58aea605d43a04331 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/conv @@ -0,0 +1 @@ +157 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..958f73677e3f3c7499c6b0a50a5745850c7dfdf3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74465651 0.01261715301 1.277945727 1.370060709 1.468999266 0.007774636589 0.02010773135 0.03888697797 +2.596558108e-18 0.001137129899 0.00239365931 0.01230705512 0.04295568363 -1.247387988e-19 1.56293665e-06 4.907378055e-06 +0.001764758915 0.005685901942 + +H atom_index 1 n_descriptor 18 +1.248290173 0.03377642062 0.107765684 0.1504172777 0.3223850091 0.02177716409 0.02837645912 0.0369702592 +1.982161233e-17 3.92671265e-05 0.1013984406 0.1147936419 0.1291463488 -1.021842258e-17 4.256661815e-06 0.01293085267 +0.02601334734 0.03079051715 + +H atom_index 2 n_descriptor 18 +1.238598326 0.03412026099 0.1044864112 0.1459864597 0.3192977442 0.02135129819 0.02781567558 0.03728377268 +5.798708147e-18 3.846831174e-05 0.09892797503 0.114472646 0.1253125044 -5.639207072e-18 4.699838185e-06 0.01302089183 +0.0256503739 0.03034989894 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f377b044f00486f916f8abde1ddff969fe93edbf Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:43 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0739654 SEC) : SETUP UNITCELL + DONE(0.074272 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0900748 SEC) : INIT PLANEWAVE + DONE(0.13218 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.376377 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651806e+02 0.000000e+00 2.160e-01 5.349e-01 + GE2 -4.664031e+02 -1.222415e+00 9.811e-02 5.143e-01 + GE3 -4.664067e+02 -3.641872e-03 6.290e-02 5.716e-01 + GE4 -4.664067e+02 1.709729e-05 2.090e-03 4.455e-01 + GE5 -4.664059e+02 7.638651e-04 8.734e-04 4.493e-01 + GE6 -4.664064e+02 -4.733794e-04 2.010e-04 4.436e-01 + GE7 -4.664062e+02 1.835455e-04 3.990e-05 4.342e-01 + GE8 -4.664063e+02 -7.012187e-05 1.757e-05 4.275e-01 + GE9 -4.664063e+02 1.995323e-05 1.994e-06 4.280e-01 + GE10 -4.664063e+02 -3.474790e-06 3.689e-07 4.313e-01 + GE11 -4.664063e+02 -2.855692e-07 1.415e-07 4.244e-01 + GE12 -4.664063e+02 -2.741122e-08 9.955e-09 3.604e-01 +E_delta_band = -7.03789812e-02 Ry = -9.57555163e-01 eV +E_delta_NN= -1.94711129e-01 Ry = -2.64918082e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4164 11 0.67 1e+02 % + Run_lcao lcao_line 7.4088 1 7.4 1e+02 % + Potential init_pot 0.24431 2 0.12 3.3 % + PW_Basis recip2real 0.28713 17 0.017 3.9 % + PW_Basis gathers_scatterp 0.11412 17 0.0067 1.5 % + Potential v_of_rho 0.9992 14 0.071 13 % + XC_Functional v_xc 0.29052 15 0.019 3.9 % + H_Hartree_pw v_hartree 0.66686 14 0.048 9 % + PW_Basis real2recip 0.652 41 0.016 8.8 % + PW_Basis gatherp_scatters 0.24216 41 0.0059 3.3 % + ORB_control set_orb_tables 0.89545 1 0.9 12 % + ORB_gen_tables gen_tables 0.89545 1 0.9 12 % + ORB_table_phi init_Table 0.37168 1 0.37 5 % + ORB_table_phi cal_ST_Phi12_R 0.36738 126 0.0029 5 % + ORB_table_beta init_Table_Beta 0.15616 1 0.16 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15485 56 0.0028 2.1 % + ORB_table_alpha init_Table_Alpha 0.21038 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20868 66 0.0032 2.8 % + LOOP_ions opt_ions 6.0676 1 6.1 82 % + ESolver_KS_LCAO Run 5.5187 1 5.5 74 % + HSolverLCAO solve 3.1509 12 0.26 42 % + HamiltLCAO updateHk 1.5811 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.5459 12 0.13 21 % + Gint_interface cal_gint 3.022 25 0.12 41 % + Gint_Gamma distri_vl 2.8646 6 0.48 39 % + LCAO_Deepks cal_projected_DM 5.9072 14 0.42 80 % + LCAO_gen_fixedH add_v_delta 2.7353 6 0.46 37 % + LCAO_DESCRIPTOR add_v_delta 2.7352 6 0.46 37 % + ElecStateLCAO psiToRho 1.552 12 0.13 21 % + Charge mix_rho 0.82758 11 0.075 11 % + LOOP_ions force_stress 0.54883 1 0.55 7.4 % + Force_Stress_LCAO getForceStress 0.54881 1 0.55 7.4 % + Force_LCAO_gamma ftable_gamma 0.35012 1 0.35 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.34294 1 0.34 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:43 2022 + FINISH Time : Wed Sep 28 11:05:50 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/157/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9823fe8a1b8b98917d030e4e0afa79a7578c6e48 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.216118 0.531234 0.221475 +H 0.170663 0.489182 0.200277 +H 0.196194 0.589244 0.193713 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..caa3a4c1ec0542494a59310a9c89874e26cf2b04 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1763 2 + 2 -12.8355 2 + 3 -9.18387 2 + 4 -6.72064 2 + 5 1.16061 0 + 6 4.19749 0 + 7 11.1073 0 + 8 11.3658 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fe76a53c7966821cac9547c7e867951de8063059 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/running_scf.log @@ -0,0 +1,802 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:46 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.05129104706 14.8745399153 6.20128886955 0 0 0 0 + tauc_H1 4.77856263587 13.6971062025 5.60775024996 0 0 0 0 + tauc_H2 5.49343547864 16.4988205513 5.42396900844 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0861955858886 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0964413695206 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.114779504189 (SEC) + + DONE : INIT CHARGE Time : 0.164303709715 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446647 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 144 0 25 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00138 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000723 + + Density error is 0.212230614542 + + Energy Rydberg eV + E_KohnSham -34.1930390427 -465.220162917 + E_Harris -34.3790473128 -467.750935266 + E_Fermi -0.396500143448 -5.39466120871 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00129951614267 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000928192544457 + + Density error is 0.0980674438953 + + Energy Rydberg eV + E_KohnSham -34.2803623119 -466.408256946 + E_Harris -34.2872250424 -466.501629185 + E_Fermi -0.207502013333 -2.82320972781 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00120182241947 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000893302490143 + + Density error is 0.0630361685774 + + Energy Rydberg eV + E_KohnSham -34.2805938239 -466.411406829 + E_Harris -34.2850298669 -466.471762291 + E_Fermi -0.197863575436 -2.69207205258 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00102172654192 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856034117699 + + Density error is 0.00194466369524 + + Energy Rydberg eV + E_KohnSham -34.2805464083 -466.410761706 + E_Harris -34.2805472293 -466.410772877 + E_Fermi -0.16246644306 -2.21046935941 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00101892721057 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856185155853 + + Density error is 0.000809204177089 + + Energy Rydberg eV + E_KohnSham -34.2805072522 -466.41022896 + E_Harris -34.2805079257 -466.410238124 + E_Fermi -0.162079334816 -2.20520248155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.001016755408 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000855762221487 + + Density error is 0.000153468314184 + + Energy Rydberg eV + E_KohnSham -34.2805310891 -466.410553278 + E_Harris -34.2805309638 -466.410551574 + E_Fermi -0.161851109955 -2.20209732301 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00101682429252 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856028544493 + + Density error is 3.03338084949e-05 + + Energy Rydberg eV + E_KohnSham -34.2805226831 -466.410438909 + E_Harris -34.2805226867 -466.410438958 + E_Fermi -0.161794463881 -2.20132661364 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00101678690254 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000855950451399 + + Density error is 1.46227896976e-05 + + Energy Rydberg eV + E_KohnSham -34.2805259724 -466.410483661 + E_Harris -34.2805259733 -466.410483674 + E_Fermi -0.161819559274 -2.20166805398 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00101676550545 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000855958467552 + + Density error is 2.41146228754e-06 + + Energy Rydberg eV + E_KohnSham -34.2805248082 -466.410467822 + E_Harris -34.2805248082 -466.410467822 + E_Fermi -0.16180545011 -2.20147608895 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00101676017326 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000855960288076 + + Density error is 4.68555151346e-07 + + Energy Rydberg eV + E_KohnSham -34.2805250283 -466.410470816 + E_Harris -34.2805250283 -466.410470816 + E_Fermi -0.161803187064 -2.20144529864 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00101676033599 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000855960748342 + + Density error is 1.61139901599e-07 + + Energy Rydberg eV + E_KohnSham -34.2805250533 -466.410471157 + E_Harris -34.2805250533 -466.410471157 + E_Fermi -0.161802982066 -2.20144250949 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00101676015334 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000855960910844 + + Density error is 1.06814306353e-08 + + Energy Rydberg eV + E_KohnSham -34.2805250569 -466.410471205 + E_Harris -34.2805250569 -466.410471205 + E_band -7.9255576502 -107.83274387 + E_one_elec -68.9939290088 -938.710561927 + E_Hartree +35.8967695399 +488.400605535 + E_xc -8.18663056447 -111.384823098 + E_Ewald +7.12819385949 +96.9840529376 + E_demet -5.70238273265e-69 -7.75848973409e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194298348756 -2.64356465508 + E_Fermi -0.161802828577 -2.20144042117 + + charge density convergence is achieved + final etot is -466.410471205 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1763 2.00000 + 2 -12.8355 2.00000 + 3 -9.18387 2.00000 + 4 -6.72064 2.00000 + 5 1.16061 0.00000 + 6 4.19749 0.00000 + 7 11.1073 0.00000 + 8 11.3658 0.00000 + + EFERMI = -2.201440421167420 eV + OUT.ABACUS/ final etot is -466.4104712051919 eV + correction force for each atom along direction 1 is -3.91533e-05 + correction force for each atom along direction 2 is 1.46802e-05 + correction force for each atom along direction 3 is -0.000185933 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.17053296 +1.0921709 -0.38937533 + H1 -0.19767659 -0.30957073 -0.057492354 + H2 +0.36820955 -0.78260018 +0.44686769 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4104712051919 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9803 11 0.73 1.0e+02% + Run_lcao lcao_line 7.9713 1 8.0 1.e+02% + Potential init_pot 0.28368 2 0.14 3.6% + PW_Basis recip2real 0.30606 17 0.018 3.8% + PW_Basis gathers_scatterp 0.13180 17 0.0078 1.7% + Potential v_of_rho 1.0650 14 0.076 13.% + XC_Functional v_xc 0.30093 15 0.020 3.8% + H_Hartree_pw v_hartree 0.71926 14 0.051 9.0% + PW_Basis real2recip 0.70745 41 0.017 8.9% + PW_Basis gatherp_scatters 0.27289 41 0.0067 3.4% + ORB_control read_orb_first 0.11239 1 0.11 1.4% + LCAO_Orbitals Read_Orbitals 0.11238 1 0.11 1.4% + ORB_control set_orb_tables 1.0974 1 1.1 14.% + ORB_gen_tables gen_tables 1.0974 1 1.1 14.% + ORB_table_phi init_Table 0.47424 1 0.47 5.9% + ORB_table_phi cal_ST_Phi12_R 0.46904 126 0.0037 5.9% + ORB_table_beta init_Table_Beta 0.18543 1 0.19 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18388 56 0.0033 2.3% + ORB_table_alpha init_Table_Alpha 0.25136 1 0.25 3.1% + ORB_table_alpha S_PhiAlpha_R 0.24941 66 0.0038 3.1% + LOOP_ions opt_ions 6.3111 1 6.3 79.% + ESolver_KS_LCAO Run 5.7265 1 5.7 72.% + HSolverLCAO solve 3.2384 12 0.27 41.% + HamiltLCAO updateHk 1.6384 12 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.6078 12 0.13 20.% + Gint_interface cal_gint 3.0780 25 0.12 39.% + Gint_Gamma distri_vl 2.9758 6 0.50 37.% + LCAO_Deepks cal_projected_DM 6.1321 14 0.44 77.% + LCAO_gen_fixedH add_v_delta 2.8311 6 0.47 35.% + LCAO_DESCRIPTOR add_v_delta 2.8312 6 0.47 35.% + ElecStateLCAO psiToRho 1.5821 12 0.13 20.% + Charge mix_rho 0.85606 11 0.078 11.% + LOOP_ions force_stress 0.58441 1 0.58 7.3% + Force_Stress_LCAO getForceStress 0.58438 1 0.58 7.3% + Force_LCAO_gamma ftable_gamma 0.36653 1 0.37 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.35860 1 0.36 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:46 2022 + Finish Time : Wed Sep 28 11:01:54 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..288b07fe5825756d8e78c46b6462611bf4015f09 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123644 ima = 3.69777e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123008630626 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111925306677 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112542781967 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112751205844 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112722116104 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112740848533 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112734877878 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112737159056 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112736500402 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112736424296 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112736406647 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001127363984 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c95b188462a9b9732c8850dac1a792a97356d1d4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.948708952918 14.874539915306 6.201288869554 0 0 0 +H +0.0 +2 +-23.221437364123 13.697106202474 5.607750249942 0 0 0 +-22.506564521352 16.498820551288 5.423969008435 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/conv new file mode 100644 index 0000000000000000000000000000000000000000..ff18f737180cb4b1b5e32c3368193a79b8675cb8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/conv @@ -0,0 +1 @@ +158 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7d0744583d691272580de308d1820693bcffca03 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750842341 0.01260201378 1.259307867 1.349757419 1.468807909 0.008686525334 0.01778657446 0.03908977161 +-9.818261462e-19 0.0009482443803 0.002568271608 0.01213921731 0.04401104181 4.423480675e-19 2.004139692e-06 5.848642133e-06 +0.00161221092 0.00597998712 + +H atom_index 1 n_descriptor 18 +1.247675394 0.03450371348 0.1075798471 0.1488323437 0.320231301 0.02220212147 0.02816312651 0.03768290659 +2.06571867e-17 4.430047513e-05 0.09997245291 0.115163009 0.1276313768 -1.195894666e-17 3.985000639e-06 0.0132356203 +0.0260264198 0.03063841422 + +H atom_index 2 n_descriptor 18 +1.206233985 0.03589152522 0.09409484251 0.1306930604 0.3057373508 0.02025214842 0.02573428952 0.03922347327 +-4.834683277e-17 4.058152916e-05 0.08924096967 0.111814708 0.1136889021 -5.849314762e-20 5.901265033e-06 0.01401833017 +0.02438980475 0.02859215558 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..110f2fa6291a178bed0918af8570c47650302f8a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/log.scf @@ -0,0 +1,104 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:46 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0862199 SEC) : SETUP UNITCELL + DONE(0.0964606 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.114802 SEC) : INIT PLANEWAVE + DONE(0.164441 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44671 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652202e+02 0.000000e+00 2.122e-01 5.766e-01 + GE2 -4.664083e+02 -1.188094e+00 9.807e-02 5.338e-01 + GE3 -4.664114e+02 -3.149883e-03 6.304e-02 6.015e-01 + GE4 -4.664108e+02 6.451226e-04 1.945e-03 4.608e-01 + GE5 -4.664102e+02 5.327459e-04 8.092e-04 4.607e-01 + GE6 -4.664106e+02 -3.243178e-04 1.535e-04 4.568e-01 + GE7 -4.664104e+02 1.143697e-04 3.033e-05 4.449e-01 + GE8 -4.664105e+02 -4.475289e-05 1.462e-05 4.407e-01 + GE9 -4.664105e+02 1.583924e-05 2.411e-06 4.404e-01 + GE10 -4.664105e+02 -2.993763e-06 4.686e-07 4.391e-01 + GE11 -4.664105e+02 -3.407843e-07 1.611e-07 4.385e-01 + GE12 -4.664105e+02 -4.845877e-08 1.068e-08 3.706e-01 +E_delta_band = -6.93694658e-02 Ry = -9.43820002e-01 eV +E_delta_NN= -1.94298349e-01 Ry = -2.64356466e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9803 11 0.73 1e+02 % + Run_lcao lcao_line 7.9713 1 8 1e+02 % + Potential init_pot 0.28368 2 0.14 3.6 % + PW_Basis recip2real 0.30606 17 0.018 3.8 % + PW_Basis gathers_scatterp 0.1318 17 0.0078 1.7 % + Potential v_of_rho 1.065 14 0.076 13 % + XC_Functional v_xc 0.30093 15 0.02 3.8 % + H_Hartree_pw v_hartree 0.71926 14 0.051 9 % + PW_Basis real2recip 0.70745 41 0.017 8.9 % + PW_Basis gatherp_scatters 0.27289 41 0.0067 3.4 % + ORB_control read_orb_first 0.11239 1 0.11 1.4 % + LCAO_Orbitals Read_Orbitals 0.11238 1 0.11 1.4 % + ORB_control set_orb_tables 1.0974 1 1.1 14 % + ORB_gen_tables gen_tables 1.0974 1 1.1 14 % + ORB_table_phi init_Table 0.47424 1 0.47 5.9 % + ORB_table_phi cal_ST_Phi12_R 0.46904 126 0.0037 5.9 % + ORB_table_beta init_Table_Beta 0.18543 1 0.19 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.18388 56 0.0033 2.3 % + ORB_table_alpha init_Table_Alpha 0.25136 1 0.25 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.24941 66 0.0038 3.1 % + LOOP_ions opt_ions 6.3111 1 6.3 79 % + ESolver_KS_LCAO Run 5.7265 1 5.7 72 % + HSolverLCAO solve 3.2384 12 0.27 41 % + HamiltLCAO updateHk 1.6384 12 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.6078 12 0.13 20 % + Gint_interface cal_gint 3.078 25 0.12 39 % + Gint_Gamma distri_vl 2.9758 6 0.5 37 % + LCAO_Deepks cal_projected_DM 6.1321 14 0.44 77 % + LCAO_gen_fixedH add_v_delta 2.8311 6 0.47 35 % + LCAO_DESCRIPTOR add_v_delta 2.8312 6 0.47 35 % + ElecStateLCAO psiToRho 1.5821 12 0.13 20 % + Charge mix_rho 0.85606 11 0.078 11 % + LOOP_ions force_stress 0.58441 1 0.58 7.3 % + Force_Stress_LCAO getForceStress 0.58438 1 0.58 7.3 % + Force_LCAO_gamma ftable_gamma 0.36653 1 0.37 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.3586 1 0.36 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:46 2022 + FINISH Time : Wed Sep 28 11:01:54 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/158/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5b13e313772573349a9b8a15b33139380e801286 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.194929 0.527372 0.231109 +H 0.145138 0.485967 0.210168 +H 0.172505 0.559469 0.280458 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0d2f9ad074d55f72548608b89a2203c7c2d8fa4c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2568 2 + 2 -13.171 2 + 3 -8.97401 2 + 4 -6.73107 2 + 5 1.23194 0 + 6 4.48262 0 + 7 11.0759 0 + 8 11.3004 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..961f007b2c973eefde222e5964b61a6b5130df43 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:40 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.458015661 14.7664073423 6.47104462973 0 0 0 0 + tauc_H1 4.06387010981 13.6070662671 5.88470545338 0 0 0 0 + tauc_H2 4.83015067036 15.6651232533 7.85283448936 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0735472090302 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0861833110555 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.101935116 (SEC) + + DONE : INIT CHARGE Time : 0.143372927353 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.389931 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 0 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000836 + + Density error is 0.216001959173 + + Energy Rydberg eV + E_KohnSham -34.1847948699 -465.107995192 + E_Harris -34.379207444 -467.753113962 + E_Fermi -0.406893784899 -5.53607395541 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00108477154275 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959783662036 + + Density error is 0.0983325510622 + + Energy Rydberg eV + E_KohnSham -34.2754699819 -466.341693382 + E_Harris -34.2822316676 -466.433690835 + E_Fermi -0.214458211866 -2.91785366426 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00101651368294 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00091820151184 + + Density error is 0.0630938130185 + + Energy Rydberg eV + E_KohnSham -34.275757733 -466.345608437 + E_Harris -34.2801102425 -466.404827366 + E_Fermi -0.203428187389 -2.7677824823 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000907259875654 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000864457791955 + + Density error is 0.00205232319949 + + Energy Rydberg eV + E_KohnSham -34.2757427427 -466.345404482 + E_Harris -34.2757455043 -466.345442057 + E_Fermi -0.167885400879 -2.28419806297 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000906168666448 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000866481356867 + + Density error is 0.000887258193843 + + Energy Rydberg eV + E_KohnSham -34.2756883517 -466.344664455 + E_Harris -34.2756890298 -466.344673681 + E_Fermi -0.167222391183 -2.27517735327 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00090486350084 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865684472348 + + Density error is 0.0001822629374 + + Energy Rydberg eV + E_KohnSham -34.2757190467 -466.345082082 + E_Harris -34.2757191269 -466.345083173 + E_Fermi -0.167126612069 -2.27387421157 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00090505816776 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865883562893 + + Density error is 4.22032568365e-05 + + Energy Rydberg eV + E_KohnSham -34.2757071984 -466.344920878 + E_Harris -34.2757072073 -466.344920999 + E_Fermi -0.167005599205 -2.27222774709 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000904995321133 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865852095742 + + Density error is 1.78714476943e-05 + + Energy Rydberg eV + E_KohnSham -34.2757121981 -466.344988902 + E_Harris -34.2757121992 -466.344988918 + E_Fermi -0.167046277327 -2.27278120133 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000904982873917 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865852897522 + + Density error is 3.03718016225e-06 + + Energy Rydberg eV + E_KohnSham -34.2757107024 -466.344968552 + E_Harris -34.2757107024 -466.344968552 + E_Fermi -0.16702868556 -2.27254185306 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000904981992662 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865849455347 + + Density error is 4.76384302432e-07 + + Energy Rydberg eV + E_KohnSham -34.2757109101 -466.344971378 + E_Harris -34.2757109101 -466.344971378 + E_Fermi -0.167025687934 -2.27250106827 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000904981964874 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865849924046 + + Density error is 1.85683542392e-07 + + Energy Rydberg eV + E_KohnSham -34.2757109522 -466.344971951 + E_Harris -34.2757109522 -466.344971951 + E_Fermi -0.167025518628 -2.27249876475 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000904981883719 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865850029252 + + Density error is 1.10284035498e-08 + + Energy Rydberg eV + E_KohnSham -34.2757109539 -466.344971974 + E_Harris -34.2757109539 -466.344971974 + E_band -7.95739479084 -108.265910391 + E_one_elec -69.2861388947 -942.686281387 + E_Hartree +36.0427035124 +490.386139093 + E_xc -8.21048338752 -111.709357405 + E_Ewald +7.30257492901 +99.3566291065 + E_demet -1.05050534194e-74 -1.42928584298e-73 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194826421075 -2.65074944757 + E_Fermi -0.167025338542 -2.27249631455 + + charge density convergence is achieved + final etot is -466.344971974 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2568 2.00000 + 2 -13.1710 2.00000 + 3 -8.97401 2.00000 + 4 -6.73107 2.00000 + 5 1.23194 0.00000 + 6 4.48262 0.00000 + 7 11.0759 0.00000 + 8 11.3004 0.00000 + + EFERMI = -2.272496314549614 eV + OUT.ABACUS/ final etot is -466.3449719738296 eV + correction force for each atom along direction 1 is -5.45299e-05 + correction force for each atom along direction 2 is -7.45729e-06 + correction force for each atom along direction 3 is 9.86987e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.0015932770 -2.1354568 -2.4691001 + H1 +1.0311147 +1.0176513 +0.61743721 + H2 -1.0295214 +1.1178055 +1.8516629 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3449719738296 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9078 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9002 1 6.9 1.e+02% + Potential init_pot 0.24409 2 0.12 3.5% + PW_Basis recip2real 0.28130 17 0.017 4.1% + PW_Basis gathers_scatterp 0.11461 17 0.0067 1.7% + Potential v_of_rho 0.99510 14 0.071 14.% + XC_Functional v_xc 0.29091 15 0.019 4.2% + H_Hartree_pw v_hartree 0.66077 14 0.047 9.6% + PW_Basis real2recip 0.64390 41 0.016 9.3% + PW_Basis gatherp_scatters 0.24236 41 0.0059 3.5% + ORB_control set_orb_tables 0.89061 1 0.89 13.% + ORB_gen_tables gen_tables 0.89060 1 0.89 13.% + ORB_table_phi init_Table 0.36973 1 0.37 5.4% + ORB_table_phi cal_ST_Phi12_R 0.36540 126 0.0029 5.3% + ORB_table_beta init_Table_Beta 0.15462 1 0.15 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15333 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20859 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20697 66 0.0031 3.0% + LOOP_ions opt_ions 5.5513 1 5.6 80.% + ESolver_KS_LCAO Run 5.0310 1 5.0 73.% + HSolverLCAO solve 2.6693 12 0.22 39.% + HamiltLCAO updateHk 1.3608 12 0.11 20.% + LCAO_Hamilt cal_Hgamma 1.3275 12 0.11 19.% + Gint_interface cal_gint 2.5165 25 0.10 36.% + Gint_Gamma distri_vl 2.6204 6 0.44 38.% + LCAO_Deepks cal_projected_DM 5.4058 14 0.39 78.% + LCAO_gen_fixedH add_v_delta 2.4919 6 0.42 36.% + LCAO_DESCRIPTOR add_v_delta 2.4918 6 0.42 36.% + ElecStateLCAO psiToRho 1.2904 12 0.11 19.% + Charge mix_rho 0.82994 11 0.075 12.% + LOOP_ions force_stress 0.52023 1 0.52 7.5% + Force_Stress_LCAO getForceStress 0.52021 1 0.52 7.5% + Force_LCAO_gamma ftable_gamma 0.32122 1 0.32 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.31395 1 0.31 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:40 2022 + Finish Time : Wed Sep 28 11:01:47 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..335c6ba28d675fee2bdf748a03975f76d33ac2c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123934 ima = 3.68725e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123523459738 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112458567989 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113008195678 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113249633716 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113208501923 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113233633472 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113224516189 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113227592764 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011322692895 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113226813618 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113226799849 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113226790458 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5f881af62bd19afd792c6f907e0581e442cba3c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.541984338973 14.766407342287 6.471044629731 0 0 0 +H +0.0 +2 +-23.936129890172 13.607066267048 5.884705453370 0 0 0 +-23.169849329648 15.665123253301 7.852834489368 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/conv new file mode 100644 index 0000000000000000000000000000000000000000..7fa1f3ec92e9f01a2a0913032246a4fd9227934e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/conv @@ -0,0 +1 @@ +159 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..354fa4d71d830c4c6416923ae0d72d29f8eb5aaf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747142662 0.01256069657 1.266450568 1.373766497 1.469289317 0.008198421005 0.01948507165 0.0389929203 +-5.006726241e-18 0.001095236478 0.002495060361 0.01207871801 0.04410084451 2.438783513e-19 1.672618656e-06 5.266311631e-06 +0.001680624663 0.005729086293 + +H atom_index 1 n_descriptor 18 +1.185670017 0.03610606129 0.08767415041 0.1231768016 0.299721939 0.01903238315 0.0246586728 0.03960736502 +-2.615871123e-17 3.654952913e-05 0.08447241829 0.1053063045 0.112779758 -8.258073918e-18 6.728118952e-06 0.01438608135 +0.02348730327 0.02761378638 + +H atom_index 2 n_descriptor 18 +1.298249452 0.03236681039 0.1257622472 0.174632071 0.3361095795 0.02405335827 0.0311529842 0.03629961608 +1.60115076e-19 4.621864026e-05 0.10771575 0.1221349884 0.1497460913 2.994664906e-18 1.761036497e-06 0.01350551438 +0.02768186502 0.03271933689 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c722e1b70ae1b5ec2cbaf3b45e10c177096dc295 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:40 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0735627 SEC) : SETUP UNITCELL + DONE(0.0861952 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.101949 SEC) : INIT PLANEWAVE + DONE(0.143475 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.389972 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651080e+02 0.000000e+00 2.160e-01 4.959e-01 + GE2 -4.663417e+02 -1.233698e+00 9.833e-02 4.707e-01 + GE3 -4.663456e+02 -3.915055e-03 6.309e-02 5.340e-01 + GE4 -4.663454e+02 2.039543e-04 2.052e-03 4.054e-01 + GE5 -4.663447e+02 7.400270e-04 8.873e-04 4.052e-01 + GE6 -4.663451e+02 -4.176263e-04 1.823e-04 4.049e-01 + GE7 -4.663449e+02 1.612034e-04 4.220e-05 3.990e-01 + GE8 -4.663450e+02 -6.802336e-05 1.787e-05 3.884e-01 + GE9 -4.663450e+02 2.034982e-05 3.037e-06 3.838e-01 + GE10 -4.663450e+02 -2.825735e-06 4.764e-07 3.843e-01 + GE11 -4.663450e+02 -5.738323e-07 1.857e-07 3.859e-01 + GE12 -4.663450e+02 -2.239218e-08 1.103e-08 3.197e-01 +E_delta_band = -7.04593080e-02 Ry = -9.58648066e-01 eV +E_delta_NN= -1.94826421e-01 Ry = -2.65074945e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9078 11 0.63 1e+02 % + Run_lcao lcao_line 6.9002 1 6.9 1e+02 % + Potential init_pot 0.24409 2 0.12 3.5 % + PW_Basis recip2real 0.2813 17 0.017 4.1 % + PW_Basis gathers_scatterp 0.11461 17 0.0067 1.7 % + Potential v_of_rho 0.9951 14 0.071 14 % + XC_Functional v_xc 0.29091 15 0.019 4.2 % + H_Hartree_pw v_hartree 0.66077 14 0.047 9.6 % + PW_Basis real2recip 0.6439 41 0.016 9.3 % + PW_Basis gatherp_scatters 0.24236 41 0.0059 3.5 % + ORB_control set_orb_tables 0.89061 1 0.89 13 % + ORB_gen_tables gen_tables 0.8906 1 0.89 13 % + ORB_table_phi init_Table 0.36973 1 0.37 5.4 % + ORB_table_phi cal_ST_Phi12_R 0.3654 126 0.0029 5.3 % + ORB_table_beta init_Table_Beta 0.15462 1 0.15 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15333 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20859 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20697 66 0.0031 3 % + LOOP_ions opt_ions 5.5513 1 5.6 80 % + ESolver_KS_LCAO Run 5.031 1 5 73 % + HSolverLCAO solve 2.6693 12 0.22 39 % + HamiltLCAO updateHk 1.3608 12 0.11 20 % + LCAO_Hamilt cal_Hgamma 1.3275 12 0.11 19 % + Gint_interface cal_gint 2.5165 25 0.1 36 % + Gint_Gamma distri_vl 2.6204 6 0.44 38 % + LCAO_Deepks cal_projected_DM 5.4058 14 0.39 78 % + LCAO_gen_fixedH add_v_delta 2.4919 6 0.42 36 % + LCAO_DESCRIPTOR add_v_delta 2.4918 6 0.42 36 % + ElecStateLCAO psiToRho 1.2904 12 0.11 19 % + Charge mix_rho 0.82994 11 0.075 12 % + LOOP_ions force_stress 0.52023 1 0.52 7.5 % + Force_Stress_LCAO getForceStress 0.52021 1 0.52 7.5 % + Force_LCAO_gamma ftable_gamma 0.32122 1 0.32 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.31395 1 0.31 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:40 2022 + FINISH Time : Wed Sep 28 11:01:47 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/159/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c8f47a82e9c81995c76eae43d543f31b22a22091 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.58541 0.287059 0.406293 +H 0.564606 0.309753 0.464206 +H 0.579698 0.337994 0.359961 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1050459456b3cefe99211a4368cbacf1c19069a8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9214 2 + 2 -12.9666 2 + 3 -8.86549 2 + 4 -6.65623 2 + 5 1.00047 0 + 6 4.03357 0 + 7 11.1536 0 + 8 11.3805 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d3a293a9b9fce4177f59c2ae96118d7bf0542d61 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:49 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.3914872173 8.03764492162 11.3762157356 0 0 0 0 + tauc_H1 15.8089790095 8.67307931045 12.9977671985 0 0 0 0 + tauc_H2 16.2315519898 9.46382135032 10.0789024666 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101356355287 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101729293823 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119731891496 (SEC) + + DONE : INIT CHARGE Time : 0.162683541589 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.444175 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000751 + + Density error is 0.212477546759 + + Energy Rydberg eV + E_KohnSham -34.1886403643 -465.160315827 + E_Harris -34.374710884 -467.691935125 + E_Fermi -0.386537423613 -5.25911145138 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105088935574 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107210142834 + + Density error is 0.0989699647435 + + Energy Rydberg eV + E_KohnSham -34.2764075635 -466.354449833 + E_Harris -34.283439142 -466.450119367 + E_Fermi -0.197250729102 -2.68373385044 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000988334651352 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103961216753 + + Density error is 0.0637632895858 + + Energy Rydberg eV + E_KohnSham -34.2767295363 -466.358830498 + E_Harris -34.281220053 -466.419927113 + E_Fermi -0.189750238506 -2.58168444053 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00088504501759 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101219935002 + + Density error is 0.00209710503377 + + Energy Rydberg eV + E_KohnSham -34.2766480337 -466.357721598 + E_Harris -34.2766530092 -466.357789294 + E_Fermi -0.154783370262 -2.1059357912 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883352516218 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101019854725 + + Density error is 0.000845255849129 + + Energy Rydberg eV + E_KohnSham -34.2766236466 -466.357389795 + E_Harris -34.276623752 -466.357391229 + E_Fermi -0.154519079264 -2.10233992771 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882125690867 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101009614888 + + Density error is 0.00019551255353 + + Energy Rydberg eV + E_KohnSham -34.276634917 -466.357543137 + E_Harris -34.276634919 -466.357543164 + E_Fermi -0.154121744983 -2.09693391747 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882257948211 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101032861461 + + Density error is 2.60490471724e-05 + + Energy Rydberg eV + E_KohnSham -34.2766320064 -466.357503536 + E_Harris -34.2766320077 -466.357503554 + E_Fermi -0.15410263145 -2.09667386452 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882200624935 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101023541139 + + Density error is 1.0582389481e-05 + + Energy Rydberg eV + E_KohnSham -34.276634315 -466.357534946 + E_Harris -34.2766343155 -466.357534953 + E_Fermi -0.154113890849 -2.0968270565 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882200070193 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101024577666 + + Density error is 2.4116781188e-06 + + Energy Rydberg eV + E_KohnSham -34.276633518 -466.357524102 + E_Harris -34.276633518 -466.357524102 + E_Fermi -0.154103499015 -2.09668566834 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882197116726 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101024435707 + + Density error is 5.88847074256e-07 + + Energy Rydberg eV + E_KohnSham -34.2766337363 -466.357527073 + E_Harris -34.2766337363 -466.357527073 + E_Fermi -0.154102436698 -2.09667121478 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882197025539 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101024507996 + + Density error is 2.04345658796e-07 + + Energy Rydberg eV + E_KohnSham -34.2766337103 -466.357526719 + E_Harris -34.2766337103 -466.357526719 + E_Fermi -0.154102139732 -2.09666717435 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882196909387 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101024537082 + + Density error is 1.05106217387e-08 + + Energy Rydberg eV + E_KohnSham -34.2766337141 -466.35752677 + E_Harris -34.2766337141 -466.35752677 + E_band -7.85108424336 -106.819481188 + E_one_elec -68.6530526524 -934.072701166 + E_Hartree +35.7477912827 +486.37365236 + E_xc -8.16269608723 -111.059177829 + E_Ewald +6.91696669648 +94.1101599484 + E_demet -6.19683038074e-59 -8.43122027176e-58 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193601923907 -2.6340893089 + E_Fermi -0.154101937158 -2.09666441819 + + charge density convergence is achieved + final etot is -466.35752677 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9214 2.00000 + 2 -12.9666 2.00000 + 3 -8.86549 2.00000 + 4 -6.65623 2.00000 + 5 1.00047 0.00000 + 6 4.03357 0.00000 + 7 11.1536 0.00000 + 8 11.3805 0.00000 + + EFERMI = -2.096664418191872 eV + OUT.ABACUS/ final etot is -466.3575267704626 eV + correction force for each atom along direction 1 is 5.11435e-05 + correction force for each atom along direction 2 is 0.000191153 + correction force for each atom along direction 3 is 1.60500e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.061964025 +1.0035492 -1.6388188 + H1 -0.11297830 +0.36299075 -0.032144715 + H2 +0.051014279 -1.3665399 +1.6709635 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3575267704626 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3119 11 0.66 1.0e+02% + Run_lcao lcao_line 7.3028 1 7.3 1.e+02% + Potential init_pot 0.28310 2 0.14 3.9% + PW_Basis recip2real 0.26749 17 0.016 3.7% + PW_Basis gathers_scatterp 0.12104 17 0.0071 1.7% + Potential v_of_rho 0.85872 14 0.061 12.% + XC_Functional v_xc 0.21378 15 0.014 2.9% + H_Hartree_pw v_hartree 0.60507 14 0.043 8.3% + PW_Basis real2recip 0.70108 41 0.017 9.6% + PW_Basis gatherp_scatters 0.28546 41 0.0070 3.9% + ORB_control set_orb_tables 1.0946 1 1.1 15.% + ORB_gen_tables gen_tables 1.0946 1 1.1 15.% + ORB_table_phi init_Table 0.47249 1 0.47 6.5% + ORB_table_phi cal_ST_Phi12_R 0.46726 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18446 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18297 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24809 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24615 66 0.0037 3.4% + LOOP_ions opt_ions 5.6861 1 5.7 78.% + ESolver_KS_LCAO Run 5.1243 1 5.1 70.% + HSolverLCAO solve 2.7592 12 0.23 38.% + HamiltLCAO updateHk 1.4191 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.3896 12 0.12 19.% + Gint_interface cal_gint 0.32775 25 0.013 4.5% + Gint_Gamma distri_vl_value 0.83602 12 0.070 11.% + Gint_Gamma distri_vl 2.6610 6 0.44 36.% + LCAO_Deepks cal_projected_DM 5.2709 14 0.38 72.% + LCAO_gen_fixedH add_v_delta 2.5235 6 0.42 35.% + LCAO_DESCRIPTOR add_v_delta 2.5237 6 0.42 35.% + ElecStateLCAO psiToRho 1.3120 12 0.11 18.% + Charge mix_rho 0.90304 11 0.082 12.% + LOOP_ions force_stress 0.56166 1 0.56 7.7% + Force_Stress_LCAO getForceStress 0.56164 1 0.56 7.7% + Force_LCAO_gamma ftable_gamma 0.37041 1 0.37 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.11029 1 0.11 1.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:49 2022 + Finish Time : Wed Sep 28 11:12:57 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..571659613a1f68395d2fcf535147995500a80ff4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123195 ima = 3.7078e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123889702515 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112747783985 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113438237464 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001136108913 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113601368461 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011360886495 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011360524488 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011360672267 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011360619545 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113606243756 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113606223021 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113606212218 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/STRU new file mode 100644 index 0000000000000000000000000000000000000000..489b274a10797b565afdb2bbbf3b10665d809237 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.608512782741 8.037644921642 11.376215735621 0 0 0 +H +0.0 +2 +-12.191020990462 8.673079310465 12.997767198519 0 0 0 +-11.768448010210 9.463821350306 10.078902466581 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/conv new file mode 100644 index 0000000000000000000000000000000000000000..5ee3e21c77d906b92c7bfb134ecf6b8ff8ea3ce3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/conv @@ -0,0 +1 @@ +16 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..90334d5919ec4f306eea23ac217086c9506b6427 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746259886 0.01233830534 1.245605619 1.350324224 1.467757922 0.007817837066 0.01924833264 0.03897599715 +1.917003211e-18 0.0009667135357 0.002258562921 0.0112709024 0.04021020067 -5.444987798e-19 1.291185551e-06 4.2940342e-06 +0.001695195733 0.005625930408 + +H atom_index 1 n_descriptor 18 +1.239854468 0.03426023523 0.1038898638 0.14660955 0.3200043913 0.02117960338 0.02789504814 0.03751916073 +3.594326749e-18 3.508615492e-05 0.09666974749 0.1148734004 0.1256339737 -4.467699712e-18 4.396060005e-06 0.01304268876 +0.02508644667 0.03037604744 + +H atom_index 2 n_descriptor 18 +1.162041959 0.03674006451 0.08065365886 0.1147264579 0.2916764184 0.01772519227 0.0233769612 0.04062810716 +-5.359749217e-17 2.92799544e-05 0.07655789254 0.09759893875 0.1119022007 -3.386544883e-18 6.468635417e-06 0.0150932087 +0.02190465414 0.02633853841 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3d67eec17cf73c895da3dc906416dd0d241a97ae Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:49 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101379 SEC) : SETUP UNITCELL + DONE(0.101745 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11975 SEC) : INIT PLANEWAVE + DONE(0.162811 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444245 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651603e+02 0.000000e+00 2.125e-01 5.233e-01 + GE2 -4.663544e+02 -1.194134e+00 9.897e-02 4.779e-01 + GE3 -4.663588e+02 -4.380665e-03 6.376e-02 5.464e-01 + GE4 -4.663577e+02 1.108900e-03 2.097e-03 4.095e-01 + GE5 -4.663574e+02 3.318033e-04 8.453e-04 4.099e-01 + GE6 -4.663575e+02 -1.533421e-04 1.955e-04 4.060e-01 + GE7 -4.663575e+02 3.960102e-05 2.605e-05 3.917e-01 + GE8 -4.663575e+02 -3.141012e-05 1.058e-05 3.926e-01 + GE9 -4.663575e+02 1.084387e-05 2.412e-06 3.921e-01 + GE10 -4.663575e+02 -2.971010e-06 5.888e-07 3.894e-01 + GE11 -4.663575e+02 3.540359e-07 2.043e-07 3.881e-01 + GE12 -4.663575e+02 -5.124492e-08 1.051e-08 3.328e-01 +E_delta_band = -6.79589702e-02 Ry = -9.24629225e-01 eV +E_delta_NN= -1.93601924e-01 Ry = -2.63408931e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3119 11 0.66 1e+02 % + Run_lcao lcao_line 7.3028 1 7.3 1e+02 % + Potential init_pot 0.2831 2 0.14 3.9 % + PW_Basis recip2real 0.26749 17 0.016 3.7 % + PW_Basis gathers_scatterp 0.12104 17 0.0071 1.7 % + Potential v_of_rho 0.85872 14 0.061 12 % + XC_Functional v_xc 0.21378 15 0.014 2.9 % + H_Hartree_pw v_hartree 0.60507 14 0.043 8.3 % + PW_Basis real2recip 0.70108 41 0.017 9.6 % + PW_Basis gatherp_scatters 0.28546 41 0.007 3.9 % + ORB_control set_orb_tables 1.0946 1 1.1 15 % + ORB_gen_tables gen_tables 1.0946 1 1.1 15 % + ORB_table_phi init_Table 0.47249 1 0.47 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.46726 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18446 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18297 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24809 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24615 66 0.0037 3.4 % + LOOP_ions opt_ions 5.6861 1 5.7 78 % + ESolver_KS_LCAO Run 5.1243 1 5.1 70 % + HSolverLCAO solve 2.7592 12 0.23 38 % + HamiltLCAO updateHk 1.4191 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.3896 12 0.12 19 % + Gint_interface cal_gint 0.32775 25 0.013 4.5 % + Gint_Gamma distri_vl_value 0.83602 12 0.07 11 % + Gint_Gamma distri_vl 2.661 6 0.44 36 % + LCAO_Deepks cal_projected_DM 5.2709 14 0.38 72 % + LCAO_gen_fixedH add_v_delta 2.5235 6 0.42 35 % + LCAO_DESCRIPTOR add_v_delta 2.5237 6 0.42 35 % + ElecStateLCAO psiToRho 1.312 12 0.11 18 % + Charge mix_rho 0.90304 11 0.082 12 % + LOOP_ions force_stress 0.56166 1 0.56 7.7 % + Force_Stress_LCAO getForceStress 0.56164 1 0.56 7.7 % + Force_LCAO_gamma ftable_gamma 0.37041 1 0.37 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.11029 1 0.11 1.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:49 2022 + FINISH Time : Wed Sep 28 11:12:57 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/16/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..67c8acadcc7235161ffec90f24ab5cedcd7b7631 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.171549 0.524844 0.238201 +H 0.154688 0.466108 0.221899 +H 0.140297 0.533245 0.297732 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..80ee2c03782fee990a07e24a2c135b54bcfdd771 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3414 2 + 2 -12.9704 2 + 3 -9.19306 2 + 4 -6.75343 2 + 5 1.2367 0 + 6 4.45481 0 + 7 11.068 0 + 8 11.3145 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..77e94c37dfc3a21902055affc6aadfaa5c0da829 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:46 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.80336837663 14.6956262753 6.66962771102 0 0 0 0 + tauc_H1 4.33125085597 13.0510290063 6.21317665852 0 0 0 0 + tauc_H2 3.9283035064 14.9308580484 8.3364966489 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0846978085943 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.099702151578 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117750127385 (SEC) + + DONE : INIT CHARGE Time : 0.165751504011 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443775 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000506 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000963 + + Density error is 0.214693223348 + + Energy Rydberg eV + E_KohnSham -34.1873228257 -465.142389795 + E_Harris -34.3791402074 -467.752199162 + E_Fermi -0.406793273826 -5.53470643211 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000810318093967 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115942217695 + + Density error is 0.0979232982857 + + Energy Rydberg eV + E_KohnSham -34.2768188624 -466.360045842 + E_Harris -34.2836070651 -466.452404079 + E_Fermi -0.216518119582 -2.94588014656 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000783588555845 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110579836529 + + Density error is 0.0628169901583 + + Energy Rydberg eV + E_KohnSham -34.2770661974 -466.363411007 + E_Harris -34.2814488835 -466.423040511 + E_Fermi -0.205224201821 -2.79221851226 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000756684813708 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103394771748 + + Density error is 0.00198499590234 + + Energy Rydberg eV + E_KohnSham -34.2770514634 -466.363210542 + E_Harris -34.2770526437 -466.3632266 + E_Fermi -0.169491071176 -2.30604432812 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000757390693503 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103495061744 + + Density error is 0.000851974469222 + + Energy Rydberg eV + E_KohnSham -34.2769980602 -466.362483954 + E_Harris -34.2769988244 -466.362494351 + E_Fermi -0.168878599517 -2.29771122369 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000756818582245 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103390605785 + + Density error is 0.000130864889605 + + Energy Rydberg eV + E_KohnSham -34.2770296292 -466.362913471 + E_Harris -34.2770296517 -466.362913778 + E_Fermi -0.168793454773 -2.29655277002 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000756981639281 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010340854289 + + Density error is 4.04460291393e-05 + + Energy Rydberg eV + E_KohnSham -34.2770192078 -466.362771682 + E_Harris -34.2770192165 -466.3627718 + E_Fermi -0.1686865724 -2.29509856073 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000756898169383 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103398701062 + + Density error is 1.42448786021e-05 + + Energy Rydberg eV + E_KohnSham -34.2770227339 -466.362819656 + E_Harris -34.2770227347 -466.362819667 + E_Fermi -0.168725741031 -2.29563147729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000756902440655 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010339824677 + + Density error is 1.9695302531e-06 + + Energy Rydberg eV + E_KohnSham -34.2770213434 -466.362800738 + E_Harris -34.2770213434 -466.362800738 + E_Fermi -0.168710596059 -2.29542541937 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000756906373884 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010339860777 + + Density error is 2.7612799673e-07 + + Energy Rydberg eV + E_KohnSham -34.2770215198 -466.362803138 + E_Harris -34.2770215198 -466.362803138 + E_Fermi -0.168709051296 -2.2954044018 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000756906838178 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103398647701 + + Density error is 1.25915622569e-07 + + Energy Rydberg eV + E_KohnSham -34.2770215565 -466.362803637 + E_Harris -34.2770215565 -466.362803637 + E_Fermi -0.168709034661 -2.29540417547 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000756907029005 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103398654579 + + Density error is 1.10500303094e-08 + + Energy Rydberg eV + E_KohnSham -34.2770215565 -466.362803638 + E_Harris -34.2770215565 -466.362803638 + E_band -7.97582544989 -108.516672372 + E_one_elec -69.3120582977 -943.038932957 + E_Hartree +36.0469151833 +490.443441816 + E_xc -8.21120091261 -111.719119834 + E_Ewald +7.32360789834 +99.6427973352 + E_demet -7.57808439848e-76 -1.03105127744e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19493661474 -2.65224870929 + E_Fermi -0.168708920947 -2.29540262831 + + charge density convergence is achieved + final etot is -466.362803638 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3414 2.00000 + 2 -12.9704 2.00000 + 3 -9.19306 2.00000 + 4 -6.75343 2.00000 + 5 1.23670 0.00000 + 6 4.45481 0.00000 + 7 11.0680 0.00000 + 8 11.3145 0.00000 + + EFERMI = -2.295402628306837 eV + OUT.ABACUS/ final etot is -466.3628036377393 eV + correction force for each atom along direction 1 is -1.24453e-06 + correction force for each atom along direction 2 is -0.000126384 + correction force for each atom along direction 3 is 7.16333e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.099651768 +2.1125345 +1.7940170 + H1 -0.52841753 -2.0746180 -0.69400976 + H2 +0.62806930 -0.037916511 -1.1000072 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3628036377393 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4529 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4442 1 6.4 1.e+02% + Potential init_pot 0.28352 2 0.14 4.4% + PW_Basis recip2real 0.28321 17 0.017 4.4% + PW_Basis gathers_scatterp 0.12256 17 0.0072 1.9% + Potential v_of_rho 0.93009 14 0.066 14.% + XC_Functional v_xc 0.25161 15 0.017 3.9% + H_Hartree_pw v_hartree 0.63607 14 0.045 9.9% + PW_Basis real2recip 0.59534 41 0.015 9.2% + PW_Basis gatherp_scatters 0.23099 41 0.0056 3.6% + ORB_control set_orb_tables 1.1086 1 1.1 17.% + ORB_gen_tables gen_tables 1.1086 1 1.1 17.% + ORB_table_phi init_Table 0.48129 1 0.48 7.5% + ORB_table_phi cal_ST_Phi12_R 0.47637 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.19132 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18976 56 0.0034 2.9% + ORB_table_alpha init_Table_Alpha 0.25761 1 0.26 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25571 66 0.0039 4.0% + LOOP_ions opt_ions 4.8115 1 4.8 75.% + ESolver_KS_LCAO Run 4.2875 1 4.3 66.% + HSolverLCAO solve 2.1656 12 0.18 34.% + HamiltLCAO updateHk 1.1451 12 0.095 18.% + LCAO_Hamilt cal_Hgamma 1.1039 12 0.092 17.% + Gint_interface cal_gint 1.8991 25 0.076 29.% + Gint_Gamma distri_vl 2.2388 6 0.37 35.% + LCAO_Deepks cal_projected_DM 4.6506 14 0.33 72.% + LCAO_gen_fixedH add_v_delta 2.1048 6 0.35 33.% + LCAO_DESCRIPTOR add_v_delta 2.1048 6 0.35 33.% + ElecStateLCAO psiToRho 1.0054 12 0.084 16.% + Charge mix_rho 0.71087 11 0.065 11.% + LOOP_ions force_stress 0.52383 1 0.52 8.1% + Force_Stress_LCAO getForceStress 0.52380 1 0.52 8.1% + Force_LCAO_gamma ftable_gamma 0.30966 1 0.31 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.29725 1 0.30 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:46 2022 + Finish Time : Wed Sep 28 11:07:52 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..661ebe965bf148fedef6579479427d3639eab27c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123793 ima = 3.67265e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123033273657 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011199810615 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112553005711 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112798185619 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112754251156 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011277866834 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112772869764 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112775812999 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011277525748 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112775164519 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112775158225 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112775152182 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/STRU new file mode 100644 index 0000000000000000000000000000000000000000..53596e49d2bf16d5083cfd632e1197be0de97537 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.196631623382 14.695626275327 6.669627711035 0 0 0 +H +0.0 +2 +-23.668749144024 13.051029006319 6.213176658503 0 0 0 +-24.071696493608 14.930858048410 8.336496648883 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/conv new file mode 100644 index 0000000000000000000000000000000000000000..06c6ef3556d094ae45c3aa6daf5413886ffae1b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/conv @@ -0,0 +1 @@ +160 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..da6089f6774609ab80e7846da94b41fc99dd4d4d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750717553 0.01265401619 1.26588588 1.367038382 1.469601979 0.008808701635 0.01821608456 0.03909490348 +-6.745770913e-18 0.001020186652 0.002671077809 0.01244461921 0.04578613095 -1.594838775e-19 2.138380508e-06 6.198712309e-06 +0.001609072455 0.005945164339 + +H atom_index 1 n_descriptor 18 +1.295956691 0.03289236707 0.1257205075 0.1726484228 0.3344981662 0.02453605587 0.0309357491 0.03663521842 +-1.748097033e-17 5.118893401e-05 0.1078179052 0.1220447284 0.1480481085 2.810968919e-19 1.497159548e-06 0.01358436999 +0.02794409677 0.0326178979 + +H atom_index 2 n_descriptor 18 +1.196247159 0.03616578029 0.09126245804 0.1265699986 0.3018244725 0.01986544207 0.02514449565 0.03956077855 +2.239696145e-17 4.194022416e-05 0.08778696768 0.1082930062 0.1130526618 7.056419725e-18 6.482825741e-06 0.01430647039 +0.02424752938 0.02808236313 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5d7448e56925fe17cb5793c063fbea91c7a641de Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:46 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0847224 SEC) : SETUP UNITCELL + DONE(0.099719 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11777 SEC) : INIT PLANEWAVE + DONE(0.165868 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443831 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651424e+02 0.000000e+00 2.147e-01 4.764e-01 + GE2 -4.663600e+02 -1.217656e+00 9.792e-02 3.970e-01 + GE3 -4.663634e+02 -3.365165e-03 6.282e-02 4.519e-01 + GE4 -4.663632e+02 2.004652e-04 1.985e-03 3.418e-01 + GE5 -4.663625e+02 7.265878e-04 8.520e-04 3.477e-01 + GE6 -4.663629e+02 -4.295172e-04 1.309e-04 3.385e-01 + GE7 -4.663628e+02 1.417894e-04 4.045e-05 3.257e-01 + GE8 -4.663628e+02 -4.797456e-05 1.424e-05 3.213e-01 + GE9 -4.663628e+02 1.891887e-05 1.970e-06 3.236e-01 + GE10 -4.663628e+02 -2.400533e-06 2.761e-07 3.218e-01 + GE11 -4.663628e+02 -4.992186e-07 1.259e-07 3.178e-01 + GE12 -4.663628e+02 -3.546013e-10 1.105e-08 2.623e-01 +E_delta_band = -7.06511868e-02 Ry = -9.61258712e-01 eV +E_delta_NN= -1.94936615e-01 Ry = -2.65224871e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4529 11 0.59 1e+02 % + Run_lcao lcao_line 6.4442 1 6.4 1e+02 % + Potential init_pot 0.28352 2 0.14 4.4 % + PW_Basis recip2real 0.28321 17 0.017 4.4 % + PW_Basis gathers_scatterp 0.12256 17 0.0072 1.9 % + Potential v_of_rho 0.93009 14 0.066 14 % + XC_Functional v_xc 0.25161 15 0.017 3.9 % + H_Hartree_pw v_hartree 0.63607 14 0.045 9.9 % + PW_Basis real2recip 0.59534 41 0.015 9.2 % + PW_Basis gatherp_scatters 0.23099 41 0.0056 3.6 % + ORB_control set_orb_tables 1.1086 1 1.1 17 % + ORB_gen_tables gen_tables 1.1086 1 1.1 17 % + ORB_table_phi init_Table 0.48129 1 0.48 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.47637 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.19132 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18976 56 0.0034 2.9 % + ORB_table_alpha init_Table_Alpha 0.25761 1 0.26 4 % + ORB_table_alpha S_PhiAlpha_R 0.25571 66 0.0039 4 % + LOOP_ions opt_ions 4.8115 1 4.8 75 % + ESolver_KS_LCAO Run 4.2875 1 4.3 66 % + HSolverLCAO solve 2.1656 12 0.18 34 % + HamiltLCAO updateHk 1.1451 12 0.095 18 % + LCAO_Hamilt cal_Hgamma 1.1039 12 0.092 17 % + Gint_interface cal_gint 1.8991 25 0.076 29 % + Gint_Gamma distri_vl 2.2388 6 0.37 35 % + LCAO_Deepks cal_projected_DM 4.6506 14 0.33 72 % + LCAO_gen_fixedH add_v_delta 2.1048 6 0.35 33 % + LCAO_DESCRIPTOR add_v_delta 2.1048 6 0.35 33 % + ElecStateLCAO psiToRho 1.0054 12 0.084 16 % + Charge mix_rho 0.71087 11 0.065 11 % + LOOP_ions force_stress 0.52383 1 0.52 8.1 % + Force_Stress_LCAO getForceStress 0.5238 1 0.52 8.1 % + Force_LCAO_gamma ftable_gamma 0.30966 1 0.31 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.29725 1 0.3 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:46 2022 + FINISH Time : Wed Sep 28 11:07:52 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/160/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..96ab7c660a64c8588d38ce0282c91f65ccfe4e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.16099 0.54003 0.247385 +H 0.186787 0.478975 0.236471 +H 0.131103 0.535483 0.301771 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..00d0d12683468829fe7c3d9b7ae284d738c23e63 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4355 2 + 2 -13.2058 2 + 3 -9.08909 2 + 4 -6.77188 2 + 5 1.35026 0 + 6 4.66721 0 + 7 11.038 0 + 8 11.2683 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a6ef15a331863d0ce028bc7085d858394d1a0d8e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:14 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.50771385016 15.1208525798 6.92676715998 0 0 0 0 + tauc_H1 5.23002423377 13.4113023394 6.62118725808 0 0 0 0 + tauc_H2 3.67088406885 14.9935331329 8.44958946027 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871819851621 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.087531857381 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105902548171 (SEC) + + DONE : INIT CHARGE Time : 0.148787421648 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.431163 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0006 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126 + + Density error is 0.216781156641 + + Energy Rydberg eV + E_KohnSham -34.1842330989 -465.100351905 + E_Harris -34.3804564949 -467.770108171 + E_Fermi -0.415329474322 -5.65084739813 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000892007380337 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00140909037359 + + Density error is 0.0976842972144 + + Energy Rydberg eV + E_KohnSham -34.2746548551 -466.330603012 + E_Harris -34.2813241832 -466.421343877 + E_Fermi -0.223435640858 -3.03999785195 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00085636012564 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133011721197 + + Density error is 0.0624137356541 + + Energy Rydberg eV + E_KohnSham -34.274864441 -466.333454575 + E_Harris -34.279135797 -466.391569355 + E_Fermi -0.21009945272 -2.85854970368 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000812893003629 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012099335046 + + Density error is 0.00205436157106 + + Energy Rydberg eV + E_KohnSham -34.2748902233 -466.333805361 + E_Harris -34.2748922109 -466.333832404 + E_Fermi -0.174400673317 -2.37284289215 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000816088106976 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121267693688 + + Density error is 0.000854352434882 + + Energy Rydberg eV + E_KohnSham -34.2748277466 -466.332955322 + E_Harris -34.2748292934 -466.332976367 + E_Fermi -0.173422555651 -2.35953491857 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000815169765378 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121091531232 + + Density error is 0.000192468437445 + + Energy Rydberg eV + E_KohnSham -34.2748693464 -466.333521316 + E_Harris -34.2748693217 -466.333520981 + E_Fermi -0.173570917089 -2.3615534795 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000815366446079 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121101731541 + + Density error is 4.48860544032e-05 + + Energy Rydberg eV + E_KohnSham -34.2748524335 -466.333291205 + E_Harris -34.2748524437 -466.333291343 + E_Fermi -0.173396311841 -2.35917785322 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000815325765588 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121097052035 + + Density error is 1.90056611051e-05 + + Energy Rydberg eV + E_KohnSham -34.274858213 -466.333369839 + E_Harris -34.2748582144 -466.333369858 + E_Fermi -0.173444324061 -2.35983109298 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00081533130778 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121095833008 + + Density error is 2.95142710352e-06 + + Energy Rydberg eV + E_KohnSham -34.2748566386 -466.333348418 + E_Harris -34.2748566386 -466.333348418 + E_Fermi -0.173424984306 -2.35956796212 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000815330422119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121095344323 + + Density error is 2.82740731421e-07 + + Energy Rydberg eV + E_KohnSham -34.2748568573 -466.333351393 + E_Harris -34.2748568573 -466.333351393 + E_Fermi -0.173421811826 -2.35952479832 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000815331013902 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121095424497 + + Density error is 1.31215065221e-07 + + Energy Rydberg eV + E_KohnSham -34.2748569073 -466.333352074 + E_Harris -34.2748569073 -466.333352074 + E_Fermi -0.173421769132 -2.35952421743 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000815331202592 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121095435949 + + Density error is 1.01843776744e-08 + + Energy Rydberg eV + E_KohnSham -34.2748569076 -466.333352078 + E_Harris -34.2748569076 -466.333352078 + E_band -8.01167633606 -109.004448702 + E_one_elec -69.5843479029 -946.743623094 + E_Hartree +36.1792969968 +492.244588791 + E_xc -8.23266129612 -112.011103331 + E_Ewald +7.4866195852 +101.860685117 + E_demet -2.15245720788e-83 -2.92856827284e-82 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195424385596 -2.65888517225 + E_Fermi -0.17342165657 -2.35952268595 + + charge density convergence is achieved + final etot is -466.333352078 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4355 2.00000 + 2 -13.2058 2.00000 + 3 -9.08909 2.00000 + 4 -6.77188 2.00000 + 5 1.35026 0.00000 + 6 4.66721 0.00000 + 7 11.0380 0.00000 + 8 11.2683 0.00000 + + EFERMI = -2.359522685953652 eV + OUT.ABACUS/ final etot is -466.3333520780565 eV + correction force for each atom along direction 1 is 5.76731e-05 + correction force for each atom along direction 2 is -0.000114570 + correction force for each atom along direction 3 is 0.000142267 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.9250696 -0.62954573 -2.9828147 + H1 -0.38655809 +0.88564710 +0.17560718 + H2 -1.5385115 -0.25610137 +2.8072075 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3333520780565 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5494 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5397 1 7.5 1.e+02% + Potential init_pot 0.28413 2 0.14 3.8% + PW_Basis recip2real 0.27744 17 0.016 3.7% + PW_Basis gathers_scatterp 0.12396 17 0.0073 1.6% + Potential v_of_rho 1.0288 14 0.073 14.% + XC_Functional v_xc 0.31657 15 0.021 4.2% + H_Hartree_pw v_hartree 0.66556 14 0.048 8.8% + PW_Basis real2recip 0.73917 41 0.018 9.8% + PW_Basis gatherp_scatters 0.29148 41 0.0071 3.9% + ORB_control set_orb_tables 1.0939 1 1.1 14.% + ORB_gen_tables gen_tables 1.0939 1 1.1 14.% + ORB_table_phi init_Table 0.47379 1 0.47 6.3% + ORB_table_phi cal_ST_Phi12_R 0.46859 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18153 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18002 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24671 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24474 66 0.0037 3.2% + LOOP_ions opt_ions 5.9370 1 5.9 79.% + ESolver_KS_LCAO Run 5.3710 1 5.4 71.% + HSolverLCAO solve 2.7472 12 0.23 36.% + HamiltLCAO updateHk 1.4198 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.3904 12 0.12 18.% + Gint_interface cal_gint 2.1660 25 0.087 29.% + Gint_Gamma distri_vl_value 0.14269 12 0.012 1.9% + Gint_Gamma distri_vl 2.8019 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.7362 14 0.41 76.% + LCAO_gen_fixedH add_v_delta 2.6545 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6545 6 0.44 35.% + ElecStateLCAO psiToRho 1.3042 12 0.11 17.% + Charge mix_rho 0.98083 11 0.089 13.% + LOOP_ions force_stress 0.56582 1 0.57 7.5% + Force_Stress_LCAO getForceStress 0.56579 1 0.57 7.5% + Force_LCAO_gamma ftable_gamma 0.35698 1 0.36 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.30806 1 0.31 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:14 2022 + Finish Time : Wed Sep 28 11:02:21 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..60c28a702ec5549e606008a7ca34a51dca698e7f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123958 ima = 3.67027e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123111965201 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112275619507 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112727774392 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112991940376 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112935864608 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112971023081 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112960154564 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112963362841 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112962650882 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112962526448 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112962519313 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112962513404 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/STRU new file mode 100644 index 0000000000000000000000000000000000000000..cdb61ace79ea812ce4ebb2b68fb4a8ff87cb39a9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.492286149827 15.120852579779 6.926767159960 0 0 0 +H +0.0 +2 +-22.769975766250 13.411302339459 6.621187258061 0 0 0 +-24.329115931159 14.993533132891 8.449589460261 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/conv new file mode 100644 index 0000000000000000000000000000000000000000..6c122c8b78082b1826a48c1f930574498b1b073b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/conv @@ -0,0 +1 @@ +161 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5ed067757319cdb22b6c2e805d670c82f0e72bd1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74872335 0.01267531643 1.277174707 1.380915775 1.470103761 0.00856886309 0.01922735667 0.03903695694 +4.094066986e-18 0.001133947451 0.002659461886 0.01259210635 0.0463786149 -3.898171355e-19 2.023614434e-06 5.985143398e-06 +0.00164819994 0.005831490081 + +H atom_index 1 n_descriptor 18 +1.206855399 0.03558715244 0.09432888208 0.1312073619 0.306468589 0.02023902347 0.02581584578 0.03884416998 +-3.610698448e-17 4.279550936e-05 0.09131381106 0.1124982204 0.113374782 -3.241028184e-18 6.322946214e-06 0.01388935397 +0.02478332925 0.02870034591 + +H atom_index 2 n_descriptor 18 +1.316506458 0.03206336245 0.1338525139 0.1840726718 0.3399437794 0.02521266652 0.03210543688 0.03647286413 +-3.945053612e-17 5.292794021e-05 0.1074590813 0.1287975207 0.1577116775 -7.938879728e-18 8.395437868e-07 0.01425840175 +0.02860850877 0.03328337928 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..b863bf8b008e4e6a93afc8d26fbb1ca05a7571b7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:14 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872043 SEC) : SETUP UNITCELL + DONE(0.0875469 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105923 SEC) : INIT PLANEWAVE + DONE(0.148926 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.431233 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651004e+02 0.000000e+00 2.168e-01 5.404e-01 + GE2 -4.663306e+02 -1.230251e+00 9.768e-02 5.046e-01 + GE3 -4.663335e+02 -2.851563e-03 6.241e-02 5.756e-01 + GE4 -4.663338e+02 -3.507860e-04 2.054e-03 4.314e-01 + GE5 -4.663330e+02 8.500392e-04 8.544e-04 4.332e-01 + GE6 -4.663335e+02 -5.659944e-04 1.925e-04 4.266e-01 + GE7 -4.663333e+02 2.301115e-04 4.489e-05 4.213e-01 + GE8 -4.663334e+02 -7.863398e-05 1.901e-05 4.083e-01 + GE9 -4.663333e+02 2.142137e-05 2.951e-06 4.097e-01 + GE10 -4.663334e+02 -2.975853e-06 2.827e-07 4.068e-01 + GE11 -4.663334e+02 -6.811196e-07 1.312e-07 4.101e-01 + GE12 -4.663334e+02 -3.580913e-09 1.018e-08 3.407e-01 +E_delta_band = -7.16600950e-02 Ry = -9.74985612e-01 eV +E_delta_NN= -1.95424386e-01 Ry = -2.65888517e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5494 11 0.69 1e+02 % + Run_lcao lcao_line 7.5397 1 7.5 1e+02 % + Potential init_pot 0.28413 2 0.14 3.8 % + PW_Basis recip2real 0.27744 17 0.016 3.7 % + PW_Basis gathers_scatterp 0.12396 17 0.0073 1.6 % + Potential v_of_rho 1.0288 14 0.073 14 % + XC_Functional v_xc 0.31657 15 0.021 4.2 % + H_Hartree_pw v_hartree 0.66556 14 0.048 8.8 % + PW_Basis real2recip 0.73917 41 0.018 9.8 % + PW_Basis gatherp_scatters 0.29148 41 0.0071 3.9 % + ORB_control set_orb_tables 1.0939 1 1.1 14 % + ORB_gen_tables gen_tables 1.0939 1 1.1 14 % + ORB_table_phi init_Table 0.47379 1 0.47 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.46859 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18153 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18002 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24671 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24474 66 0.0037 3.2 % + LOOP_ions opt_ions 5.937 1 5.9 79 % + ESolver_KS_LCAO Run 5.371 1 5.4 71 % + HSolverLCAO solve 2.7472 12 0.23 36 % + HamiltLCAO updateHk 1.4198 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.3904 12 0.12 18 % + Gint_interface cal_gint 2.166 25 0.087 29 % + Gint_Gamma distri_vl_value 0.14269 12 0.012 1.9 % + Gint_Gamma distri_vl 2.8019 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.7362 14 0.41 76 % + LCAO_gen_fixedH add_v_delta 2.6545 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6545 6 0.44 35 % + ElecStateLCAO psiToRho 1.3042 12 0.11 17 % + Charge mix_rho 0.98083 11 0.089 13 % + LOOP_ions force_stress 0.56582 1 0.57 7.5 % + Force_Stress_LCAO getForceStress 0.56579 1 0.57 7.5 % + Force_LCAO_gamma ftable_gamma 0.35698 1 0.36 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.30806 1 0.31 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:14 2022 + FINISH Time : Wed Sep 28 11:02:21 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/161/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e755789d3c20533d84700194abfcb8df9c4511d5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.157946 0.535303 0.24058 +H 0.217428 0.510077 0.231047 +H 0.172599 0.573847 0.294054 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..52958f92f46ff283a48f6f5b81dfce853e141dd1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2653 2 + 2 -12.6089 2 + 3 -9.41466 2 + 4 -6.7424 2 + 5 1.12475 0 + 6 4.17103 0 + 7 11.1 0 + 8 11.3794 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c93ad710d7afca22e2cc9f373d567c57461c0f12 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:00 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.42248699123 14.9884962657 6.73624715075 0 0 0 0 + tauc_H1 6.08797783782 14.282162971 6.46931949008 0 0 0 0 + tauc_H2 4.83277748548 16.0677030565 8.23349876998 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871962529994 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0951464503971 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.113326614562 (SEC) + + DONE : INIT CHARGE Time : 0.163270176635 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445696 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00105 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000601 + + Density error is 0.212224586891 + + Energy Rydberg eV + E_KohnSham -34.1894515941 -465.171353175 + E_Harris -34.3762790292 -467.713270836 + E_Fermi -0.397969732421 -5.41465599246 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00127037817197 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000809245403817 + + Density error is 0.0980910293133 + + Energy Rydberg eV + E_KohnSham -34.278357858 -466.380984952 + E_Harris -34.2853906798 -466.476671401 + E_Fermi -0.208215587212 -2.83291839849 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00120183732753 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000778080511474 + + Density error is 0.0631636561956 + + Energy Rydberg eV + E_KohnSham -34.2787691018 -466.38658021 + E_Harris -34.2833060285 -466.448308266 + E_Fermi -0.199846573008 -2.71905211868 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109708100257 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000751646846878 + + Density error is 0.00190052761365 + + Energy Rydberg eV + E_KohnSham -34.2787015275 -466.385660815 + E_Harris -34.2787015287 -466.385660832 + E_Fermi -0.164156613512 -2.23346530815 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109756972329 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000752603452028 + + Density error is 0.000966125851236 + + Energy Rydberg eV + E_KohnSham -34.2786516952 -466.384982812 + E_Harris -34.278652682 -466.384996239 + E_Fermi -0.163970992626 -2.23093980643 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109598007885 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000752157445309 + + Density error is 0.000106314030276 + + Energy Rydberg eV + E_KohnSham -34.2786798759 -466.385366231 + E_Harris -34.2786798787 -466.385366269 + E_Fermi -0.163690851772 -2.22712829457 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109601544852 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00075231758681 + + Density error is 3.04280348916e-05 + + Energy Rydberg eV + E_KohnSham -34.2786715085 -466.385252385 + E_Harris -34.2786715123 -466.385252438 + E_Fermi -0.163617759115 -2.22613381796 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109593329458 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00075224721448 + + Density error is 1.46841657502e-05 + + Energy Rydberg eV + E_KohnSham -34.2786734713 -466.385279091 + E_Harris -34.2786734723 -466.385279104 + E_Fermi -0.163644526303 -2.22649800423 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109593385709 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000752258816257 + + Density error is 2.71367460752e-06 + + Energy Rydberg eV + E_KohnSham -34.2786722864 -466.38526297 + E_Harris -34.2786722865 -466.385262971 + E_Fermi -0.163631345764 -2.22631867379 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109593396399 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000752262296296 + + Density error is 1.59864030542e-07 + + Energy Rydberg eV + E_KohnSham -34.2786724843 -466.385265663 + E_Harris -34.2786724843 -466.385265663 + E_Fermi -0.163628495324 -2.22627989157 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109593433361 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000752262512123 + + Density error is 5.3410687527e-08 + + Energy Rydberg eV + E_KohnSham -34.2786725368 -466.385266377 + E_Harris -34.2786725368 -466.385266377 + E_band -7.94245002151 -108.062576373 + E_one_elec -69.0088061575 -938.912975919 + E_Hartree +35.895602036 +488.384720829 + E_xc -8.18639547027 -111.381624477 + E_Ewald +7.14579206624 +97.2234888241 + E_demet -1.54810844536e-68 -2.10630959788e-67 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194366478175 -2.64449160338 + E_Fermi -0.16362844181 -2.22627916348 + + charge density convergence is achieved + final etot is -466.385266377 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2653 2.00000 + 2 -12.6089 2.00000 + 3 -9.41466 2.00000 + 4 -6.74240 2.00000 + 5 1.12475 0.00000 + 6 4.17103 0.00000 + 7 11.1000 0.00000 + 8 11.3794 0.00000 + + EFERMI = -2.226279163478385 eV + OUT.ABACUS/ final etot is -466.3852663768000 eV + correction force for each atom along direction 1 is 3.82082e-05 + correction force for each atom along direction 2 is 4.25528e-05 + correction force for each atom along direction 3 is 0.000120282 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.26940856 +0.88225866 +1.2024782 + H1 +0.37319795 -0.47563888 -0.45680762 + H2 -0.64260651 -0.40661978 -0.74567062 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3852663768000 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0124 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0028 1 7.0 1.e+02% + Potential init_pot 0.28700 2 0.14 4.1% + PW_Basis recip2real 0.28018 16 0.018 4.0% + PW_Basis gathers_scatterp 0.12868 16 0.0080 1.8% + Potential v_of_rho 0.97330 13 0.075 14.% + XC_Functional v_xc 0.28696 14 0.020 4.1% + H_Hartree_pw v_hartree 0.64502 13 0.050 9.2% + PW_Basis real2recip 0.65044 38 0.017 9.3% + PW_Basis gatherp_scatters 0.25324 38 0.0067 3.6% + ORB_control set_orb_tables 1.1106 1 1.1 16.% + ORB_gen_tables gen_tables 1.1106 1 1.1 16.% + ORB_table_phi init_Table 0.48370 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47848 126 0.0038 6.8% + ORB_table_beta init_Table_Beta 0.19001 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18840 56 0.0034 2.7% + ORB_table_alpha init_Table_Alpha 0.25208 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.25009 66 0.0038 3.6% + LOOP_ions opt_ions 5.3646 1 5.4 77.% + ESolver_KS_LCAO Run 4.8130 1 4.8 69.% + HSolverLCAO solve 2.5448 11 0.23 36.% + HamiltLCAO updateHk 1.3234 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2958 11 0.12 18.% + Gint_interface cal_gint 2.1782 23 0.095 31.% + Gint_Gamma distri_vl 2.3151 6 0.39 33.% + LCAO_Deepks cal_projected_DM 5.1886 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1702 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1702 6 0.36 31.% + ElecStateLCAO psiToRho 1.2042 11 0.11 17.% + Charge mix_rho 0.78524 10 0.079 11.% + LOOP_ions force_stress 0.55146 1 0.55 7.9% + Force_Stress_LCAO getForceStress 0.55142 1 0.55 7.9% + Force_LCAO_gamma ftable_gamma 0.33538 1 0.34 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.31446 1 0.31 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:00 2022 + Finish Time : Wed Sep 28 11:12:07 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a7d6bb7a736751474ab7e3f27d49534ec32cb382 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123798 ima = 3.67231e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122876114151 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111475308958 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112194933488 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112438013078 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112399031 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112420804297 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112418150012 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112420476885 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001124198099 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112419675775 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112419666435 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/STRU new file mode 100644 index 0000000000000000000000000000000000000000..78a152f4441a253d33e9d9068726e93417255233 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.577513008749 14.988496265761 6.736247150747 0 0 0 +H +0.0 +2 +-21.912022162181 14.282162971002 6.469319490059 0 0 0 +-23.167222514526 16.067703056444 8.233498769959 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/conv new file mode 100644 index 0000000000000000000000000000000000000000..75d753d3d85af3f7764ab761b5c2b21adeae0c73 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/conv @@ -0,0 +1 @@ +162 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f668ce040b9cfa469736b236ac2320216b3a08f3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75437187 0.01268233001 1.257503957 1.343228737 1.469145525 0.009416529374 0.01650662729 0.03919721961 +9.822189691e-19 0.0008470764374 0.002741596881 0.01280122462 0.0451934603 7.764584467e-19 2.504236441e-06 6.908868243e-06 +0.001576956288 0.006103072111 + +H atom_index 1 n_descriptor 18 +1.253499143 0.03475880111 0.1119311775 0.1512379544 0.3210792721 0.02322207027 0.02844588211 0.03791123155 +6.687437286e-17 4.747898845e-05 0.1022765572 0.115843507 0.1296089764 -1.407112439e-18 2.872544732e-06 0.0133565325 +0.02675133011 0.03088411824 + +H atom_index 2 n_descriptor 18 +1.20486372 0.03635038808 0.09565210587 0.1297592371 0.3038348306 0.0208266535 0.02558082732 0.03968767105 +4.950505147e-17 4.305721253e-05 0.09016975351 0.1109098102 0.1135030979 6.177219399e-18 5.295774418e-06 0.01425143986 +0.02483522235 0.02847549152 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c2d08b3dc1c4ca3f08206a367340a3ddd623c5e5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:00 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087222 SEC) : SETUP UNITCELL + DONE(0.0951636 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.113347 SEC) : INIT PLANEWAVE + DONE(0.163401 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445758 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651714e+02 0.000000e+00 2.122e-01 5.335e-01 + GE2 -4.663810e+02 -1.209632e+00 9.809e-02 4.869e-01 + GE3 -4.663866e+02 -5.595258e-03 6.316e-02 5.524e-01 + GE4 -4.663857e+02 9.193952e-04 1.901e-03 4.203e-01 + GE5 -4.663850e+02 6.780032e-04 9.661e-04 4.182e-01 + GE6 -4.663854e+02 -3.834187e-04 1.063e-04 4.158e-01 + GE7 -4.663853e+02 1.138453e-04 3.043e-05 4.028e-01 + GE8 -4.663853e+02 -2.670601e-05 1.468e-05 3.987e-01 + GE9 -4.663853e+02 1.612108e-05 2.714e-06 3.986e-01 + GE10 -4.663853e+02 -2.692311e-06 1.599e-07 3.972e-01 + GE11 -4.663853e+02 -7.141070e-07 5.341e-08 3.266e-01 +E_delta_band = -6.95014669e-02 Ry = -9.45615969e-01 eV +E_delta_NN= -1.94366478e-01 Ry = -2.64449160e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0124 11 0.64 1e+02 % + Run_lcao lcao_line 7.0028 1 7 1e+02 % + Potential init_pot 0.287 2 0.14 4.1 % + PW_Basis recip2real 0.28018 16 0.018 4 % + PW_Basis gathers_scatterp 0.12868 16 0.008 1.8 % + Potential v_of_rho 0.9733 13 0.075 14 % + XC_Functional v_xc 0.28696 14 0.02 4.1 % + H_Hartree_pw v_hartree 0.64502 13 0.05 9.2 % + PW_Basis real2recip 0.65044 38 0.017 9.3 % + PW_Basis gatherp_scatters 0.25324 38 0.0067 3.6 % + ORB_control set_orb_tables 1.1106 1 1.1 16 % + ORB_gen_tables gen_tables 1.1106 1 1.1 16 % + ORB_table_phi init_Table 0.4837 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47848 126 0.0038 6.8 % + ORB_table_beta init_Table_Beta 0.19001 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.1884 56 0.0034 2.7 % + ORB_table_alpha init_Table_Alpha 0.25208 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.25009 66 0.0038 3.6 % + LOOP_ions opt_ions 5.3646 1 5.4 77 % + ESolver_KS_LCAO Run 4.813 1 4.8 69 % + HSolverLCAO solve 2.5448 11 0.23 36 % + HamiltLCAO updateHk 1.3234 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2958 11 0.12 18 % + Gint_interface cal_gint 2.1782 23 0.095 31 % + Gint_Gamma distri_vl 2.3151 6 0.39 33 % + LCAO_Deepks cal_projected_DM 5.1886 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.1702 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1702 6 0.36 31 % + ElecStateLCAO psiToRho 1.2042 11 0.11 17 % + Charge mix_rho 0.78524 10 0.079 11 % + LOOP_ions force_stress 0.55146 1 0.55 7.9 % + Force_Stress_LCAO getForceStress 0.55142 1 0.55 7.9 % + Force_LCAO_gamma ftable_gamma 0.33538 1 0.34 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.31446 1 0.31 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:00 2022 + FINISH Time : Wed Sep 28 11:12:07 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/162/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a04ca07f8887bef0880b0f917bbcabd5f01eee03 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.160954 0.518372 0.22396 +H 0.223634 0.503102 0.216264 +H 0.151599 0.580772 0.221347 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9c06be4c94e818e1a6fa2832c86414ab48a0429d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3849 2 + 2 -13.6171 2 + 3 -8.77402 2 + 4 -6.76332 2 + 5 1.51651 0 + 6 4.81164 0 + 7 11.028 0 + 8 11.2345 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4311ab6f5aeacd52c5ecfbc747cb9fe99e28d72e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:24 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.50671162201 14.5144256081 6.27088014437 0 0 0 0 + tauc_H1 6.26175636704 14.0868507957 6.05539160377 0 0 0 0 + tauc_H2 4.24478258307 16.2616185403 6.19771946454 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0869197652553 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0971189447378 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115162268207 (SEC) + + DONE : INIT CHARGE Time : 0.162814652756 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.442741 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 0 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0018 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000656 + + Density error is 0.2188237999 + + Energy Rydberg eV + E_KohnSham -34.1847275315 -465.107079006 + E_Harris -34.384718192 -467.828091536 + E_Fermi -0.418842209398 -5.69864061072 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00143823259203 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834344878976 + + Density error is 0.0975859883037 + + Energy Rydberg eV + E_KohnSham -34.2759296088 -466.347946926 + E_Harris -34.2824276755 -466.43635766 + E_Fermi -0.224973000363 -3.06091470109 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00131767674508 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803804384642 + + Density error is 0.0622084537561 + + Energy Rydberg eV + E_KohnSham -34.2761287169 -466.350655931 + E_Harris -34.2802461556 -466.406676559 + E_Fermi -0.210071501644 -2.85816940977 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111592221194 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000760749989785 + + Density error is 0.00216909811306 + + Energy Rydberg eV + E_KohnSham -34.2761848208 -466.351419263 + E_Harris -34.2761890822 -466.351477243 + E_Fermi -0.17479424251 -2.37819767573 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111234813864 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00076068614555 + + Density error is 0.000881908939253 + + Energy Rydberg eV + E_KohnSham -34.2761136385 -466.35045078 + E_Harris -34.2761154795 -466.350475827 + E_Fermi -0.173458208774 -2.3600200042 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011108475963 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000760068767269 + + Density error is 0.000222002868533 + + Energy Rydberg eV + E_KohnSham -34.2761619008 -466.351107421 + E_Harris -34.2761620498 -466.351109448 + E_Fermi -0.173784148806 -2.36445464585 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111043786071 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000760322969585 + + Density error is 5.20148194285e-05 + + Energy Rydberg eV + E_KohnSham -34.2761427719 -466.350847159 + E_Harris -34.2761427874 -466.35084737 + E_Fermi -0.173542948615 -2.36117294888 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111047668718 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000760266035726 + + Density error is 1.92078329906e-05 + + Energy Rydberg eV + E_KohnSham -34.2761491928 -466.350934521 + E_Harris -34.2761491944 -466.350934542 + E_Fermi -0.173606422233 -2.36203655176 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111043508669 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00076026148138 + + Density error is 1.39233255199e-06 + + Energy Rydberg eV + E_KohnSham -34.2761474431 -466.350910714 + E_Harris -34.2761474431 -466.350910714 + E_Fermi -0.173585098131 -2.36174642247 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111043019439 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000760262483421 + + Density error is 1.62601015854e-07 + + Energy Rydberg eV + E_KohnSham -34.2761477292 -466.350914606 + E_Harris -34.2761477292 -466.350914606 + E_Fermi -0.173583890897 -2.3617299972 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011104306265 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000760262830884 + + Density error is 6.49998226925e-08 + + Energy Rydberg eV + E_KohnSham -34.2761477459 -466.350914834 + E_Harris -34.2761477459 -466.350914834 + E_band -8.01713260992 -109.078685117 + E_one_elec -69.7593926819 -949.125229494 + E_Hartree +36.2735873915 +493.527475425 + E_xc -8.24704739216 -112.206836209 + E_Ewald +7.58013566157 +103.13303661 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195510191589 -2.66005262268 + E_Fermi -0.173583899895 -2.36173011964 + + charge density convergence is achieved + final etot is -466.350914834 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3849 2.00000 + 2 -13.6171 2.00000 + 3 -8.77402 2.00000 + 4 -6.76332 2.00000 + 5 1.51651 0.00000 + 6 4.81164 0.00000 + 7 11.0280 0.00000 + 8 11.2345 0.00000 + + EFERMI = -2.361730119636269 eV + OUT.ABACUS/ final etot is -466.3509148337922 eV + correction force for each atom along direction 1 is 0.000130913 + correction force for each atom along direction 2 is 4.25282e-05 + correction force for each atom along direction 3 is 0.000111113 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.68903861 -2.4712517 +0.25637465 + H1 +0.52291588 +0.35535843 -0.097748812 + H2 +0.16612273 +2.1158933 -0.15862584 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3509148337922 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4491 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4391 1 6.4 1.e+02% + Potential init_pot 0.28370 2 0.14 4.4% + PW_Basis recip2real 0.27047 16 0.017 4.2% + PW_Basis gathers_scatterp 0.11902 16 0.0074 1.8% + Potential v_of_rho 0.88582 13 0.068 14.% + XC_Functional v_xc 0.25296 14 0.018 3.9% + H_Hartree_pw v_hartree 0.59330 13 0.046 9.2% + PW_Basis real2recip 0.55802 38 0.015 8.7% + PW_Basis gatherp_scatters 0.21736 38 0.0057 3.4% + ORB_control set_orb_tables 1.1090 1 1.1 17.% + ORB_gen_tables gen_tables 1.1090 1 1.1 17.% + ORB_table_phi init_Table 0.48464 1 0.48 7.5% + ORB_table_phi cal_ST_Phi12_R 0.47982 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18866 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18719 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25740 1 0.26 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25550 66 0.0039 4.0% + LOOP_ions opt_ions 4.8103 1 4.8 75.% + ESolver_KS_LCAO Run 4.2706 1 4.3 66.% + HSolverLCAO solve 2.2929 11 0.21 36.% + HamiltLCAO updateHk 1.1998 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.1662 11 0.11 18.% + Gint_interface cal_gint 2.1628 23 0.094 34.% + Gint_Gamma distri_vl 2.0470 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.6424 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9154 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9154 6 0.32 30.% + ElecStateLCAO psiToRho 1.0795 11 0.098 17.% + Charge mix_rho 0.65496 10 0.065 10.% + LOOP_ions force_stress 0.53946 1 0.54 8.4% + Force_Stress_LCAO getForceStress 0.53943 1 0.54 8.4% + Force_LCAO_gamma ftable_gamma 0.32754 1 0.33 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.32073 1 0.32 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:24 2022 + Finish Time : Wed Sep 28 11:07:30 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..70d5dc8167c5849cb288dc669c18d8ed0ed9ceaa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124158 ima = 3.70135e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123547732892 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112926201759 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113270134852 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113530700436 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011346602108 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113504832074 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113493091242 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113496687588 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113495919436 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113495877831 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113495872382 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/STRU new file mode 100644 index 0000000000000000000000000000000000000000..56646e8c67ea52b4fc30b80868a0756f6eb3f021 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.493288377982 14.514425608100 6.270880144349 0 0 0 +H +0.0 +2 +-21.738243632980 14.086850795672 6.055391603748 0 0 0 +-23.755217416950 16.261618540298 6.197719464521 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/conv new file mode 100644 index 0000000000000000000000000000000000000000..2c90c84e9853e20362d1789173a186d24bd0e2d5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/conv @@ -0,0 +1 @@ +163 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..db653799f8e42d33e4843fdbefd101309f35633e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74248226 0.01269911675 1.297814932 1.388387587 1.470009735 0.007657799072 0.02131910842 0.03883861137 +-2.069822502e-19 0.001271188382 0.002411314647 0.01300499282 0.04387234938 -2.943091413e-19 1.552985722e-06 4.931383022e-06 +0.001833841166 0.00551100665 + +H atom_index 1 n_descriptor 18 +1.249165838 0.03343312386 0.1092137275 0.1513395557 0.3231688314 0.02190046802 0.02848836914 0.03659288689 +1.106927781e-17 3.93174677e-05 0.1034747998 0.1146979815 0.1301077878 4.418482444e-19 4.211582894e-06 0.01282165551 +0.02642398618 0.03090059794 + +H atom_index 2 n_descriptor 18 +1.289956628 0.03204102685 0.1241717692 0.1713479144 0.3346838262 0.02359206224 0.03080039009 0.03583811594 +5.634884334e-18 4.262953235e-05 0.1081295904 0.1216367867 0.1471693374 4.90751818e-18 2.233703705e-06 0.01317377882 +0.02780267889 0.03250542167 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9ada641182ef7fe0734f66b1864cd8d316add2f7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:24 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0869426 SEC) : SETUP UNITCELL + DONE(0.0971386 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115179 SEC) : INIT PLANEWAVE + DONE(0.162945 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.442808 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651071e+02 0.000000e+00 2.188e-01 5.041e-01 + GE2 -4.663479e+02 -1.240868e+00 9.759e-02 4.291e-01 + GE3 -4.663507e+02 -2.709004e-03 6.221e-02 4.788e-01 + GE4 -4.663514e+02 -7.633328e-04 2.169e-03 3.746e-01 + GE5 -4.663505e+02 9.684837e-04 8.819e-04 3.712e-01 + GE6 -4.663511e+02 -6.566416e-04 2.220e-04 3.597e-01 + GE7 -4.663508e+02 2.602623e-04 5.201e-05 3.558e-01 + GE8 -4.663509e+02 -8.736154e-05 1.921e-05 3.480e-01 + GE9 -4.663509e+02 2.380660e-05 1.392e-06 3.426e-01 + GE10 -4.663509e+02 -3.892397e-06 1.626e-07 3.517e-01 + GE11 -4.663509e+02 -2.273978e-07 6.500e-08 2.936e-01 +E_delta_band = -7.20794668e-02 Ry = -9.80691457e-01 eV +E_delta_NN= -1.95510192e-01 Ry = -2.66005262e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4491 11 0.59 1e+02 % + Run_lcao lcao_line 6.4391 1 6.4 1e+02 % + Potential init_pot 0.2837 2 0.14 4.4 % + PW_Basis recip2real 0.27047 16 0.017 4.2 % + PW_Basis gathers_scatterp 0.11902 16 0.0074 1.8 % + Potential v_of_rho 0.88582 13 0.068 14 % + XC_Functional v_xc 0.25296 14 0.018 3.9 % + H_Hartree_pw v_hartree 0.5933 13 0.046 9.2 % + PW_Basis real2recip 0.55802 38 0.015 8.7 % + PW_Basis gatherp_scatters 0.21736 38 0.0057 3.4 % + ORB_control set_orb_tables 1.109 1 1.1 17 % + ORB_gen_tables gen_tables 1.109 1 1.1 17 % + ORB_table_phi init_Table 0.48464 1 0.48 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.47982 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18866 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18719 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.2574 1 0.26 4 % + ORB_table_alpha S_PhiAlpha_R 0.2555 66 0.0039 4 % + LOOP_ions opt_ions 4.8103 1 4.8 75 % + ESolver_KS_LCAO Run 4.2706 1 4.3 66 % + HSolverLCAO solve 2.2929 11 0.21 36 % + HamiltLCAO updateHk 1.1998 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.1662 11 0.11 18 % + Gint_interface cal_gint 2.1628 23 0.094 34 % + Gint_Gamma distri_vl 2.047 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.6424 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9154 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9154 6 0.32 30 % + ElecStateLCAO psiToRho 1.0795 11 0.098 17 % + Charge mix_rho 0.65496 10 0.065 10 % + LOOP_ions force_stress 0.53946 1 0.54 8.4 % + Force_Stress_LCAO getForceStress 0.53943 1 0.54 8.4 % + Force_LCAO_gamma ftable_gamma 0.32754 1 0.33 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.32073 1 0.32 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:24 2022 + FINISH Time : Wed Sep 28 11:07:30 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/163/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..01d065ab9b75a28bebf6b75a1b2ccfa49ebd04ad --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.15798 0.505006 0.203273 +H 0.19513 0.520087 0.257052 +H 0.127788 0.565199 0.200942 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d885fd87694b1e36fbb75b66ffaf81d4e732fa14 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2011 2 + 2 -12.3124 2 + 3 -9.58972 2 + 4 -6.73231 2 + 5 0.993968 0 + 6 3.93878 0 + 7 11.1258 0 + 8 11.425 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e2cb727388a9b7fec20c6be823cd3e2670107d98 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:55 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.42345177862 14.1401667114 5.69164685694 0 0 0 0 + tauc_H1 5.46365133567 14.5624297808 7.19746113251 0 0 0 0 + tauc_H2 3.57806387898 15.8255786557 5.62637543638 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0873530841124 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0969938644735 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115240614145 (SEC) + + DONE : INIT CHARGE Time : 0.166319895835 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446507 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00143 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101 + + Density error is 0.209483930078 + + Energy Rydberg eV + E_KohnSham -34.1888729739 -465.163480644 + E_Harris -34.37041934 -467.633545674 + E_Fermi -0.389078457453 -5.29368399041 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00132075376744 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121441847334 + + Density error is 0.0979624014652 + + Energy Rydberg eV + E_KohnSham -34.2757579772 -466.345611758 + E_Harris -34.2829656849 -466.443677653 + E_Fermi -0.202430399088 -2.75420687601 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122068121474 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115383944706 + + Density error is 0.063204164145 + + Energy Rydberg eV + E_KohnSham -34.2761759004 -466.351297896 + E_Harris -34.2808057887 -466.414290758 + E_Fermi -0.195656354961 -2.66204127738 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00103583710229 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107202536405 + + Density error is 0.00185138714463 + + Energy Rydberg eV + E_KohnSham -34.2760707044 -466.349866631 + E_Harris -34.2760702633 -466.349860629 + E_Fermi -0.160092533925 -2.17817066864 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00103602387849 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107279039204 + + Density error is 0.000940809139283 + + Energy Rydberg eV + E_KohnSham -34.276040979 -466.349462196 + E_Harris -34.2760416341 -466.349471109 + E_Fermi -0.160304401013 -2.18105326826 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00103351366712 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107165579753 + + Density error is 9.6563661736e-05 + + Energy Rydberg eV + E_KohnSham -34.2760547932 -466.349650147 + E_Harris -34.2760547942 -466.349650162 + E_Fermi -0.15982655726 -2.17455187046 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00103341488447 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107162975078 + + Density error is 2.23088083784e-05 + + Energy Rydberg eV + E_KohnSham -34.2760522299 -466.349615272 + E_Harris -34.2760522313 -466.349615291 + E_Fermi -0.159760161536 -2.17364851029 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00103337141611 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107156059466 + + Density error is 9.21675749132e-06 + + Energy Rydberg eV + E_KohnSham -34.2760530348 -466.349626224 + E_Harris -34.2760530352 -466.349626229 + E_Fermi -0.159773753425 -2.17383343743 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00103336719263 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107156593669 + + Density error is 2.32781799452e-06 + + Energy Rydberg eV + E_KohnSham -34.2760522866 -466.349616043 + E_Harris -34.2760522866 -466.349616044 + E_Fermi -0.159766913936 -2.17374038141 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00103336215203 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107156644781 + + Density error is 2.86431345874e-07 + + Energy Rydberg eV + E_KohnSham -34.2760524141 -466.349617779 + E_Harris -34.2760524141 -466.349617778 + E_Fermi -0.159764717971 -2.17371050378 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00103336206472 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107156684718 + + Density error is 5.10523294943e-08 + + Energy Rydberg eV + E_KohnSham -34.2760524463 -466.349618217 + E_Harris -34.2760524463 -466.349618217 + E_band -7.91367756309 -107.671106993 + E_one_elec -68.7503398556 -935.396361472 + E_Hartree +35.766981462 +486.634748143 + E_xc -8.16552132509 -111.097617162 + E_Ewald +6.99819476271 +95.2153244866 + E_demet -1.58512916824e-61 -2.15667887541e-60 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193895692793 -2.63808623965 + E_Fermi -0.159764511836 -2.17370769916 + + charge density convergence is achieved + final etot is -466.349618217 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2011 2.00000 + 2 -12.3124 2.00000 + 3 -9.58972 2.00000 + 4 -6.73231 2.00000 + 5 0.993968 0.00000 + 6 3.93878 0.00000 + 7 11.1258 0.00000 + 8 11.4250 0.00000 + + EFERMI = -2.173707699160181 eV + OUT.ABACUS/ final etot is -466.3496182166348 eV + correction force for each atom along direction 1 is -8.65046e-05 + correction force for each atom along direction 2 is 0.000172606 + correction force for each atom along direction 3 is 3.57844e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.049618672 +1.6771136 +1.0203972 + H1 -0.0090405444 -0.79317193 -0.46511434 + H2 -0.040578128 -0.88394168 -0.55528289 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3496182166348 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2381 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2282 1 7.2 1.e+02% + Potential init_pot 0.28462 2 0.14 3.9% + PW_Basis recip2real 0.28699 16 0.018 4.0% + PW_Basis gathers_scatterp 0.11939 16 0.0075 1.6% + Potential v_of_rho 0.99722 13 0.077 14.% + XC_Functional v_xc 0.28549 14 0.020 3.9% + H_Hartree_pw v_hartree 0.66994 13 0.052 9.3% + PW_Basis real2recip 0.66399 38 0.017 9.2% + PW_Basis gatherp_scatters 0.25632 38 0.0067 3.5% + ORB_control set_orb_tables 1.0990 1 1.1 15.% + ORB_gen_tables gen_tables 1.0990 1 1.1 15.% + ORB_table_phi init_Table 0.47721 1 0.48 6.6% + ORB_table_phi cal_ST_Phi12_R 0.47202 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18445 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18290 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.25003 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24800 66 0.0038 3.4% + LOOP_ions opt_ions 5.6037 1 5.6 77.% + ESolver_KS_LCAO Run 5.0129 1 5.0 69.% + HSolverLCAO solve 2.7097 11 0.25 37.% + HamiltLCAO updateHk 1.3945 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.3604 11 0.12 19.% + Gint_interface cal_gint 2.5503 23 0.11 35.% + Gint_Gamma distri_vl 2.4006 6 0.40 33.% + LCAO_Deepks cal_projected_DM 5.4356 13 0.42 75.% + LCAO_gen_fixedH add_v_delta 2.2555 6 0.38 31.% + LCAO_DESCRIPTOR add_v_delta 2.2556 6 0.38 31.% + ElecStateLCAO psiToRho 1.2990 11 0.12 18.% + Charge mix_rho 0.78968 10 0.079 11.% + LOOP_ions force_stress 0.59060 1 0.59 8.2% + Force_Stress_LCAO getForceStress 0.59057 1 0.59 8.2% + Force_LCAO_gamma ftable_gamma 0.36216 1 0.36 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.35439 1 0.35 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:55 2022 + Finish Time : Wed Sep 28 11:02:02 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a1a081cc955a931120672a30c471ff26fee957c0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123579 ima = 3.68645e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122682891815 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111237117982 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112043888308 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112259562586 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112242226446 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112251074916 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112250290123 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112251771185 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112251331673 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112251239831 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112251222753 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4757f979e6726bb5c348c28e565ef47619722a8b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.576548221360 14.140166711433 5.691646856945 0 0 0 +H +0.0 +2 +-22.536348664310 14.562429780758 7.197461132497 0 0 0 +-24.421936121043 15.825578655665 5.626375436357 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/conv new file mode 100644 index 0000000000000000000000000000000000000000..c515675dda6ee26729fd036e5fd62f4e01bd0e46 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/conv @@ -0,0 +1 @@ +164 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ab4ecdf061c8889dd6b2e6e329af6ed35252e7e5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.757247783 0.01266461031 1.24915601 1.324520129 1.468880028 0.01000290019 0.01523183876 0.03930426395 +3.29507727e-18 0.0007095151535 0.002777800667 0.01323695651 0.04418001879 3.933581458e-20 2.679882813e-06 7.419014381e-06 +0.001582189994 0.006110964496 + +H atom_index 1 n_descriptor 18 +1.216564027 0.03633884104 0.1019656508 0.1347537859 0.307672302 0.02204842289 0.0262571465 0.03958142207 +-3.980750421e-17 4.179759622e-05 0.09351836728 0.1142534209 0.1150910253 4.919223664e-18 3.596073066e-06 0.01404726738 +0.02558271031 0.0290763049 + +H atom_index 2 n_descriptor 18 +1.210012502 0.03654232922 0.09981543207 0.1319664376 0.3051983353 0.02171510582 0.02586813056 0.03983888271 +4.163904415e-18 4.124748439e-05 0.091869919 0.1126498086 0.1139071287 2.375351982e-18 3.888614236e-06 0.01421545821 +0.02531347486 0.02873245292 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..57efec32bf59eb6650e1135088ba09b62bb12f37 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:55 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0873772 SEC) : SETUP UNITCELL + DONE(0.0970118 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115259 SEC) : INIT PLANEWAVE + DONE(0.166443 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446573 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651635e+02 0.000000e+00 2.095e-01 5.551e-01 + GE2 -4.663456e+02 -1.182131e+00 9.796e-02 5.041e-01 + GE3 -4.663513e+02 -5.686137e-03 6.320e-02 5.719e-01 + GE4 -4.663499e+02 1.431264e-03 1.851e-03 4.362e-01 + GE5 -4.663495e+02 4.044356e-04 9.408e-04 4.331e-01 + GE6 -4.663497e+02 -1.879518e-04 9.656e-05 4.340e-01 + GE7 -4.663496e+02 3.487500e-05 2.231e-05 4.106e-01 + GE8 -4.663496e+02 -1.095117e-05 9.217e-06 4.155e-01 + GE9 -4.663496e+02 1.018030e-05 2.328e-06 4.172e-01 + GE10 -4.663496e+02 -1.735177e-06 2.864e-07 4.193e-01 + GE11 -4.663496e+02 -4.381307e-07 5.105e-08 3.531e-01 +E_delta_band = -6.85282025e-02 Ry = -9.32374027e-01 eV +E_delta_NN= -1.93895693e-01 Ry = -2.63808624e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2381 11 0.66 1e+02 % + Run_lcao lcao_line 7.2282 1 7.2 1e+02 % + Potential init_pot 0.28462 2 0.14 3.9 % + PW_Basis recip2real 0.28699 16 0.018 4 % + PW_Basis gathers_scatterp 0.11939 16 0.0075 1.6 % + Potential v_of_rho 0.99722 13 0.077 14 % + XC_Functional v_xc 0.28549 14 0.02 3.9 % + H_Hartree_pw v_hartree 0.66994 13 0.052 9.3 % + PW_Basis real2recip 0.66399 38 0.017 9.2 % + PW_Basis gatherp_scatters 0.25632 38 0.0067 3.5 % + ORB_control set_orb_tables 1.099 1 1.1 15 % + ORB_gen_tables gen_tables 1.099 1 1.1 15 % + ORB_table_phi init_Table 0.47721 1 0.48 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.47202 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.18445 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.1829 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.25003 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.248 66 0.0038 3.4 % + LOOP_ions opt_ions 5.6037 1 5.6 77 % + ESolver_KS_LCAO Run 5.0129 1 5 69 % + HSolverLCAO solve 2.7097 11 0.25 37 % + HamiltLCAO updateHk 1.3945 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.3604 11 0.12 19 % + Gint_interface cal_gint 2.5503 23 0.11 35 % + Gint_Gamma distri_vl 2.4006 6 0.4 33 % + LCAO_Deepks cal_projected_DM 5.4356 13 0.42 75 % + LCAO_gen_fixedH add_v_delta 2.2555 6 0.38 31 % + LCAO_DESCRIPTOR add_v_delta 2.2556 6 0.38 31 % + ElecStateLCAO psiToRho 1.299 11 0.12 18 % + Charge mix_rho 0.78968 10 0.079 11 % + LOOP_ions force_stress 0.5906 1 0.59 8.2 % + Force_Stress_LCAO getForceStress 0.59057 1 0.59 8.2 % + Force_LCAO_gamma ftable_gamma 0.36216 1 0.36 5 % + Force_LCAO_gamma cal_fvl_dphi 0.35439 1 0.35 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:55 2022 + FINISH Time : Wed Sep 28 11:02:02 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/164/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..aa58f43cc374fb159c80769a927741ad42eff0f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.172146 0.500962 0.204936 +H 0.194401 0.483862 0.263222 +H 0.111043 0.52374 0.206084 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d0f7e4d5469a2894d3bfc59dbc9800ed3ded7aea --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1934 2 + 2 -13.5543 2 + 3 -8.65971 2 + 4 -6.71786 2 + 5 1.3886 0 + 6 4.60876 0 + 7 11.0712 0 + 8 11.2748 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c0a13f23721761c7c34972ed9f11af76d776c742 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:09 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.82007472172 14.0269425082 5.73819814487 0 0 0 0 + tauc_H1 5.44322153016 13.5481233142 7.37021292453 0 0 0 0 + tauc_H2 3.10920379981 14.6647064391 5.77035826448 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0893392772804 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0897687894364 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.108899013016 (SEC) + + DONE : INIT CHARGE Time : 0.158638721566 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.442458 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000932 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00176 + + Density error is 0.218362546546 + + Energy Rydberg eV + E_KohnSham -34.1849636518 -465.110291587 + E_Harris -34.3835038832 -467.811570017 + E_Fermi -0.409151333307 -5.56678947727 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00128157760231 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00144576057546 + + Density error is 0.098252709047 + + Energy Rydberg eV + E_KohnSham -34.276999599 -466.36250489 + E_Harris -34.2835951794 -466.452242366 + E_Fermi -0.214695778742 -2.92108592744 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00123016566922 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133256889455 + + Density error is 0.0629322695388 + + Energy Rydberg eV + E_KohnSham -34.2773417413 -466.367159974 + E_Harris -34.2815593777 -466.424543862 + E_Fermi -0.202685246176 -2.75767424853 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115546613394 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113355641634 + + Density error is 0.00218852333669 + + Energy Rydberg eV + E_KohnSham -34.2773514565 -466.367292158 + E_Harris -34.2773567357 -466.367363984 + E_Fermi -0.167533613166 -2.27941174559 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.001155675455 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113007072291 + + Density error is 0.000917214584312 + + Energy Rydberg eV + E_KohnSham -34.2772878657 -466.366426959 + E_Harris -34.2772889021 -466.366441061 + E_Fermi -0.166548563679 -2.26600945975 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115454639784 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112792392735 + + Density error is 0.000228230409989 + + Energy Rydberg eV + E_KohnSham -34.2773263587 -466.366950684 + E_Harris -34.2773264828 -466.366952373 + E_Fermi -0.166615894925 -2.26692554835 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115486778063 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112766024473 + + Density error is 4.35088597376e-05 + + Energy Rydberg eV + E_KohnSham -34.2773109268 -466.366740722 + E_Harris -34.2773109373 -466.366740865 + E_Fermi -0.16642361263 -2.26430941351 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115477737276 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112766958533 + + Density error is 2.00016772024e-05 + + Energy Rydberg eV + E_KohnSham -34.2773169977 -466.366823321 + E_Harris -34.2773169994 -466.366823344 + E_Fermi -0.166475688692 -2.26501794468 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115477000838 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112762638484 + + Density error is 1.52456803613e-06 + + Energy Rydberg eV + E_KohnSham -34.2773153926 -466.366801482 + E_Harris -34.2773153926 -466.366801482 + E_Fermi -0.166453913246 -2.26472167454 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115477053023 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112762224401 + + Density error is 1.79786503729e-07 + + Energy Rydberg eV + E_KohnSham -34.2773156835 -466.366805441 + E_Harris -34.2773156835 -466.366805441 + E_Fermi -0.166452490426 -2.26470231608 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115477120901 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112762270329 + + Density error is 3.11779514108e-08 + + Energy Rydberg eV + E_KohnSham -34.2773157037 -466.366805715 + E_Harris -34.2773157037 -466.366805715 + E_band -7.95626248485 -108.250504578 + E_one_elec -69.4327320946 -944.680784194 + E_Hartree +36.1245080192 +491.499146507 + E_xc -8.22251804458 -111.873097314 + E_Ewald +7.37754744867 +100.376682567 + E_demet -5.9133154007e-81 -8.04547835207e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194790051605 -2.65025461554 + E_Fermi -0.166452433998 -2.26470154835 + + charge density convergence is achieved + final etot is -466.366805715 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1934 2.00000 + 2 -13.5543 2.00000 + 3 -8.65971 2.00000 + 4 -6.71786 2.00000 + 5 1.38860 0.00000 + 6 4.60876 0.00000 + 7 11.0712 0.00000 + 8 11.2748 0.00000 + + EFERMI = -2.264701548348085 eV + OUT.ABACUS/ final etot is -466.3668057147171 eV + correction force for each atom along direction 1 is -5.65172e-05 + correction force for each atom along direction 2 is -9.63466e-05 + correction force for each atom along direction 3 is 1.23368e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.54712958 +0.0091308069 -1.4698313 + H1 -0.32179058 -0.0035621845 +0.84861300 + H2 -0.22533900 -0.0055686224 +0.62121833 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3668057147171 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1073 11 0.65 1.0e+02% + Run_lcao lcao_line 7.0982 1 7.1 1.e+02% + Potential init_pot 0.28435 2 0.14 4.0% + PW_Basis recip2real 0.28895 16 0.018 4.1% + PW_Basis gathers_scatterp 0.12330 16 0.0077 1.7% + Potential v_of_rho 1.0077 13 0.078 14.% + XC_Functional v_xc 0.29658 14 0.021 4.2% + H_Hartree_pw v_hartree 0.67005 13 0.052 9.4% + PW_Basis real2recip 0.64552 38 0.017 9.1% + PW_Basis gatherp_scatters 0.24682 38 0.0065 3.5% + ORB_control set_orb_tables 1.1034 1 1.1 16.% + ORB_gen_tables gen_tables 1.1034 1 1.1 16.% + ORB_table_phi init_Table 0.47917 1 0.48 6.7% + ORB_table_phi cal_ST_Phi12_R 0.47400 126 0.0038 6.7% + ORB_table_beta init_Table_Beta 0.18669 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18510 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.25070 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24876 66 0.0038 3.5% + LOOP_ions opt_ions 5.4725 1 5.5 77.% + ESolver_KS_LCAO Run 4.8994 1 4.9 69.% + HSolverLCAO solve 2.6111 11 0.24 37.% + HamiltLCAO updateHk 1.3549 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.3217 11 0.12 19.% + Gint_interface cal_gint 2.4478 23 0.11 34.% + Gint_Gamma distri_vl 2.3626 6 0.39 33.% + LCAO_Deepks cal_projected_DM 5.3069 13 0.41 75.% + LCAO_gen_fixedH add_v_delta 2.2179 6 0.37 31.% + LCAO_DESCRIPTOR add_v_delta 2.2178 6 0.37 31.% + ElecStateLCAO psiToRho 1.2403 11 0.11 17.% + Charge mix_rho 0.77918 10 0.078 11.% + LOOP_ions force_stress 0.57285 1 0.57 8.1% + Force_Stress_LCAO getForceStress 0.57282 1 0.57 8.1% + Force_LCAO_gamma ftable_gamma 0.35359 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.34577 1 0.35 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:09 2022 + Finish Time : Wed Sep 28 11:14:17 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..af7b35237eb38206037a9e880fafe4067a9a8ab4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123469 ima = 3.68834e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124072317004 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113188223194 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113652817342 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113893334784 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113843063959 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113873765956 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113862655136 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113865856388 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113865051633 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113864996658 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113864986231 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9e38fe6004342517095b20ad5b7aceff4f3e0030 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.179925278291 14.026942508154 5.738198144854 0 0 0 +H +0.0 +2 +-22.556778469821 13.548123314184 7.370212924550 0 0 0 +-24.890796200200 14.664706439093 5.770358264467 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/conv new file mode 100644 index 0000000000000000000000000000000000000000..28406643c0f3bb06e6c6285cae395598d348232f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/conv @@ -0,0 +1 @@ +165 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a5855a6ed2ba04e594518af00de0f9a020454c2e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.740572965 0.01259281288 1.286623548 1.380068672 1.469012718 0.007278069844 0.02152408073 0.03876986766 +1.389904992e-19 0.001198536725 0.002250293572 0.0126757162 0.04126506816 2.176609977e-19 1.308881382e-06 4.30103296e-06 +0.001889151997 0.005398370567 + +H atom_index 1 n_descriptor 18 +1.25350636 0.03313835464 0.1111049532 0.1542391147 0.325583843 0.02194459861 0.02884701731 0.0363978919 +-2.192077851e-17 3.468423447e-05 0.1038095162 0.1150377714 0.1324493084 -3.607944209e-19 3.743323386e-06 0.01269546376 +0.02630588084 0.03113521166 + +H atom_index 2 n_descriptor 18 +1.24159148 0.03356806541 0.1070116802 0.148732403 0.3219818128 0.02144850729 0.02816557457 0.03674837518 +2.189023525e-17 3.381437976e-05 0.1009581539 0.1144875081 0.1276995183 -3.716882525e-18 4.232280111e-06 0.01275761548 +0.02586896595 0.03061596329 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..32bd4117ca90b2cfce6471cfd3d7eb8c7b36089d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:09 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0893701 SEC) : SETUP UNITCELL + DONE(0.0897889 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.10892 SEC) : INIT PLANEWAVE + DONE(0.158773 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44252 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651103e+02 0.000000e+00 2.184e-01 5.483e-01 + GE2 -4.663625e+02 -1.252213e+00 9.825e-02 4.954e-01 + GE3 -4.663672e+02 -4.655084e-03 6.293e-02 5.610e-01 + GE4 -4.663673e+02 -1.321832e-04 2.189e-03 4.260e-01 + GE5 -4.663664e+02 8.651983e-04 9.172e-04 4.259e-01 + GE6 -4.663670e+02 -5.237246e-04 2.282e-04 4.196e-01 + GE7 -4.663667e+02 2.099624e-04 4.351e-05 4.154e-01 + GE8 -4.663668e+02 -8.259913e-05 2.000e-05 4.041e-01 + GE9 -4.663668e+02 2.183828e-05 1.525e-06 4.024e-01 + GE10 -4.663668e+02 -3.958135e-06 1.798e-07 4.034e-01 + GE11 -4.663668e+02 -2.741835e-07 3.118e-08 3.357e-01 +E_delta_band = -7.06690192e-02 Ry = -9.61501334e-01 eV +E_delta_NN= -1.94790052e-01 Ry = -2.65025462e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1073 11 0.65 1e+02 % + Run_lcao lcao_line 7.0982 1 7.1 1e+02 % + Potential init_pot 0.28435 2 0.14 4 % + PW_Basis recip2real 0.28895 16 0.018 4.1 % + PW_Basis gathers_scatterp 0.1233 16 0.0077 1.7 % + Potential v_of_rho 1.0077 13 0.078 14 % + XC_Functional v_xc 0.29658 14 0.021 4.2 % + H_Hartree_pw v_hartree 0.67005 13 0.052 9.4 % + PW_Basis real2recip 0.64552 38 0.017 9.1 % + PW_Basis gatherp_scatters 0.24682 38 0.0065 3.5 % + ORB_control set_orb_tables 1.1034 1 1.1 16 % + ORB_gen_tables gen_tables 1.1034 1 1.1 16 % + ORB_table_phi init_Table 0.47917 1 0.48 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.474 126 0.0038 6.7 % + ORB_table_beta init_Table_Beta 0.18669 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.1851 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.2507 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24876 66 0.0038 3.5 % + LOOP_ions opt_ions 5.4725 1 5.5 77 % + ESolver_KS_LCAO Run 4.8994 1 4.9 69 % + HSolverLCAO solve 2.6111 11 0.24 37 % + HamiltLCAO updateHk 1.3549 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.3217 11 0.12 19 % + Gint_interface cal_gint 2.4478 23 0.11 34 % + Gint_Gamma distri_vl 2.3626 6 0.39 33 % + LCAO_Deepks cal_projected_DM 5.3069 13 0.41 75 % + LCAO_gen_fixedH add_v_delta 2.2179 6 0.37 31 % + LCAO_DESCRIPTOR add_v_delta 2.2178 6 0.37 31 % + ElecStateLCAO psiToRho 1.2403 11 0.11 17 % + Charge mix_rho 0.77918 10 0.078 11 % + LOOP_ions force_stress 0.57285 1 0.57 8.1 % + Force_Stress_LCAO getForceStress 0.57282 1 0.57 8.1 % + Force_LCAO_gamma ftable_gamma 0.35359 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.34577 1 0.35 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:09 2022 + FINISH Time : Wed Sep 28 11:14:17 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/165/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..64cb3cef5dd69f5f32a653eaf234ad17f08d0fe0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.190336 0.500976 0.208362 +H 0.225943 0.463131 0.24973 +H 0.132181 0.488398 0.238517 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..fb75d040f6edf00d7a5fb0da1b753b0eb7dca37e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3106 2 + 2 -12.4072 2 + 3 -9.59515 2 + 4 -6.75452 2 + 5 1.08712 0 + 6 4.10962 0 + 7 11.101 0 + 8 11.403 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..70dde41a49bbe432658d408f8f3dce50cb968424 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:45 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.32940132391 14.0273225793 5.83414654524 0 0 0 0 + tauc_H1 6.32641180359 12.9676604587 6.99244824766 0 0 0 0 + tauc_H2 3.70107299209 13.6751511253 6.67848038628 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.104735230336 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105127803252 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123181125199 (SEC) + + DONE : INIT CHARGE Time : 0.166491778673 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449511 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 337 ; sender_size of each process is: +144 144 0 49 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000665 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00161 + + Density error is 0.211460681435 + + Energy Rydberg eV + E_KohnSham -34.1874250969 -465.143781266 + E_Harris -34.3732692822 -467.672321126 + E_Fermi -0.396345870403 -5.39256221624 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000770523459209 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013759158873 + + Density error is 0.0979212833776 + + Energy Rydberg eV + E_KohnSham -34.2764858717 -466.355515271 + E_Harris -34.2836474195 -466.452953128 + E_Fermi -0.207476810173 -2.82286682122 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000781825190827 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012709585809 + + Density error is 0.0631443782079 + + Energy Rydberg eV + E_KohnSham -34.2769801368 -466.362240094 + E_Harris -34.2815910289 -466.424974498 + E_Fermi -0.199995614705 -2.721079935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000813503607159 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107503218354 + + Density error is 0.00187023865578 + + Energy Rydberg eV + E_KohnSham -34.276897751 -466.361119177 + E_Harris -34.2768973745 -466.361114055 + E_Fermi -0.164209571555 -2.23418583929 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000813759936765 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107610713442 + + Density error is 0.00109552238939 + + Energy Rydberg eV + E_KohnSham -34.2768450159 -466.360401679 + E_Harris -34.2768463722 -466.360420133 + E_Fermi -0.164221714753 -2.23435105598 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000814058785958 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107292361125 + + Density error is 0.000103918308122 + + Energy Rydberg eV + E_KohnSham -34.2768749327 -466.360808718 + E_Harris -34.276874941 -466.360808831 + E_Fermi -0.163872859844 -2.22960464144 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000813982968545 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107245985196 + + Density error is 3.22035280967e-05 + + Energy Rydberg eV + E_KohnSham -34.2768670032 -466.360700832 + E_Harris -34.2768670084 -466.360700903 + E_Fermi -0.163766534822 -2.22815801529 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000814005016708 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107249938969 + + Density error is 1.11997300813e-05 + + Energy Rydberg eV + E_KohnSham -34.2768678839 -466.360712814 + E_Harris -34.2768678845 -466.360712822 + E_Fermi -0.163805595788 -2.228689467 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000814020613249 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107249653814 + + Density error is 2.29535494924e-06 + + Energy Rydberg eV + E_KohnSham -34.276866856 -466.360698829 + E_Harris -34.276866856 -466.36069883 + E_Fermi -0.163796806178 -2.22856987822 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000814020941223 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107249243144 + + Density error is 4.52936648658e-07 + + Energy Rydberg eV + E_KohnSham -34.2768670292 -466.360701185 + E_Harris -34.2768670292 -466.360701185 + E_Fermi -0.163794780251 -2.22854231407 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00081402130504 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107249264721 + + Density error is 8.64226456074e-08 + + Energy Rydberg eV + E_KohnSham -34.2768670579 -466.360701576 + E_Harris -34.2768670579 -466.360701576 + E_band -7.94777288049 -108.134997585 + E_one_elec -68.9754902432 -938.459689651 + E_Hartree +35.873763623 +488.087593979 + E_xc -8.18258131591 -111.329730245 + E_Ewald +7.13235239229 +97.0406326791 + E_demet -3.74063712373e-67 -5.0893979033e-66 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194279901092 -2.64331366173 + E_Fermi -0.16379449966 -2.22853849644 + + charge density convergence is achieved + final etot is -466.360701576 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3106 2.00000 + 2 -12.4072 2.00000 + 3 -9.59515 2.00000 + 4 -6.75452 2.00000 + 5 1.08712 0.00000 + 6 4.10962 0.00000 + 7 11.1010 0.00000 + 8 11.4030 0.00000 + + EFERMI = -2.228538496437905 eV + OUT.ABACUS/ final etot is -466.3607015764818 eV + correction force for each atom along direction 1 is -7.72147e-05 + correction force for each atom along direction 2 is -0.000118232 + correction force for each atom along direction 3 is 0.000194652 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.48990006 -0.75116117 +1.1024136 + H1 +0.56635562 +0.24782217 -0.45872482 + H2 -0.076455566 +0.50333899 -0.64368877 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3607015764818 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1310 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1219 1 7.1 1.e+02% + Potential init_pot 0.28386 2 0.14 4.0% + PW_Basis recip2real 0.28856 16 0.018 4.0% + PW_Basis gathers_scatterp 0.12440 16 0.0078 1.7% + Potential v_of_rho 1.0124 13 0.078 14.% + XC_Functional v_xc 0.28668 14 0.020 4.0% + H_Hartree_pw v_hartree 0.68098 13 0.052 9.5% + PW_Basis real2recip 0.70394 38 0.019 9.9% + PW_Basis gatherp_scatters 0.27106 38 0.0071 3.8% + ORB_control set_orb_tables 1.0996 1 1.1 15.% + ORB_gen_tables gen_tables 1.0995 1 1.1 15.% + ORB_table_phi init_Table 0.47562 1 0.48 6.7% + ORB_table_phi cal_ST_Phi12_R 0.47043 126 0.0037 6.6% + ORB_table_beta init_Table_Beta 0.18350 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18195 56 0.0032 2.6% + ORB_table_alpha init_Table_Alpha 0.25064 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24864 66 0.0038 3.5% + LOOP_ions opt_ions 5.4969 1 5.5 77.% + ESolver_KS_LCAO Run 4.9322 1 4.9 69.% + HSolverLCAO solve 2.4728 11 0.22 35.% + HamiltLCAO updateHk 1.2987 11 0.12 18.% + LCAO_Hamilt cal_Hgamma 1.2711 11 0.12 18.% + Gint_interface cal_gint 2.2876 23 0.099 32.% + Gint_Gamma distri_vl 2.3747 6 0.40 33.% + LCAO_Deepks cal_projected_DM 5.3377 13 0.41 75.% + LCAO_gen_fixedH add_v_delta 2.2265 6 0.37 31.% + LCAO_DESCRIPTOR add_v_delta 2.2265 6 0.37 31.% + ElecStateLCAO psiToRho 1.1566 11 0.11 16.% + Charge mix_rho 0.90516 10 0.091 13.% + LOOP_ions force_stress 0.56452 1 0.56 7.9% + Force_Stress_LCAO getForceStress 0.56449 1 0.56 7.9% + Force_LCAO_gamma ftable_gamma 0.34584 1 0.35 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.33766 1 0.34 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:45 2022 + Finish Time : Wed Sep 28 11:02:52 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a356c5e54a44053438a3343ec2da6e5785cc180d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123721 ima = 3.67993e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122705449875 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111132597526 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111916018617 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112169275434 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112125208567 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011214844371 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112148098178 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112150208213 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112149655737 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112149563902 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011214953973 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/STRU new file mode 100644 index 0000000000000000000000000000000000000000..baa7c0c41d90afe892da6a7e37ef1c8e6ddb2015 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.670598676090 14.027322579321 5.834146545224 0 0 0 +H +0.0 +2 +-21.673588196401 12.967660458714 6.992448247662 0 0 0 +-24.298927007920 13.675151125308 6.678480386288 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/conv new file mode 100644 index 0000000000000000000000000000000000000000..145fe01fca993f69d4f0c84fedbf8073df53a1fa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/conv @@ -0,0 +1 @@ +166 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4a80cff847b282954f82825edc83f5b41675e10e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.756900326 0.01275408049 1.257705014 1.333417722 1.469273235 0.01000511383 0.01545202621 0.0392710121 +8.290960028e-18 0.0007519818527 0.002857860431 0.01355947128 0.04546127722 -8.948903088e-19 2.898789875e-06 7.80360066e-06 +0.001591989193 0.006158584019 + +H atom_index 1 n_descriptor 18 +1.230797823 0.03588469896 0.1068938776 0.140929521 0.3126821713 0.02284140953 0.02709830264 0.03902469318 +4.076401505e-17 4.500222893e-05 0.09817401306 0.1147763987 0.1205484955 -9.289632247e-18 3.028537922e-06 0.01375116121 +0.02640853413 0.02981188463 + +H atom_index 2 n_descriptor 18 +1.224566634 0.03608638963 0.1047637063 0.1381782421 0.3104274122 0.02252230789 0.02672883218 0.0392576311 +2.86267981e-17 4.44630886e-05 0.09663878765 0.1144407975 0.1181524564 -1.107119858e-18 3.335078034e-06 0.01387547782 +0.02616128365 0.0294985903 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..76d4517a7e50ac9a7d63e5f439a0e2fb3fde5b38 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:45 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.104788 SEC) : SETUP UNITCELL + DONE(0.105143 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123201 SEC) : INIT PLANEWAVE + DONE(0.166629 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449574 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651438e+02 0.000000e+00 2.115e-01 5.408e-01 + GE2 -4.663555e+02 -1.211734e+00 9.792e-02 5.048e-01 + GE3 -4.663622e+02 -6.724822e-03 6.314e-02 5.738e-01 + GE4 -4.663611e+02 1.120917e-03 1.870e-03 4.329e-01 + GE5 -4.663604e+02 7.174980e-04 1.096e-03 4.299e-01 + GE6 -4.663608e+02 -4.070392e-04 1.039e-04 4.116e-01 + GE7 -4.663607e+02 1.078861e-04 3.220e-05 4.085e-01 + GE8 -4.663607e+02 -1.198264e-05 1.120e-05 4.096e-01 + GE9 -4.663607e+02 1.398516e-05 2.295e-06 4.113e-01 + GE10 -4.663607e+02 -2.355942e-06 4.529e-07 4.096e-01 + GE11 -4.663607e+02 -3.911996e-07 8.642e-08 3.372e-01 +E_delta_band = -6.93683869e-02 Ry = -9.43805323e-01 eV +E_delta_NN= -1.94279901e-01 Ry = -2.64331366e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.131 11 0.65 1e+02 % + Run_lcao lcao_line 7.1219 1 7.1 1e+02 % + Potential init_pot 0.28386 2 0.14 4 % + PW_Basis recip2real 0.28856 16 0.018 4 % + PW_Basis gathers_scatterp 0.1244 16 0.0078 1.7 % + Potential v_of_rho 1.0124 13 0.078 14 % + XC_Functional v_xc 0.28668 14 0.02 4 % + H_Hartree_pw v_hartree 0.68098 13 0.052 9.5 % + PW_Basis real2recip 0.70394 38 0.019 9.9 % + PW_Basis gatherp_scatters 0.27106 38 0.0071 3.8 % + ORB_control set_orb_tables 1.0996 1 1.1 15 % + ORB_gen_tables gen_tables 1.0995 1 1.1 15 % + ORB_table_phi init_Table 0.47562 1 0.48 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.47043 126 0.0037 6.6 % + ORB_table_beta init_Table_Beta 0.1835 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18195 56 0.0032 2.6 % + ORB_table_alpha init_Table_Alpha 0.25064 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24864 66 0.0038 3.5 % + LOOP_ions opt_ions 5.4969 1 5.5 77 % + ESolver_KS_LCAO Run 4.9322 1 4.9 69 % + HSolverLCAO solve 2.4728 11 0.22 35 % + HamiltLCAO updateHk 1.2987 11 0.12 18 % + LCAO_Hamilt cal_Hgamma 1.2711 11 0.12 18 % + Gint_interface cal_gint 2.2876 23 0.099 32 % + Gint_Gamma distri_vl 2.3747 6 0.4 33 % + LCAO_Deepks cal_projected_DM 5.3377 13 0.41 75 % + LCAO_gen_fixedH add_v_delta 2.2265 6 0.37 31 % + LCAO_DESCRIPTOR add_v_delta 2.2265 6 0.37 31 % + ElecStateLCAO psiToRho 1.1566 11 0.11 16 % + Charge mix_rho 0.90516 10 0.091 13 % + LOOP_ions force_stress 0.56452 1 0.56 7.9 % + Force_Stress_LCAO getForceStress 0.56449 1 0.56 7.9 % + Force_LCAO_gamma ftable_gamma 0.34584 1 0.35 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.33766 1 0.34 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:45 2022 + FINISH Time : Wed Sep 28 11:02:52 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/166/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..34bf8f9632515b6af6a1fc4d88f7025d26291797 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.195596 0.503158 0.205416 +H 0.221885 0.447424 0.230392 +H 0.145675 0.523312 0.241139 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..dd32fa3e0fd2855bf1645a8a5c4dac73bc9c2e3a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.145 2 + 2 -13.357 2 + 3 -8.76396 2 + 4 -6.70706 2 + 5 1.29392 0 + 6 4.45908 0 + 7 11.0905 0 + 8 11.3072 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1cf6f6f6f7673518e4f651df69d09ed862b5ddd5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:01 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.47668361874 14.0884138144 5.75164698459 0 0 0 0 + tauc_H1 6.21276876179 12.527871616 6.45096429507 0 0 0 0 + tauc_H2 4.07888617749 14.6527332343 6.75188585936 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0865907612407 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0998659122182 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118348441212 (SEC) + + DONE : INIT CHARGE Time : 0.16843003998 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449687 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 337 ; sender_size of each process is: +144 144 0 49 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000357 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00152 + + Density error is 0.216005346833 + + Energy Rydberg eV + E_KohnSham -34.1887111164 -465.161278459 + E_Harris -34.3822024202 -467.793862704 + E_Fermi -0.403126793697 -5.48482141075 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000529955270886 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00140778406839 + + Density error is 0.0982662200225 + + Energy Rydberg eV + E_KohnSham -34.2783973381 -466.381522106 + E_Harris -34.2850602865 -466.47217617 + E_Fermi -0.211173311879 -2.87316030708 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00057994780338 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131260592 + + Density error is 0.0629759346163 + + Energy Rydberg eV + E_KohnSham -34.2786412263 -466.384840375 + E_Harris -34.2829139687 -466.442974018 + E_Fermi -0.19973668341 -2.71755699399 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000677778120476 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115000291184 + + Density error is 0.00213070647562 + + Energy Rydberg eV + E_KohnSham -34.2786357381 -466.384765705 + E_Harris -34.2786399765 -466.384823371 + E_Fermi -0.164614444905 -2.23969442381 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000672279284529 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114819865184 + + Density error is 0.000856173511181 + + Energy Rydberg eV + E_KohnSham -34.2785847265 -466.384071656 + E_Harris -34.2785854238 -466.384081143 + E_Fermi -0.163788697408 -2.22845955274 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000673444755248 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114629188747 + + Density error is 0.000212195867927 + + Energy Rydberg eV + E_KohnSham -34.2786168214 -466.38450833 + E_Harris -34.27861692 -466.384509671 + E_Fermi -0.163767940944 -2.22817714656 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000673585052391 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114626605902 + + Density error is 3.79587332436e-05 + + Energy Rydberg eV + E_KohnSham -34.2786038145 -466.384331362 + E_Harris -34.2786038218 -466.384331461 + E_Fermi -0.163614386314 -2.22608792864 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000673529268284 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114624569497 + + Density error is 1.8638865949e-05 + + Energy Rydberg eV + E_KohnSham -34.2786092303 -466.384405048 + E_Harris -34.2786092318 -466.384405068 + E_Fermi -0.163656372683 -2.2266591825 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00067353006141 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114622365541 + + Density error is 2.64146063393e-06 + + Energy Rydberg eV + E_KohnSham -34.2786077698 -466.384385176 + E_Harris -34.2786077698 -466.384385177 + E_Fermi -0.163637680137 -2.22640485736 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000673530313853 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114621498356 + + Density error is 4.9929648644e-07 + + Energy Rydberg eV + E_KohnSham -34.2786080456 -466.384388929 + E_Harris -34.2786080456 -466.384388929 + E_Fermi -0.163635132484 -2.22637019477 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00067353118963 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114621535501 + + Density error is 1.85134627128e-07 + + Energy Rydberg eV + E_KohnSham -34.2786080678 -466.384389231 + E_Harris -34.2786080678 -466.384389231 + E_Fermi -0.163634922797 -2.22636734183 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000673531421476 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114621520212 + + Density error is 9.61908757304e-09 + + Energy Rydberg eV + E_KohnSham -34.2786080701 -466.384389263 + E_Harris -34.2786080701 -466.384389263 + E_band -7.93389316751 -107.946154401 + E_one_elec -69.2396048998 -942.053153905 + E_Hartree +36.0291754877 +490.202080875 + E_xc -8.20743386074 -111.667866464 + E_Ewald +7.26375520114 +98.8284596127 + E_demet -2.33593092274e-75 -3.17819706837e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194528759306 -2.64669955143 + E_Fermi -0.163634740797 -2.22636486559 + + charge density convergence is achieved + final etot is -466.384389263 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1450 2.00000 + 2 -13.3570 2.00000 + 3 -8.76396 2.00000 + 4 -6.70706 2.00000 + 5 1.29392 0.00000 + 6 4.45908 0.00000 + 7 11.0905 0.00000 + 8 11.3072 0.00000 + + EFERMI = -2.226364865592311 eV + OUT.ABACUS/ final etot is -466.3843892627266 eV + correction force for each atom along direction 1 is -4.56194e-05 + correction force for each atom along direction 2 is -0.000107999 + correction force for each atom along direction 3 is 9.08176e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.1385516 -0.42429906 -0.85654524 + H1 -0.58239223 +0.55628500 +0.10855520 + H2 -0.55615934 -0.13198593 +0.74799004 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3843892627266 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6508 11 0.70 1.0e+02% + Run_lcao lcao_line 7.6414 1 7.6 1.e+02% + Potential init_pot 0.28246 2 0.14 3.7% + PW_Basis recip2real 0.30059 17 0.018 3.9% + PW_Basis gathers_scatterp 0.13031 17 0.0077 1.7% + Potential v_of_rho 1.0543 14 0.075 14.% + XC_Functional v_xc 0.29921 15 0.020 3.9% + H_Hartree_pw v_hartree 0.70887 14 0.051 9.3% + PW_Basis real2recip 0.70532 41 0.017 9.2% + PW_Basis gatherp_scatters 0.27130 41 0.0066 3.5% + ORB_control set_orb_tables 1.1087 1 1.1 14.% + ORB_gen_tables gen_tables 1.1087 1 1.1 14.% + ORB_table_phi init_Table 0.48372 1 0.48 6.3% + ORB_table_phi cal_ST_Phi12_R 0.47829 126 0.0038 6.3% + ORB_table_beta init_Table_Beta 0.18696 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18533 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.25199 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24995 66 0.0038 3.3% + LOOP_ions opt_ions 6.0029 1 6.0 78.% + ESolver_KS_LCAO Run 5.4383 1 5.4 71.% + HSolverLCAO solve 2.9797 12 0.25 39.% + HamiltLCAO updateHk 1.5182 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4887 12 0.12 19.% + Gint_interface cal_gint 2.8029 25 0.11 37.% + Gint_Gamma distri_vl 2.8338 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.8315 14 0.42 76.% + LCAO_gen_fixedH add_v_delta 2.6883 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.6883 6 0.45 35.% + ElecStateLCAO psiToRho 1.4436 12 0.12 19.% + Charge mix_rho 0.85373 11 0.078 11.% + LOOP_ions force_stress 0.56445 1 0.56 7.4% + Force_Stress_LCAO getForceStress 0.56442 1 0.56 7.4% + Force_LCAO_gamma ftable_gamma 0.34976 1 0.35 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.34184 1 0.34 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:01 2022 + Finish Time : Wed Sep 28 11:14:09 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6a217bf181d3693fff2511c011d22a9a0eb40e0e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123604 ima = 3.69174e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123772558988 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112926125463 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113417919411 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011363479955 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113594297425 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113620345313 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113610311992 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113613189635 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113612400023 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113612331621 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113612316183 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113612306953 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d105aff0ffb18905d5324e39efb4eabd2d4a438a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.523316381253 14.088413814417 5.751646984587 0 0 0 +H +0.0 +2 +-21.787231238200 12.527871615965 6.450964295052 0 0 0 +-23.921113822518 14.652733234335 6.751885859348 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/conv new file mode 100644 index 0000000000000000000000000000000000000000..1662137751fd30dc91f891638b99e9c4b1f73528 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/conv @@ -0,0 +1 @@ +167 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e9d1f7296d57b2c9fc0106fc6eccb0ff38c0f9ce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.7430087 0.01255382824 1.275191564 1.371558703 1.468721802 0.007528513615 0.02060406461 0.03884158639 +-1.202451665e-17 0.001136594226 0.002302839211 0.0122216838 0.04171677268 2.828279992e-20 1.384228221e-06 4.499844445e-06 +0.001808735946 0.005552715917 + +H atom_index 1 n_descriptor 18 +1.21607539 0.03474665851 0.09755819548 0.1367488805 0.3127151685 0.02028452806 0.0265948025 0.0379660688 +-1.21779925e-17 3.382404259e-05 0.0929188355 0.1139679859 0.117222787 9.655020015e-19 5.364265457e-06 0.01329352289 +0.02467890166 0.02932499754 + +H atom_index 2 n_descriptor 18 +1.258282918 0.03324901233 0.1115851351 0.1557350431 0.3262357708 0.02210598689 0.0290293554 0.03654921889 +-3.913664507e-17 3.706290833e-05 0.103738577 0.1153117257 0.1336837694 -2.742283371e-19 3.6688979e-06 0.01280464734 +0.02628110117 0.03126808357 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a7cb37a63983a520901cd32e8e5bc636d596d9f3 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:01 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0866132 SEC) : SETUP UNITCELL + DONE(0.0998854 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118368 SEC) : INIT PLANEWAVE + DONE(0.168565 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449751 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651613e+02 0.000000e+00 2.160e-01 5.554e-01 + GE2 -4.663815e+02 -1.220244e+00 9.827e-02 5.057e-01 + GE3 -4.663848e+02 -3.318269e-03 6.298e-02 5.747e-01 + GE4 -4.663848e+02 7.467041e-05 2.131e-03 4.373e-01 + GE5 -4.663841e+02 6.940493e-04 8.562e-04 4.376e-01 + GE6 -4.663845e+02 -4.366740e-04 2.122e-04 4.305e-01 + GE7 -4.663843e+02 1.769682e-04 3.796e-05 4.217e-01 + GE8 -4.663844e+02 -7.368629e-05 1.864e-05 4.150e-01 + GE9 -4.663844e+02 1.987158e-05 2.641e-06 4.176e-01 + GE10 -4.663844e+02 -3.752729e-06 4.993e-07 4.154e-01 + GE11 -4.663844e+02 -3.019728e-07 1.851e-07 4.171e-01 + GE12 -4.663844e+02 -3.177588e-08 9.619e-09 3.475e-01 +E_delta_band = -7.00287608e-02 Ry = -9.52790170e-01 eV +E_delta_NN= -1.94528759e-01 Ry = -2.64669955e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6508 11 0.7 1e+02 % + Run_lcao lcao_line 7.6414 1 7.6 1e+02 % + Potential init_pot 0.28246 2 0.14 3.7 % + PW_Basis recip2real 0.30059 17 0.018 3.9 % + PW_Basis gathers_scatterp 0.13031 17 0.0077 1.7 % + Potential v_of_rho 1.0543 14 0.075 14 % + XC_Functional v_xc 0.29921 15 0.02 3.9 % + H_Hartree_pw v_hartree 0.70887 14 0.051 9.3 % + PW_Basis real2recip 0.70532 41 0.017 9.2 % + PW_Basis gatherp_scatters 0.2713 41 0.0066 3.5 % + ORB_control set_orb_tables 1.1087 1 1.1 14 % + ORB_gen_tables gen_tables 1.1087 1 1.1 14 % + ORB_table_phi init_Table 0.48372 1 0.48 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.47829 126 0.0038 6.3 % + ORB_table_beta init_Table_Beta 0.18696 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18533 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.25199 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24995 66 0.0038 3.3 % + LOOP_ions opt_ions 6.0029 1 6 78 % + ESolver_KS_LCAO Run 5.4383 1 5.4 71 % + HSolverLCAO solve 2.9797 12 0.25 39 % + HamiltLCAO updateHk 1.5182 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4887 12 0.12 19 % + Gint_interface cal_gint 2.8029 25 0.11 37 % + Gint_Gamma distri_vl 2.8338 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.8315 14 0.42 76 % + LCAO_gen_fixedH add_v_delta 2.6883 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.6883 6 0.45 35 % + ElecStateLCAO psiToRho 1.4436 12 0.12 19 % + Charge mix_rho 0.85373 11 0.078 11 % + LOOP_ions force_stress 0.56445 1 0.56 7.4 % + Force_Stress_LCAO getForceStress 0.56442 1 0.56 7.4 % + Force_LCAO_gamma ftable_gamma 0.34976 1 0.35 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.34184 1 0.34 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:01 2022 + FINISH Time : Wed Sep 28 11:14:09 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/167/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9ab6b01aadec105c0b55fff124efedecb90bc409 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.186442 0.508606 0.207322 +H 0.227511 0.486028 0.253842 +H 0.167858 0.563666 0.234846 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0c654b3117f6592dc4ffaf5e69259b4d26c9fcef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4384 2 + 2 -12.8765 2 + 3 -9.34712 2 + 4 -6.77847 2 + 5 1.3178 0 + 6 4.48781 0 + 7 11.0535 0 + 8 11.3261 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4a6c4cc5a1e1d4905f6aa12d59613ef7b0577398 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:43 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.22036727708 14.2409755771 5.80502679559 0 0 0 0 + tauc_H1 6.37030350439 13.6087910378 7.10756687701 0 0 0 0 + tauc_H2 4.70003377381 15.7826571153 6.57568894614 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.087320032789 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0971489905925 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115317194128 (SEC) + + DONE : INIT CHARGE Time : 0.163952405882 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443125 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 337 ; sender_size of each process is: +144 144 0 49 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000329 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000941 + + Density error is 0.214350593737 + + Energy Rydberg eV + E_KohnSham -34.1901600423 -465.180992107 + E_Harris -34.381190115 -467.780089586 + E_Fermi -0.409344660702 -5.56941983142 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000460423411291 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120229930991 + + Density error is 0.0975487021702 + + Energy Rydberg eV + E_KohnSham -34.2792337846 -466.392902545 + E_Harris -34.2859961995 -466.484909919 + E_Fermi -0.219313581098 -2.98391435172 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000489063535359 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114837209607 + + Density error is 0.0624888611701 + + Energy Rydberg eV + E_KohnSham -34.2794785694 -466.396233012 + E_Harris -34.2838533184 -466.455754526 + E_Fermi -0.207424961757 -2.82216138733 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000553150245419 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107596148068 + + Density error is 0.00195626993192 + + Energy Rydberg eV + E_KohnSham -34.2794756173 -466.396192847 + E_Harris -34.2794762378 -466.39620129 + E_Fermi -0.171627966257 -2.33511827724 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000553276739387 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107856113623 + + Density error is 0.000872800271482 + + Energy Rydberg eV + E_KohnSham -34.2794132613 -466.395344451 + E_Harris -34.2794150086 -466.395368223 + E_Fermi -0.1708755513 -2.32488114657 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000553702773471 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107719046479 + + Density error is 9.39912719697e-05 + + Energy Rydberg eV + E_KohnSham -34.2794556225 -466.395920804 + E_Harris -34.2794556241 -466.395920826 + E_Fermi -0.170921090518 -2.32550073941 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000553751831294 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107708443041 + + Density error is 4.03413473621e-05 + + Energy Rydberg eV + E_KohnSham -34.279442879 -466.39574742 + E_Harris -34.2794428878 -466.39574754 + E_Fermi -0.170809803506 -2.32398660195 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00055371508609 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107703287468 + + Density error is 8.44721347731e-06 + + Energy Rydberg eV + E_KohnSham -34.2794447404 -466.395772746 + E_Harris -34.2794447408 -466.395772751 + E_Fermi -0.170855878165 -2.32461347984 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000553719995836 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107704122623 + + Density error is 6.9402185278e-07 + + Energy Rydberg eV + E_KohnSham -34.2794435329 -466.395756316 + E_Harris -34.2794435329 -466.395756316 + E_Fermi -0.170847899453 -2.32450492389 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00055372047444 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107704010583 + + Density error is 2.60753047902e-07 + + Energy Rydberg eV + E_KohnSham -34.2794437361 -466.395759081 + E_Harris -34.2794437361 -466.395759081 + E_Fermi -0.170847498091 -2.32449946308 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000553720384994 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107704062905 + + Density error is 4.56356868164e-08 + + Energy Rydberg eV + E_KohnSham -34.2794437227 -466.395758899 + E_Harris -34.2794437227 -466.395758899 + E_band -8.00260115373 -108.880974512 + E_one_elec -69.4289835581 -944.629782738 + E_Hartree +36.0970209688 +491.125166001 + E_xc -8.21883852787 -111.823034921 + E_Ewald +7.39537309821 +100.619212972 + E_demet -1.74834516583e-80 -2.37874563261e-79 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19510917946 -2.65459657276 + E_Fermi -0.170847424591 -2.32449846306 + + charge density convergence is achieved + final etot is -466.395758899 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4384 2.00000 + 2 -12.8765 2.00000 + 3 -9.34712 2.00000 + 4 -6.77847 2.00000 + 5 1.31780 0.00000 + 6 4.48781 0.00000 + 7 11.0535 0.00000 + 8 11.3261 0.00000 + + EFERMI = -2.324498463061217 eV + OUT.ABACUS/ final etot is -466.3957588987216 eV + correction force for each atom along direction 1 is 9.12555e-05 + correction force for each atom along direction 2 is -5.10458e-06 + correction force for each atom along direction 3 is 0.000166203 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.56611775 -0.94049674 -0.039976074 + H1 +0.050325165 -0.29368477 -0.23128839 + H2 -0.61644292 +1.2341815 +0.27126446 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3957588987216 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3111 11 0.57 1.0e+02% + Run_lcao lcao_line 6.3013 1 6.3 1.e+02% + Potential init_pot 0.28378 2 0.14 4.5% + PW_Basis recip2real 0.26923 16 0.017 4.3% + PW_Basis gathers_scatterp 0.11180 16 0.0070 1.8% + Potential v_of_rho 0.85430 13 0.066 14.% + XC_Functional v_xc 0.22401 14 0.016 3.5% + H_Hartree_pw v_hartree 0.59058 13 0.045 9.4% + PW_Basis real2recip 0.55703 38 0.015 8.8% + PW_Basis gatherp_scatters 0.21699 38 0.0057 3.4% + ORB_control set_orb_tables 1.1055 1 1.1 18.% + ORB_gen_tables gen_tables 1.1055 1 1.1 18.% + ORB_table_phi init_Table 0.48490 1 0.48 7.7% + ORB_table_phi cal_ST_Phi12_R 0.47999 126 0.0038 7.6% + ORB_table_beta init_Table_Beta 0.18819 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18668 56 0.0033 3.0% + ORB_table_alpha init_Table_Alpha 0.25494 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25307 66 0.0038 4.0% + LOOP_ions opt_ions 4.6771 1 4.7 74.% + ESolver_KS_LCAO Run 4.1421 1 4.1 66.% + HSolverLCAO solve 2.1919 11 0.20 35.% + HamiltLCAO updateHk 1.1475 11 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1122 11 0.10 18.% + Gint_interface cal_gint 2.0562 23 0.089 33.% + Gint_Gamma distri_vl 1.9953 6 0.33 32.% + LCAO_Deepks cal_projected_DM 4.5152 13 0.35 72.% + LCAO_gen_fixedH add_v_delta 1.8633 6 0.31 30.% + LCAO_DESCRIPTOR add_v_delta 1.8633 6 0.31 30.% + ElecStateLCAO psiToRho 1.0308 11 0.094 16.% + Charge mix_rho 0.65798 10 0.066 10.% + LOOP_ions force_stress 0.53477 1 0.53 8.5% + Force_Stress_LCAO getForceStress 0.53474 1 0.53 8.5% + Force_LCAO_gamma ftable_gamma 0.32300 1 0.32 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.31634 1 0.32 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:43 2022 + Finish Time : Wed Sep 28 11:02:50 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..7ddda99c513cb19d69c47c4bafd8cf2141c0b2a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123836 ima = 3.69554e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122639535383 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111618275939 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112154760455 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112414304815 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112354210105 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112386808756 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112384616656 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112387192675 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112386714869 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112386735684 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112386721659 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/STRU new file mode 100644 index 0000000000000000000000000000000000000000..873eebc58c9247dfc17f0a61d582722cb4065ba3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.779632722926 14.240975577157 5.805026795578 0 0 0 +H +0.0 +2 +-21.629696495623 13.608791037845 7.107566877003 0 0 0 +-23.299966226180 15.782657115336 6.575688946148 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/conv new file mode 100644 index 0000000000000000000000000000000000000000..93cd1187476dc604cf89164f3ddc1725d6483586 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/conv @@ -0,0 +1 @@ +168 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e69bb0aadf7527215ae47ee3f0a3d6af73312941 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752707507 0.01279647272 1.27551031 1.360570469 1.46989644 0.009220137689 0.01741087731 0.0391249836 +6.606805057e-18 0.0009810858931 0.002815444613 0.01311848312 0.04711238774 -5.095625907e-19 2.64449088e-06 7.10236556e-06 +0.001599254764 0.006111183206 + +H atom_index 1 n_descriptor 18 +1.23623022 0.03515348101 0.1053333364 0.1432526733 0.3152218522 0.02224296222 0.02743696962 0.03826178303 +1.964403432e-17 4.896901104e-05 0.09971650683 0.1144631462 0.1228964654 -4.439302895e-19 4.294472478e-06 0.01351124066 +0.02636414278 0.03009908851 + +H atom_index 2 n_descriptor 18 +1.274422477 0.03387609759 0.1190351485 0.1613172467 0.3275789432 0.02410326751 0.02966622434 0.03715935803 +-2.114617546e-17 5.263920953e-05 0.1072016856 0.1180926231 0.1384389968 -1.037967475e-17 2.139143141e-06 0.01334082591 +0.02775085644 0.03180385215 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..863e0cdbdcf8deb538c56fadae0d3885ca60528c Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..95aeb434f54e9c47c37ad1982b14fe06894c199c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:43 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0873493 SEC) : SETUP UNITCELL + DONE(0.0971681 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115336 SEC) : INIT PLANEWAVE + DONE(0.164082 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443187 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651810e+02 0.000000e+00 2.144e-01 4.928e-01 + GE2 -4.663929e+02 -1.211910e+00 9.755e-02 4.200e-01 + GE3 -4.663962e+02 -3.330468e-03 6.249e-02 4.721e-01 + GE4 -4.663962e+02 4.016488e-05 1.956e-03 3.588e-01 + GE5 -4.663953e+02 8.483968e-04 8.728e-04 3.664e-01 + GE6 -4.663959e+02 -5.763536e-04 9.399e-05 3.399e-01 + GE7 -4.663957e+02 1.733845e-04 4.034e-05 3.368e-01 + GE8 -4.663958e+02 -2.532640e-05 8.447e-06 3.384e-01 + GE9 -4.663958e+02 1.642958e-05 6.940e-07 3.352e-01 + GE10 -4.663958e+02 -2.764992e-06 2.608e-07 3.385e-01 + GE11 -4.663958e+02 1.826736e-07 4.564e-08 2.824e-01 +E_delta_band = -7.10934757e-02 Ry = -9.67276361e-01 eV +E_delta_NN= -1.95109179e-01 Ry = -2.65459657e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3111 11 0.57 1e+02 % + Run_lcao lcao_line 6.3013 1 6.3 1e+02 % + Potential init_pot 0.28378 2 0.14 4.5 % + PW_Basis recip2real 0.26923 16 0.017 4.3 % + PW_Basis gathers_scatterp 0.1118 16 0.007 1.8 % + Potential v_of_rho 0.8543 13 0.066 14 % + XC_Functional v_xc 0.22401 14 0.016 3.5 % + H_Hartree_pw v_hartree 0.59058 13 0.045 9.4 % + PW_Basis real2recip 0.55703 38 0.015 8.8 % + PW_Basis gatherp_scatters 0.21699 38 0.0057 3.4 % + ORB_control set_orb_tables 1.1055 1 1.1 18 % + ORB_gen_tables gen_tables 1.1055 1 1.1 18 % + ORB_table_phi init_Table 0.4849 1 0.48 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.47999 126 0.0038 7.6 % + ORB_table_beta init_Table_Beta 0.18819 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18668 56 0.0033 3 % + ORB_table_alpha init_Table_Alpha 0.25494 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.25307 66 0.0038 4 % + LOOP_ions opt_ions 4.6771 1 4.7 74 % + ESolver_KS_LCAO Run 4.1421 1 4.1 66 % + HSolverLCAO solve 2.1919 11 0.2 35 % + HamiltLCAO updateHk 1.1475 11 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1122 11 0.1 18 % + Gint_interface cal_gint 2.0562 23 0.089 33 % + Gint_Gamma distri_vl 1.9953 6 0.33 32 % + LCAO_Deepks cal_projected_DM 4.5152 13 0.35 72 % + LCAO_gen_fixedH add_v_delta 1.8633 6 0.31 30 % + LCAO_DESCRIPTOR add_v_delta 1.8633 6 0.31 30 % + ElecStateLCAO psiToRho 1.0308 11 0.094 16 % + Charge mix_rho 0.65798 10 0.066 10 % + LOOP_ions force_stress 0.53477 1 0.53 8.5 % + Force_Stress_LCAO getForceStress 0.53474 1 0.53 8.5 % + Force_LCAO_gamma ftable_gamma 0.323 1 0.32 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.31634 1 0.32 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:43 2022 + FINISH Time : Wed Sep 28 11:02:50 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/168/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..2233bca59048e263140b806e4edec28b4201e685 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.18714 0.5134 0.217815 +H 0.253316 0.509424 0.21088 +H 0.175753 0.579764 0.218634 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..853acb3eba0f3024a5d683864383dc9791d0943b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0564 2 + 2 -12.7895 2 + 3 -9.12817 2 + 4 -6.69441 2 + 5 1.08574 0 + 6 4.04587 0 + 7 11.133 0 + 8 11.3878 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3fb9b859f6ee8e32ae36b1baa6eb1ab0bfe26175 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.23993111427 14.3752113134 6.09883379668 0 0 0 0 + tauc_H1 7.09285800467 14.2638740132 5.90463901927 0 0 0 0 + tauc_H2 4.92109434045 16.2333973802 6.12176580012 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0865549588825 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0868956902501 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.10504520717 (SEC) + + DONE : INIT CHARGE Time : 0.155761195041 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438375 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00156 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000597 + + Density error is 0.211594666649 + + Energy Rydberg eV + E_KohnSham -34.1927534807 -465.216277647 + E_Harris -34.3773805498 -467.728257792 + E_Fermi -0.390181375824 -5.30868996468 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013733783585 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785135037792 + + Density error is 0.0984253063192 + + Energy Rydberg eV + E_KohnSham -34.2802463898 -466.406679745 + E_Harris -34.2872470915 -466.501929178 + E_Fermi -0.201254154012 -2.73820324074 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00126395024569 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000757382543973 + + Density error is 0.0633837947611 + + Energy Rydberg eV + E_KohnSham -34.2805711154 -466.411097863 + E_Harris -34.2850795746 -466.472438598 + E_Fermi -0.193319016994 -2.63024016288 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105571241338 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000727116691111 + + Density error is 0.00197345195059 + + Energy Rydberg eV + E_KohnSham -34.2804957059 -466.410071865 + E_Harris -34.2804977095 -466.410099125 + E_Fermi -0.158076078565 -2.15073538598 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105358561495 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000725864915584 + + Density error is 0.000875817700478 + + Energy Rydberg eV + E_KohnSham -34.2804629109 -466.409625666 + E_Harris -34.2804631532 -466.409628962 + E_Fermi -0.157886190837 -2.1481518309 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105094135812 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000725596126316 + + Density error is 0.000175138451445 + + Energy Rydberg eV + E_KohnSham -34.2804780585 -466.409831759 + E_Harris -34.2804780505 -466.409831651 + E_Fermi -0.157545422204 -2.14351543579 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105080712293 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000725779062792 + + Density error is 2.70224916876e-05 + + Energy Rydberg eV + E_KohnSham -34.280474142 -466.409778472 + E_Harris -34.2804741438 -466.409778497 + E_Fermi -0.15748478716 -2.14269045369 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105076364847 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000725724364854 + + Density error is 1.29170262364e-05 + + Energy Rydberg eV + E_KohnSham -34.2804763921 -466.409809087 + E_Harris -34.2804763929 -466.409809098 + E_Fermi -0.157501549197 -2.14291851291 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105075012283 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000725731405076 + + Density error is 2.33904450622e-06 + + Energy Rydberg eV + E_KohnSham -34.2804754209 -466.409795874 + E_Harris -34.2804754209 -466.409795874 + E_Fermi -0.157489847777 -2.14275930692 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105074313406 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000725731413314 + + Density error is 5.4853840709e-07 + + Energy Rydberg eV + E_KohnSham -34.2804756616 -466.409799148 + E_Harris -34.2804756616 -466.409799148 + E_Fermi -0.157488072246 -2.14273514959 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105074271707 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0007257319816 + + Density error is 1.84774285639e-07 + + Energy Rydberg eV + E_KohnSham -34.2804756613 -466.409799144 + E_Harris -34.2804756613 -466.409799144 + E_Fermi -0.157487802108 -2.14273147417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010507422957 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000725732212591 + + Density error is 1.13271621957e-08 + + Energy Rydberg eV + E_KohnSham -34.2804756659 -466.409799207 + E_Harris -34.2804756659 -466.409799207 + E_band -7.88911984555 -107.336982104 + E_one_elec -68.7812382611 -935.816755847 + E_Hartree +35.798185444 +487.059300099 + E_xc -8.17077392252 -111.169082416 + E_Ewald +6.99872084951 +95.2224822648 + E_demet -8.30789697016e-64 -1.13034737191e-62 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193899965219 -2.63814436899 + E_Fermi -0.157487626604 -2.14272908631 + + charge density convergence is achieved + final etot is -466.409799207 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0564 2.00000 + 2 -12.7895 2.00000 + 3 -9.12817 2.00000 + 4 -6.69441 2.00000 + 5 1.08574 0.00000 + 6 4.04587 0.00000 + 7 11.1330 0.00000 + 8 11.3878 0.00000 + + EFERMI = -2.142729086313782 eV + OUT.ABACUS/ final etot is -466.4097992066590 eV + correction force for each atom along direction 1 is 7.45281e-05 + correction force for each atom along direction 2 is 0.000155017 + correction force for each atom along direction 3 is 0.000116513 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.38442499 +0.96581529 -0.039651975 + H1 -0.53108996 +0.0096152864 +0.052633561 + H2 +0.14666497 -0.97543058 -0.012981585 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4097992066590 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7696 11 0.71 1.0e+02% + Run_lcao lcao_line 7.7607 1 7.8 1.e+02% + Potential init_pot 0.28511 2 0.14 3.7% + PW_Basis recip2real 0.30344 17 0.018 3.9% + PW_Basis gathers_scatterp 0.13336 17 0.0078 1.7% + Potential v_of_rho 1.0461 14 0.075 13.% + XC_Functional v_xc 0.29705 15 0.020 3.8% + H_Hartree_pw v_hartree 0.70629 14 0.050 9.1% + PW_Basis real2recip 0.69341 41 0.017 8.9% + PW_Basis gatherp_scatters 0.25796 41 0.0063 3.3% + ORB_control set_orb_tables 1.1004 1 1.1 14.% + ORB_gen_tables gen_tables 1.1004 1 1.1 14.% + ORB_table_phi init_Table 0.47607 1 0.48 6.1% + ORB_table_phi cal_ST_Phi12_R 0.47083 126 0.0037 6.1% + ORB_table_beta init_Table_Beta 0.18501 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18347 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.25477 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.25273 66 0.0038 3.3% + LOOP_ions opt_ions 6.1416 1 6.1 79.% + ESolver_KS_LCAO Run 5.5739 1 5.6 72.% + HSolverLCAO solve 3.1314 12 0.26 40.% + HamiltLCAO updateHk 1.5866 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.5566 12 0.13 20.% + Gint_interface cal_gint 2.9608 25 0.12 38.% + Gint_Gamma distri_vl 2.8903 6 0.48 37.% + LCAO_Deepks cal_projected_DM 5.9644 14 0.43 77.% + LCAO_gen_fixedH add_v_delta 2.7459 6 0.46 35.% + LCAO_DESCRIPTOR add_v_delta 2.7460 6 0.46 35.% + ElecStateLCAO psiToRho 1.5259 12 0.13 20.% + Charge mix_rho 0.85338 11 0.078 11.% + LOOP_ions force_stress 0.56749 1 0.57 7.3% + Force_Stress_LCAO getForceStress 0.56746 1 0.57 7.3% + Force_LCAO_gamma ftable_gamma 0.35497 1 0.35 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.34714 1 0.35 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:17 2022 + Finish Time : Wed Sep 28 11:04:24 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..37c7a7560b9851133d80683feecbdf3495b80043 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123351 ima = 3.71019e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123343325946 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011212045568 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112813584137 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113007238357 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112989166474 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112999513899 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112996226333 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112998033851 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112997378525 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011299736103 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112997339645 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112997330375 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4da130e6b8b4f347f3b6859f9d9b2b1e34dc26f6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.760068885734 14.375211313380 6.098833796696 0 0 0 +H +0.0 +2 +-20.907141995335 14.263874013163 5.904639019257 0 0 0 +-23.078905659538 16.233397380181 6.121765800096 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/conv new file mode 100644 index 0000000000000000000000000000000000000000..19b8471d3832991716d5ea10d17f9889b0496ae8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/conv @@ -0,0 +1 @@ +169 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..bd0f94164065cdd4bae2d17276bb4ac1f0f71ea4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750306416 0.01251009538 1.252244297 1.342554418 1.468324761 0.008507912691 0.01783908178 0.03908837184 +-6.17633016e-19 0.0009188432482 0.002468424635 0.01177839668 0.0425814105 1.970001747e-19 1.789320927e-06 5.370766149e-06 +0.00161599729 0.005922178762 + +H atom_index 1 n_descriptor 18 +1.22050871 0.03536367382 0.09812102376 0.1369042323 0.3114186265 0.02074779949 0.02659989292 0.03862162959 +-2.149692151e-17 3.951166456e-05 0.09202392013 0.1143624512 0.1172085838 1.052835362e-18 5.262227231e-06 0.0136193598 +0.02469705893 0.02933353522 + +H atom_index 2 n_descriptor 18 +1.205466355 0.03585559532 0.09343652741 0.1305569845 0.3059529657 0.02004749827 0.02571733943 0.03922132394 +1.493859383e-17 3.822061759e-05 0.08809097685 0.1116417163 0.1138228953 2.338252122e-18 5.842103863e-06 0.01399081392 +0.02408478006 0.02855934229 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a2d5723833e2b53cd9fb13592db7d5a98cdff8c5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.086578 SEC) : SETUP UNITCELL + DONE(0.0869114 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105065 SEC) : INIT PLANEWAVE + DONE(0.155891 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438442 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652163e+02 0.000000e+00 2.116e-01 5.675e-01 + GE2 -4.664067e+02 -1.190402e+00 9.843e-02 5.199e-01 + GE3 -4.664111e+02 -4.418119e-03 6.338e-02 5.857e-01 + GE4 -4.664101e+02 1.025998e-03 1.973e-03 4.506e-01 + GE5 -4.664096e+02 4.461997e-04 8.758e-04 4.506e-01 + GE6 -4.664098e+02 -2.060935e-04 1.751e-04 4.463e-01 + GE7 -4.664098e+02 5.328678e-05 2.702e-05 4.273e-01 + GE8 -4.664098e+02 -3.061450e-05 1.292e-05 4.267e-01 + GE9 -4.664098e+02 1.321333e-05 2.339e-06 4.262e-01 + GE10 -4.664098e+02 -3.274415e-06 5.485e-07 4.256e-01 + GE11 -4.664098e+02 3.902838e-09 1.848e-07 4.230e-01 + GE12 -4.664098e+02 -6.255185e-08 1.133e-08 3.617e-01 +E_delta_band = -6.85301894e-02 Ry = -9.32401061e-01 eV +E_delta_NN= -1.93899965e-01 Ry = -2.63814437e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7696 11 0.71 1e+02 % + Run_lcao lcao_line 7.7607 1 7.8 1e+02 % + Potential init_pot 0.28511 2 0.14 3.7 % + PW_Basis recip2real 0.30344 17 0.018 3.9 % + PW_Basis gathers_scatterp 0.13336 17 0.0078 1.7 % + Potential v_of_rho 1.0461 14 0.075 13 % + XC_Functional v_xc 0.29705 15 0.02 3.8 % + H_Hartree_pw v_hartree 0.70629 14 0.05 9.1 % + PW_Basis real2recip 0.69341 41 0.017 8.9 % + PW_Basis gatherp_scatters 0.25796 41 0.0063 3.3 % + ORB_control set_orb_tables 1.1004 1 1.1 14 % + ORB_gen_tables gen_tables 1.1004 1 1.1 14 % + ORB_table_phi init_Table 0.47607 1 0.48 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.47083 126 0.0037 6.1 % + ORB_table_beta init_Table_Beta 0.18501 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18347 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.25477 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.25273 66 0.0038 3.3 % + LOOP_ions opt_ions 6.1416 1 6.1 79 % + ESolver_KS_LCAO Run 5.5739 1 5.6 72 % + HSolverLCAO solve 3.1314 12 0.26 40 % + HamiltLCAO updateHk 1.5866 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.5566 12 0.13 20 % + Gint_interface cal_gint 2.9608 25 0.12 38 % + Gint_Gamma distri_vl 2.8903 6 0.48 37 % + LCAO_Deepks cal_projected_DM 5.9644 14 0.43 77 % + LCAO_gen_fixedH add_v_delta 2.7459 6 0.46 35 % + LCAO_DESCRIPTOR add_v_delta 2.746 6 0.46 35 % + ElecStateLCAO psiToRho 1.5259 12 0.13 20 % + Charge mix_rho 0.85338 11 0.078 11 % + LOOP_ions force_stress 0.56749 1 0.57 7.3 % + Force_Stress_LCAO getForceStress 0.56746 1 0.57 7.3 % + Force_LCAO_gamma ftable_gamma 0.35497 1 0.35 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.34714 1 0.35 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:17 2022 + FINISH Time : Wed Sep 28 11:04:24 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/169/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9dd933a79105e8b6245c400d7e8ed6c5097b94c4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.579467 0.290794 0.42553 +H 0.533631 0.250273 0.453044 +H 0.549587 0.345412 0.41975 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..289559a42bef6fad6b4fe3197a3c236ff1f0e7ff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4387 2 + 2 -13.13 2 + 3 -9.14992 2 + 4 -6.77363 2 + 5 1.34046 0 + 6 4.62958 0 + 7 11.0413 0 + 8 11.2799 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..401f32610da39d4008726791700848a2b76a9540 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/running_scf.log @@ -0,0 +1,777 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:26 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.2250710616 8.14223143136 11.9148273107 0 0 0 0 + tauc_H1 14.9416771318 7.00764100791 12.6852216443 0 0 0 0 + tauc_H2 15.3884320037 9.67152200113 11.7530092016 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0873520657187 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0880191598111 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106224324087 (SEC) + + DONE : INIT CHARGE Time : 0.155795491908 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437258 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00159 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954 + + Density error is 0.216124915921 + + Energy Rydberg eV + E_KohnSham -34.1857317987 -465.120742762 + E_Harris -34.3806634685 -467.772924192 + E_Fermi -0.414508141133 -5.63967258679 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0014824992812 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103562071039 + + Density error is 0.0977322633354 + + Energy Rydberg eV + E_KohnSham -34.2757427842 -466.345405047 + E_Harris -34.2824251587 -466.436323417 + E_Fermi -0.222773933927 -3.03099486728 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00135697304661 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000983144410711 + + Density error is 0.062489789543 + + Energy Rydberg eV + E_KohnSham -34.2759252445 -466.347887548 + E_Harris -34.2802225231 -466.406355022 + E_Fermi -0.209662439367 -2.85260383198 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011403424262 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909369231914 + + Density error is 0.00202148522523 + + Energy Rydberg eV + E_KohnSham -34.2759451263 -466.348158053 + E_Harris -34.2759466784 -466.348179171 + E_Fermi -0.173907023421 -2.36612644075 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113821948965 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000911420811516 + + Density error is 0.000856359971645 + + Energy Rydberg eV + E_KohnSham -34.2758825609 -466.347306807 + E_Harris -34.2758838794 -466.347324746 + E_Fermi -0.172991759058 -2.35367363024 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113609701832 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000910373132681 + + Density error is 0.000139246878201 + + Energy Rydberg eV + E_KohnSham -34.2759232905 -466.347860961 + E_Harris -34.2759233446 -466.347861698 + E_Fermi -0.173091759737 -2.35503420927 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113588073252 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000910426727736 + + Density error is 4.72624090437e-05 + + Energy Rydberg eV + E_KohnSham -34.2759087621 -466.347663292 + E_Harris -34.2759087749 -466.347663467 + E_Fermi -0.172947107135 -2.35306610965 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113589446659 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000910396849844 + + Density error is 1.65308810632e-05 + + Energy Rydberg eV + E_KohnSham -34.2759132202 -466.347723948 + E_Harris -34.2759132212 -466.347723962 + E_Fermi -0.17300005135 -2.35378645265 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113585171196 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000910395572223 + + Density error is 2.1560870769e-06 + + Energy Rydberg eV + E_KohnSham -34.2759116157 -466.347702117 + E_Harris -34.2759116157 -466.347702118 + E_Fermi -0.172982209419 -2.35354370073 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113584944119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000910393941543 + + Density error is 6.53890318986e-07 + + Energy Rydberg eV + E_KohnSham -34.2759118208 -466.347704908 + E_Harris -34.2759118208 -466.347704908 + E_Fermi -0.172980900138 -2.35352588704 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113584873385 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000910394010725 + + Density error is 7.88787150611e-08 + + Energy Rydberg eV + E_KohnSham -34.2759118392 -466.347705158 + E_Harris -34.2759118392 -466.347705158 + E_band -8.01021069318 -108.984507608 + E_one_elec -69.5508271692 -946.287550114 + E_Hartree +36.1612997593 +491.999723813 + E_xc -8.22968074492 -111.970550852 + E_Ewald +7.46711663187 +101.595333824 + E_demet -1.04499170595e-82 -1.42178415637e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195367869804 -2.65811623546 + E_Fermi -0.172980297668 -2.35351769002 + + charge density convergence is achieved + final etot is -466.347705158 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4387 2.00000 + 2 -13.1300 2.00000 + 3 -9.14992 2.00000 + 4 -6.77363 2.00000 + 5 1.34046 0.00000 + 6 4.62958 0.00000 + 7 11.0413 0.00000 + 8 11.2799 0.00000 + + EFERMI = -2.353517690017300 eV + OUT.ABACUS/ final etot is -466.3477051582510 eV + correction force for each atom along direction 1 is -0.000154188 + correction force for each atom along direction 2 is -2.44886e-05 + correction force for each atom along direction 3 is 2.50236e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.68856590 -3.0703404 +0.66142224 + H1 +0.64869232 +0.48202186 -0.36140001 + H2 -1.3372582 +2.5883186 -0.30002223 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3477051582510 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1309 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1212 1 6.1 1.e+02% + Potential init_pot 0.28780 2 0.14 4.7% + PW_Basis recip2real 0.26624 16 0.017 4.3% + PW_Basis gathers_scatterp 0.12200 16 0.0076 2.0% + Potential v_of_rho 0.88202 13 0.068 14.% + XC_Functional v_xc 0.25626 14 0.018 4.2% + H_Hartree_pw v_hartree 0.59170 13 0.046 9.7% + PW_Basis real2recip 0.57179 38 0.015 9.3% + PW_Basis gatherp_scatters 0.23559 38 0.0062 3.8% + ORB_control set_orb_tables 1.1093 1 1.1 18.% + ORB_gen_tables gen_tables 1.1093 1 1.1 18.% + ORB_table_phi init_Table 0.48821 1 0.49 8.0% + ORB_table_phi cal_ST_Phi12_R 0.48329 126 0.0038 7.9% + ORB_table_beta init_Table_Beta 0.18997 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18843 56 0.0034 3.1% + ORB_table_alpha init_Table_Alpha 0.25164 1 0.25 4.1% + ORB_table_alpha S_PhiAlpha_R 0.24975 66 0.0038 4.1% + LOOP_ions opt_ions 4.4971 1 4.5 73.% + ESolver_KS_LCAO Run 3.9658 1 4.0 65.% + HSolverLCAO solve 1.9651 11 0.18 32.% + HamiltLCAO updateHk 1.0407 11 0.095 17.% + LCAO_Hamilt cal_Hgamma 1.0122 11 0.092 17.% + Gint_Gamma distri_vl_value 0.61635 11 0.056 10.% + Gint_Gamma distri_vl 1.9153 6 0.32 31.% + LCAO_Deepks cal_projected_DM 4.1232 13 0.32 67.% + LCAO_gen_fixedH add_v_delta 1.7826 6 0.30 29.% + LCAO_DESCRIPTOR add_v_delta 1.7826 6 0.30 29.% + ElecStateLCAO psiToRho 0.90596 11 0.082 15.% + Charge mix_rho 0.66279 10 0.066 11.% + LOOP_ions force_stress 0.53105 1 0.53 8.7% + Force_Stress_LCAO getForceStress 0.53102 1 0.53 8.7% + Force_LCAO_gamma ftable_gamma 0.31950 1 0.32 5.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:26 2022 + Finish Time : Wed Sep 28 11:03:32 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..cafaebdbbcfa316170d122152abe4891a0766a5d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123946 ima = 3.68639e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123003085218 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112122371968 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112589042775 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112851017221 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112794001287 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112826570485 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112819014752 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112822400567 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112821796626 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112821717297 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112821681847 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b3dae1615a6d8e2d8ae70d603fed3281235911e9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.774928938393 8.142231431337 11.914827310757 0 0 0 +H +0.0 +2 +-13.058322868225 7.007641007921 12.685221644238 0 0 0 +-12.611567996281 9.671522001112 11.753009201563 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/conv new file mode 100644 index 0000000000000000000000000000000000000000..197b75185763b4532c663e0cd150875856c0e154 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/conv @@ -0,0 +1 @@ +17 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..dc10352e138458bd324f08353b44c03d24e43926 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749719711 0.01269939011 1.276082414 1.376978179 1.470065503 0.008720012017 0.01880540945 0.03905907179 +1.990446844e-18 0.001101041854 0.002699359626 0.01266695431 0.04665051584 -5.517096162e-19 2.158131702e-06 6.234566285e-06 +0.001630046823 0.005902707935 + +H atom_index 1 n_descriptor 18 +1.210045027 0.03560715275 0.0954680318 0.1323276571 0.3071502885 0.02049077793 0.02597001648 0.03884418549 +-2.680991627e-17 4.414015757e-05 0.092229825 0.1134589054 0.1134717082 -5.633012604e-18 6.143888842e-06 0.01387376426 +0.0249829479 0.02883918422 + +H atom_index 2 n_descriptor 18 +1.310826051 0.03234584582 0.1317429206 0.1807357584 0.3383398983 0.02514131796 0.03177388715 0.0365127548 +2.94683209e-18 5.361190149e-05 0.1077762778 0.1270039319 0.1549117225 -4.164487135e-18 9.521032114e-07 0.01405200939 +0.02852761888 0.03311324905 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3a738f86986bd56397ae1e7ffaeec3fb460ff7f2 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/log.scf @@ -0,0 +1,100 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:26 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0873976 SEC) : SETUP UNITCELL + DONE(0.0880353 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106244 SEC) : INIT PLANEWAVE + DONE(0.155921 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.437327 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651207e+02 0.000000e+00 2.161e-01 4.740e-01 + GE2 -4.663454e+02 -1.224662e+00 9.773e-02 3.973e-01 + GE3 -4.663479e+02 -2.482501e-03 6.249e-02 4.536e-01 + GE4 -4.663482e+02 -2.705053e-04 2.021e-03 3.451e-01 + GE5 -4.663473e+02 8.512453e-04 8.564e-04 3.421e-01 + GE6 -4.663479e+02 -5.541536e-04 1.392e-04 3.347e-01 + GE7 -4.663477e+02 1.976688e-04 4.726e-05 3.309e-01 + GE8 -4.663477e+02 -6.065601e-05 1.653e-05 3.200e-01 + GE9 -4.663477e+02 2.183100e-05 2.156e-06 3.219e-01 + GE10 -4.663477e+02 -2.790938e-06 6.539e-07 3.217e-01 + GE11 -4.663477e+02 -2.499376e-07 7.888e-08 2.630e-01 +E_delta_band = -7.15475536e-02 Ry = -9.73454407e-01 eV +E_delta_NN= -1.95367870e-01 Ry = -2.65811624e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1309 11 0.56 1e+02 % + Run_lcao lcao_line 6.1212 1 6.1 1e+02 % + Potential init_pot 0.2878 2 0.14 4.7 % + PW_Basis recip2real 0.26624 16 0.017 4.3 % + PW_Basis gathers_scatterp 0.122 16 0.0076 2 % + Potential v_of_rho 0.88202 13 0.068 14 % + XC_Functional v_xc 0.25626 14 0.018 4.2 % + H_Hartree_pw v_hartree 0.5917 13 0.046 9.7 % + PW_Basis real2recip 0.57179 38 0.015 9.3 % + PW_Basis gatherp_scatters 0.23559 38 0.0062 3.8 % + ORB_control set_orb_tables 1.1093 1 1.1 18 % + ORB_gen_tables gen_tables 1.1093 1 1.1 18 % + ORB_table_phi init_Table 0.48821 1 0.49 8 % + ORB_table_phi cal_ST_Phi12_R 0.48329 126 0.0038 7.9 % + ORB_table_beta init_Table_Beta 0.18997 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18843 56 0.0034 3.1 % + ORB_table_alpha init_Table_Alpha 0.25164 1 0.25 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.24975 66 0.0038 4.1 % + LOOP_ions opt_ions 4.4971 1 4.5 73 % + ESolver_KS_LCAO Run 3.9658 1 4 65 % + HSolverLCAO solve 1.9651 11 0.18 32 % + HamiltLCAO updateHk 1.0407 11 0.095 17 % + LCAO_Hamilt cal_Hgamma 1.0122 11 0.092 17 % + Gint_Gamma distri_vl_value 0.61635 11 0.056 10 % + Gint_Gamma distri_vl 1.9153 6 0.32 31 % + LCAO_Deepks cal_projected_DM 4.1232 13 0.32 67 % + LCAO_gen_fixedH add_v_delta 1.7826 6 0.3 29 % + LCAO_DESCRIPTOR add_v_delta 1.7826 6 0.3 29 % + ElecStateLCAO psiToRho 0.90596 11 0.082 15 % + Charge mix_rho 0.66279 10 0.066 11 % + LOOP_ions force_stress 0.53105 1 0.53 8.7 % + Force_Stress_LCAO getForceStress 0.53102 1 0.53 8.7 % + Force_LCAO_gamma ftable_gamma 0.3195 1 0.32 5.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:26 2022 + FINISH Time : Wed Sep 28 11:03:32 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/17/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..0508c6aee63a29146a976a8ed2afde67ea49e87b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.205136 0.520963 0.232115 +H 0.261083 0.494521 0.208598 +H 0.157652 0.497324 0.196241 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3a86c4444d8e7e42b43be073fe31758851f96a42 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.314 2 + 2 -13.2038 2 + 3 -9.0173 2 + 4 -6.74855 2 + 5 1.35226 0 + 6 4.53352 0 + 7 11.0627 0 + 8 11.301 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a6812e45f554b49cab8840afd138fac4779ede42 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.74379693862 14.5869763469 6.4992175253 0 0 0 0 + tauc_H1 7.31033367711 13.8465929738 5.84074115045 0 0 0 0 + tauc_H2 4.41426735099 13.9250850244 5.49475631072 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874466974028 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101461625276 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119652469498 (SEC) + + DONE : INIT CHARGE Time : 0.169018552624 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450709 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 144 0 25 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00089 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138 + + Density error is 0.216615792876 + + Energy Rydberg eV + E_KohnSham -34.1882304747 -465.154738993 + E_Harris -34.3835716878 -467.812492546 + E_Fermi -0.409257487046 -5.56823377299 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00119157521706 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124178323217 + + Density error is 0.0980944551983 + + Energy Rydberg eV + E_KohnSham -34.2795967647 -466.397841142 + E_Harris -34.2863135331 -466.489227465 + E_Fermi -0.216445113258 -2.94488684457 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00113922278455 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114920608214 + + Density error is 0.0629284863226 + + Energy Rydberg eV + E_KohnSham -34.2799669803 -466.402878183 + E_Harris -34.2842984857 -466.461811339 + E_Fermi -0.205049882347 -2.78984677415 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00106807875277 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000984928228744 + + Density error is 0.00203933305604 + + Energy Rydberg eV + E_KohnSham -34.2799634134 -466.402829654 + E_Harris -34.2799655402 -466.40285859 + E_Fermi -0.169466461473 -2.30570949593 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.0010703745944 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000982899668603 + + Density error is 0.00094609892233 + + Energy Rydberg eV + E_KohnSham -34.2798969423 -466.401925269 + E_Harris -34.2798981692 -466.401941961 + E_Fermi -0.168685152855 -2.29507924683 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00106915275334 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980987583794 + + Density error is 0.000174805813524 + + Energy Rydberg eV + E_KohnSham -34.2799360006 -466.402456683 + E_Harris -34.2799360635 -466.40245754 + E_Fermi -0.16869201434 -2.29517260212 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.001069365765 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980897135839 + + Density error is 4.24680603077e-05 + + Energy Rydberg eV + E_KohnSham -34.2799215634 -466.402260255 + E_Harris -34.2799215731 -466.402260387 + E_Fermi -0.168546809012 -2.29319698228 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00106930186536 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980879400597 + + Density error is 1.77702716527e-05 + + Energy Rydberg eV + E_KohnSham -34.2799263715 -466.402325672 + E_Harris -34.2799263727 -466.402325689 + E_Fermi -0.168593632577 -2.29383404957 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00106930132638 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980851061175 + + Density error is 2.53560073451e-06 + + Energy Rydberg eV + E_KohnSham -34.2799248645 -466.402305169 + E_Harris -34.2799248645 -466.40230517 + E_Fermi -0.168575806182 -2.29359150901 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.0010692988856 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980846836081 + + Density error is 3.66011821809e-07 + + Energy Rydberg eV + E_KohnSham -34.2799250785 -466.40230808 + E_Harris -34.2799250785 -466.40230808 + E_Fermi -0.168573220444 -2.29355632824 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00106929962547 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980847337296 + + Density error is 1.50951524435e-07 + + Energy Rydberg eV + E_KohnSham -34.2799251176 -466.402308613 + E_Harris -34.2799251176 -466.402308613 + E_Fermi -0.168573133958 -2.29355515155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00106929980589 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098084725683 + + Density error is 1.02214362694e-08 + + Energy Rydberg eV + E_KohnSham -34.2799251187 -466.402308628 + E_Harris -34.2799251187 -466.402308628 + E_band -7.97953711404 -108.567172153 + E_one_elec -69.4141226507 -944.42758972 + E_Hartree +36.1016067561 +491.187558839 + E_xc -8.21955992294 -111.832850004 + E_Ewald +7.37624724286 +100.35899236 + E_demet -1.23769988087e-80 -1.68397707938e-79 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195001132879 -2.65312652361 + E_Fermi -0.168572991389 -2.29355321179 + + charge density convergence is achieved + final etot is -466.402308628 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3140 2.00000 + 2 -13.2038 2.00000 + 3 -9.01730 2.00000 + 4 -6.74855 2.00000 + 5 1.35226 0.00000 + 6 4.53352 0.00000 + 7 11.0627 0.00000 + 8 11.3010 0.00000 + + EFERMI = -2.293553211788812 eV + OUT.ABACUS/ final etot is -466.4023086280749 eV + correction force for each atom along direction 1 is -3.06563e-05 + correction force for each atom along direction 2 is 1.73853e-05 + correction force for each atom along direction 3 is -3.42997e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.3059276 +0.52300238 +0.83152569 + H1 -0.35085816 +0.068188207 +0.029817474 + H2 -0.95506946 -0.59119059 -0.86134317 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4023086280749 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7610 11 0.71 1.0e+02% + Run_lcao lcao_line 7.7511 1 7.8 1.e+02% + Potential init_pot 0.28445 2 0.14 3.7% + PW_Basis recip2real 0.29737 17 0.017 3.8% + PW_Basis gathers_scatterp 0.12982 17 0.0076 1.7% + Potential v_of_rho 1.0478 14 0.075 14.% + XC_Functional v_xc 0.29561 15 0.020 3.8% + H_Hartree_pw v_hartree 0.70567 14 0.050 9.1% + PW_Basis real2recip 0.69972 41 0.017 9.0% + PW_Basis gatherp_scatters 0.26912 41 0.0066 3.5% + ORB_control set_orb_tables 1.1011 1 1.1 14.% + ORB_gen_tables gen_tables 1.1011 1 1.1 14.% + ORB_table_phi init_Table 0.47413 1 0.47 6.1% + ORB_table_phi cal_ST_Phi12_R 0.46887 126 0.0037 6.0% + ORB_table_beta init_Table_Beta 0.19322 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.19157 56 0.0034 2.5% + ORB_table_alpha init_Table_Alpha 0.24796 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24594 66 0.0037 3.2% + LOOP_ions opt_ions 6.1213 1 6.1 79.% + ESolver_KS_LCAO Run 5.5454 1 5.5 71.% + HSolverLCAO solve 3.1026 12 0.26 40.% + HamiltLCAO updateHk 1.5785 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.5477 12 0.13 20.% + Gint_interface cal_gint 2.9358 25 0.12 38.% + Gint_Gamma distri_vl 2.8811 6 0.48 37.% + LCAO_Deepks cal_projected_DM 5.9473 14 0.42 77.% + LCAO_gen_fixedH add_v_delta 2.7365 6 0.46 35.% + LCAO_DESCRIPTOR add_v_delta 2.7365 6 0.46 35.% + ElecStateLCAO psiToRho 1.5072 12 0.13 19.% + Charge mix_rho 0.84808 11 0.077 11.% + LOOP_ions force_stress 0.57577 1 0.58 7.4% + Force_Stress_LCAO getForceStress 0.57574 1 0.58 7.4% + Force_LCAO_gamma ftable_gamma 0.35857 1 0.36 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.35073 1 0.35 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:48 2022 + Finish Time : Wed Sep 28 11:14:56 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2755d3ae2d2fcbb6934cc741eb2cbe9a4c585f3d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012384 ima = 3.67573e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123389076649 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112272438395 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112806655052 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113064842157 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113011245194 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113042656807 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113034128254 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113037254837 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113036583016 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113036478735 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113036468307 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113036461084 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e1c1a019942df286cbcf2545bc84fec5afdd2977 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.256203061398 14.586976346884 6.499217525299 0 0 0 +H +0.0 +2 +-20.689666322867 13.846592973762 5.840741150448 0 0 0 +-23.585732648995 13.925085024332 5.494756310735 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/conv new file mode 100644 index 0000000000000000000000000000000000000000..f3c6fa7c253dba9d5669b5ed01e17b9c51b5c604 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/conv @@ -0,0 +1 @@ +170 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..043de26178dd85c956c4a871caa8e7ab87f4ee22 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747401426 0.01268027828 1.278299744 1.370476745 1.469480519 0.008242312081 0.01932151823 0.03897403243 +-9.072665851e-18 0.001119205287 0.002547184822 0.01245148272 0.04486569725 -7.517756363e-20 1.871748645e-06 5.599508303e-06 +0.001691275069 0.005843975384 + +H atom_index 1 n_descriptor 18 +1.227574574 0.03478996458 0.1007149821 0.1402918942 0.3143430371 0.02106030475 0.02706540301 0.03794066368 +-2.646800537e-17 4.203088427e-05 0.09623337644 0.1141331653 0.1203992542 2.904856961e-18 5.345459499e-06 0.01335241487 +0.02542191696 0.02975863479 + +H atom_index 2 n_descriptor 18 +1.275754515 0.03312841129 0.1174560121 0.1627987392 0.3295347835 0.02323616606 0.02985273303 0.03654028459 +-7.980764865e-17 4.635330528e-05 0.1068360226 0.1174095034 0.1397962151 -5.753340487e-18 2.857881652e-06 0.01311232499 +0.02718386708 0.03189349319 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9d0fcf3ade35a7370243db0076051d7817ec84a7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/e_base.npy new file mode 100644 index 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TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874688 SEC) : SETUP UNITCELL + DONE(0.101481 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119673 SEC) : INIT PLANEWAVE + DONE(0.16915 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450768 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651547e+02 0.000000e+00 2.166e-01 5.612e-01 + GE2 -4.663978e+02 -1.243102e+00 9.809e-02 5.168e-01 + GE3 -4.664029e+02 -5.037041e-03 6.293e-02 5.841e-01 + GE4 -4.664028e+02 4.852965e-05 2.039e-03 4.466e-01 + GE5 -4.664019e+02 9.043851e-04 9.461e-04 4.470e-01 + GE6 -4.664025e+02 -5.314143e-04 1.748e-04 4.401e-01 + GE7 -4.664023e+02 1.964277e-04 4.247e-05 4.312e-01 + GE8 -4.664023e+02 -6.541715e-05 1.777e-05 4.235e-01 + GE9 -4.664023e+02 2.050307e-05 2.536e-06 4.250e-01 + GE10 -4.664023e+02 -2.910826e-06 3.660e-07 4.246e-01 + GE11 -4.664023e+02 -5.328466e-07 1.510e-07 4.249e-01 + GE12 -4.664023e+02 -1.517158e-08 1.022e-08 3.585e-01 +E_delta_band = -7.09045887e-02 Ry = -9.64706421e-01 eV +E_delta_NN= -1.95001133e-01 Ry = -2.65312652e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.761 11 0.71 1e+02 % + Run_lcao lcao_line 7.7511 1 7.8 1e+02 % + Potential init_pot 0.28445 2 0.14 3.7 % + PW_Basis recip2real 0.29737 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.12982 17 0.0076 1.7 % + Potential v_of_rho 1.0478 14 0.075 14 % + XC_Functional v_xc 0.29561 15 0.02 3.8 % + H_Hartree_pw v_hartree 0.70567 14 0.05 9.1 % + PW_Basis real2recip 0.69972 41 0.017 9 % + PW_Basis gatherp_scatters 0.26912 41 0.0066 3.5 % + ORB_control set_orb_tables 1.1011 1 1.1 14 % + ORB_gen_tables gen_tables 1.1011 1 1.1 14 % + ORB_table_phi init_Table 0.47413 1 0.47 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.46887 126 0.0037 6 % + ORB_table_beta init_Table_Beta 0.19322 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.19157 56 0.0034 2.5 % + ORB_table_alpha init_Table_Alpha 0.24796 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24594 66 0.0037 3.2 % + LOOP_ions opt_ions 6.1213 1 6.1 79 % + ESolver_KS_LCAO Run 5.5454 1 5.5 71 % + HSolverLCAO solve 3.1026 12 0.26 40 % + HamiltLCAO updateHk 1.5785 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.5477 12 0.13 20 % + Gint_interface cal_gint 2.9358 25 0.12 38 % + Gint_Gamma distri_vl 2.8811 6 0.48 37 % + LCAO_Deepks cal_projected_DM 5.9473 14 0.42 77 % + LCAO_gen_fixedH add_v_delta 2.7365 6 0.46 35 % + LCAO_DESCRIPTOR add_v_delta 2.7365 6 0.46 35 % + ElecStateLCAO psiToRho 1.5072 12 0.13 19 % + Charge mix_rho 0.84808 11 0.077 11 % + LOOP_ions force_stress 0.57577 1 0.58 7.4 % + Force_Stress_LCAO getForceStress 0.57574 1 0.58 7.4 % + Force_LCAO_gamma ftable_gamma 0.35857 1 0.36 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.35073 1 0.35 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:48 2022 + FINISH Time : Wed Sep 28 11:14:56 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/170/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d35dc364a4818171b1bdcb8d6f7fcb2d00f9b8cb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.222177 0.517723 0.238807 +H 0.259584 0.566582 0.221081 +H 0.206761 0.534752 0.301655 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..cb521b8053e92240ed5b9131e928728909d5f783 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3543 2 + 2 -12.9212 2 + 3 -9.24977 2 + 4 -6.75884 2 + 5 1.27082 0 + 6 4.42996 0 + 7 11.068 0 + 8 11.3277 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d4891e4c8c36a2a2387107bb39df961d6c407021 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:54 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.22094870362 14.4962497228 6.68660788536 0 0 0 0 + tauc_H1 7.26834845697 15.8643095887 6.19027329505 0 0 0 0 + tauc_H2 5.78931325904 14.9730522963 8.44633060619 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.073284331971 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0735640035969 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0893183590338 (SEC) + + DONE : INIT CHARGE Time : 0.130733978996 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374246 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000599 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821 + + Density error is 0.214454748808 + + Energy Rydberg eV + E_KohnSham -34.1895956219 -465.173312774 + E_Harris -34.3806926254 -467.773320892 + E_Fermi -0.406311878893 -5.52815671803 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000895908236661 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111368009865 + + Density error is 0.0978682987986 + + Energy Rydberg eV + E_KohnSham -34.2790460021 -466.390347632 + E_Harris -34.285840711 -466.482794391 + E_Fermi -0.215988541037 -2.93867486081 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000862163556759 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107069892142 + + Density error is 0.062769153338 + + Energy Rydberg eV + E_KohnSham -34.2793416402 -466.394369996 + E_Harris -34.2837386652 -466.45419459 + E_Fermi -0.204940139972 -2.78835365253 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000826574646353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101888209541 + + Density error is 0.00195938211537 + + Energy Rydberg eV + E_KohnSham -34.2793245415 -466.394137355 + E_Harris -34.2793254109 -466.394149185 + E_Fermi -0.16921662371 -2.30231027878 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000828196312857 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102041433997 + + Density error is 0.000884202524494 + + Energy Rydberg eV + E_KohnSham -34.2792663235 -466.393345259 + E_Harris -34.2792674942 -466.393361188 + E_Fermi -0.168587067845 -2.2937447318 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827431458943 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101935615734 + + Density error is 0.000124944383487 + + Energy Rydberg eV + E_KohnSham -34.2793030528 -466.393844987 + E_Harris -34.2793030759 -466.393845302 + E_Fermi -0.168540646242 -2.29311313349 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827626364889 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101952123254 + + Density error is 3.9264880563e-05 + + Energy Rydberg eV + E_KohnSham -34.2792904973 -466.393674161 + E_Harris -34.2792905056 -466.393674273 + E_Fermi -0.168433196484 -2.29165120453 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827544260679 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101942192496 + + Density error is 1.37298739123e-05 + + Energy Rydberg eV + E_KohnSham -34.2792938832 -466.393720228 + E_Harris -34.2792938839 -466.393720238 + E_Fermi -0.168473124238 -2.29219444949 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827546933567 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101942111153 + + Density error is 2.20966731613e-06 + + Energy Rydberg eV + E_KohnSham -34.2792925551 -466.393702159 + E_Harris -34.2792925552 -466.393702159 + E_Fermi -0.168459173172 -2.2920046355 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827550464241 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101942480589 + + Density error is 1.93713318684e-07 + + Energy Rydberg eV + E_KohnSham -34.2792927071 -466.393704226 + E_Harris -34.2792927071 -466.393704226 + E_Fermi -0.168457010812 -2.29197521509 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827550736918 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101942524953 + + Density error is 9.01840562793e-08 + + Energy Rydberg eV + E_KohnSham -34.27929275 -466.39370481 + E_Harris -34.27929275 -466.39370481 + E_band -7.97960227496 -108.568058713 + E_one_elec -69.3165881055 -943.100564153 + E_Hartree +36.0471000801 +490.445957466 + E_xc -8.21091693876 -111.715256172 + E_Ewald +7.32537774981 +99.6668773998 + E_demet -4.0038704176e-77 -5.4475451733e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194910477044 -2.6518930877 + E_Fermi -0.16845702603 -2.29197542215 + + charge density convergence is achieved + final etot is -466.39370481 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3543 2.00000 + 2 -12.9212 2.00000 + 3 -9.24977 2.00000 + 4 -6.75884 2.00000 + 5 1.27082 0.00000 + 6 4.42996 0.00000 + 7 11.0680 0.00000 + 8 11.3277 0.00000 + + EFERMI = -2.291975422147655 eV + OUT.ABACUS/ final etot is -466.3937048097598 eV + correction force for each atom along direction 1 is 3.73849e-06 + correction force for each atom along direction 2 is 2.49049e-05 + correction force for each atom along direction 3 is 9.73618e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.96606257 -0.72796547 +1.2589514 + H1 +0.92530402 +1.0812501 -0.63010451 + H2 +0.040758553 -0.35328467 -0.62884687 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3937048097598 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4983 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4907 1 6.5 1.e+02% + Potential init_pot 0.24280 2 0.12 3.7% + PW_Basis recip2real 0.26343 16 0.016 4.1% + PW_Basis gathers_scatterp 0.11129 16 0.0070 1.7% + Potential v_of_rho 0.92735 13 0.071 14.% + XC_Functional v_xc 0.27391 14 0.020 4.2% + H_Hartree_pw v_hartree 0.61447 13 0.047 9.5% + PW_Basis real2recip 0.60413 38 0.016 9.3% + PW_Basis gatherp_scatters 0.22767 38 0.0060 3.5% + ORB_control set_orb_tables 0.89072 1 0.89 14.% + ORB_gen_tables gen_tables 0.89072 1 0.89 14.% + ORB_table_phi init_Table 0.37378 1 0.37 5.8% + ORB_table_phi cal_ST_Phi12_R 0.36957 126 0.0029 5.7% + ORB_table_beta init_Table_Beta 0.15159 1 0.15 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15033 56 0.0027 2.3% + ORB_table_alpha init_Table_Alpha 0.20767 1 0.21 3.2% + ORB_table_alpha S_PhiAlpha_R 0.20601 66 0.0031 3.2% + LOOP_ions opt_ions 5.1569 1 5.2 79.% + ESolver_KS_LCAO Run 4.6492 1 4.6 72.% + HSolverLCAO solve 2.4693 11 0.22 38.% + HamiltLCAO updateHk 1.2640 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2350 11 0.11 19.% + Gint_interface cal_gint 2.2080 23 0.096 34.% + Gint_Gamma distri_vl 2.2267 6 0.37 34.% + LCAO_Deepks cal_projected_DM 5.0097 13 0.39 77.% + LCAO_gen_fixedH add_v_delta 2.0988 6 0.35 32.% + LCAO_DESCRIPTOR add_v_delta 2.0988 6 0.35 32.% + ElecStateLCAO psiToRho 1.1882 11 0.11 18.% + Charge mix_rho 0.76515 10 0.077 12.% + LOOP_ions force_stress 0.50754 1 0.51 7.8% + Force_Stress_LCAO getForceStress 0.50752 1 0.51 7.8% + Force_LCAO_gamma ftable_gamma 0.31129 1 0.31 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.30395 1 0.30 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:54 2022 + Finish Time : Wed Sep 28 11:13:01 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..537150c421dbda3b6cfa8e4bdffc19704640ddd7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124094 ima = 3.66823e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122899879943 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111798016725 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112368621606 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112620768515 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112570431487 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112599678677 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112594039354 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112596884058 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112596373057 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112596266594 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112596261504 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/STRU new file mode 100644 index 0000000000000000000000000000000000000000..65cc15369df57a9e81908f42dd6fd541f5e9974c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.779051296376 14.496249722779 6.686607885378 0 0 0 +H +0.0 +2 +-20.731651543019 15.864309588663 6.190273295037 0 0 0 +-22.210686740962 14.973052296271 8.446330606205 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/conv new file mode 100644 index 0000000000000000000000000000000000000000..6e702eeccfe79359adc162934b05756babeb51e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/conv @@ -0,0 +1 @@ +171 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8b6d8e7bd1849d76d6d021b4ab4f647e9e2c00f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751436642 0.01271379963 1.269854273 1.361407611 1.469579242 0.008926025008 0.01784352505 0.03909775446 +-1.552136291e-18 0.0009987574576 0.002709624541 0.01266691582 0.04605782061 3.808469818e-19 2.315020426e-06 6.493916436e-06 +0.001607638286 0.006029654085 + +H atom_index 1 n_descriptor 18 +1.279242835 0.03352635204 0.1197562458 0.1638858738 0.3295049562 0.02396095834 0.02996685622 0.03691770231 +4.536033076e-17 5.076372973e-05 0.1071105775 0.1184622433 0.1406236246 7.578576764e-18 2.186534794e-06 0.01331658075 +0.02756218171 0.03199374859 + +H atom_index 2 n_descriptor 18 +1.215737558 0.03565473031 0.09767425033 0.1344852539 0.3086170756 0.02093735329 0.0262629739 0.03887412084 +-6.747453765e-18 4.477284833e-05 0.09328289834 0.1137905496 0.1152394559 -1.512237658e-18 5.588122968e-06 0.01383308744 +0.02520039176 0.02908710585 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..7da5c204a6ca2f53f3d879e1bdd80dd8886069a8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:54 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0732993 SEC) : SETUP UNITCELL + DONE(0.0735729 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0893309 SEC) : INIT PLANEWAVE + DONE(0.130837 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374288 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651733e+02 0.000000e+00 2.145e-01 4.935e-01 + GE2 -4.663903e+02 -1.217035e+00 9.787e-02 4.683e-01 + GE3 -4.663944e+02 -4.022364e-03 6.277e-02 5.285e-01 + GE4 -4.663941e+02 2.326409e-04 1.959e-03 4.105e-01 + GE5 -4.663933e+02 7.920962e-04 8.842e-04 4.087e-01 + GE6 -4.663938e+02 -4.997286e-04 1.249e-04 4.027e-01 + GE7 -4.663937e+02 1.708264e-04 3.926e-05 3.922e-01 + GE8 -4.663937e+02 -4.606735e-05 1.373e-05 3.880e-01 + GE9 -4.663937e+02 1.806952e-05 2.210e-06 3.903e-01 + GE10 -4.663937e+02 -2.066990e-06 1.937e-07 3.933e-01 + GE11 -4.663937e+02 -5.838918e-07 9.018e-08 3.201e-01 +E_delta_band = -7.06449414e-02 Ry = -9.61173737e-01 eV +E_delta_NN= -1.94910477e-01 Ry = -2.65189309e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4983 11 0.59 1e+02 % + Run_lcao lcao_line 6.4907 1 6.5 1e+02 % + Potential init_pot 0.2428 2 0.12 3.7 % + PW_Basis recip2real 0.26343 16 0.016 4.1 % + PW_Basis gathers_scatterp 0.11129 16 0.007 1.7 % + Potential v_of_rho 0.92735 13 0.071 14 % + XC_Functional v_xc 0.27391 14 0.02 4.2 % + H_Hartree_pw v_hartree 0.61447 13 0.047 9.5 % + PW_Basis real2recip 0.60413 38 0.016 9.3 % + PW_Basis gatherp_scatters 0.22767 38 0.006 3.5 % + ORB_control set_orb_tables 0.89072 1 0.89 14 % + ORB_gen_tables gen_tables 0.89072 1 0.89 14 % + ORB_table_phi init_Table 0.37378 1 0.37 5.8 % + ORB_table_phi cal_ST_Phi12_R 0.36957 126 0.0029 5.7 % + ORB_table_beta init_Table_Beta 0.15159 1 0.15 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15033 56 0.0027 2.3 % + ORB_table_alpha init_Table_Alpha 0.20767 1 0.21 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.20601 66 0.0031 3.2 % + LOOP_ions opt_ions 5.1569 1 5.2 79 % + ESolver_KS_LCAO Run 4.6492 1 4.6 72 % + HSolverLCAO solve 2.4693 11 0.22 38 % + HamiltLCAO updateHk 1.264 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.235 11 0.11 19 % + Gint_interface cal_gint 2.208 23 0.096 34 % + Gint_Gamma distri_vl 2.2267 6 0.37 34 % + LCAO_Deepks cal_projected_DM 5.0097 13 0.39 77 % + LCAO_gen_fixedH add_v_delta 2.0988 6 0.35 32 % + LCAO_DESCRIPTOR add_v_delta 2.0988 6 0.35 32 % + ElecStateLCAO psiToRho 1.1882 11 0.11 18 % + Charge mix_rho 0.76515 10 0.077 12 % + LOOP_ions force_stress 0.50754 1 0.51 7.8 % + Force_Stress_LCAO getForceStress 0.50752 1 0.51 7.8 % + Force_LCAO_gamma ftable_gamma 0.31129 1 0.31 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.30395 1 0.3 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:54 2022 + FINISH Time : Wed Sep 28 11:13:01 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/171/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e17920acfe70437325cd6d5db7fcf96ebf1c1436 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.248007 0.530384 0.265445 +H 0.232787 0.463154 0.26419 +H 0.223543 0.54314 0.325848 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..426c1e8d6c56bd14abf4af49cd17bf17e8118e77 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.077 2 + 2 -12.3992 2 + 3 -9.4333 2 + 4 -6.70365 2 + 5 0.936993 0 + 6 3.85663 0 + 7 11.1453 0 + 8 11.4226 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1afba15ddb8a0875c78a5fb038260aa6dedb27f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:14 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.94418289589 14.8507554017 7.43245422294 0 0 0 0 + tauc_H1 6.518027247 12.9683043217 7.39733322508 0 0 0 0 + tauc_H2 6.25920751597 15.2079078874 9.12373059168 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105024001152 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105393479192 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123493438163 (SEC) + + DONE : INIT CHARGE Time : 0.166854295409 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449548 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00063 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102 + + Density error is 0.209007376985 + + Energy Rydberg eV + E_KohnSham -34.1899550134 -465.178202545 + E_Harris -34.370148083 -467.629855033 + E_Fermi -0.384876142117 -5.23650855705 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000910614070957 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126269736004 + + Density error is 0.0982799254672 + + Energy Rydberg eV + E_KohnSham -34.2760309878 -466.349326258 + E_Harris -34.2832443572 -466.447469184 + E_Fermi -0.198580682031 -2.70182878834 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000870946861394 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120291248142 + + Density error is 0.0633910229563 + + Energy Rydberg eV + E_KohnSham -34.2763947342 -466.354275283 + E_Harris -34.2810155644 -466.417144902 + E_Fermi -0.192162267616 -2.61450178018 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000826538981907 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113016077718 + + Density error is 0.00188107133131 + + Energy Rydberg eV + E_KohnSham -34.2762787754 -466.352697582 + E_Harris -34.2762791151 -466.352702204 + E_Fermi -0.156804992645 -2.13344137482 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827389598699 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011324064544 + + Density error is 0.000836462417867 + + Energy Rydberg eV + E_KohnSham -34.276262043 -466.352469925 + E_Harris -34.2762623852 -466.352474582 + E_Fermi -0.15700255321 -2.13612932421 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827011408326 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011315090297 + + Density error is 0.000137590928173 + + Energy Rydberg eV + E_KohnSham -34.2762661398 -466.352525666 + E_Harris -34.2762661353 -466.352525604 + E_Fermi -0.156480488801 -2.12902627352 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827031883032 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113144394286 + + Density error is 2.35934231599e-05 + + Energy Rydberg eV + E_KohnSham -34.2762669884 -466.352537212 + E_Harris -34.2762669887 -466.352537215 + E_Fermi -0.156462351474 -2.12877950253 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827007423185 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113141814934 + + Density error is 5.58503541755e-06 + + Energy Rydberg eV + E_KohnSham -34.2762676701 -466.352546486 + E_Harris -34.2762676702 -466.352546488 + E_Fermi -0.156462487147 -2.12878134845 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827009877637 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113142008741 + + Density error is 2.24935760596e-06 + + Energy Rydberg eV + E_KohnSham -34.2762672256 -466.352540438 + E_Harris -34.2762672256 -466.352540438 + E_Fermi -0.156458284015 -2.12872416191 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827007526439 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113141436778 + + Density error is 3.70126834741e-07 + + Energy Rydberg eV + E_KohnSham -34.2762673073 -466.35254155 + E_Harris -34.2762673073 -466.35254155 + E_Fermi -0.156456569475 -2.12870083439 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827008092931 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113141495935 + + Density error is 1.30203203612e-07 + + Energy Rydberg eV + E_KohnSham -34.2762673131 -466.352541629 + E_Harris -34.2762673131 -466.352541629 + E_Fermi -0.15645636341 -2.12869803073 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827008395339 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113141519559 + + Density error is 1.15322884175e-08 + + Energy Rydberg eV + E_KohnSham -34.2762673172 -466.352541685 + E_Harris -34.2762673172 -466.352541685 + E_band -7.88099770774 -107.22647475 + E_one_elec -68.5919243479 -933.241007917 + E_Hartree +35.6969714838 +485.682213524 + E_xc -8.15468732034 -110.950212965 + E_Ewald +6.89906066279 +93.8665358616 + E_demet -8.48484541395e-58 -1.15442244279e-56 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193662313163 -2.63491094688 + E_Fermi -0.156456292603 -2.12869706735 + + charge density convergence is achieved + final etot is -466.352541685 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0770 2.00000 + 2 -12.3992 2.00000 + 3 -9.43330 2.00000 + 4 -6.70365 2.00000 + 5 0.936993 0.00000 + 6 3.85663 0.00000 + 7 11.1453 0.00000 + 8 11.4226 0.00000 + + EFERMI = -2.128697067352264 eV + OUT.ABACUS/ final etot is -466.3525416846557 eV + correction force for each atom along direction 1 is 9.21131e-05 + correction force for each atom along direction 2 is -2.24881e-05 + correction force for each atom along direction 3 is 6.63545e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.75649933 -2.0861650 +0.60087266 + H1 +0.56447991 +1.6643271 -0.38905135 + H2 +0.19201941 +0.42183791 -0.21182131 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3525416846557 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4893 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4794 1 7.5 1.e+02% + Potential init_pot 0.28427 2 0.14 3.8% + PW_Basis recip2real 0.27498 17 0.016 3.7% + PW_Basis gathers_scatterp 0.12346 17 0.0073 1.6% + Potential v_of_rho 0.94353 14 0.067 13.% + XC_Functional v_xc 0.26427 15 0.018 3.5% + H_Hartree_pw v_hartree 0.63442 14 0.045 8.5% + PW_Basis real2recip 0.71878 41 0.018 9.6% + PW_Basis gatherp_scatters 0.28638 41 0.0070 3.8% + ORB_control set_orb_tables 1.1003 1 1.1 15.% + ORB_gen_tables gen_tables 1.1003 1 1.1 15.% + ORB_table_phi init_Table 0.47781 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47246 126 0.0037 6.3% + ORB_table_beta init_Table_Beta 0.18557 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18401 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24716 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24518 66 0.0037 3.3% + LOOP_ions opt_ions 5.8540 1 5.9 78.% + ESolver_KS_LCAO Run 5.2665 1 5.3 70.% + HSolverLCAO solve 2.7376 12 0.23 37.% + HamiltLCAO updateHk 1.4083 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.3789 12 0.11 18.% + Gint_interface cal_gint 1.5813 25 0.063 21.% + Gint_Gamma distri_vl_value 0.36113 12 0.030 4.8% + Gint_Gamma distri_vl 2.7364 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.5800 14 0.40 75.% + LCAO_gen_fixedH add_v_delta 2.5885 6 0.43 35.% + LCAO_DESCRIPTOR add_v_delta 2.5885 6 0.43 35.% + ElecStateLCAO psiToRho 1.3046 12 0.11 17.% + Charge mix_rho 0.97747 11 0.089 13.% + LOOP_ions force_stress 0.58734 1 0.59 7.8% + Force_Stress_LCAO getForceStress 0.58731 1 0.59 7.8% + Force_LCAO_gamma ftable_gamma 0.38491 1 0.38 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.26242 1 0.26 3.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:14 2022 + Finish Time : Wed Sep 28 11:09:21 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b603723e7a50b1a3fcdd1616380c2a0c6a82d4cd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123439 ima = 3.63769e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122923024161 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111600456328 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112407659605 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112600388119 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112599333499 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112599727979 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011259909237 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112599936832 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112599687866 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112599665656 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112599650948 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112599646909 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/STRU new file mode 100644 index 0000000000000000000000000000000000000000..bda62526ab61554faac89852ced7c377b10fe6f3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.055817104120 14.850755401649 7.432454222967 0 0 0 +H +0.0 +2 +-21.481972753015 12.968304321664 7.397333225092 0 0 0 +-21.740792484050 15.207907887433 9.123730591698 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/conv new file mode 100644 index 0000000000000000000000000000000000000000..a52361aed1986bda335c75eae1524f6c9c89d90c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/conv @@ -0,0 +1 @@ +172 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..10231c79bfffceae89a5bd2b200f373785144884 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755490859 0.01251938073 1.240476873 1.326716689 1.468474576 0.009514072368 0.01593719282 0.03927570474 +-6.158524382e-18 0.0007477448752 0.002624899168 0.01232214561 0.0429956597 5.84399794e-19 2.219607011e-06 6.401050672e-06 +0.001552869743 0.006024264177 + +H atom_index 1 n_descriptor 18 +1.174793676 0.0372745979 0.08669264288 0.1178333207 0.2921431039 0.01933191367 0.02381071337 0.04100625359 +-1.635040861e-17 3.72425953e-05 0.08101503562 0.1002343361 0.1120749932 -3.188276367e-18 5.903155619e-06 0.01522182691 +0.02318616809 0.0267998238 + +H atom_index 2 n_descriptor 18 +1.230151311 0.03561469494 0.1039053907 0.1406491686 0.3133399415 0.02203910018 0.027074572 0.03881874402 +-2.656703245e-17 4.193472922e-05 0.09494089569 0.1149777113 0.1202957274 -8.768042017e-18 3.762697943e-06 0.01365821036 +0.02549238173 0.02975604291 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..54c0da7c9689bf40a92680acd65d61d703b45ba8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:14 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105047 SEC) : SETUP UNITCELL + DONE(0.105409 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123515 SEC) : INIT PLANEWAVE + DONE(0.166995 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449614 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651782e+02 0.000000e+00 2.090e-01 5.319e-01 + GE2 -4.663493e+02 -1.171124e+00 9.828e-02 4.939e-01 + GE3 -4.663543e+02 -4.949025e-03 6.339e-02 5.663e-01 + GE4 -4.663527e+02 1.577701e-03 1.881e-03 4.214e-01 + GE5 -4.663525e+02 2.276570e-04 8.365e-04 4.207e-01 + GE6 -4.663525e+02 -5.574080e-05 1.376e-04 4.185e-01 + GE7 -4.663525e+02 -1.154611e-05 2.359e-05 4.023e-01 + GE8 -4.663525e+02 -9.274087e-06 5.585e-06 4.025e-01 + GE9 -4.663525e+02 6.048056e-06 2.249e-06 4.025e-01 + GE10 -4.663525e+02 -1.111689e-06 3.701e-07 4.035e-01 + GE11 -4.663525e+02 -7.935926e-08 1.302e-07 4.009e-01 + GE12 -4.663525e+02 -5.537223e-08 1.153e-08 3.394e-01 +E_delta_band = -6.79745176e-02 Ry = -9.24840759e-01 eV +E_delta_NN= -1.93662313e-01 Ry = -2.63491095e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4893 11 0.68 1e+02 % + Run_lcao lcao_line 7.4794 1 7.5 1e+02 % + Potential init_pot 0.28427 2 0.14 3.8 % + PW_Basis recip2real 0.27498 17 0.016 3.7 % + PW_Basis gathers_scatterp 0.12346 17 0.0073 1.6 % + Potential v_of_rho 0.94353 14 0.067 13 % + XC_Functional v_xc 0.26427 15 0.018 3.5 % + H_Hartree_pw v_hartree 0.63442 14 0.045 8.5 % + PW_Basis real2recip 0.71878 41 0.018 9.6 % + PW_Basis gatherp_scatters 0.28638 41 0.007 3.8 % + ORB_control set_orb_tables 1.1003 1 1.1 15 % + ORB_gen_tables gen_tables 1.1003 1 1.1 15 % + ORB_table_phi init_Table 0.47781 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47246 126 0.0037 6.3 % + ORB_table_beta init_Table_Beta 0.18557 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18401 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24716 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24518 66 0.0037 3.3 % + LOOP_ions opt_ions 5.854 1 5.9 78 % + ESolver_KS_LCAO Run 5.2665 1 5.3 70 % + HSolverLCAO solve 2.7376 12 0.23 37 % + HamiltLCAO updateHk 1.4083 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.3789 12 0.11 18 % + Gint_interface cal_gint 1.5813 25 0.063 21 % + Gint_Gamma distri_vl_value 0.36113 12 0.03 4.8 % + Gint_Gamma distri_vl 2.7364 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.58 14 0.4 75 % + LCAO_gen_fixedH add_v_delta 2.5885 6 0.43 35 % + LCAO_DESCRIPTOR add_v_delta 2.5885 6 0.43 35 % + ElecStateLCAO psiToRho 1.3046 12 0.11 17 % + Charge mix_rho 0.97747 11 0.089 13 % + LOOP_ions force_stress 0.58734 1 0.59 7.8 % + Force_Stress_LCAO getForceStress 0.58731 1 0.59 7.8 % + Force_LCAO_gamma ftable_gamma 0.38491 1 0.38 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.26242 1 0.26 3.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:14 2022 + FINISH Time : Wed Sep 28 11:09:21 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/172/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c3b8195d47c378e7d1d077b120da79ae94b41754 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.255654 0.53369 0.294576 +H 0.318413 0.526578 0.278353 +H 0.236935 0.592498 0.272291 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ece2fda619829569c058b91a7de2835002368175 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2487 2 + 2 -13.1817 2 + 3 -8.98647 2 + 4 -6.73451 2 + 5 1.32444 0 + 6 4.45558 0 + 7 11.077 0 + 8 11.3159 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c9cbc962d72b09620d389961e3a6a596abd310f4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.15829948925 14.9433307624 8.24812132597 0 0 0 0 + tauc_H1 8.91555051407 14.7441759853 7.79389594261 0 0 0 0 + tauc_H2 6.63417388526 16.589947192 7.6241344439 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0727306081665 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0730473587392 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0888042876861 (SEC) + + DONE : INIT CHARGE Time : 0.130396001822 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374233 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 337 ; sender_size of each process is: +144 144 49 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000651 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000706 + + Density error is 0.215326992366 + + Energy Rydberg eV + E_KohnSham -34.1912978514 -465.196472794 + E_Harris -34.3835761321 -467.812553013 + E_Fermi -0.405368902656 -5.51532686813 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000969658618401 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000873599279357 + + Density error is 0.0980066059412 + + Energy Rydberg eV + E_KohnSham -34.2808501648 -466.414894525 + E_Harris -34.2875466596 -466.506005012 + E_Fermi -0.213842210668 -2.909472538 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00103700438643 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000837653533871 + + Density error is 0.0628721546205 + + Energy Rydberg eV + E_KohnSham -34.2811165015 -466.418518222 + E_Harris -34.2854327787 -466.477244187 + E_Fermi -0.202369714725 -2.7533812229 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.0011668575538 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000786594297412 + + Density error is 0.00203980096257 + + Energy Rydberg eV + E_KohnSham -34.2811106415 -466.418438493 + E_Harris -34.2811130723 -466.418471566 + E_Fermi -0.166981873159 -2.27190493768 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115691365931 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785722379335 + + Density error is 0.00087853924594 + + Energy Rydberg eV + E_KohnSham -34.2810538467 -466.417665759 + E_Harris -34.2810548006 -466.417678739 + E_Fermi -0.166214520904 -2.26146457463 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115827914768 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785061915431 + + Density error is 0.00017926582885 + + Energy Rydberg eV + E_KohnSham -34.2810889061 -466.418142768 + E_Harris -34.2810889558 -466.418143444 + E_Fermi -0.166207933336 -2.26137494617 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115870043183 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785253655515 + + Density error is 3.86592924995e-05 + + Energy Rydberg eV + E_KohnSham -34.2810759539 -466.417966543 + E_Harris -34.2810759616 -466.417966649 + E_Fermi -0.166068801748 -2.2594819638 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115861499 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785188719669 + + Density error is 1.8580689298e-05 + + Energy Rydberg eV + E_KohnSham -34.2810805178 -466.418028639 + E_Harris -34.2810805194 -466.41802866 + E_Fermi -0.166111547391 -2.26006354811 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115861518668 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785188609858 + + Density error is 2.44824272017e-06 + + Energy Rydberg eV + E_KohnSham -34.2810789982 -466.418007963 + E_Harris -34.2810789982 -466.418007964 + E_Fermi -0.166093007136 -2.259811295 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115861486128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785188995708 + + Density error is 4.61145960339e-07 + + Energy Rydberg eV + E_KohnSham -34.2810792894 -466.418011926 + E_Harris -34.2810792894 -466.418011926 + E_Fermi -0.166090630584 -2.25977896035 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115861655648 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785189547038 + + Density error is 1.67870361347e-07 + + Energy Rydberg eV + E_KohnSham -34.2810793127 -466.418012242 + E_Harris -34.2810793127 -466.418012242 + E_Fermi -0.166090444764 -2.25977643214 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.0011586170454 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00078518971379 + + Density error is 1.03601994616e-08 + + Energy Rydberg eV + E_KohnSham -34.2810793157 -466.418012284 + E_Harris -34.2810793157 -466.418012284 + E_band -7.96011254035 -108.30288727 + E_one_elec -69.3048623598 -942.941027198 + E_Hartree +36.0512295737 +490.502142109 + E_xc -8.21128611997 -111.72027914 + E_Ewald +7.30816313787 +99.4326605886 + E_demet -5.0644910585e-78 -6.89059358657e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194767428091 -2.64994680684 + E_Fermi -0.166090283887 -2.2597742433 + + charge density convergence is achieved + final etot is -466.418012284 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2487 2.00000 + 2 -13.1817 2.00000 + 3 -8.98647 2.00000 + 4 -6.73451 2.00000 + 5 1.32444 0.00000 + 6 4.45558 0.00000 + 7 11.0770 0.00000 + 8 11.3159 0.00000 + + EFERMI = -2.259774243300376 eV + OUT.ABACUS/ final etot is -466.4180122839947 eV + correction force for each atom along direction 1 is 0.000119764 + correction force for each atom along direction 2 is 2.20961e-05 + correction force for each atom along direction 3 is 6.16320e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.52324177 -0.22744693 +0.27806080 + H1 +0.39002202 +0.11583848 -0.18022377 + H2 +0.13321975 +0.11160845 -0.097837025 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4180122839947 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3676 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3598 1 7.4 1.e+02% + Potential init_pot 0.24226 2 0.12 3.3% + PW_Basis recip2real 0.24219 17 0.014 3.3% + PW_Basis gathers_scatterp 0.11123 17 0.0065 1.5% + Potential v_of_rho 0.93796 14 0.067 13.% + XC_Functional v_xc 0.29163 15 0.019 4.0% + H_Hartree_pw v_hartree 0.60813 14 0.043 8.3% + PW_Basis real2recip 0.64580 41 0.016 8.8% + PW_Basis gatherp_scatters 0.25943 41 0.0063 3.5% + ORB_control set_orb_tables 0.89913 1 0.90 12.% + ORB_gen_tables gen_tables 0.89913 1 0.90 12.% + ORB_table_phi init_Table 0.37748 1 0.38 5.1% + ORB_table_phi cal_ST_Phi12_R 0.37324 126 0.0030 5.1% + ORB_table_beta init_Table_Beta 0.15626 1 0.16 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15494 56 0.0028 2.1% + ORB_table_alpha init_Table_Alpha 0.20812 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20649 66 0.0031 2.8% + LOOP_ions opt_ions 6.0142 1 6.0 82.% + ESolver_KS_LCAO Run 5.4716 1 5.5 74.% + HSolverLCAO solve 3.0948 12 0.26 42.% + HamiltLCAO updateHk 1.5550 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.5299 12 0.13 21.% + Gint_interface cal_gint 1.9468 25 0.078 26.% + Gint_Gamma distri_vl_value 0.40428 12 0.034 5.5% + Gint_Gamma distri_vl 2.8442 6 0.47 39.% + LCAO_Deepks cal_projected_DM 5.7924 14 0.41 79.% + LCAO_gen_fixedH add_v_delta 2.7158 6 0.45 37.% + LCAO_DESCRIPTOR add_v_delta 2.7158 6 0.45 37.% + ElecStateLCAO psiToRho 1.5196 12 0.13 21.% + Charge mix_rho 0.82991 11 0.075 11.% + LOOP_ions force_stress 0.54254 1 0.54 7.4% + Force_Stress_LCAO getForceStress 0.54251 1 0.54 7.4% + Force_LCAO_gamma ftable_gamma 0.34621 1 0.35 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.27438 1 0.27 3.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:48 2022 + Finish Time : Wed Sep 28 11:09:55 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..83070530415e620ce631ef0750931aab66754a14 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123775 ima = 3.65615e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001233294791 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011239412113 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112908677742 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113145786056 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011309922667 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113126968688 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113119038485 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113122025665 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113121195722 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113121124934 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113121108642 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113121100528 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c549c750e54a771a1b6e7aadbccc8b996ec239fd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.841700510734 14.943330762396 8.248121325958 0 0 0 +H +0.0 +2 +-19.084449485915 14.744175985272 7.793895942589 0 0 0 +-21.365826114740 16.589947192052 7.624134443896 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/conv new file mode 100644 index 0000000000000000000000000000000000000000..308edcb8aabb5f08639e9027a430429d29ac29fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/conv @@ -0,0 +1 @@ +173 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5b45b5256df839df0f7f04692c6174b730d95fd3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746946758 0.01265357772 1.27583221 1.366012258 1.469158618 0.008118720004 0.01933705974 0.03895571948 +1.889807435e-18 0.001101130181 0.002493542055 0.01231831655 0.04406947926 1.883061298e-19 1.781072787e-06 5.38272558e-06 +0.00170357382 0.005830723552 + +H atom_index 1 n_descriptor 18 +1.249247831 0.03399780663 0.1078490338 0.1502003105 0.3217569033 0.02197091234 0.02834591642 0.0371750117 +-4.941261665e-17 4.252958187e-05 0.101434882 0.1148915719 0.1289582027 -3.916021289e-18 4.25452389e-06 0.01304852634 +0.02612778081 0.03077946739 + +H atom_index 2 n_descriptor 18 +1.240234326 0.034313908 0.1047859852 0.1460704826 0.3188531836 0.02156442598 0.0278228279 0.03746694582 +-1.376869415e-17 4.174053668e-05 0.09916203737 0.1145631883 0.1253854052 -8.088990385e-18 4.70183156e-06 0.01313315284 +0.02579024404 0.030367576 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e0cc450684d543067282e1cb6250845d2e83bf00 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0727463 SEC) : SETUP UNITCELL + DONE(0.0730558 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0888195 SEC) : INIT PLANEWAVE + DONE(0.130528 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374278 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651965e+02 0.000000e+00 2.153e-01 5.263e-01 + GE2 -4.664149e+02 -1.218422e+00 9.801e-02 5.062e-01 + GE3 -4.664185e+02 -3.623696e-03 6.287e-02 5.693e-01 + GE4 -4.664184e+02 7.972849e-05 2.040e-03 4.468e-01 + GE5 -4.664177e+02 7.727337e-04 8.785e-04 4.442e-01 + GE6 -4.664181e+02 -4.770086e-04 1.793e-04 4.406e-01 + GE7 -4.664180e+02 1.762246e-04 3.866e-05 4.330e-01 + GE8 -4.664180e+02 -6.209553e-05 1.858e-05 4.256e-01 + GE9 -4.664180e+02 2.067548e-05 2.448e-06 4.239e-01 + GE10 -4.664180e+02 -3.962678e-06 4.611e-07 4.217e-01 + GE11 -4.664180e+02 -3.161440e-07 1.679e-07 4.239e-01 + GE12 -4.664180e+02 -4.171071e-08 1.036e-08 3.572e-01 +E_delta_band = -7.04438805e-02 Ry = -9.58438164e-01 eV +E_delta_NN= -1.94767428e-01 Ry = -2.64994681e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3676 11 0.67 1e+02 % + Run_lcao lcao_line 7.3598 1 7.4 1e+02 % + Potential init_pot 0.24226 2 0.12 3.3 % + PW_Basis recip2real 0.24219 17 0.014 3.3 % + PW_Basis gathers_scatterp 0.11123 17 0.0065 1.5 % + Potential v_of_rho 0.93796 14 0.067 13 % + XC_Functional v_xc 0.29163 15 0.019 4 % + H_Hartree_pw v_hartree 0.60813 14 0.043 8.3 % + PW_Basis real2recip 0.6458 41 0.016 8.8 % + PW_Basis gatherp_scatters 0.25943 41 0.0063 3.5 % + ORB_control set_orb_tables 0.89913 1 0.9 12 % + ORB_gen_tables gen_tables 0.89913 1 0.9 12 % + ORB_table_phi init_Table 0.37748 1 0.38 5.1 % + ORB_table_phi cal_ST_Phi12_R 0.37324 126 0.003 5.1 % + ORB_table_beta init_Table_Beta 0.15626 1 0.16 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15494 56 0.0028 2.1 % + ORB_table_alpha init_Table_Alpha 0.20812 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20649 66 0.0031 2.8 % + LOOP_ions opt_ions 6.0142 1 6 82 % + ESolver_KS_LCAO Run 5.4716 1 5.5 74 % + HSolverLCAO solve 3.0948 12 0.26 42 % + HamiltLCAO updateHk 1.555 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.5299 12 0.13 21 % + Gint_interface cal_gint 1.9468 25 0.078 26 % + Gint_Gamma distri_vl_value 0.40428 12 0.034 5.5 % + Gint_Gamma distri_vl 2.8442 6 0.47 39 % + LCAO_Deepks cal_projected_DM 5.7924 14 0.41 79 % + LCAO_gen_fixedH add_v_delta 2.7158 6 0.45 37 % + LCAO_DESCRIPTOR add_v_delta 2.7158 6 0.45 37 % + ElecStateLCAO psiToRho 1.5196 12 0.13 21 % + Charge mix_rho 0.82991 11 0.075 11 % + LOOP_ions force_stress 0.54254 1 0.54 7.4 % + Force_Stress_LCAO getForceStress 0.54251 1 0.54 7.4 % + Force_LCAO_gamma ftable_gamma 0.34621 1 0.35 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.27438 1 0.27 3.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:48 2022 + FINISH Time : Wed Sep 28 11:09:55 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/173/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c05753b71b04140bcc4e5165155c16534d3ef098 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.26594 0.547454 0.306223 +H 0.314786 0.504832 0.291492 +H 0.206879 0.513267 0.299819 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e878b0f13d001f6e3e8f546019e1fea9b103f24e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9055 2 + 2 -12.8948 2 + 3 -8.91746 2 + 4 -6.6554 2 + 5 1.00107 0 + 6 3.96255 0 + 7 11.1597 0 + 8 11.3941 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4d4212a41cfc7327f70abf3c99331bc934081463 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:46 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.44632602169 15.3287149335 8.57423653299 0 0 0 0 + tauc_H1 8.81401195935 14.1352831208 8.16177603413 0 0 0 0 + tauc_H2 5.79260148946 14.3714720303 8.39493450685 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.124674856873 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.125045164585 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.143082336165 (SEC) + + DONE : INIT CHARGE Time : 0.186096047974 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.468541 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00145 + + Density error is 0.212294683997 + + Energy Rydberg eV + E_KohnSham -34.1894969289 -465.171969986 + E_Harris -34.3750651339 -467.696754942 + E_Fermi -0.384674183639 -5.23376077099 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000871776016355 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121313048223 + + Density error is 0.0990387219902 + + Energy Rydberg eV + E_KohnSham -34.277766409 -466.372937875 + E_Harris -34.2848925622 -466.469894164 + E_Fermi -0.19521766853 -2.65607264229 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00083122608149 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112764470696 + + Density error is 0.0639779397346 + + Energy Rydberg eV + E_KohnSham -34.278185887 -466.378645166 + E_Harris -34.2827292496 -466.440460786 + E_Fermi -0.188648695075 -2.56669717329 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0007786763235 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000956659668169 + + Density error is 0.00205900219043 + + Energy Rydberg eV + E_KohnSham -34.2780917898 -466.377364908 + E_Harris -34.2780959462 -466.377421459 + E_Fermi -0.15365716296 -2.09061295477 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000778360504978 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000953150064387 + + Density error is 0.000919544650011 + + Energy Rydberg eV + E_KohnSham -34.2780622833 -466.376963452 + E_Harris -34.2780624498 -466.376965718 + E_Fermi -0.153490412803 -2.08834420249 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000777736846079 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950502548945 + + Density error is 0.000200607889886 + + Energy Rydberg eV + E_KohnSham -34.2780745822 -466.377130787 + E_Harris -34.278074585 -466.377130825 + E_Fermi -0.153064328371 -2.08254702638 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000777910425484 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00095047301938 + + Density error is 2.75811855354e-05 + + Energy Rydberg eV + E_KohnSham -34.2780711267 -466.377083773 + E_Harris -34.278071129 -466.377083804 + E_Fermi -0.153039137268 -2.08220428385 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00077785866102 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950425919184 + + Density error is 1.19297062202e-05 + + Energy Rydberg eV + E_KohnSham -34.2780737854 -466.377119946 + E_Harris -34.2780737861 -466.377119955 + E_Fermi -0.153053421988 -2.08239863743 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000777860968685 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950407435719 + + Density error is 1.77467062633e-06 + + Energy Rydberg eV + E_KohnSham -34.2780728387 -466.377107065 + E_Harris -34.2780728387 -466.377107065 + E_Fermi -0.153041734328 -2.08223961867 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000777861563768 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950404282686 + + Density error is 5.14150648333e-07 + + Energy Rydberg eV + E_KohnSham -34.2780730232 -466.377109576 + E_Harris -34.2780730232 -466.377109576 + E_Fermi -0.153040406751 -2.08222155606 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000777861815748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950404270651 + + Density error is 1.50289129313e-07 + + Energy Rydberg eV + E_KohnSham -34.2780730315 -466.377109689 + E_Harris -34.2780730315 -466.377109689 + E_Fermi -0.153040128558 -2.08221777105 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00077786181243 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000950404059897 + + Density error is 1.08585302676e-08 + + Energy Rydberg eV + E_KohnSham -34.2780730366 -466.377109758 + E_Harris -34.2780730366 -466.377109758 + E_band -7.84572085353 -106.746508525 + E_one_elec -68.5943665848 -933.274236254 + E_Hartree +35.7179217248 +485.967256176 + E_xc -8.1578381446 -110.993082128 + E_Ewald +6.88197165102 +93.6340279284 + E_demet -1.96802556723e-58 -2.67763615241e-57 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193504322666 -2.63276137589 + E_Fermi -0.153039984219 -2.08221580721 + + charge density convergence is achieved + final etot is -466.377109758 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9055 2.00000 + 2 -12.8948 2.00000 + 3 -8.91746 2.00000 + 4 -6.65540 2.00000 + 5 1.00107 0.00000 + 6 3.96255 0.00000 + 7 11.1597 0.00000 + 8 11.3941 0.00000 + + EFERMI = -2.082215807209022 eV + OUT.ABACUS/ final etot is -466.3771097581784 eV + correction force for each atom along direction 1 is -2.17010e-05 + correction force for each atom along direction 2 is -0.000109138 + correction force for each atom along direction 3 is -0.000185740 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.1325286 -0.78130268 -0.16610251 + H1 -0.55414116 +0.11221091 +0.066082126 + H2 +1.6866697 +0.66909178 +0.10002038 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3771097581784 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3449 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3338 1 7.3 1.e+02% + Potential init_pot 0.28443 2 0.14 3.9% + PW_Basis recip2real 0.27310 17 0.016 3.7% + PW_Basis gathers_scatterp 0.12220 17 0.0072 1.7% + Potential v_of_rho 0.88197 14 0.063 12.% + XC_Functional v_xc 0.23242 15 0.015 3.2% + H_Hartree_pw v_hartree 0.60696 14 0.043 8.3% + PW_Basis real2recip 0.70450 41 0.017 9.6% + PW_Basis gatherp_scatters 0.28855 41 0.0070 3.9% + ORB_control set_orb_tables 1.0963 1 1.1 15.% + ORB_gen_tables gen_tables 1.0963 1 1.1 15.% + ORB_table_phi init_Table 0.47535 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47014 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18543 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18390 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24691 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24488 66 0.0037 3.3% + LOOP_ions opt_ions 5.6922 1 5.7 77.% + ESolver_KS_LCAO Run 5.1169 1 5.1 70.% + HSolverLCAO solve 2.6400 12 0.22 36.% + HamiltLCAO updateHk 1.3620 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.3324 12 0.11 18.% + Gint_interface cal_gint 1.1458 25 0.046 16.% + Gint_Gamma distri_vl_value 0.48101 12 0.040 6.5% + Gint_Gamma distri_vl 2.6647 6 0.44 36.% + LCAO_Deepks cal_projected_DM 5.3742 14 0.38 73.% + LCAO_gen_fixedH add_v_delta 2.5180 6 0.42 34.% + LCAO_DESCRIPTOR add_v_delta 2.5180 6 0.42 34.% + ElecStateLCAO psiToRho 1.2537 12 0.10 17.% + Charge mix_rho 0.97095 11 0.088 13.% + LOOP_ions force_stress 0.57517 1 0.58 7.8% + Force_Stress_LCAO getForceStress 0.57514 1 0.58 7.8% + Force_LCAO_gamma ftable_gamma 0.37871 1 0.38 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.20853 1 0.21 2.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:46 2022 + Finish Time : Wed Sep 28 11:09:53 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0114a2163fdc7cbbb08e650b555cff4434ad342e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123118 ima = 3.64948e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123909270209 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011255366916 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113299359773 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113479210963 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113467258936 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113476061355 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113471923825 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113473790643 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001134732534 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113473213946 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113473193038 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113473185292 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/STRU new file mode 100644 index 0000000000000000000000000000000000000000..016ecee9e88ab1a1afc2b6eacb476eda0a7cc4f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.553673978308 15.328714933505 8.574236532998 0 0 0 +H +0.0 +2 +-19.185988040658 14.135283120744 8.161776034140 0 0 0 +-22.207398510547 14.371472030283 8.394934506867 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/conv new file mode 100644 index 0000000000000000000000000000000000000000..8b95303caf53a871615c639f3ca6fdf201565c52 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/conv @@ -0,0 +1 @@ +174 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ad3466d761af4cb93cfe32f33b80e1e34fb6d561 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747215247 0.01235024961 1.245077519 1.344045969 1.467677044 0.007929065774 0.01885075355 0.03900261328 +1.903451415e-19 0.000940385817 0.002276360279 0.0112702482 0.04026721936 -1.615472348e-19 1.355450849e-06 4.395106906e-06 +0.001673964454 0.005695705431 + +H atom_index 1 n_descriptor 18 +1.221102285 0.03501792918 0.09771066744 0.1380452883 0.3132930168 0.0203897212 0.02676537976 0.03830898319 +-1.479154575e-17 3.446185675e-05 0.09143867212 0.1144813068 0.1181657421 -1.081237944e-17 5.13812353e-06 0.0134080837 +0.02434771869 0.02944499869 + +H atom_index 2 n_descriptor 18 +1.175406325 0.03646511049 0.08418094061 0.1194800512 0.2964021819 0.01834085877 0.02410432203 0.04018233218 +8.47558291e-19 3.098032837e-05 0.07963490428 0.1018109973 0.1126697349 8.060015088e-18 6.348033473e-06 0.01469955024 +0.02246072053 0.02703956579 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fa5c6a6b1340a24dee97ddcfad9521717e1af950 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:46 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.124699 SEC) : SETUP UNITCELL + DONE(0.12506 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.143103 SEC) : INIT PLANEWAVE + DONE(0.186232 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.468607 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651720e+02 0.000000e+00 2.123e-01 5.213e-01 + GE2 -4.663729e+02 -1.200968e+00 9.904e-02 4.790e-01 + GE3 -4.663786e+02 -5.707291e-03 6.398e-02 5.500e-01 + GE4 -4.663774e+02 1.280258e-03 2.059e-03 4.067e-01 + GE5 -4.663770e+02 4.014555e-04 9.195e-04 4.079e-01 + GE6 -4.663771e+02 -1.673345e-04 2.006e-04 4.037e-01 + GE7 -4.663771e+02 4.701423e-05 2.758e-05 3.924e-01 + GE8 -4.663771e+02 -3.617388e-05 1.193e-05 3.896e-01 + GE9 -4.663771e+02 1.288152e-05 1.775e-06 3.907e-01 + GE10 -4.663771e+02 -2.510952e-06 5.142e-07 3.897e-01 + GE11 -4.663771e+02 -1.133094e-07 1.503e-07 3.895e-01 + GE12 -4.663771e+02 -6.896918e-08 1.086e-08 3.331e-01 +E_delta_band = -6.77426396e-02 Ry = -9.21685895e-01 eV +E_delta_NN= -1.93504323e-01 Ry = -2.63276138e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3449 11 0.67 1e+02 % + Run_lcao lcao_line 7.3338 1 7.3 1e+02 % + Potential init_pot 0.28443 2 0.14 3.9 % + PW_Basis recip2real 0.2731 17 0.016 3.7 % + PW_Basis gathers_scatterp 0.1222 17 0.0072 1.7 % + Potential v_of_rho 0.88197 14 0.063 12 % + XC_Functional v_xc 0.23242 15 0.015 3.2 % + H_Hartree_pw v_hartree 0.60696 14 0.043 8.3 % + PW_Basis real2recip 0.7045 41 0.017 9.6 % + PW_Basis gatherp_scatters 0.28855 41 0.007 3.9 % + ORB_control set_orb_tables 1.0963 1 1.1 15 % + ORB_gen_tables gen_tables 1.0963 1 1.1 15 % + ORB_table_phi init_Table 0.47535 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.47014 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18543 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.1839 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24691 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24488 66 0.0037 3.3 % + LOOP_ions opt_ions 5.6922 1 5.7 77 % + ESolver_KS_LCAO Run 5.1169 1 5.1 70 % + HSolverLCAO solve 2.64 12 0.22 36 % + HamiltLCAO updateHk 1.362 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.3324 12 0.11 18 % + Gint_interface cal_gint 1.1458 25 0.046 16 % + Gint_Gamma distri_vl_value 0.48101 12 0.04 6.5 % + Gint_Gamma distri_vl 2.6647 6 0.44 36 % + LCAO_Deepks cal_projected_DM 5.3742 14 0.38 73 % + LCAO_gen_fixedH add_v_delta 2.518 6 0.42 34 % + LCAO_DESCRIPTOR add_v_delta 2.518 6 0.42 34 % + ElecStateLCAO psiToRho 1.2537 12 0.1 17 % + Charge mix_rho 0.97095 11 0.088 13 % + LOOP_ions force_stress 0.57517 1 0.58 7.8 % + Force_Stress_LCAO getForceStress 0.57514 1 0.58 7.8 % + Force_LCAO_gamma ftable_gamma 0.37871 1 0.38 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.20853 1 0.21 2.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:46 2022 + FINISH Time : Wed Sep 28 11:09:53 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/174/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..f9abb8add44be388fdc70af2d505291a5c367025 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.274304 0.547706 0.301889 +H 0.328112 0.541394 0.338984 +H 0.234093 0.566447 0.350019 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..135114d40aae6eeb3daaaf8abfa62ee3c98082ac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4372 2 + 2 -12.6535 2 + 3 -9.5058 2 + 4 -6.7796 2 + 5 1.2453 0 + 6 4.37155 0 + 7 11.0651 0 + 8 11.3578 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7f799c1c9b5a4577f8d9852240ac957e1afdc430 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:12 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.68050295307 15.3357809042 8.45290365191 0 0 0 0 + tauc_H1 9.1871313162 15.1590250052 9.49155018388 0 0 0 0 + tauc_H2 6.55459689134 15.8605192361 9.80052876195 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874720360614 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0991958860292 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117732694974 (SEC) + + DONE : INIT CHARGE Time : 0.168743534466 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450557 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000916 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115 + + Density error is 0.213973472278 + + Energy Rydberg eV + E_KohnSham -34.18747298 -465.14443275 + E_Harris -34.3783907001 -467.742001592 + E_Fermi -0.40655950647 -5.53152586406 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00133282233104 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117596425964 + + Density error is 0.0977653535927 + + Energy Rydberg eV + E_KohnSham -34.2781469515 -466.378115422 + E_Harris -34.2851101667 -466.472854825 + E_Fermi -0.215552797324 -2.93274626345 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127319331488 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011002278308 + + Density error is 0.0628907132829 + + Energy Rydberg eV + E_KohnSham -34.2786003258 -466.384283896 + E_Harris -34.2831093758 -466.445632668 + E_Fermi -0.205933577558 -2.80187006431 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011992580198 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000976196179075 + + Density error is 0.00192388521754 + + Energy Rydberg eV + E_KohnSham -34.2785624434 -466.383768479 + E_Harris -34.2785628357 -466.383773817 + E_Fermi -0.169971860561 -2.31258580329 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120369544938 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000978055871161 + + Density error is 0.00107987444095 + + Energy Rydberg eV + E_KohnSham -34.2784932282 -466.382826758 + E_Harris -34.2784953277 -466.382855324 + E_Fermi -0.169566516011 -2.30707080776 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120178296146 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000975888417751 + + Density error is 0.000104816000404 + + Energy Rydberg eV + E_KohnSham -34.2785359291 -466.383407734 + E_Harris -34.2785359397 -466.383407878 + E_Fermi -0.169440186776 -2.30535201034 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120148039231 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000975483417285 + + Density error is 4.10135554326e-05 + + Energy Rydberg eV + E_KohnSham -34.2785238306 -466.383243125 + E_Harris -34.2785238397 -466.383243248 + E_Fermi -0.16932627877 -2.30380221241 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120144458768 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000975510197141 + + Density error is 1.63304838968e-05 + + Energy Rydberg eV + E_KohnSham -34.2785250595 -466.383259845 + E_Harris -34.2785250607 -466.383259861 + E_Fermi -0.16938179011 -2.30455748294 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120145861851 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000975509300857 + + Density error is 2.33280529154e-06 + + Energy Rydberg eV + E_KohnSham -34.2785236968 -466.383241305 + E_Harris -34.2785236968 -466.383241305 + E_Fermi -0.169365939249 -2.30434182091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120146029758 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000975508765473 + + Density error is 3.09962335403e-07 + + Energy Rydberg eV + E_KohnSham -34.2785239408 -466.383244625 + E_Harris -34.2785239408 -466.383244625 + E_Fermi -0.169363628417 -2.30431038042 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001201461327 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000975509581037 + + Density error is 3.35804408549e-08 + + Energy Rydberg eV + E_KohnSham -34.2785239785 -466.383245137 + E_Harris -34.2785239785 -466.383245137 + E_band -7.99314444313 -108.752309364 + E_one_elec -69.3082355062 -942.98692121 + E_Hartree +36.0345819614 +490.275639722 + E_xc -8.20854778886 -111.683022234 + E_Ewald +7.32791611081 +99.701413573 + E_demet -1.42041383958e-76 -1.93257217364e-75 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194877939221 -2.6514503879 + E_Fermi -0.169363511263 -2.30430878646 + + charge density convergence is achieved + final etot is -466.383245137 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4372 2.00000 + 2 -12.6535 2.00000 + 3 -9.50580 2.00000 + 4 -6.77960 2.00000 + 5 1.24530 0.00000 + 6 4.37155 0.00000 + 7 11.0651 0.00000 + 8 11.3578 0.00000 + + EFERMI = -2.304308786459388 eV + OUT.ABACUS/ final etot is -466.3832451373469 eV + correction force for each atom along direction 1 is -2.30949e-05 + correction force for each atom along direction 2 is -9.10501e-05 + correction force for each atom along direction 3 is 0.000197133 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.16750261 +0.018413871 +0.35727040 + H1 +0.62221212 -0.20687149 -0.31288333 + H2 -0.78971474 +0.18845762 -0.044387075 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3832451373469 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8633 11 0.71 1.0e+02% + Run_lcao lcao_line 7.8533 1 7.9 1.e+02% + Potential init_pot 0.28424 2 0.14 3.6% + PW_Basis recip2real 0.27059 16 0.017 3.4% + PW_Basis gathers_scatterp 0.13159 16 0.0082 1.7% + Potential v_of_rho 1.0238 13 0.079 13.% + XC_Functional v_xc 0.35162 14 0.025 4.5% + H_Hartree_pw v_hartree 0.63631 13 0.049 8.1% + PW_Basis real2recip 0.65184 38 0.017 8.3% + PW_Basis gatherp_scatters 0.28632 38 0.0075 3.6% + ORB_control set_orb_tables 1.1003 1 1.1 14.% + ORB_gen_tables gen_tables 1.1003 1 1.1 14.% + ORB_table_phi init_Table 0.48000 1 0.48 6.1% + ORB_table_phi cal_ST_Phi12_R 0.47471 126 0.0038 6.0% + ORB_table_beta init_Table_Beta 0.18637 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18484 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24891 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24690 66 0.0037 3.1% + LOOP_ions opt_ions 6.2231 1 6.2 79.% + ESolver_KS_LCAO Run 5.6048 1 5.6 71.% + HSolverLCAO solve 3.3161 11 0.30 42.% + HamiltLCAO updateHk 1.6404 11 0.15 21.% + LCAO_Hamilt cal_Hgamma 1.6132 11 0.15 21.% + Gint_interface cal_gint 1.1668 23 0.051 15.% + Gint_Gamma distri_vl_value 0.76473 11 0.070 9.7% + Gint_Gamma distri_vl 2.6859 6 0.45 34.% + LCAO_Deepks cal_projected_DM 5.8681 13 0.45 75.% + LCAO_gen_fixedH add_v_delta 2.5560 6 0.43 33.% + LCAO_DESCRIPTOR add_v_delta 2.5561 6 0.43 33.% + ElecStateLCAO psiToRho 1.6396 11 0.15 21.% + Charge mix_rho 0.71461 10 0.071 9.1% + LOOP_ions force_stress 0.61821 1 0.62 7.9% + Force_Stress_LCAO getForceStress 0.61818 1 0.62 7.9% + Force_LCAO_gamma ftable_gamma 0.39670 1 0.40 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.22769 1 0.23 2.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:12 2022 + Finish Time : Wed Sep 28 11:08:20 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..49c8c676598365bec564ca00b2a27be6bdd33f4d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012374 ima = 3.65523e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122671376806 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111234066506 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111907661723 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112187717194 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112123803453 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011215742193 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112157029078 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112159734808 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112158976776 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112158870012 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112158850936 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/STRU new file mode 100644 index 0000000000000000000000000000000000000000..fd0e96eab074cc1ac261c017c0024077d257ec95 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.319497046946 15.335780904267 8.452903651923 0 0 0 +H +0.0 +2 +-18.812868683805 15.159025005165 9.491550183856 0 0 0 +-21.445403108668 15.860519236095 9.800528761969 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/conv new file mode 100644 index 0000000000000000000000000000000000000000..ad4a6110c8cded68a272de28f0e173e2829c927e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/conv @@ -0,0 +1 @@ +175 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..078bb50b5b8785d77398c54e48cdf3a1620a371b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755143307 0.01282899703 1.270858323 1.349633281 1.469805204 0.009708909933 0.01634362558 0.03919620711 +-1.996081936e-18 0.0008700454055 0.002900800893 0.01357670829 0.04708702673 -9.800284112e-19 2.978134696e-06 7.795067019e-06 +0.001591626513 0.006183831164 + +H atom_index 1 n_descriptor 18 +1.246286768 0.0351662058 0.1108554301 0.147817301 0.3180982463 0.02330489733 0.0280098498 0.03826185243 +-3.962410871e-17 4.981853341e-05 0.1026963866 0.1152923878 0.126709974 -4.031557728e-18 2.922410928e-06 0.01348698857 +0.02707378154 0.03057008086 + +H atom_index 2 n_descriptor 18 +1.250739385 0.03501779426 0.1124481906 0.1498874559 0.3195920402 0.02352957605 0.02827146793 0.03811916106 +3.045212615e-17 5.022655891e-05 0.1036559648 0.1156405836 0.128496767 1.388425046e-17 2.678818543e-06 0.01344573219 +0.02723959513 0.03077650648 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..6ac5be04e3c65b279125de4ee014e90c20b84111 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:12 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874936 SEC) : SETUP UNITCELL + DONE(0.0992246 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.117754 SEC) : INIT PLANEWAVE + DONE(0.168876 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450628 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651444e+02 0.000000e+00 2.140e-01 6.078e-01 + GE2 -4.663781e+02 -1.233683e+00 9.777e-02 5.624e-01 + GE3 -4.663843e+02 -6.168474e-03 6.289e-02 6.277e-01 + GE4 -4.663838e+02 5.154167e-04 1.924e-03 4.915e-01 + GE5 -4.663828e+02 9.417209e-04 1.080e-03 4.909e-01 + GE6 -4.663834e+02 -5.809756e-04 1.048e-04 4.749e-01 + GE7 -4.663832e+02 1.646089e-04 4.101e-05 4.736e-01 + GE8 -4.663833e+02 -1.671981e-05 1.633e-05 4.687e-01 + GE9 -4.663832e+02 1.854036e-05 2.333e-06 4.710e-01 + GE10 -4.663832e+02 -3.320351e-06 3.100e-07 4.720e-01 + GE11 -4.663832e+02 -5.124827e-07 3.358e-08 3.969e-01 +E_delta_band = -7.06391836e-02 Ry = -9.61095399e-01 eV +E_delta_NN= -1.94877939e-01 Ry = -2.65145039e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8633 11 0.71 1e+02 % + Run_lcao lcao_line 7.8533 1 7.9 1e+02 % + Potential init_pot 0.28424 2 0.14 3.6 % + PW_Basis recip2real 0.27059 16 0.017 3.4 % + PW_Basis gathers_scatterp 0.13159 16 0.0082 1.7 % + Potential v_of_rho 1.0238 13 0.079 13 % + XC_Functional v_xc 0.35162 14 0.025 4.5 % + H_Hartree_pw v_hartree 0.63631 13 0.049 8.1 % + PW_Basis real2recip 0.65184 38 0.017 8.3 % + PW_Basis gatherp_scatters 0.28632 38 0.0075 3.6 % + ORB_control set_orb_tables 1.1003 1 1.1 14 % + ORB_gen_tables gen_tables 1.1003 1 1.1 14 % + ORB_table_phi init_Table 0.48 1 0.48 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.47471 126 0.0038 6 % + ORB_table_beta init_Table_Beta 0.18637 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18484 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24891 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.2469 66 0.0037 3.1 % + LOOP_ions opt_ions 6.2231 1 6.2 79 % + ESolver_KS_LCAO Run 5.6048 1 5.6 71 % + HSolverLCAO solve 3.3161 11 0.3 42 % + HamiltLCAO updateHk 1.6404 11 0.15 21 % + LCAO_Hamilt cal_Hgamma 1.6132 11 0.15 21 % + Gint_interface cal_gint 1.1668 23 0.051 15 % + Gint_Gamma distri_vl_value 0.76473 11 0.07 9.7 % + Gint_Gamma distri_vl 2.6859 6 0.45 34 % + LCAO_Deepks cal_projected_DM 5.8681 13 0.45 75 % + LCAO_gen_fixedH add_v_delta 2.556 6 0.43 33 % + LCAO_DESCRIPTOR add_v_delta 2.5561 6 0.43 33 % + ElecStateLCAO psiToRho 1.6396 11 0.15 21 % + Charge mix_rho 0.71461 10 0.071 9.1 % + LOOP_ions force_stress 0.61821 1 0.62 7.9 % + Force_Stress_LCAO getForceStress 0.61818 1 0.62 7.9 % + Force_LCAO_gamma ftable_gamma 0.3967 1 0.4 5 % + Force_LCAO_gamma cal_fvl_dphi 0.22769 1 0.23 2.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:12 2022 + FINISH Time : Wed Sep 28 11:08:20 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/175/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..824025b7f7f57f506f17841bffa6d648fc87a174 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.281105 0.542467 0.306653 +H 0.344883 0.55707 0.32192 +H 0.247685 0.596408 0.318925 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..44bee17458ac36a7e7d8c10334ecd63e2a0e6a06 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1985 2 + 2 -13.0494 2 + 3 -9.03839 2 + 4 -6.72273 2 + 5 1.23034 0 + 6 4.34116 0 + 7 11.0934 0 + 8 11.3355 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..55fe36dca9440257eec4faafee7feda918e2ee19 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:28 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.87093753002 15.1890690265 8.58628897189 0 0 0 0 + tauc_H1 9.65671558205 15.5979666983 9.01377168023 0 0 0 0 + tauc_H2 6.93517167751 16.6994312772 8.92990924058 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.107001301497 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.107364704665 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.125522809832 (SEC) + + DONE : INIT CHARGE Time : 0.168783229042 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.45189 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00138 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000979 + + Density error is 0.214509205947 + + Energy Rydberg eV + E_KohnSham -34.1902553982 -465.182289491 + E_Harris -34.3810830084 -467.778632325 + E_Fermi -0.400919131383 -5.45478462402 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00130464865075 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103000155526 + + Density error is 0.0982841787305 + + Energy Rydberg eV + E_KohnSham -34.2798406943 -466.401159975 + E_Harris -34.2866541503 -466.493861799 + E_Fermi -0.210106991451 -2.85865227338 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121162426363 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968981461215 + + Density error is 0.0631622925515 + + Energy Rydberg eV + E_KohnSham -34.2801682653 -466.405616806 + E_Harris -34.2845661946 -466.465453705 + E_Fermi -0.200023687961 -2.72146189125 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105146856884 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000866821367812 + + Density error is 0.00201082306862 + + Energy Rydberg eV + E_KohnSham -34.2801372448 -466.405194751 + E_Harris -34.2801391419 -466.405220563 + E_Fermi -0.164583943352 -2.2392794289 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010508210481 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865530731902 + + Density error is 0.000904340774919 + + Energy Rydberg eV + E_KohnSham -34.2800854895 -466.404490584 + E_Harris -34.2800861254 -466.404499237 + E_Fermi -0.164046622428 -2.23196880268 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010488363079 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000864283370845 + + Density error is 0.000170982369221 + + Energy Rydberg eV + E_KohnSham -34.2801142242 -466.40488154 + E_Harris -34.280114253 -466.404881931 + E_Fermi -0.163896400871 -2.22992493353 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104881490625 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000864369325034 + + Density error is 3.73950541121e-05 + + Energy Rydberg eV + E_KohnSham -34.2801041581 -466.404744583 + E_Harris -34.280104165 -466.404744678 + E_Fermi -0.163788010838 -2.22845021148 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104878796802 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000864320373342 + + Density error is 1.58736755821e-05 + + Energy Rydberg eV + E_KohnSham -34.28010818 -466.404799304 + E_Harris -34.2801081811 -466.404799319 + E_Fermi -0.163823856749 -2.22893792012 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104876775334 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000864306146653 + + Density error is 1.7399654373e-06 + + Energy Rydberg eV + E_KohnSham -34.280106795 -466.40478046 + E_Harris -34.280106795 -466.40478046 + E_Fermi -0.163807217011 -2.22871152488 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104876421566 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000864306200876 + + Density error is 2.40820675068e-07 + + Energy Rydberg eV + E_KohnSham -34.2801070269 -466.404783616 + E_Harris -34.2801070269 -466.404783616 + E_Fermi -0.163805743044 -2.22869147052 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104876449745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000864306770032 + + Density error is 5.13238955985e-08 + + Energy Rydberg eV + E_KohnSham -34.2801070531 -466.404783972 + E_Harris -34.2801070531 -466.404783972 + E_band -7.93918661374 -108.018175432 + E_one_elec -69.145325811 -940.770421097 + E_Hartree +35.9738241054 +489.448986683 + E_xc -8.19900806185 -111.553227589 + E_Ewald +7.21504575349 +98.1657335782 + E_demet -7.51937557023e-73 -1.02306353157e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194527264938 -2.64667921952 + E_Fermi -0.163805663917 -2.22869039395 + + charge density convergence is achieved + final etot is -466.404783972 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1985 2.00000 + 2 -13.0494 2.00000 + 3 -9.03839 2.00000 + 4 -6.72273 2.00000 + 5 1.23034 0.00000 + 6 4.34116 0.00000 + 7 11.0934 0.00000 + 8 11.3355 0.00000 + + EFERMI = -2.228690393945226 eV + OUT.ABACUS/ final etot is -466.4047839721508 eV + correction force for each atom along direction 1 is 3.93859e-05 + correction force for each atom along direction 2 is 0.000102329 + correction force for each atom along direction 3 is -0.000106847 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.3407027 -0.70538757 -0.019643217 + H1 -0.94917174 -0.11769890 -0.19062158 + H2 -0.39153093 +0.82308647 +0.21026480 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4047839721508 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7595 11 0.61 1.0e+02% + Run_lcao lcao_line 6.7497 1 6.7 1.e+02% + Potential init_pot 0.28574 2 0.14 4.2% + PW_Basis recip2real 0.25674 16 0.016 3.8% + PW_Basis gathers_scatterp 0.11379 16 0.0071 1.7% + Potential v_of_rho 0.81531 13 0.063 12.% + XC_Functional v_xc 0.21105 14 0.015 3.1% + H_Hartree_pw v_hartree 0.56461 13 0.043 8.4% + PW_Basis real2recip 0.65229 38 0.017 9.6% + PW_Basis gatherp_scatters 0.26881 38 0.0071 4.0% + ORB_control set_orb_tables 1.1021 1 1.1 16.% + ORB_gen_tables gen_tables 1.1020 1 1.1 16.% + ORB_table_phi init_Table 0.47568 1 0.48 7.0% + ORB_table_phi cal_ST_Phi12_R 0.47043 126 0.0037 7.0% + ORB_table_beta init_Table_Beta 0.18555 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18401 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25088 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.24887 66 0.0038 3.7% + LOOP_ions opt_ions 5.1193 1 5.1 76.% + ESolver_KS_LCAO Run 4.5590 1 4.6 67.% + HSolverLCAO solve 2.3062 11 0.21 34.% + HamiltLCAO updateHk 1.2177 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1902 11 0.11 18.% + Gint_interface cal_gint 0.80071 23 0.035 12.% + Gint_Gamma distri_vl_value 0.47833 11 0.043 7.1% + Gint_Gamma distri_vl 2.1942 6 0.37 32.% + LCAO_Deepks cal_projected_DM 4.7920 13 0.37 71.% + LCAO_gen_fixedH add_v_delta 2.0466 6 0.34 30.% + LCAO_DESCRIPTOR add_v_delta 2.0466 6 0.34 30.% + ElecStateLCAO psiToRho 1.0685 11 0.097 16.% + Charge mix_rho 0.88873 10 0.089 13.% + LOOP_ions force_stress 0.56006 1 0.56 8.3% + Force_Stress_LCAO getForceStress 0.56003 1 0.56 8.3% + Force_LCAO_gamma ftable_gamma 0.36234 1 0.36 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.17813 1 0.18 2.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:28 2022 + Finish Time : Wed Sep 28 11:08:35 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..52751661fd586d80afeb3f6cf3a6871eafb5520f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012369 ima = 3.6417e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123375281483 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112227494184 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112817182483 + charge after normalized = 8.00000000000004 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113044142393 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011300567254 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113028054315 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113021181743 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113024010103 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113023323583 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113023251294 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113023240349 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9df04c3180739dcac893fb72b8cc9550eadb7bd9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.129062469983 15.189069026472 8.586288971894 0 0 0 +H +0.0 +2 +-18.343284417944 15.597966698244 9.013771680204 0 0 0 +-21.064828322483 16.699431277164 8.929909240582 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/conv new file mode 100644 index 0000000000000000000000000000000000000000..acdb5930bf741df45fc070d1b399b82cbcab0e17 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/conv @@ -0,0 +1 @@ +176 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e428804740d9fe6060d1f9964269afe8e1225871 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748205898 0.0125982695 1.266075257 1.360930927 1.468937716 0.008279897193 0.01883570891 0.0390060923 +2.556430555e-19 0.00104113051 0.002499793185 0.01209301363 0.04380051527 -1.916231612e-19 1.788472798e-06 5.41971418e-06 +0.001665726832 0.005859073107 + +H atom_index 1 n_descriptor 18 +1.206591653 0.03559315432 0.09384070954 0.1313110858 0.3069136594 0.02004606408 0.02583155939 0.03890104696 +-1.626420968e-17 3.89351634e-05 0.08959099416 0.1124337589 0.1136683051 -6.451376967e-19 6.060475046e-06 0.01385488918 +0.02434157779 0.02867662703 + +H atom_index 2 n_descriptor 18 +1.263343985 0.03365143908 0.1126146541 0.1566771974 0.3259292293 0.02263686499 0.0291355866 0.03693536196 +6.671617386e-18 4.390482548e-05 0.1039528293 0.1158299655 0.1344657395 5.667839179e-18 3.443003843e-06 0.01305455504 +0.0265256639 0.0313706486 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f47a4ce201a80745841079af915fd11529a70d41 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..b2dc13d3db9a1c51e93b86b76152c37794bf5d73 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..e3294d80dc325ba6d9122c8118a42e1af69340d4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..9d80dd1299de53b076a960416682193bd01cd00e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:28 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.107026 SEC) : SETUP UNITCELL + DONE(0.107381 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.125543 SEC) : INIT PLANEWAVE + DONE(0.168921 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451959 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651823e+02 0.000000e+00 2.145e-01 5.069e-01 + GE2 -4.664012e+02 -1.218870e+00 9.828e-02 4.638e-01 + GE3 -4.664056e+02 -4.456832e-03 6.316e-02 5.330e-01 + GE4 -4.664052e+02 4.220553e-04 2.011e-03 3.900e-01 + GE5 -4.664045e+02 7.041671e-04 9.043e-04 3.891e-01 + GE6 -4.664049e+02 -3.909560e-04 1.710e-04 3.866e-01 + GE7 -4.664047e+02 1.369569e-04 3.740e-05 3.802e-01 + GE8 -4.664048e+02 -5.472069e-05 1.587e-05 3.755e-01 + GE9 -4.664048e+02 1.884382e-05 1.740e-06 3.761e-01 + GE10 -4.664048e+02 -3.155970e-06 2.408e-07 3.752e-01 + GE11 -4.664048e+02 -3.562511e-07 5.132e-08 3.207e-01 +E_delta_band = -6.98842258e-02 Ry = -9.50823671e-01 eV +E_delta_NN= -1.94527265e-01 Ry = -2.64667922e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7595 11 0.61 1e+02 % + Run_lcao lcao_line 6.7497 1 6.7 1e+02 % + Potential init_pot 0.28574 2 0.14 4.2 % + PW_Basis recip2real 0.25674 16 0.016 3.8 % + PW_Basis gathers_scatterp 0.11379 16 0.0071 1.7 % + Potential v_of_rho 0.81531 13 0.063 12 % + XC_Functional v_xc 0.21105 14 0.015 3.1 % + H_Hartree_pw v_hartree 0.56461 13 0.043 8.4 % + PW_Basis real2recip 0.65229 38 0.017 9.6 % + PW_Basis gatherp_scatters 0.26881 38 0.0071 4 % + ORB_control set_orb_tables 1.1021 1 1.1 16 % + ORB_gen_tables gen_tables 1.102 1 1.1 16 % + ORB_table_phi init_Table 0.47568 1 0.48 7 % + ORB_table_phi cal_ST_Phi12_R 0.47043 126 0.0037 7 % + ORB_table_beta init_Table_Beta 0.18555 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18401 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.25088 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.24887 66 0.0038 3.7 % + LOOP_ions opt_ions 5.1193 1 5.1 76 % + ESolver_KS_LCAO Run 4.559 1 4.6 67 % + HSolverLCAO solve 2.3062 11 0.21 34 % + HamiltLCAO updateHk 1.2177 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1902 11 0.11 18 % + Gint_interface cal_gint 0.80071 23 0.035 12 % + Gint_Gamma distri_vl_value 0.47833 11 0.043 7.1 % + Gint_Gamma distri_vl 2.1942 6 0.37 32 % + LCAO_Deepks cal_projected_DM 4.792 13 0.37 71 % + LCAO_gen_fixedH add_v_delta 2.0466 6 0.34 30 % + LCAO_DESCRIPTOR add_v_delta 2.0466 6 0.34 30 % + ElecStateLCAO psiToRho 1.0685 11 0.097 16 % + Charge mix_rho 0.88873 10 0.089 13 % + LOOP_ions force_stress 0.56006 1 0.56 8.3 % + Force_Stress_LCAO getForceStress 0.56003 1 0.56 8.3 % + Force_LCAO_gamma ftable_gamma 0.36234 1 0.36 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.17813 1 0.18 2.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:28 2022 + FINISH Time : Wed Sep 28 11:08:35 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/176/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b104ec8265ff3a7b0fd383c3bd9fe7f21c35e755 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.292688 0.544366 0.307001 +H 0.350781 0.516752 0.317377 +H 0.298855 0.609445 0.32416 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2a5630c34fc5d8217405b0752ff13f33679f727e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0981 2 + 2 -13.0389 2 + 3 -8.96546 2 + 4 -6.69924 2 + 5 1.16657 0 + 6 4.23713 0 + 7 11.1144 0 + 8 11.3513 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..2f4e48fa1cb9beef1e78257e4af13da54ceab5f3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:19 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 8.19526586495 15.2422522479 8.59602171944 0 0 0 0 + tauc_H1 9.82187416506 14.4690523609 8.88654815711 0 0 0 0 + tauc_H2 8.36793481121 17.0644632066 9.07647261745 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0733589841229 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0736839254438 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0895133655656 (SEC) + + DONE : INIT CHARGE Time : 0.132029862113 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374495 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00154 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000546 + + Density error is 0.213258204249 + + Energy Rydberg eV + E_KohnSham -34.1916311265 -465.201007235 + E_Harris -34.3796405478 -467.759006641 + E_Fermi -0.396267665093 -5.39149817843 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00138122481535 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000749509074437 + + Density error is 0.0984269467029 + + Energy Rydberg eV + E_KohnSham -34.2796118342 -466.398046173 + E_Harris -34.286434766 -466.490876923 + E_Fermi -0.206050100266 -2.80345543708 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127220955378 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000728609359678 + + Density error is 0.0631898293465 + + Energy Rydberg eV + E_KohnSham -34.2798415831 -466.401172067 + E_Harris -34.2842394437 -466.46100803 + E_Fermi -0.196288985292 -2.67064865461 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010683247413 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000711665434622 + + Density error is 0.00203410778768 + + Energy Rydberg eV + E_KohnSham -34.2798005546 -466.400613847 + E_Harris -34.279803427 -466.400652927 + E_Fermi -0.161082590192 -2.19164107521 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010644964412 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00071070819185 + + Density error is 0.000830410725045 + + Energy Rydberg eV + E_KohnSham -34.279762115 -466.400090849 + E_Harris -34.2797624811 -466.400095829 + E_Fermi -0.16059598211 -2.1850204326 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106210893964 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000710591117389 + + Density error is 0.000180417154657 + + Energy Rydberg eV + E_KohnSham -34.2797842696 -466.400392277 + E_Harris -34.2797842958 -466.400392634 + E_Fermi -0.160387413477 -2.18218271076 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106201766628 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000710837525436 + + Density error is 3.04229540679e-05 + + Energy Rydberg eV + E_KohnSham -34.2797764425 -466.400285784 + E_Harris -34.2797764458 -466.400285828 + E_Fermi -0.160307152965 -2.18109071048 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106198636189 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000710769038405 + + Density error is 1.65955463235e-05 + + Energy Rydberg eV + E_KohnSham -34.2797800268 -466.400334551 + E_Harris -34.2797800281 -466.400334569 + E_Fermi -0.160333437981 -2.18144833647 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106196427604 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000710781629667 + + Density error is 2.61013459098e-06 + + Energy Rydberg eV + E_KohnSham -34.2797788057 -466.400317937 + E_Harris -34.2797788057 -466.400317938 + E_Fermi -0.160317908517 -2.18123704727 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010619561469 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000710782768031 + + Density error is 5.74907006698e-07 + + Energy Rydberg eV + E_KohnSham -34.2797791003 -466.400321945 + E_Harris -34.2797791003 -466.400321945 + E_Fermi -0.160315672529 -2.1812066251 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106195584883 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000710783311773 + + Density error is 1.85933516463e-07 + + Energy Rydberg eV + E_KohnSham -34.2797791073 -466.400322041 + E_Harris -34.2797791073 -466.400322041 + E_Fermi -0.160315384544 -2.18120270687 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106195549534 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000710783548684 + + Density error is 1.03686023619e-08 + + Energy Rydberg eV + E_KohnSham -34.2797791119 -466.400322103 + E_Harris -34.2797791119 -466.400322103 + E_band -7.90869865511 -107.603365474 + E_one_elec -68.981359242 -938.539541476 + E_Hartree +35.8990932033 +488.432220598 + E_xc -8.18689136608 -111.388371486 + E_Ewald +7.11436263154 +96.7958694272 + E_demet -2.07972863898e-68 -2.8296159784e-67 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194199796651 -2.64222378489 + E_Fermi -0.160315200757 -2.18120020631 + + charge density convergence is achieved + final etot is -466.400322103 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0981 2.00000 + 2 -13.0389 2.00000 + 3 -8.96546 2.00000 + 4 -6.69924 2.00000 + 5 1.16657 0.00000 + 6 4.23713 0.00000 + 7 11.1144 0.00000 + 8 11.3513 0.00000 + + EFERMI = -2.181200206312925 eV + OUT.ABACUS/ final etot is -466.4003221028518 eV + correction force for each atom along direction 1 is 0.000106338 + correction force for each atom along direction 2 is 9.66734e-05 + correction force for each atom along direction 3 is -8.94495e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.58897402 +1.2495631 +0.11649750 + H1 +0.50586966 -0.017160225 +0.14658467 + H2 +0.083104355 -1.2324029 -0.26308217 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4003221028518 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5967 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5890 1 7.6 1.e+02% + Potential init_pot 0.24199 2 0.12 3.2% + PW_Basis recip2real 0.23874 17 0.014 3.1% + PW_Basis gathers_scatterp 0.11160 17 0.0066 1.5% + Potential v_of_rho 0.94770 14 0.068 12.% + XC_Functional v_xc 0.30776 15 0.021 4.1% + H_Hartree_pw v_hartree 0.60573 14 0.043 8.0% + PW_Basis real2recip 0.64893 41 0.016 8.5% + PW_Basis gatherp_scatters 0.28888 41 0.0070 3.8% + ORB_control set_orb_tables 0.90221 1 0.90 12.% + ORB_gen_tables gen_tables 0.90221 1 0.90 12.% + ORB_table_phi init_Table 0.37787 1 0.38 5.0% + ORB_table_phi cal_ST_Phi12_R 0.37363 126 0.0030 4.9% + ORB_table_beta init_Table_Beta 0.15642 1 0.16 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15506 56 0.0028 2.0% + ORB_table_alpha init_Table_Alpha 0.20947 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20778 66 0.0031 2.7% + LOOP_ions opt_ions 6.2422 1 6.2 82.% + ESolver_KS_LCAO Run 5.6786 1 5.7 75.% + HSolverLCAO solve 3.3211 12 0.28 44.% + HamiltLCAO updateHk 1.6513 12 0.14 22.% + LCAO_Hamilt cal_Hgamma 1.6262 12 0.14 21.% + Gint_interface cal_gint 1.4205 25 0.057 19.% + Gint_Gamma distri_vl_value 0.69537 12 0.058 9.2% + Gint_Gamma distri_vl 2.9431 6 0.49 39.% + LCAO_Deepks cal_projected_DM 5.9477 14 0.42 78.% + LCAO_gen_fixedH add_v_delta 2.8145 6 0.47 37.% + LCAO_DESCRIPTOR add_v_delta 2.8144 6 0.47 37.% + ElecStateLCAO psiToRho 1.6522 12 0.14 22.% + Charge mix_rho 0.81614 11 0.074 11.% + LOOP_ions force_stress 0.56355 1 0.56 7.4% + Force_Stress_LCAO getForceStress 0.56352 1 0.56 7.4% + Force_LCAO_gamma ftable_gamma 0.36730 1 0.37 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.23243 1 0.23 3.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:19 2022 + Finish Time : Wed Sep 28 11:10:26 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6acfdb155a25e01fe25ef1f8cfe2b80d06eb3f74 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123735 ima = 3.63732e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123485032836 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112495360659 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011308335812 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011328438726 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113257550159 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113274589134 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113268390868 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113270650161 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113269841173 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113269805701 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113269784373 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113269774794 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/STRU new file mode 100644 index 0000000000000000000000000000000000000000..774dabc4169178818e04f67635048ad0f13336f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-19.804734135054 15.242252247932 8.596021719438 0 0 0 +H +0.0 +2 +-18.178125834966 14.469052360907 8.886548157137 0 0 0 +-19.632065188783 17.064463206571 9.076472617461 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/conv new file mode 100644 index 0000000000000000000000000000000000000000..c2cf5bf8c6967a6d46b842d127d03340e0f14bda --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/conv @@ -0,0 +1 @@ +177 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..27979bcc919f85ba96bed3ca4586f74154185aa5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747232353 0.01251892184 1.260342578 1.357091522 1.46848891 0.008061258724 0.0190498504 0.03898062093 +-7.582962003e-19 0.001022726091 0.002404169191 0.01181564268 0.04246227431 -3.665979022e-19 1.589796291e-06 4.974887659e-06 +0.001685003147 0.005781357479 + +H atom_index 1 n_descriptor 18 +1.250762488 0.03398186096 0.1079323873 0.1510578605 0.322594686 0.02189737765 0.02845318208 0.03721346504 +9.46264932e-18 4.011147577e-05 0.1005276949 0.115097518 0.1295833107 -3.559587544e-18 4.075317549e-06 0.01302496017 +0.0258541445 0.03084067099 + +H atom_index 2 n_descriptor 18 +1.196696371 0.03581851426 0.09066848492 0.1275965057 0.3039668992 0.01945675192 0.02530438791 0.03923586281 +1.799419994e-17 3.562331587e-05 0.08636955072 0.1091098849 0.1134335055 -2.15125669e-18 6.213949345e-06 0.01405600155 +0.02371838856 0.02818510348 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..2677912da97301b9ce5629449ff421fb465ad926 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:19 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733741 SEC) : SETUP UNITCELL + DONE(0.073694 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0895272 SEC) : INIT PLANEWAVE + DONE(0.13217 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374543 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652010e+02 0.000000e+00 2.133e-01 5.471e-01 + GE2 -4.663980e+02 -1.197039e+00 9.843e-02 5.267e-01 + GE3 -4.664012e+02 -3.125894e-03 6.319e-02 5.870e-01 + GE4 -4.664006e+02 5.582209e-04 2.034e-03 4.598e-01 + GE5 -4.664001e+02 5.229978e-04 8.304e-04 4.615e-01 + GE6 -4.664004e+02 -3.014285e-04 1.804e-04 4.585e-01 + GE7 -4.664003e+02 1.064933e-04 3.042e-05 4.395e-01 + GE8 -4.664003e+02 -4.876704e-05 1.660e-05 4.388e-01 + GE9 -4.664003e+02 1.661366e-05 2.610e-06 4.434e-01 + GE10 -4.664003e+02 -4.007977e-06 5.749e-07 4.447e-01 + GE11 -4.664003e+02 -9.586939e-08 1.859e-07 4.432e-01 + GE12 -4.664003e+02 -6.162097e-08 1.037e-08 3.752e-01 +E_delta_band = -6.92154580e-02 Ry = -9.41724619e-01 eV +E_delta_NN= -1.94199797e-01 Ry = -2.64222378e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5967 11 0.69 1e+02 % + Run_lcao lcao_line 7.589 1 7.6 1e+02 % + Potential init_pot 0.24199 2 0.12 3.2 % + PW_Basis recip2real 0.23874 17 0.014 3.1 % + PW_Basis gathers_scatterp 0.1116 17 0.0066 1.5 % + Potential v_of_rho 0.9477 14 0.068 12 % + XC_Functional v_xc 0.30776 15 0.021 4.1 % + H_Hartree_pw v_hartree 0.60573 14 0.043 8 % + PW_Basis real2recip 0.64893 41 0.016 8.5 % + PW_Basis gatherp_scatters 0.28888 41 0.007 3.8 % + ORB_control set_orb_tables 0.90221 1 0.9 12 % + ORB_gen_tables gen_tables 0.90221 1 0.9 12 % + ORB_table_phi init_Table 0.37787 1 0.38 5 % + ORB_table_phi cal_ST_Phi12_R 0.37363 126 0.003 4.9 % + ORB_table_beta init_Table_Beta 0.15642 1 0.16 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15506 56 0.0028 2 % + ORB_table_alpha init_Table_Alpha 0.20947 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20778 66 0.0031 2.7 % + LOOP_ions opt_ions 6.2422 1 6.2 82 % + ESolver_KS_LCAO Run 5.6786 1 5.7 75 % + HSolverLCAO solve 3.3211 12 0.28 44 % + HamiltLCAO updateHk 1.6513 12 0.14 22 % + LCAO_Hamilt cal_Hgamma 1.6262 12 0.14 21 % + Gint_interface cal_gint 1.4205 25 0.057 19 % + Gint_Gamma distri_vl_value 0.69537 12 0.058 9.2 % + Gint_Gamma distri_vl 2.9431 6 0.49 39 % + LCAO_Deepks cal_projected_DM 5.9477 14 0.42 78 % + LCAO_gen_fixedH add_v_delta 2.8145 6 0.47 37 % + LCAO_DESCRIPTOR add_v_delta 2.8144 6 0.47 37 % + ElecStateLCAO psiToRho 1.6522 12 0.14 22 % + Charge mix_rho 0.81614 11 0.074 11 % + LOOP_ions force_stress 0.56355 1 0.56 7.4 % + Force_Stress_LCAO getForceStress 0.56352 1 0.56 7.4 % + Force_LCAO_gamma ftable_gamma 0.3673 1 0.37 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.23243 1 0.23 3.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:19 2022 + FINISH Time : Wed Sep 28 11:10:26 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/177/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..7287c3b4172c1e479d3244431d870dcfe66f16c3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.300571 0.55299 0.308429 +H 0.361658 0.539068 0.288956 +H 0.312907 0.580971 0.363971 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..7b9e09da65cefd01f606fb11d30b8c53d3c71468 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5566 2 + 2 -12.9735 2 + 3 -9.35975 2 + 4 -6.80305 2 + 5 1.40249 0 + 6 4.65789 0 + 7 11.0256 0 + 8 11.2951 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b47b645d201670f02a104acdceaee20eee0d130c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:49 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 8.4159829737 15.4837109834 8.63601560231 0 0 0 0 + tauc_H1 10.1264229865 15.0939071605 8.09076443138 0 0 0 0 + tauc_H2 8.76140949852 16.2672019905 10.1911787511 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0730691528564 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0778704893971 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0936765137412 (SEC) + + DONE : INIT CHARGE Time : 0.135182217434 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.380656 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00066 + + Density error is 0.216487368897 + + Energy Rydberg eV + E_KohnSham -34.1857815752 -465.121420007 + E_Harris -34.3819307039 -467.790165815 + E_Fermi -0.417931221365 -5.68624598266 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00140347014904 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000864690542654 + + Density error is 0.0975249029017 + + Energy Rydberg eV + E_KohnSham -34.2773943794 -466.367876152 + E_Harris -34.284149148 -466.459779494 + E_Fermi -0.224944549831 -3.06052761175 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00133082857564 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830015296067 + + Density error is 0.0624728981067 + + Energy Rydberg eV + E_KohnSham -34.2777393613 -466.372569873 + E_Harris -34.2820997825 -466.431896447 + E_Fermi -0.212432211147 -2.89028851034 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122467518605 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000791540650203 + + Density error is 0.00200392052928 + + Energy Rydberg eV + E_KohnSham -34.277753766 -466.372765859 + E_Harris -34.2777551272 -466.372784378 + E_Fermi -0.176382489889 -2.39980688992 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122844056323 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000794828579535 + + Density error is 0.000973578560563 + + Energy Rydberg eV + E_KohnSham -34.2776771054 -466.371722837 + E_Harris -34.2776795426 -466.371755998 + E_Fermi -0.175509710623 -2.3879321188 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122652157746 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000793813724345 + + Density error is 0.000100110385721 + + Energy Rydberg eV + E_KohnSham -34.2777258208 -466.372385645 + E_Harris -34.2777258307 -466.37238578 + E_Fermi -0.175613558694 -2.3893450443 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122621749858 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000793735755974 + + Density error is 4.99467614784e-05 + + Energy Rydberg eV + E_KohnSham -34.2777112747 -466.372187735 + E_Harris -34.277711289 -466.37218793 + E_Fermi -0.175486713149 -2.38761922212 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122620076014 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000793697139236 + + Density error is 1.69082257413e-05 + + Energy Rydberg eV + E_KohnSham -34.2777135625 -466.372218862 + E_Harris -34.2777135638 -466.372218879 + E_Fermi -0.175552947516 -2.38852038692 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122620657389 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000793713039452 + + Density error is 2.05559977519e-06 + + Energy Rydberg eV + E_KohnSham -34.2777119451 -466.372196856 + E_Harris -34.2777119451 -466.372196856 + E_Fermi -0.175535460994 -2.38828247058 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122620607374 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000793714282376 + + Density error is 1.61933743926e-07 + + Energy Rydberg eV + E_KohnSham -34.2777121962 -466.372200272 + E_Harris -34.2777121962 -466.372200272 + E_Fermi -0.175533443114 -2.38825501591 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122620684781 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000793714760154 + + Density error is 6.46480398894e-08 + + Energy Rydberg eV + E_KohnSham -34.2777122365 -466.372200821 + E_Harris -34.2777122365 -466.372200821 + E_band -8.03971066495 -109.385875315 + E_one_elec -69.6629199774 -947.81265101 + E_Hartree +36.2072173022 +492.624464034 + E_xc -8.2366943593 -112.065975971 + E_Ewald +7.53822436573 +102.562804176 + E_demet -6.01416224671e-87 -8.18268752517e-86 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19555497172 -2.66066188761 + E_Fermi -0.17553347439 -2.38825544144 + + charge density convergence is achieved + final etot is -466.372200821 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5566 2.00000 + 2 -12.9735 2.00000 + 3 -9.35975 2.00000 + 4 -6.80305 2.00000 + 5 1.40249 0.00000 + 6 4.65789 0.00000 + 7 11.0256 0.00000 + 8 11.2951 0.00000 + + EFERMI = -2.388255441444581 eV + OUT.ABACUS/ final etot is -466.3722008212032 eV + correction force for each atom along direction 1 is 0.000120123 + correction force for each atom along direction 2 is 0.000134033 + correction force for each atom along direction 3 is 6.45633e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.11634841 -0.77759217 -1.5265195 + H1 +0.10953839 -0.22827672 -0.42235500 + H2 +0.0068100197 +1.0058689 +1.9488745 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3722008212032 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1085 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1010 1 7.1 1.e+02% + Potential init_pot 0.24714 2 0.12 3.5% + PW_Basis recip2real 0.23150 16 0.014 3.3% + PW_Basis gathers_scatterp 0.11177 16 0.0070 1.6% + Potential v_of_rho 0.91020 13 0.070 13.% + XC_Functional v_xc 0.31312 14 0.022 4.4% + H_Hartree_pw v_hartree 0.56774 13 0.044 8.0% + PW_Basis real2recip 0.61834 38 0.016 8.7% + PW_Basis gatherp_scatters 0.28415 38 0.0075 4.0% + ORB_control set_orb_tables 0.89632 1 0.90 13.% + ORB_gen_tables gen_tables 0.89632 1 0.90 13.% + ORB_table_phi init_Table 0.37407 1 0.37 5.3% + ORB_table_phi cal_ST_Phi12_R 0.36982 126 0.0029 5.2% + ORB_table_beta init_Table_Beta 0.15445 1 0.15 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15315 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.21017 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20848 66 0.0032 2.9% + LOOP_ions opt_ions 5.7534 1 5.8 81.% + ESolver_KS_LCAO Run 5.1779 1 5.2 73.% + HSolverLCAO solve 3.0243 11 0.27 43.% + HamiltLCAO updateHk 1.5058 11 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.4821 11 0.13 21.% + Gint_interface cal_gint 1.2126 23 0.053 17.% + Gint_Gamma distri_vl_value 0.64636 11 0.059 9.1% + Gint_Gamma distri_vl 2.4799 6 0.41 35.% + LCAO_Deepks cal_projected_DM 5.4393 13 0.42 77.% + LCAO_gen_fixedH add_v_delta 2.3544 6 0.39 33.% + LCAO_DESCRIPTOR add_v_delta 2.3545 6 0.39 33.% + ElecStateLCAO psiToRho 1.4978 11 0.14 21.% + Charge mix_rho 0.71960 10 0.072 10.% + LOOP_ions force_stress 0.57538 1 0.58 8.1% + Force_Stress_LCAO getForceStress 0.57536 1 0.58 8.1% + Force_LCAO_gamma ftable_gamma 0.37036 1 0.37 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.21568 1 0.22 3.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:49 2022 + Finish Time : Wed Sep 28 11:04:56 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ca30e74e5b705e7064013f866da7f2eda803cdf4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124242 ima = 3.65694e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122691708851 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111510088805 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112037139032 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112332483635 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112260018063 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112297875375 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112295594479 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298898799 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298137888 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298038937 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298034446 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ee610f5788ae3dc968bd258ac5bfd8a1332ec876 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-19.584017026324 15.483710983425 8.636015602325 0 0 0 +H +0.0 +2 +-17.873577013561 15.093907160540 8.090764431364 0 0 0 +-19.238590501470 16.267201990490 10.191178751111 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/conv new file mode 100644 index 0000000000000000000000000000000000000000..55a577b4eacf1b7a5cacf0822148f6f084a7e34e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/conv @@ -0,0 +1 @@ +178 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..da07efed0b14899a0021c3cd3155b268db3b0812 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752674266 0.01284896904 1.283887333 1.36953071 1.470443284 0.0093062359 0.01766987339 0.03912184949 +3.488973943e-18 0.001032971881 0.002894461739 0.01343642376 0.04839016487 -9.542355546e-21 2.821046006e-06 7.410772675e-06 +0.001600043089 0.006107944181 + +H atom_index 1 n_descriptor 18 +1.245358444 0.0348436691 0.1087296947 0.1473500647 0.3181022688 0.02278651247 0.02796694104 0.03792406488 +-5.316524304e-18 5.202585777e-05 0.1031069193 0.1147446746 0.1265383909 -5.880708174e-18 3.823471723e-06 0.0134114676 +0.02698498314 0.03054620402 + +H atom_index 2 n_descriptor 18 +1.293904327 0.03327296756 0.1269363217 0.1712360663 0.3329957513 0.02515038484 0.03077682847 0.03685584526 +-5.840209179e-18 5.675705282e-05 0.1085428038 0.1233337458 0.1469274656 -2.294057726e-18 1.14810934e-06 0.01366488806 +0.02864359536 0.0325608399 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3036a96fdb1cf307fabb59c4aa632282468fe3dd Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..3933e5c47e56d924f211445177133719ae02cd22 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..d8f403634ceb06f628c349c13ed92be5cea6d271 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..2cdc1f5c92eb47b70d2b36f2c4905cd495a4b1c1 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..134b0cca44c387f8687c01092fff397865f234d5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:49 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.073086 SEC) : SETUP UNITCELL + DONE(0.0778826 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0936903 SEC) : INIT PLANEWAVE + DONE(0.135285 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.380701 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651214e+02 0.000000e+00 2.165e-01 5.417e-01 + GE2 -4.663679e+02 -1.246456e+00 9.752e-02 5.183e-01 + GE3 -4.663726e+02 -4.693721e-03 6.247e-02 5.787e-01 + GE4 -4.663728e+02 -1.959857e-04 2.004e-03 4.592e-01 + GE5 -4.663717e+02 1.043022e-03 9.736e-04 4.520e-01 + GE6 -4.663724e+02 -6.628083e-04 1.001e-04 4.307e-01 + GE7 -4.663722e+02 1.979099e-04 4.995e-05 4.536e-01 + GE8 -4.663722e+02 -3.112672e-05 1.691e-05 4.367e-01 + GE9 -4.663722e+02 2.200659e-05 2.056e-06 4.415e-01 + GE10 -4.663722e+02 -3.416742e-06 1.619e-07 4.493e-01 + GE11 -4.663722e+02 -5.489353e-07 6.465e-08 3.620e-01 +E_delta_band = -7.20154039e-02 Ry = -9.79819837e-01 eV +E_delta_NN= -1.95554972e-01 Ry = -2.66066189e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1085 11 0.65 1e+02 % + Run_lcao lcao_line 7.101 1 7.1 1e+02 % + Potential init_pot 0.24714 2 0.12 3.5 % + PW_Basis recip2real 0.2315 16 0.014 3.3 % + PW_Basis gathers_scatterp 0.11177 16 0.007 1.6 % + Potential v_of_rho 0.9102 13 0.07 13 % + XC_Functional v_xc 0.31312 14 0.022 4.4 % + H_Hartree_pw v_hartree 0.56774 13 0.044 8 % + PW_Basis real2recip 0.61834 38 0.016 8.7 % + PW_Basis gatherp_scatters 0.28415 38 0.0075 4 % + ORB_control set_orb_tables 0.89632 1 0.9 13 % + ORB_gen_tables gen_tables 0.89632 1 0.9 13 % + ORB_table_phi init_Table 0.37407 1 0.37 5.3 % + ORB_table_phi cal_ST_Phi12_R 0.36982 126 0.0029 5.2 % + ORB_table_beta init_Table_Beta 0.15445 1 0.15 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15315 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.21017 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20848 66 0.0032 2.9 % + LOOP_ions opt_ions 5.7534 1 5.8 81 % + ESolver_KS_LCAO Run 5.1779 1 5.2 73 % + HSolverLCAO solve 3.0243 11 0.27 43 % + HamiltLCAO updateHk 1.5058 11 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.4821 11 0.13 21 % + Gint_interface cal_gint 1.2126 23 0.053 17 % + Gint_Gamma distri_vl_value 0.64636 11 0.059 9.1 % + Gint_Gamma distri_vl 2.4799 6 0.41 35 % + LCAO_Deepks cal_projected_DM 5.4393 13 0.42 77 % + LCAO_gen_fixedH add_v_delta 2.3544 6 0.39 33 % + LCAO_DESCRIPTOR add_v_delta 2.3545 6 0.39 33 % + ElecStateLCAO psiToRho 1.4978 11 0.14 21 % + Charge mix_rho 0.7196 10 0.072 10 % + LOOP_ions force_stress 0.57538 1 0.58 8.1 % + Force_Stress_LCAO getForceStress 0.57536 1 0.58 8.1 % + Force_LCAO_gamma ftable_gamma 0.37036 1 0.37 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.21568 1 0.22 3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:49 2022 + FINISH Time : Wed Sep 28 11:04:56 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/178/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9979ad8b3a296d9ee1a127bc7c5e91afc3f87b7c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.323627 0.551562 0.313414 +H 0.348134 0.608365 0.291289 +H 0.332771 0.560678 0.380942 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..fb3036d4f4ac6f6e6232d1d49dfc542197d6a978 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1015 2 + 2 -12.585 2 + 3 -9.30941 2 + 4 -6.70587 2 + 5 1.00865 0 + 6 3.98931 0 + 7 11.1329 0 + 8 11.3984 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..67c13c4098204d69bbc9a9689bce414824f1b169 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:05 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.06155006716 15.4437223328 8.7755974471 0 0 0 0 + tauc_H1 9.74775057279 17.0342138095 8.15610016519 0 0 0 0 + tauc_H2 9.31757544186 15.6989721061 10.666362784 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0742176517649 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0880342623261 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104364383374 (SEC) + + DONE : INIT CHARGE Time : 0.146057617782 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.393291 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000516 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000775 + + Density error is 0.210718386727 + + Energy Rydberg eV + E_KohnSham -34.1902079117 -465.181643403 + E_Harris -34.3736040013 -467.676875214 + E_Fermi -0.388906630619 -5.2913461664 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000816474005807 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110777819489 + + Density error is 0.098392860032 + + Energy Rydberg eV + E_KohnSham -34.2775476852 -466.369961985 + E_Harris -34.2846677448 -466.466835367 + E_Fermi -0.201352374412 -2.73953959783 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000787126016159 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010660885916 + + Density error is 0.0634418536049 + + Energy Rydberg eV + E_KohnSham -34.2779232919 -466.375072377 + E_Harris -34.2824948424 -466.437271513 + E_Fermi -0.194130714051 -2.6412838679 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000765425349737 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102955286764 + + Density error is 0.00190934549909 + + Energy Rydberg eV + E_KohnSham -34.2778292767 -466.373793235 + E_Harris -34.2778295905 -466.373797504 + E_Fermi -0.158707076995 -2.15932056005 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000765744238176 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103019052718 + + Density error is 0.000870964807807 + + Energy Rydberg eV + E_KohnSham -34.2777993498 -466.373386057 + E_Harris -34.2777998257 -466.373392533 + E_Fermi -0.158701005432 -2.1592379522 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000765603687378 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102981728851 + + Density error is 0.000142113981049 + + Energy Rydberg eV + E_KohnSham -34.2778121558 -466.373560292 + E_Harris -34.2778119961 -466.37355812 + E_Fermi -0.158267444222 -2.15333904931 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000765754296272 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102998932215 + + Density error is 2.7026822045e-05 + + Energy Rydberg eV + E_KohnSham -34.2778092474 -466.373520721 + E_Harris -34.2778092492 -466.373520747 + E_Fermi -0.158244674348 -2.15302924929 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000765695828972 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102990267996 + + Density error is 1.0443334446e-05 + + Energy Rydberg eV + E_KohnSham -34.2778110828 -466.373545693 + E_Harris -34.2778110833 -466.3735457 + E_Fermi -0.158254745086 -2.15316626871 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000765703403176 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102990998796 + + Density error is 1.60887133355e-06 + + Energy Rydberg eV + E_KohnSham -34.277810207 -466.373533778 + E_Harris -34.2778102071 -466.373533778 + E_Fermi -0.158244481431 -2.15302662452 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0007657062399 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102991318315 + + Density error is 3.53227457786e-07 + + Energy Rydberg eV + E_KohnSham -34.2778103691 -466.373535983 + E_Harris -34.2778103691 -466.373535983 + E_Fermi -0.158243470195 -2.15301286594 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000765706782794 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010299138634 + + Density error is 8.69735090516e-08 + + Energy Rydberg eV + E_KohnSham -34.2778103881 -466.373536241 + E_Harris -34.2778103881 -466.373536241 + E_band -7.89401943283 -107.403644409 + E_one_elec -68.7300247909 -935.119960838 + E_Hartree +35.7669520852 +486.634348451 + E_xc -8.1659628774 -111.103624789 + E_Ewald +6.97665373037 +94.922243706 + E_demet -2.65036754101e-61 -3.6060100352e-60 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193893077932 -2.63805066264 + E_Fermi -0.158243295522 -2.1530104894 + + charge density convergence is achieved + final etot is -466.373536241 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1015 2.00000 + 2 -12.5850 2.00000 + 3 -9.30941 2.00000 + 4 -6.70587 2.00000 + 5 1.00865 0.00000 + 6 3.98931 0.00000 + 7 11.1329 0.00000 + 8 11.3984 0.00000 + + EFERMI = -2.153010489401165 eV + OUT.ABACUS/ final etot is -466.3735362412510 eV + correction force for each atom along direction 1 is 1.28086e-05 + correction force for each atom along direction 2 is 0.000153804 + correction force for each atom along direction 3 is 2.21577e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.30364072 +0.34864765 +1.9979200 + H1 +0.036648311 +0.13339055 -0.35931517 + H2 -0.34028903 -0.48203819 -1.6386049 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3735362412510 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1532 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1456 1 7.1 1.e+02% + Potential init_pot 0.24551 2 0.12 3.4% + PW_Basis recip2real 0.22864 16 0.014 3.2% + PW_Basis gathers_scatterp 0.10882 16 0.0068 1.5% + Potential v_of_rho 0.89488 13 0.069 13.% + XC_Functional v_xc 0.29503 14 0.021 4.1% + H_Hartree_pw v_hartree 0.56886 13 0.044 8.0% + PW_Basis real2recip 0.61633 38 0.016 8.6% + PW_Basis gatherp_scatters 0.28048 38 0.0074 3.9% + ORB_control set_orb_tables 0.90357 1 0.90 13.% + ORB_gen_tables gen_tables 0.90357 1 0.90 13.% + ORB_table_phi init_Table 0.37775 1 0.38 5.3% + ORB_table_phi cal_ST_Phi12_R 0.37346 126 0.0030 5.2% + ORB_table_beta init_Table_Beta 0.15666 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15537 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.21101 1 0.21 2.9% + ORB_table_alpha S_PhiAlpha_R 0.20931 66 0.0032 2.9% + LOOP_ions opt_ions 5.7779 1 5.8 81.% + ESolver_KS_LCAO Run 5.2131 1 5.2 73.% + HSolverLCAO solve 3.0169 11 0.27 42.% + HamiltLCAO updateHk 1.5154 11 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.4920 11 0.14 21.% + Gint_interface cal_gint 1.1695 23 0.051 16.% + Gint_Gamma distri_vl_value 0.66754 11 0.061 9.3% + Gint_Gamma distri_vl 2.4917 6 0.42 35.% + LCAO_Deepks cal_projected_DM 5.4641 13 0.42 76.% + LCAO_gen_fixedH add_v_delta 2.3620 6 0.39 33.% + LCAO_DESCRIPTOR add_v_delta 2.3623 6 0.39 33.% + ElecStateLCAO psiToRho 1.4840 11 0.13 21.% + Charge mix_rho 0.75460 10 0.075 11.% + LOOP_ions force_stress 0.56464 1 0.56 7.9% + Force_Stress_LCAO getForceStress 0.56462 1 0.56 7.9% + Force_LCAO_gamma ftable_gamma 0.36354 1 0.36 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.20749 1 0.21 2.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:05 2022 + Finish Time : Wed Sep 28 11:11:12 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2cc6745fa5733b66586b2f4fa3b12e15b066c5ad --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123769 ima = 3.66564e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123074912887 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111737996977 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112497592734 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112703497498 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011268938834 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112697857537 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112695057625 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112696790062 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112696299118 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112696240174 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112696224449 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c10aab3d5833a30da3e5f65ab9486c3d91958bac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.938449932824 15.443722332811 8.775597447075 0 0 0 +H +0.0 +2 +-18.252249427196 17.034213809451 8.156100165191 0 0 0 +-18.682424558140 15.698972106068 10.666362784004 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/conv new file mode 100644 index 0000000000000000000000000000000000000000..0badf0f9b940e381be113876de96da970a91168d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/conv @@ -0,0 +1 @@ +179 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..bbd9d71498a8b59e138fefb0ddf132d28d816b2e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753407431 0.01252549555 1.245414665 1.337617866 1.468543691 0.009108449733 0.0167839496 0.03919610672 +7.309841529e-19 0.0008315105228 0.002585527205 0.01206937792 0.04332549339 -1.002272136e-19 2.071026916e-06 6.044565714e-06 +0.001565950866 0.005997752706 + +H atom_index 1 n_descriptor 18 +1.244124589 0.03490224794 0.1071796382 0.1470167175 0.3186244845 0.02231496008 0.02792012704 0.0380880449 +-5.965096058e-18 4.353923829e-05 0.098350629 0.1153393469 0.1259281735 2.758908616e-18 3.680450677e-06 0.01336495867 +0.02586455473 0.0304446519 + +H atom_index 2 n_descriptor 18 +1.177243344 0.03699456033 0.08618426259 0.1188999605 0.2938328511 0.01911047313 0.02398889978 0.04068432624 +-1.345409722e-17 3.77045636e-05 0.08133928944 0.1012743443 0.1122877425 -1.052024755e-18 6.385377571e-06 0.01504000193 +0.02313025494 0.02696906049 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..28fc843727e75ae2bbed1cea1bedbf25af63e2e6 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..713b2ab2aea80182114ccc5a7430fe411bd0a2f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:05 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0742332 SEC) : SETUP UNITCELL + DONE(0.088046 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104378 SEC) : INIT PLANEWAVE + DONE(0.146165 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.393345 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651816e+02 0.000000e+00 2.107e-01 5.475e-01 + GE2 -4.663700e+02 -1.188319e+00 9.839e-02 5.237e-01 + GE3 -4.663751e+02 -5.110391e-03 6.344e-02 5.880e-01 + GE4 -4.663738e+02 1.279142e-03 1.909e-03 4.614e-01 + GE5 -4.663734e+02 4.071773e-04 8.710e-04 4.611e-01 + GE6 -4.663736e+02 -1.742348e-04 1.421e-04 4.544e-01 + GE7 -4.663735e+02 3.957116e-05 2.703e-05 4.366e-01 + GE8 -4.663735e+02 -2.497223e-05 1.044e-05 4.367e-01 + GE9 -4.663735e+02 1.191499e-05 1.609e-06 4.406e-01 + GE10 -4.663735e+02 -2.204385e-06 3.532e-07 4.421e-01 + GE11 -4.663735e+02 -2.584922e-07 8.697e-08 3.675e-01 +E_delta_band = -6.84645427e-02 Ry = -9.31507891e-01 eV +E_delta_NN= -1.93893078e-01 Ry = -2.63805066e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1532 11 0.65 1e+02 % + Run_lcao lcao_line 7.1456 1 7.1 1e+02 % + Potential init_pot 0.24551 2 0.12 3.4 % + PW_Basis recip2real 0.22864 16 0.014 3.2 % + PW_Basis gathers_scatterp 0.10882 16 0.0068 1.5 % + Potential v_of_rho 0.89488 13 0.069 13 % + XC_Functional v_xc 0.29503 14 0.021 4.1 % + H_Hartree_pw v_hartree 0.56886 13 0.044 8 % + PW_Basis real2recip 0.61633 38 0.016 8.6 % + PW_Basis gatherp_scatters 0.28048 38 0.0074 3.9 % + ORB_control set_orb_tables 0.90357 1 0.9 13 % + ORB_gen_tables gen_tables 0.90357 1 0.9 13 % + ORB_table_phi init_Table 0.37775 1 0.38 5.3 % + ORB_table_phi cal_ST_Phi12_R 0.37346 126 0.003 5.2 % + ORB_table_beta init_Table_Beta 0.15666 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15537 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.21101 1 0.21 2.9 % + ORB_table_alpha S_PhiAlpha_R 0.20931 66 0.0032 2.9 % + LOOP_ions opt_ions 5.7779 1 5.8 81 % + ESolver_KS_LCAO Run 5.2131 1 5.2 73 % + HSolverLCAO solve 3.0169 11 0.27 42 % + HamiltLCAO updateHk 1.5154 11 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.492 11 0.14 21 % + Gint_interface cal_gint 1.1695 23 0.051 16 % + Gint_Gamma distri_vl_value 0.66754 11 0.061 9.3 % + Gint_Gamma distri_vl 2.4917 6 0.42 35 % + LCAO_Deepks cal_projected_DM 5.4641 13 0.42 76 % + LCAO_gen_fixedH add_v_delta 2.362 6 0.39 33 % + LCAO_DESCRIPTOR add_v_delta 2.3623 6 0.39 33 % + ElecStateLCAO psiToRho 1.484 11 0.13 21 % + Charge mix_rho 0.7546 10 0.075 11 % + LOOP_ions force_stress 0.56464 1 0.56 7.9 % + Force_Stress_LCAO getForceStress 0.56462 1 0.56 7.9 % + Force_LCAO_gamma ftable_gamma 0.36354 1 0.36 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.20749 1 0.21 2.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:05 2022 + FINISH Time : Wed Sep 28 11:11:12 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/179/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9daffe1ea24ea25e56451f14112eed5470b08405 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.567867 0.298167 0.436392 +H 0.520968 0.261573 0.411139 +H 0.541626 0.321638 0.496115 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9cb3910e19cec967ffb7cddb24c6c8394e8b74b2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0555 2 + 2 -12.8634 2 + 3 -9.04909 2 + 4 -6.68882 2 + 5 1.02458 0 + 6 4.11645 0 + 7 11.1301 0 + 8 11.3673 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4be8c0b9b73ba8333ec32e4e70a7e0b2a588cf92 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:42 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.9002762062 8.34867109948 12.2189668727 0 0 0 0 + tauc_H1 14.5870910095 7.32403189032 11.511885798 0 0 0 0 + tauc_H2 15.1655141483 9.00585921948 13.8912210039 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0745674933637 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0748592206927 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0906564765654 (SEC) + + DONE : INIT CHARGE Time : 0.131979459708 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.376324 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 +receiver_size is 324 ; receiver_size of each process is: +81 81 81 81 +sender_size is 369 ; sender_size of each process is: +81 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000746 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00116 + + Density error is 0.213145685124 + + Energy Rydberg eV + E_KohnSham -34.1867232408 -465.134232024 + E_Harris -34.3749451445 -467.695122403 + E_Fermi -0.392521529555 -5.34052938962 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00106261812123 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00135530704946 + + Density error is 0.0988876710917 + + Energy Rydberg eV + E_KohnSham -34.2761790695 -466.351341014 + E_Harris -34.2832581802 -466.447657256 + E_Fermi -0.201825403211 -2.74597548482 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00102077513061 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00128040319582 + + Density error is 0.0637799919178 + + Energy Rydberg eV + E_KohnSham -34.2765895572 -466.356925985 + E_Harris -34.281120921 -466.418578353 + E_Fermi -0.194360976841 -2.64441675388 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000969499833757 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115996754511 + + Density error is 0.00200068903988 + + Energy Rydberg eV + E_KohnSham -34.2765086871 -466.355825691 + E_Harris -34.2765112053 -466.355859953 + E_Fermi -0.159012103332 -2.16347065628 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000968143595857 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00116049119701 + + Density error is 0.000931101174295 + + Energy Rydberg eV + E_KohnSham -34.2764692212 -466.355288729 + E_Harris -34.2764697226 -466.355295552 + E_Fermi -0.158812273015 -2.16075182533 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967444540369 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115868302191 + + Density error is 0.00018545545468 + + Energy Rydberg eV + E_KohnSham -34.276486937 -466.355529766 + E_Harris -34.2764868075 -466.355528004 + E_Fermi -0.158425925774 -2.15549530145 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967691108108 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115892913214 + + Density error is 3.39644576397e-05 + + Energy Rydberg eV + E_KohnSham -34.2764810753 -466.355450014 + E_Harris -34.2764810788 -466.355450061 + E_Fermi -0.158401071899 -2.15515714713 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967594178409 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115886834344 + + Density error is 1.33386227512e-05 + + Energy Rydberg eV + E_KohnSham -34.2764842989 -466.355493873 + E_Harris -34.2764842996 -466.355493883 + E_Fermi -0.158418575813 -2.15539530011 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967597978307 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115885882325 + + Density error is 2.42469193992e-06 + + Energy Rydberg eV + E_KohnSham -34.2764832196 -466.355479189 + E_Harris -34.2764832197 -466.355479189 + E_Fermi -0.158405685785 -2.15521992228 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967597970153 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115885083315 + + Density error is 6.02476511422e-07 + + Energy Rydberg eV + E_KohnSham -34.2764834135 -466.355481827 + E_Harris -34.2764834135 -466.355481827 + E_Fermi -0.158403687307 -2.15519273159 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967598785379 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115885143484 + + Density error is 1.99984732025e-07 + + Energy Rydberg eV + E_KohnSham -34.2764834232 -466.355481958 + E_Harris -34.2764834232 -466.355481958 + E_Fermi -0.158403383049 -2.15518859195 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00096759901944 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115885146409 + + Density error is 1.13927119179e-08 + + Energy Rydberg eV + E_KohnSham -34.2764834278 -466.35548202 + E_Harris -34.2764834277 -466.35548202 + E_band -7.88740203918 -107.31361015 + E_one_elec -68.7985322646 -936.052052836 + E_Hartree +35.809135006 +487.208276533 + E_xc -8.17295348123 -111.198736834 + E_Ewald +7.01118342297 +95.3920442755 + E_demet -5.62159277097e-62 -7.64856935208e-61 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193982225124 -2.6392635724 + E_Fermi -0.158403187833 -2.1551859359 + + charge density convergence is achieved + final etot is -466.35548202 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0555 2.00000 + 2 -12.8634 2.00000 + 3 -9.04909 2.00000 + 4 -6.68882 2.00000 + 5 1.02458 0.00000 + 6 4.11645 0.00000 + 7 11.1301 0.00000 + 8 11.3673 0.00000 + + EFERMI = -2.155185935896291 eV + OUT.ABACUS/ final etot is -466.3554820199714 eV + correction force for each atom along direction 1 is -4.59559e-05 + correction force for each atom along direction 2 is -0.000109659 + correction force for each atom along direction 3 is 8.59095e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.023984315 +1.3121342 +2.1985415 + H1 -0.76862009 -0.53144135 -0.30506558 + H2 +0.74463578 -0.78069287 -1.8934760 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3554820199714 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2656 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2584 1 6.3 1.e+02% + Potential init_pot 0.24225 2 0.12 3.9% + PW_Basis recip2real 0.23924 17 0.014 3.8% + PW_Basis gathers_scatterp 0.11443 17 0.0067 1.8% + Potential v_of_rho 0.95456 14 0.068 15.% + XC_Functional v_xc 0.30724 15 0.020 4.9% + H_Hartree_pw v_hartree 0.61397 14 0.044 9.8% + PW_Basis real2recip 0.66079 41 0.016 11.% + PW_Basis gatherp_scatters 0.30382 41 0.0074 4.8% + ORB_control set_orb_tables 0.89277 1 0.89 14.% + ORB_gen_tables gen_tables 0.89277 1 0.89 14.% + ORB_table_phi init_Table 0.37300 1 0.37 6.0% + ORB_table_phi cal_ST_Phi12_R 0.36880 126 0.0029 5.9% + ORB_table_beta init_Table_Beta 0.15286 1 0.15 2.4% + ORB_table_beta VNL_PhiBeta_R 0.15149 56 0.0027 2.4% + ORB_table_alpha init_Table_Alpha 0.20884 1 0.21 3.3% + ORB_table_alpha S_PhiAlpha_R 0.20723 66 0.0031 3.3% + LOOP_ions opt_ions 4.9195 1 4.9 79.% + ESolver_KS_LCAO Run 4.4305 1 4.4 71.% + HSolverLCAO solve 2.0449 12 0.17 33.% + HamiltLCAO updateHk 1.0858 12 0.090 17.% + LCAO_Hamilt cal_Hgamma 1.0605 12 0.088 17.% + Gint_Gamma distri_vl_value 0.65310 12 0.054 10.% + Gint_Gamma distri_vl 2.3102 6 0.39 37.% + LCAO_Deepks cal_projected_DM 4.5706 14 0.33 73.% + LCAO_gen_fixedH add_v_delta 2.1819 6 0.36 35.% + LCAO_DESCRIPTOR add_v_delta 2.1817 6 0.36 35.% + ElecStateLCAO psiToRho 0.94093 12 0.078 15.% + Charge mix_rho 0.83629 11 0.076 13.% + LOOP_ions force_stress 0.48888 1 0.49 7.8% + Force_Stress_LCAO getForceStress 0.48886 1 0.49 7.8% + Force_LCAO_gamma ftable_gamma 0.29487 1 0.29 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:42 2022 + Finish Time : Wed Sep 28 11:10:49 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1ef0b613285f26c2dc337dfee1ef31b82b794183 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123508 ima = 3.67362e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123619221965 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112237971409 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112967611499 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113180181474 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113158939227 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113172788305 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113167150081 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113169308137 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113168748911 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113168706048 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113168683715 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113168673152 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c6f62d6014df4dee925b018a4e173299ee6fead9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.099723793790 8.348671099459 12.218966872664 0 0 0 +H +0.0 +2 +-13.412908990469 7.324031890304 11.511885797971 0 0 0 +-12.834485851710 9.005859219475 13.891221003868 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/conv new file mode 100644 index 0000000000000000000000000000000000000000..a5ba3576af98e1979de7087648176871473b8b43 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/conv @@ -0,0 +1 @@ +18 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..54c9fb014e339c81bbbb96014399481ddceb0e7c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749288093 0.01242990216 1.24629099 1.352780457 1.468392095 0.008373049601 0.01838367543 0.03907558636 +-5.817857274e-20 0.0009472874047 0.002430224839 0.01152467235 0.04236020715 -1.128830682e-19 1.6012893e-06 5.07997866e-06 +0.001621443923 0.005792594334 + +H atom_index 1 n_descriptor 18 +1.264255707 0.0337180738 0.112466784 0.1571559725 0.3264341526 0.02257006445 0.02919133755 0.03705534968 +-2.472344261e-18 4.179223658e-05 0.1027719074 0.1159571581 0.1347596571 7.63454732e-19 3.286751731e-06 0.01306506511 +0.02621299622 0.03139539902 + +H atom_index 2 n_descriptor 18 +1.160325306 0.03702061425 0.08021074885 0.113250676 0.2891048498 0.01783144083 0.02313800499 0.04093132317 +1.103914212e-17 3.317152289e-05 0.07648844366 0.09633012423 0.1114572019 -4.187409532e-18 6.954367394e-06 0.01537246473 +0.02203635038 0.0261282176 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..75547467ac23d73be2fe6589631a2b48b6f186e0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:42 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.074582 SEC) : SETUP UNITCELL + DONE(0.0748673 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0906708 SEC) : INIT PLANEWAVE + DONE(0.132082 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.376371 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651342e+02 0.000000e+00 2.131e-01 4.534e-01 + GE2 -4.663513e+02 -1.217109e+00 9.889e-02 4.156e-01 + GE3 -4.663569e+02 -5.584971e-03 6.378e-02 4.772e-01 + GE4 -4.663558e+02 1.100294e-03 2.001e-03 3.558e-01 + GE5 -4.663553e+02 5.369616e-04 9.311e-04 3.539e-01 + GE6 -4.663555e+02 -2.410366e-04 1.855e-04 3.546e-01 + GE7 -4.663555e+02 7.975227e-05 3.396e-05 3.360e-01 + GE8 -4.663555e+02 -4.385918e-05 1.334e-05 3.380e-01 + GE9 -4.663555e+02 1.468437e-05 2.425e-06 3.418e-01 + GE10 -4.663555e+02 -2.638194e-06 6.025e-07 3.416e-01 + GE11 -4.663555e+02 -1.315871e-07 2.000e-07 3.418e-01 + GE12 -4.663555e+02 -6.161401e-08 1.139e-08 2.678e-01 +E_delta_band = -6.86661143e-02 Ry = -9.34250414e-01 eV +E_delta_NN= -1.93982225e-01 Ry = -2.63926357e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2656 11 0.57 1e+02 % + Run_lcao lcao_line 6.2584 1 6.3 1e+02 % + Potential init_pot 0.24225 2 0.12 3.9 % + PW_Basis recip2real 0.23924 17 0.014 3.8 % + PW_Basis gathers_scatterp 0.11443 17 0.0067 1.8 % + Potential v_of_rho 0.95456 14 0.068 15 % + XC_Functional v_xc 0.30724 15 0.02 4.9 % + H_Hartree_pw v_hartree 0.61397 14 0.044 9.8 % + PW_Basis real2recip 0.66079 41 0.016 11 % + PW_Basis gatherp_scatters 0.30382 41 0.0074 4.8 % + ORB_control set_orb_tables 0.89277 1 0.89 14 % + ORB_gen_tables gen_tables 0.89277 1 0.89 14 % + ORB_table_phi init_Table 0.373 1 0.37 6 % + ORB_table_phi cal_ST_Phi12_R 0.3688 126 0.0029 5.9 % + ORB_table_beta init_Table_Beta 0.15286 1 0.15 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.15149 56 0.0027 2.4 % + ORB_table_alpha init_Table_Alpha 0.20884 1 0.21 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.20723 66 0.0031 3.3 % + LOOP_ions opt_ions 4.9195 1 4.9 79 % + ESolver_KS_LCAO Run 4.4305 1 4.4 71 % + HSolverLCAO solve 2.0449 12 0.17 33 % + HamiltLCAO updateHk 1.0858 12 0.09 17 % + LCAO_Hamilt cal_Hgamma 1.0605 12 0.088 17 % + Gint_Gamma distri_vl_value 0.6531 12 0.054 10 % + Gint_Gamma distri_vl 2.3102 6 0.39 37 % + LCAO_Deepks cal_projected_DM 4.5706 14 0.33 73 % + LCAO_gen_fixedH add_v_delta 2.1819 6 0.36 35 % + LCAO_DESCRIPTOR add_v_delta 2.1817 6 0.36 35 % + ElecStateLCAO psiToRho 0.94093 12 0.078 15 % + Charge mix_rho 0.83629 11 0.076 13 % + LOOP_ions force_stress 0.48888 1 0.49 7.8 % + Force_Stress_LCAO getForceStress 0.48886 1 0.49 7.8 % + Force_LCAO_gamma ftable_gamma 0.29487 1 0.29 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:42 2022 + FINISH Time : Wed Sep 28 11:10:49 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/18/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..8ccc902700681f4445babccf625c82096c0b75a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.336468 0.559977 0.322239 +H 0.314434 0.61569 0.347853 +H 0.372493 0.53051 0.370012 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..611b96bcb3c236b8f53787fe4b52276f668467d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1756 2 + 2 -13.0818 2 + 3 -8.99984 2 + 4 -6.71805 2 + 5 1.24217 0 + 6 4.33256 0 + 7 11.0963 0 + 8 11.3375 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..711682f142e2958738145137c2cacb86796ccb52 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:04 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.42109664509 15.6793494147 9.02270583517 0 0 0 0 + tauc_H1 8.8041611782 17.2393170994 9.73989634577 0 0 0 0 + tauc_H2 10.4297973531 14.8542863572 10.3603433921 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871143557099 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0897035083465 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.108020318337 (SEC) + + DONE : INIT CHARGE Time : 0.159036721093 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.440276 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000806 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114 + + Density error is 0.214044463654 + + Energy Rydberg eV + E_KohnSham -34.1922054553 -465.208821379 + E_Harris -34.3817135494 -467.787211276 + E_Fermi -0.399872673083 -5.44054682842 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010090545789 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127391461222 + + Density error is 0.0981726848469 + + Energy Rydberg eV + E_KohnSham -34.2806522983 -466.412202414 + E_Harris -34.287410076 -466.504146696 + E_Fermi -0.209829256979 -2.85487350202 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000959985137042 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120925968833 + + Density error is 0.0630028871549 + + Energy Rydberg eV + E_KohnSham -34.2808857005 -466.415378013 + E_Harris -34.2852449089 -466.474688087 + E_Fermi -0.199205040775 -2.71032362487 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883464447166 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111049477749 + + Density error is 0.00201784015851 + + Energy Rydberg eV + E_KohnSham -34.2808610713 -466.415042916 + E_Harris -34.2808632279 -466.415072258 + E_Fermi -0.163899267123 -2.2299639309 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882291021908 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111009136055 + + Density error is 0.000837985815002 + + Energy Rydberg eV + E_KohnSham -34.2808139825 -466.41440224 + E_Harris -34.2808146171 -466.414410874 + E_Fermi -0.163281235924 -2.22155518504 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000881309568065 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110877889577 + + Density error is 0.00017707302332 + + Energy Rydberg eV + E_KohnSham -34.2808430215 -466.414797336 + E_Harris -34.2808430782 -466.414798107 + E_Fermi -0.163174334414 -2.22010071538 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000881455356363 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110896972842 + + Density error is 3.60238736906e-05 + + Energy Rydberg eV + E_KohnSham -34.2808319341 -466.414646483 + E_Harris -34.2808319405 -466.414646571 + E_Fermi -0.163065118476 -2.21861475632 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000881395617667 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001108894697 + + Density error is 1.55284235574e-05 + + Energy Rydberg eV + E_KohnSham -34.2808363443 -466.414706488 + E_Harris -34.2808363453 -466.414706502 + E_Fermi -0.163100463167 -2.21909564552 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000881386666131 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110888369245 + + Density error is 1.609914898e-06 + + Energy Rydberg eV + E_KohnSham -34.2808350163 -466.414688419 + E_Harris -34.2808350163 -466.41468842 + E_Fermi -0.163083682259 -2.21886732954 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000881388178744 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011088844506 + + Density error is 1.63465395389e-07 + + Energy Rydberg eV + E_KohnSham -34.2808352381 -466.414691438 + E_Harris -34.2808352381 -466.414691438 + E_Fermi -0.16308231251 -2.21884869315 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000881388597604 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110888493807 + + Density error is 3.10363755683e-08 + + Energy Rydberg eV + E_KohnSham -34.2808352636 -466.414691784 + E_Harris -34.2808352636 -466.414691784 + E_band -7.93421896771 -107.950587141 + E_one_elec -69.1319459473 -940.588378712 + E_Hartree +35.9690306719 +489.383768675 + E_xc -8.19811805449 -111.541118418 + E_Ewald +7.2048767374 +98.0273770163 + E_demet -6.243968962e-73 -8.49535560183e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194469638139 -2.64589516669 + E_Fermi -0.1630822642 -2.21884803586 + + charge density convergence is achieved + final etot is -466.414691784 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1756 2.00000 + 2 -13.0818 2.00000 + 3 -8.99984 2.00000 + 4 -6.71805 2.00000 + 5 1.24217 0.00000 + 6 4.33256 0.00000 + 7 11.0963 0.00000 + 8 11.3375 0.00000 + + EFERMI = -2.218848035856790 eV + OUT.ABACUS/ final etot is -466.4146917839414 eV + correction force for each atom along direction 1 is -2.72245e-05 + correction force for each atom along direction 2 is 0.000106336 + correction force for each atom along direction 3 is 2.58548e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.47339591 -0.78316741 +0.048545471 + H1 -0.085922771 +0.37271099 +0.32748996 + H2 -0.38747314 +0.41045642 -0.37603543 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4146917839414 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7777 11 0.71 1.0e+02% + Run_lcao lcao_line 7.7680 1 7.8 1.e+02% + Potential init_pot 0.28561 2 0.14 3.7% + PW_Basis recip2real 0.26683 16 0.017 3.4% + PW_Basis gathers_scatterp 0.12555 16 0.0078 1.6% + Potential v_of_rho 1.0405 13 0.080 13.% + XC_Functional v_xc 0.36261 14 0.026 4.7% + H_Hartree_pw v_hartree 0.64101 13 0.049 8.2% + PW_Basis real2recip 0.66054 38 0.017 8.5% + PW_Basis gatherp_scatters 0.29232 38 0.0077 3.8% + ORB_control set_orb_tables 1.0979 1 1.1 14.% + ORB_gen_tables gen_tables 1.0979 1 1.1 14.% + ORB_table_phi init_Table 0.47945 1 0.48 6.2% + ORB_table_phi cal_ST_Phi12_R 0.47418 126 0.0038 6.1% + ORB_table_beta init_Table_Beta 0.18413 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18257 56 0.0033 2.3% + ORB_table_alpha init_Table_Alpha 0.24735 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24540 66 0.0037 3.2% + LOOP_ions opt_ions 6.1518 1 6.2 79.% + ESolver_KS_LCAO Run 5.5324 1 5.5 71.% + HSolverLCAO solve 3.2216 11 0.29 41.% + HamiltLCAO updateHk 1.5915 11 0.14 20.% + LCAO_Hamilt cal_Hgamma 1.5640 11 0.14 20.% + Gint_interface cal_gint 0.93450 23 0.041 12.% + Gint_Gamma distri_vl_value 0.80175 11 0.073 10.% + Gint_Gamma distri_vl 2.6458 6 0.44 34.% + LCAO_Deepks cal_projected_DM 5.7697 13 0.44 74.% + LCAO_gen_fixedH add_v_delta 2.5101 6 0.42 32.% + LCAO_DESCRIPTOR add_v_delta 2.5102 6 0.42 32.% + ElecStateLCAO psiToRho 1.5971 11 0.15 21.% + Charge mix_rho 0.72157 10 0.072 9.3% + LOOP_ions force_stress 0.61922 1 0.62 8.0% + Force_Stress_LCAO getForceStress 0.61920 1 0.62 8.0% + Force_LCAO_gamma ftable_gamma 0.40109 1 0.40 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.19803 1 0.20 2.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:04 2022 + Finish Time : Wed Sep 28 11:10:12 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a7e46c866a2fa778e9575fe5a52442e87f0178be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123518 ima = 3.66419e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001233484065 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240985815 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112960448412 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113176840858 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113140251691 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113163517489 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113155481272 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113158173145 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113157526799 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113157459079 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113157449888 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/STRU new file mode 100644 index 0000000000000000000000000000000000000000..569332e155bfe4cdba92a53fc05f008b1cedda7d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.578903354903 15.679349414679 9.022705835157 0 0 0 +H +0.0 +2 +-19.195838821819 17.239317099351 9.739896345762 0 0 0 +-17.570202646927 14.854286357181 10.360343392091 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/conv new file mode 100644 index 0000000000000000000000000000000000000000..c7832a97106a22f4c579c6c521d6f45cdc243a15 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/conv @@ -0,0 +1 @@ +180 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c09ebe7514c841f6f2acb4545e59fcd4ed68de3c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747498288 0.01259481981 1.267521658 1.360239836 1.468829348 0.008149997705 0.01903056548 0.03898143008 +-1.734724077e-18 0.001051236579 0.002464588045 0.01207306024 0.04340385181 -7.827941009e-20 1.725228612e-06 5.259622877e-06 +0.001684736906 0.005835388805 + +H atom_index 1 n_descriptor 18 +1.25101702 0.03400367735 0.1082375768 0.1509885591 0.3223347475 0.02201455803 0.02844368334 0.03720936556 +-3.538087291e-18 4.188575111e-05 0.1011682476 0.1150600027 0.1295766147 -2.580333416e-18 4.105328524e-06 0.0130517844 +0.02603971993 0.03084582539 + +H atom_index 2 n_descriptor 18 +1.216791021 0.0351883228 0.09697263893 0.1357473726 0.3108748642 0.02046138229 0.02645105662 0.0384238031 +-8.712637061e-18 3.893567221e-05 0.09225787849 0.1140166804 0.1163274613 8.159839898e-18 5.656181166e-06 0.01356258861 +0.02471752785 0.02921512287 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/dm_eig.npy new file mode 100644 index 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..51410933526ba21a4ac8e0a4fb6f2ce71d2f8658 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:04 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871376 SEC) : SETUP UNITCELL + DONE(0.0897199 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.108041 SEC) : INIT PLANEWAVE + DONE(0.159167 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.440342 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652088e+02 0.000000e+00 2.140e-01 6.008e-01 + GE2 -4.664122e+02 -1.203381e+00 9.817e-02 5.542e-01 + GE3 -4.664154e+02 -3.175599e-03 6.300e-02 6.234e-01 + GE4 -4.664150e+02 3.350973e-04 2.018e-03 4.808e-01 + GE5 -4.664144e+02 6.406759e-04 8.380e-04 4.800e-01 + GE6 -4.664148e+02 -3.950961e-04 1.771e-04 4.762e-01 + GE7 -4.664146e+02 1.508526e-04 3.602e-05 4.662e-01 + GE8 -4.664147e+02 -6.000453e-05 1.553e-05 4.632e-01 + GE9 -4.664147e+02 1.806854e-05 1.610e-06 4.619e-01 + GE10 -4.664147e+02 -3.018115e-06 1.635e-07 4.659e-01 + GE11 -4.664147e+02 -3.463604e-07 3.104e-08 3.935e-01 +E_delta_band = -6.97909671e-02 Ry = -9.49554821e-01 eV +E_delta_NN= -1.94469638e-01 Ry = -2.64589517e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7777 11 0.71 1e+02 % + Run_lcao lcao_line 7.768 1 7.8 1e+02 % + Potential init_pot 0.28561 2 0.14 3.7 % + PW_Basis recip2real 0.26683 16 0.017 3.4 % + PW_Basis gathers_scatterp 0.12555 16 0.0078 1.6 % + Potential v_of_rho 1.0405 13 0.08 13 % + XC_Functional v_xc 0.36261 14 0.026 4.7 % + H_Hartree_pw v_hartree 0.64101 13 0.049 8.2 % + PW_Basis real2recip 0.66054 38 0.017 8.5 % + PW_Basis gatherp_scatters 0.29232 38 0.0077 3.8 % + ORB_control set_orb_tables 1.0979 1 1.1 14 % + ORB_gen_tables gen_tables 1.0979 1 1.1 14 % + ORB_table_phi init_Table 0.47945 1 0.48 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.47418 126 0.0038 6.1 % + ORB_table_beta init_Table_Beta 0.18413 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18257 56 0.0033 2.3 % + ORB_table_alpha init_Table_Alpha 0.24735 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.2454 66 0.0037 3.2 % + LOOP_ions opt_ions 6.1518 1 6.2 79 % + ESolver_KS_LCAO Run 5.5324 1 5.5 71 % + HSolverLCAO solve 3.2216 11 0.29 41 % + HamiltLCAO updateHk 1.5915 11 0.14 20 % + LCAO_Hamilt cal_Hgamma 1.564 11 0.14 20 % + Gint_interface cal_gint 0.9345 23 0.041 12 % + Gint_Gamma distri_vl_value 0.80175 11 0.073 10 % + Gint_Gamma distri_vl 2.6458 6 0.44 34 % + LCAO_Deepks cal_projected_DM 5.7697 13 0.44 74 % + LCAO_gen_fixedH add_v_delta 2.5101 6 0.42 32 % + LCAO_DESCRIPTOR add_v_delta 2.5102 6 0.42 32 % + ElecStateLCAO psiToRho 1.5971 11 0.15 21 % + Charge mix_rho 0.72157 10 0.072 9.3 % + LOOP_ions force_stress 0.61922 1 0.62 8 % + Force_Stress_LCAO getForceStress 0.6192 1 0.62 8 % + Force_LCAO_gamma ftable_gamma 0.40109 1 0.4 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.19803 1 0.2 2.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:04 2022 + FINISH Time : Wed Sep 28 11:10:12 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/180/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..0ecc822653cef3628827cea40b240ffff4cd81d6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.344515 0.572134 0.3132 +H 0.293654 0.544754 0.344496 +H 0.392011 0.557229 0.351059 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e96ccfe77e9474960344822b2283034f4e1559da --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5969 2 + 2 -13.1141 2 + 3 -9.28595 2 + 4 -6.8105 2 + 5 1.45261 0 + 6 4.76827 0 + 7 11.0104 0 + 8 11.266 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c5f426d03847bdb5a63f1cc95dca3ab62026e87e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:36 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.64641104836 16.0197474376 8.76960715189 0 0 0 0 + tauc_H1 8.22231969362 15.2531174827 9.6458941339 0 0 0 0 + tauc_H2 10.9762976628 15.602424624 9.82965770457 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0878244923275 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0882328284762 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106420563693 (SEC) + + DONE : INIT CHARGE Time : 0.151332447873 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.430438 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000879 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00149 + + Density error is 0.217961444869 + + Energy Rydberg eV + E_KohnSham -34.1832257579 -465.086646328 + E_Harris -34.3822957794 -467.795132922 + E_Fermi -0.421964306411 -5.74111891981 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127370696953 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134281462425 + + Density error is 0.097538058583 + + Energy Rydberg eV + E_KohnSham -34.2757152399 -466.345030287 + E_Harris -34.2824211468 -466.436268832 + E_Fermi -0.228431715049 -3.10797292858 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121741184267 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123621201102 + + Density error is 0.0623741050282 + + Energy Rydberg eV + E_KohnSham -34.2760624007 -466.349753653 + E_Harris -34.2803764272 -466.408448995 + E_Fermi -0.215008020169 -2.92533418999 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114277857866 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105592535197 + + Density error is 0.00203929426676 + + Energy Rydberg eV + E_KohnSham -34.2760946378 -466.350192261 + E_Harris -34.2760968623 -466.350222527 + E_Fermi -0.178922793901 -2.43436949914 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114801048007 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105573495133 + + Density error is 0.00097490925745 + + Energy Rydberg eV + E_KohnSham -34.276014153 -466.34909721 + E_Harris -34.2760166623 -466.349131351 + E_Fermi -0.177893004722 -2.42035849856 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114626539835 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105366479406 + + Density error is 0.000113700328641 + + Energy Rydberg eV + E_KohnSham -34.2760656689 -466.349798119 + E_Harris -34.2760656979 -466.349798514 + E_Fermi -0.178081715131 -2.4229260354 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114611204652 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105333260102 + + Density error is 4.97582561329e-05 + + Energy Rydberg eV + E_KohnSham -34.2760487929 -466.34956851 + E_Harris -34.276048807 -466.349568701 + E_Fermi -0.177941671101 -2.42102063862 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114606151982 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105334996157 + + Density error is 1.96192999794e-05 + + Energy Rydberg eV + E_KohnSham -34.2760522796 -466.349615948 + E_Harris -34.2760522811 -466.349615969 + E_Fermi -0.17800315654 -2.42185719093 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114606547284 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105331872223 + + Density error is 2.30179272e-06 + + Energy Rydberg eV + E_KohnSham -34.2760505759 -466.349592768 + E_Harris -34.2760505759 -466.349592768 + E_Fermi -0.177982102356 -2.42157073406 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114606662897 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105331796465 + + Density error is 3.32912855977e-07 + + Energy Rydberg eV + E_KohnSham -34.2760508218 -466.349596114 + E_Harris -34.2760508218 -466.349596114 + E_Fermi -0.177980265256 -2.42154573903 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114606701804 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105331773009 + + Density error is 1.34188051275e-07 + + Energy Rydberg eV + E_KohnSham -34.2760508595 -466.349596628 + E_Harris -34.2760508595 -466.349596628 + E_Fermi -0.177980088212 -2.42154333023 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114606707924 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105331752048 + + Density error is 1.0697326021e-08 + + Energy Rydberg eV + E_KohnSham -34.2760508611 -466.349596649 + E_Harris -34.2760508611 -466.349596649 + E_band -8.05654975293 -109.61498286 + E_one_elec -69.7970746853 -949.637919452 + E_Hartree +36.2730591812 +493.520288756 + E_xc -8.24757917173 -112.214071442 + E_Ewald +7.61883060422 +103.659508314 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195822853604 -2.66430660763 + E_Fermi -0.177979937882 -2.42154128488 + + charge density convergence is achieved + final etot is -466.349596649 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5969 2.00000 + 2 -13.1141 2.00000 + 3 -9.28595 2.00000 + 4 -6.81050 2.00000 + 5 1.45261 0.00000 + 6 4.76827 0.00000 + 7 11.0104 0.00000 + 8 11.2660 0.00000 + + EFERMI = -2.421541284878023 eV + OUT.ABACUS/ final etot is -466.3495966485715 eV + correction force for each atom along direction 1 is -3.19671e-05 + correction force for each atom along direction 2 is -0.000195356 + correction force for each atom along direction 3 is 1.13470e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -2.1452936 +0.52276259 -1.4758371 + H1 -0.29694003 +0.034741560 -0.13239664 + H2 +2.4422337 -0.55750415 +1.6082337 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3495966485715 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8261 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8154 1 6.8 1.e+02% + Potential init_pot 0.28070 2 0.14 4.1% + PW_Basis recip2real 0.27322 17 0.016 4.0% + PW_Basis gathers_scatterp 0.12296 17 0.0072 1.8% + Potential v_of_rho 0.83695 14 0.060 12.% + XC_Functional v_xc 0.19781 15 0.013 2.9% + H_Hartree_pw v_hartree 0.60241 14 0.043 8.8% + PW_Basis real2recip 0.69532 41 0.017 10.% + PW_Basis gatherp_scatters 0.27592 41 0.0067 4.0% + ORB_control set_orb_tables 1.0991 1 1.1 16.% + ORB_gen_tables gen_tables 1.0991 1 1.1 16.% + ORB_table_phi init_Table 0.47599 1 0.48 7.0% + ORB_table_phi cal_ST_Phi12_R 0.47076 126 0.0037 6.9% + ORB_table_beta init_Table_Beta 0.18714 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18559 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24906 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24704 66 0.0037 3.6% + LOOP_ions opt_ions 5.2113 1 5.2 76.% + ESolver_KS_LCAO Run 4.7122 1 4.7 69.% + HSolverLCAO solve 2.3497 12 0.20 34.% + HamiltLCAO updateHk 1.2291 12 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1997 12 0.10 18.% + Gint_interface cal_gint 0.59493 25 0.024 8.7% + Gint_Gamma distri_vl_value 0.56388 12 0.047 8.3% + Gint_Gamma distri_vl 2.4588 6 0.41 36.% + LCAO_Deepks cal_projected_DM 4.9161 14 0.35 72.% + LCAO_gen_fixedH add_v_delta 2.3156 6 0.39 34.% + LCAO_DESCRIPTOR add_v_delta 2.3158 6 0.39 34.% + ElecStateLCAO psiToRho 1.1020 12 0.092 16.% + Charge mix_rho 0.92707 11 0.084 14.% + LOOP_ions force_stress 0.49890 1 0.50 7.3% + Force_Stress_LCAO getForceStress 0.49887 1 0.50 7.3% + Force_LCAO_gamma ftable_gamma 0.30160 1 0.30 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.14381 1 0.14 2.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:36 2022 + Finish Time : Wed Sep 28 11:04:42 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..bdbfeea0eea91371e9bae5eb41ec89b4cf17ac57 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123849 ima = 3.64919e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122838989649 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111729706022 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112210641652 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112514114612 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011243868993 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112479660686 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112474682891 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112478190003 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112477437381 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112477337663 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112477327605 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112477320929 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5f045957b06f82a4afa89c59a4c87b3c484e01b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.353588951638 16.019747437653 8.769607151888 0 0 0 +H +0.0 +2 +-19.777680306385 15.253117482643 9.645894133887 0 0 0 +-17.023702337140 15.602424623966 9.829657704565 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/conv new file mode 100644 index 0000000000000000000000000000000000000000..fa13ed94fcd165bcf854ba302a644e3953684ff1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/conv @@ -0,0 +1 @@ +181 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8ba5afe78d0e93734d0946506cf35b38516edc98 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751499789 0.01283198867 1.288066807 1.378380897 1.47071973 0.009132957862 0.01831785493 0.03909751085 +2.879620233e-18 0.00110526968 0.002872960508 0.01335178311 0.0486738476 7.076801517e-19 2.671944691e-06 7.139019601e-06 +0.001609414416 0.00603126814 + +H atom_index 1 n_descriptor 18 +1.242329085 0.03476518842 0.1070484596 0.1460338535 0.3173621351 0.02243676319 0.02780425044 0.03783862426 +3.889536881e-17 5.18051742e-05 0.1025086949 0.1144226418 0.1254889902 -5.696899317e-18 4.320157578e-06 0.01339043896 +0.02681420602 0.03041942291 + +H atom_index 2 n_descriptor 18 +1.311789192 0.03259456199 0.1335493481 0.1809296484 0.3378728794 0.02574175261 0.03178873847 0.03668059713 +-2.322963193e-17 5.860236477e-05 0.1080336029 0.1288785486 0.1551299929 -5.445363712e-18 6.323109144e-07 0.01419465079 +0.02909835187 0.0331555655 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d302c7fd6ca99c5cda54991f9931d8e456da6981 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:36 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0878563 SEC) : SETUP UNITCELL + DONE(0.0882482 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106444 SEC) : INIT PLANEWAVE + DONE(0.151464 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.430505 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650866e+02 0.000000e+00 2.180e-01 4.853e-01 + GE2 -4.663450e+02 -1.258384e+00 9.754e-02 4.446e-01 + GE3 -4.663498e+02 -4.723366e-03 6.237e-02 5.100e-01 + GE4 -4.663502e+02 -4.386072e-04 2.039e-03 3.750e-01 + GE5 -4.663491e+02 1.095051e-03 9.749e-04 3.727e-01 + GE6 -4.663498e+02 -7.009088e-04 1.137e-04 3.668e-01 + GE7 -4.663496e+02 2.296089e-04 4.976e-05 3.637e-01 + GE8 -4.663496e+02 -4.743837e-05 1.962e-05 3.564e-01 + GE9 -4.663496e+02 2.318048e-05 2.302e-06 3.566e-01 + GE10 -4.663496e+02 -3.346038e-06 3.329e-07 3.571e-01 + GE11 -4.663496e+02 -5.137792e-07 1.342e-07 3.587e-01 + GE12 -4.663496e+02 -2.097243e-08 1.070e-08 3.046e-01 +E_delta_band = -7.25360641e-02 Ry = -9.86903782e-01 eV +E_delta_NN= -1.95822854e-01 Ry = -2.66430661e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8261 11 0.62 1e+02 % + Run_lcao lcao_line 6.8154 1 6.8 1e+02 % + Potential init_pot 0.2807 2 0.14 4.1 % + PW_Basis recip2real 0.27322 17 0.016 4 % + PW_Basis gathers_scatterp 0.12296 17 0.0072 1.8 % + Potential v_of_rho 0.83695 14 0.06 12 % + XC_Functional v_xc 0.19781 15 0.013 2.9 % + H_Hartree_pw v_hartree 0.60241 14 0.043 8.8 % + PW_Basis real2recip 0.69532 41 0.017 10 % + PW_Basis gatherp_scatters 0.27592 41 0.0067 4 % + ORB_control set_orb_tables 1.0991 1 1.1 16 % + ORB_gen_tables gen_tables 1.0991 1 1.1 16 % + ORB_table_phi init_Table 0.47599 1 0.48 7 % + ORB_table_phi cal_ST_Phi12_R 0.47076 126 0.0037 6.9 % + ORB_table_beta init_Table_Beta 0.18714 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18559 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24906 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24704 66 0.0037 3.6 % + LOOP_ions opt_ions 5.2113 1 5.2 76 % + ESolver_KS_LCAO Run 4.7122 1 4.7 69 % + HSolverLCAO solve 2.3497 12 0.2 34 % + HamiltLCAO updateHk 1.2291 12 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1997 12 0.1 18 % + Gint_interface cal_gint 0.59493 25 0.024 8.7 % + Gint_Gamma distri_vl_value 0.56388 12 0.047 8.3 % + Gint_Gamma distri_vl 2.4588 6 0.41 36 % + LCAO_Deepks cal_projected_DM 4.9161 14 0.35 72 % + LCAO_gen_fixedH add_v_delta 2.3156 6 0.39 34 % + LCAO_DESCRIPTOR add_v_delta 2.3158 6 0.39 34 % + ElecStateLCAO psiToRho 1.102 12 0.092 16 % + Charge mix_rho 0.92707 11 0.084 14 % + LOOP_ions force_stress 0.4989 1 0.5 7.3 % + Force_Stress_LCAO getForceStress 0.49887 1 0.5 7.3 % + Force_LCAO_gamma ftable_gamma 0.3016 1 0.3 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.14381 1 0.14 2.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:36 2022 + FINISH Time : Wed Sep 28 11:04:42 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/181/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..7d9fd24e4ea227f4f3e24c7e7ab33b683557851e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.34157 0.59186 0.303552 +H 0.32036 0.533023 0.281193 +H 0.387758 0.583387 0.353927 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..edf585569b8e3a07061f106c7b4d875130173027 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.8219 2 + 2 -13.0287 2 + 3 -8.73267 2 + 4 -6.63063 2 + 5 0.966327 0 + 6 3.96972 0 + 7 11.1721 0 + 8 11.3907 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3047cac7349e636c5da0811a578e5f501d589d7f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:16 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.56394666462 16.5720844387 8.49944274659 0 0 0 0 + tauc_H1 8.97007043293 14.9246318474 7.87339419653 0 0 0 0 + tauc_H2 10.8572379456 16.3348406772 9.90994468996 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.073341187453 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0736688650179 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0901589962016 (SEC) + + DONE : INIT CHARGE Time : 0.13291706747 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.376777 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 100 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000449 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122 + + Density error is 0.212536969336 + + Energy Rydberg eV + E_KohnSham -34.1875895672 -465.146018999 + E_Harris -34.3734689183 -467.675037315 + E_Fermi -0.38266304868 -5.2063978761 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000685174844485 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122737433446 + + Density error is 0.0993331915213 + + Energy Rydberg eV + E_KohnSham -34.2753409551 -466.339937883 + E_Harris -34.2824219405 -466.43627963 + E_Fermi -0.193227812564 -2.62899926295 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000665771711191 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116115584779 + + Density error is 0.0640135706063 + + Energy Rydberg eV + E_KohnSham -34.2756625554 -466.344313478 + E_Harris -34.2801662016 -466.405588728 + E_Fermi -0.186357130388 -2.53551883621 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000652393340902 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105118966343 + + Density error is 0.00217781313213 + + Energy Rydberg eV + E_KohnSham -34.2755729667 -466.343094562 + E_Harris -34.2755800804 -466.343191349 + E_Fermi -0.151596560951 -2.06257702613 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000651353186713 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104878195711 + + Density error is 0.000868568397561 + + Energy Rydberg eV + E_KohnSham -34.2755525203 -466.342816375 + E_Harris -34.275552727 -466.342819187 + E_Fermi -0.151338451705 -2.05906526968 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000651287736758 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104728803878 + + Density error is 0.000206390298596 + + Energy Rydberg eV + E_KohnSham -34.2755619341 -466.342944456 + E_Harris -34.2755619177 -466.342944233 + E_Fermi -0.150923898762 -2.05342498754 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000651418333158 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104729961298 + + Density error is 2.36846938037e-05 + + Energy Rydberg eV + E_KohnSham -34.2755600224 -466.342918445 + E_Harris -34.2755600238 -466.342918465 + E_Fermi -0.15089084314 -2.05297524273 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000651378972977 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010472373837 + + Density error is 1.06981920256e-05 + + Energy Rydberg eV + E_KohnSham -34.2755621512 -466.342947409 + E_Harris -34.2755621517 -466.342947416 + E_Fermi -0.150901518095 -2.05312048294 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000651384462509 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104723269181 + + Density error is 1.36602525624e-06 + + Energy Rydberg eV + E_KohnSham -34.275561326 -466.342936182 + E_Harris -34.275561326 -466.342936183 + E_Fermi -0.150891040681 -2.05297793041 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000651385844115 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104723194773 + + Density error is 3.1643596203e-07 + + Energy Rydberg eV + E_KohnSham -34.2755615061 -466.342938633 + E_Harris -34.2755615061 -466.342938633 + E_Fermi -0.150890086652 -2.05296495018 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000651386255353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010472323097 + + Density error is 4.28177970921e-08 + + Energy Rydberg eV + E_KohnSham -34.2755615145 -466.342938746 + E_Harris -34.2755615145 -466.342938746 + E_band -7.82229106417 -106.427729887 + E_one_elec -68.5359592275 -932.47956339 + E_Hartree +35.6981154361 +485.697777792 + E_xc -8.15431593211 -110.945159969 + E_Ewald +6.84250435153 +93.0970477705 + E_demet -3.84299318645e-56 -5.22866047109e-55 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193292334713 -2.62987713182 + E_Fermi -0.150889882366 -2.05296217073 + + charge density convergence is achieved + final etot is -466.342938746 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.8219 2.00000 + 2 -13.0287 2.00000 + 3 -8.73267 2.00000 + 4 -6.63063 2.00000 + 5 0.966327 0.00000 + 6 3.96972 0.00000 + 7 11.1721 0.00000 + 8 11.3907 0.00000 + + EFERMI = -2.052962170727010 eV + OUT.ABACUS/ final etot is -466.3429387463186 eV + correction force for each atom along direction 1 is 0.000131312 + correction force for each atom along direction 2 is -3.04855e-05 + correction force for each atom along direction 3 is 9.02749e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.94596448 +0.039598894 +1.0264764 + H1 +0.48241505 +0.21735274 +0.52378673 + H2 -1.4283795 -0.25695164 -1.5502632 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3429387463186 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8866 11 0.63 1.0e+02% + Run_lcao lcao_line 6.8789 1 6.9 1.e+02% + Potential init_pot 0.24101 2 0.12 3.5% + PW_Basis recip2real 0.22133 16 0.014 3.2% + PW_Basis gathers_scatterp 0.10334 16 0.0065 1.5% + Potential v_of_rho 0.87996 13 0.068 13.% + XC_Functional v_xc 0.28549 14 0.020 4.1% + H_Hartree_pw v_hartree 0.56277 13 0.043 8.2% + PW_Basis real2recip 0.60464 38 0.016 8.8% + PW_Basis gatherp_scatters 0.26823 38 0.0071 3.9% + ORB_control set_orb_tables 0.89808 1 0.90 13.% + ORB_gen_tables gen_tables 0.89807 1 0.90 13.% + ORB_table_phi init_Table 0.37621 1 0.38 5.5% + ORB_table_phi cal_ST_Phi12_R 0.37193 126 0.0030 5.4% + ORB_table_beta init_Table_Beta 0.15584 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15453 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.20804 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20641 66 0.0031 3.0% + LOOP_ions opt_ions 5.5345 1 5.5 80.% + ESolver_KS_LCAO Run 4.9779 1 5.0 72.% + HSolverLCAO solve 2.8182 11 0.26 41.% + HamiltLCAO updateHk 1.4095 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3861 11 0.13 20.% + Gint_interface cal_gint 1.3316 23 0.058 19.% + Gint_Gamma distri_vl_value 0.51263 11 0.047 7.4% + Gint_Gamma distri_vl 2.3775 6 0.40 35.% + LCAO_Deepks cal_projected_DM 5.2570 13 0.40 76.% + LCAO_gen_fixedH add_v_delta 2.2493 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2492 6 0.37 33.% + ElecStateLCAO psiToRho 1.3924 11 0.13 20.% + Charge mix_rho 0.74314 10 0.074 11.% + LOOP_ions force_stress 0.55646 1 0.56 8.1% + Force_Stress_LCAO getForceStress 0.55644 1 0.56 8.1% + Force_LCAO_gamma ftable_gamma 0.35651 1 0.36 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.23025 1 0.23 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:16 2022 + Finish Time : Wed Sep 28 11:13:23 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6ccfc39ec1c709937e4b1b23681e4aa0a3f38a7b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123275 ima = 3.65961e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124217052023 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113063149059 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113769120887 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113927253736 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113921321167 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113926909079 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113924031857 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113925605737 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113925090198 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113925055346 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113925037763 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/STRU new file mode 100644 index 0000000000000000000000000000000000000000..195d982a6de38b8d0e96c0e329cc2055fa094423 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.436053335401 16.572084438696 8.499442746562 0 0 0 +H +0.0 +2 +-19.029929567058 14.924631847372 7.873394196542 0 0 0 +-17.142762054376 16.334840677232 9.909944689952 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/conv new file mode 100644 index 0000000000000000000000000000000000000000..696f28ef1dde34dd34be749f2375f1e0fea50974 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/conv @@ -0,0 +1 @@ +182 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..da017bf9f4c6ca677eca95c0b7f5a190dbb3ab73 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74400588 0.01225888685 1.244158418 1.348719987 1.467245697 0.007443833266 0.01987635817 0.03889699419 +5.690168625e-19 0.0009657046246 0.002135529177 0.01117691944 0.03847277267 3.159226743e-19 1.101322107e-06 3.759170411e-06 +0.001757531305 0.005473031109 + +H atom_index 1 n_descriptor 18 +1.218632043 0.03479899716 0.09744670409 0.1380905675 0.3140729071 0.02014892123 0.02677788755 0.03811267177 +2.67706595e-17 3.006714278e-05 0.09118263581 0.1144281745 0.1181644201 -3.057536313e-18 4.879985589e-06 0.01326134274 +0.02417124855 0.02943480998 + +H atom_index 2 n_descriptor 18 +1.164110214 0.03651851134 0.08160815656 0.1162874367 0.2939975799 0.01776655759 0.02362283377 0.04037729243 +4.210907331e-17 2.63830707e-05 0.07712578878 0.0989321993 0.1122675724 6.773231684e-18 5.969730757e-06 0.01485300612 +0.02191642706 0.02655889914 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9b2eeb4f36a00ca3676476d083dd3ce7685d7e8c Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..142f0529db701770ae023fe00c45aea93619d9e5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:16 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733559 SEC) : SETUP UNITCELL + DONE(0.0736789 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.090174 SEC) : INIT PLANEWAVE + DONE(0.133023 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.376819 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651460e+02 0.000000e+00 2.125e-01 5.267e-01 + GE2 -4.663399e+02 -1.193919e+00 9.933e-02 4.998e-01 + GE3 -4.663443e+02 -4.375595e-03 6.401e-02 5.652e-01 + GE4 -4.663431e+02 1.218916e-03 2.178e-03 4.404e-01 + GE5 -4.663428e+02 2.781868e-04 8.686e-04 4.400e-01 + GE6 -4.663429e+02 -1.280811e-04 2.064e-04 4.370e-01 + GE7 -4.663429e+02 2.601068e-05 2.368e-05 4.153e-01 + GE8 -4.663429e+02 -2.896359e-05 1.070e-05 4.200e-01 + GE9 -4.663429e+02 1.122650e-05 1.366e-06 4.151e-01 + GE10 -4.663429e+02 -2.450463e-06 3.164e-07 4.154e-01 + GE11 -4.663429e+02 -1.134185e-07 4.282e-08 3.498e-01 +E_delta_band = -6.73861923e-02 Ry = -9.16836181e-01 eV +E_delta_NN= -1.93292335e-01 Ry = -2.62987713e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8866 11 0.63 1e+02 % + Run_lcao lcao_line 6.8789 1 6.9 1e+02 % + Potential init_pot 0.24101 2 0.12 3.5 % + PW_Basis recip2real 0.22133 16 0.014 3.2 % + PW_Basis gathers_scatterp 0.10334 16 0.0065 1.5 % + Potential v_of_rho 0.87996 13 0.068 13 % + XC_Functional v_xc 0.28549 14 0.02 4.1 % + H_Hartree_pw v_hartree 0.56277 13 0.043 8.2 % + PW_Basis real2recip 0.60464 38 0.016 8.8 % + PW_Basis gatherp_scatters 0.26823 38 0.0071 3.9 % + ORB_control set_orb_tables 0.89808 1 0.9 13 % + ORB_gen_tables gen_tables 0.89807 1 0.9 13 % + ORB_table_phi init_Table 0.37621 1 0.38 5.5 % + ORB_table_phi cal_ST_Phi12_R 0.37193 126 0.003 5.4 % + ORB_table_beta init_Table_Beta 0.15584 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15453 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.20804 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20641 66 0.0031 3 % + LOOP_ions opt_ions 5.5345 1 5.5 80 % + ESolver_KS_LCAO Run 4.9779 1 5 72 % + HSolverLCAO solve 2.8182 11 0.26 41 % + HamiltLCAO updateHk 1.4095 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3861 11 0.13 20 % + Gint_interface cal_gint 1.3316 23 0.058 19 % + Gint_Gamma distri_vl_value 0.51263 11 0.047 7.4 % + Gint_Gamma distri_vl 2.3775 6 0.4 35 % + LCAO_Deepks cal_projected_DM 5.257 13 0.4 76 % + LCAO_gen_fixedH add_v_delta 2.2493 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2492 6 0.37 33 % + ElecStateLCAO psiToRho 1.3924 11 0.13 20 % + Charge mix_rho 0.74314 10 0.074 11 % + LOOP_ions force_stress 0.55646 1 0.56 8.1 % + Force_Stress_LCAO getForceStress 0.55644 1 0.56 8.1 % + Force_LCAO_gamma ftable_gamma 0.35651 1 0.36 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.23025 1 0.23 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:16 2022 + FINISH Time : Wed Sep 28 11:13:23 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/182/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..afb9ef8945e9477461af5e5776348c2820b9bc93 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.333262 0.605089 0.285342 +H 0.381271 0.610065 0.240587 +H 0.366481 0.626032 0.335582 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e5b6ee0f2bcf38ff9e9b3eaad4283c9b06401e6b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5589 2 + 2 -12.8049 2 + 3 -9.47819 2 + 4 -6.80346 2 + 5 1.34354 0 + 6 4.57767 0 + 7 11.0344 0 + 8 11.318 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d91dd55bb5ae5fbefd562456ac92946d2b5603b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:35 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.33133003982 16.942498834 7.98958685189 0 0 0 0 + tauc_H1 10.6755776235 17.0818128585 6.73644323307 0 0 0 0 + tauc_H2 10.2614658162 17.5288912925 9.39630007 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0995937682598 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100008940922 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118164319363 (SEC) + + DONE : INIT CHARGE Time : 0.162697583992 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443987 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 100 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000985 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000983 + + Density error is 0.215581963957 + + Energy Rydberg eV + E_KohnSham -34.1853337022 -465.115326382 + E_Harris -34.379806115 -467.7612593 + E_Fermi -0.415550841651 -5.65385925516 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00138013162438 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104795454977 + + Density error is 0.0974814041696 + + Energy Rydberg eV + E_KohnSham -34.2767117687 -466.358588759 + E_Harris -34.2835497327 -466.451624031 + E_Fermi -0.223011917148 -3.03423279511 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00131494489203 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000988819256373 + + Density error is 0.0625351028105 + + Energy Rydberg eV + E_KohnSham -34.2770911525 -466.363750539 + E_Harris -34.2815156844 -466.423949384 + E_Fermi -0.211415129234 -2.87645040099 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00122775243902 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000905700265381 + + Density error is 0.00197964578666 + + Energy Rydberg eV + E_KohnSham -34.2770884325 -466.363713531 + E_Harris -34.2770895236 -466.363728377 + E_Fermi -0.175292571297 -2.38497778671 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00123287746682 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908522912739 + + Density error is 0.000998829112891 + + Energy Rydberg eV + E_KohnSham -34.2770148265 -466.36271207 + E_Harris -34.2770171154 -466.362743213 + E_Fermi -0.174608615768 -2.37567209433 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00123088626559 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000907067763685 + + Density error is 0.000107093268674 + + Energy Rydberg eV + E_KohnSham -34.2770610706 -466.363341254 + E_Harris -34.2770610877 -466.363341487 + E_Fermi -0.174624820476 -2.37589257071 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00123060161381 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906936959431 + + Density error is 4.15562946716e-05 + + Energy Rydberg eV + E_KohnSham -34.2770471946 -466.363152461 + E_Harris -34.2770472045 -466.363152596 + E_Fermi -0.174512031879 -2.37435800311 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00123054764543 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906914839871 + + Density error is 2.33115531533e-05 + + Energy Rydberg eV + E_KohnSham -34.2770494507 -466.363183157 + E_Harris -34.2770494531 -466.363183189 + E_Fermi -0.174568723234 -2.37512932856 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00123054838626 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906913502998 + + Density error is 1.81908491499e-06 + + Energy Rydberg eV + E_KohnSham -34.2770477244 -466.36315967 + E_Harris -34.2770477244 -466.36315967 + E_Fermi -0.174542862388 -2.37477747371 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00123054914847 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906912929473 + + Density error is 2.75801851053e-07 + + Energy Rydberg eV + E_KohnSham -34.2770480831 -466.36316455 + E_Harris -34.2770480831 -466.36316455 + E_Fermi -0.174541590997 -2.37476017554 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00123055014749 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906913512617 + + Density error is 9.59435281199e-08 + + Energy Rydberg eV + E_KohnSham -34.2770481126 -466.363164951 + E_Harris -34.2770481126 -466.363164951 + E_band -8.03272367273 -109.290812409 + E_one_elec -69.5741763254 -946.605231683 + E_Hartree +36.1613349232 +492.000202242 + E_xc -8.22911514724 -111.962855501 + E_Ewald +7.48861302996 +101.887807325 + E_demet -9.15688352249e-84 -1.24585791828e-82 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195387084046 -2.65837765864 + E_Fermi -0.174541526246 -2.37475929457 + + charge density convergence is achieved + final etot is -466.363164951 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5589 2.00000 + 2 -12.8049 2.00000 + 3 -9.47819 2.00000 + 4 -6.80346 2.00000 + 5 1.34354 0.00000 + 6 4.57767 0.00000 + 7 11.0344 0.00000 + 8 11.3180 0.00000 + + EFERMI = -2.374759294566133 eV + OUT.ABACUS/ final etot is -466.3631649511196 eV + correction force for each atom along direction 1 is 0.000180410 + correction force for each atom along direction 2 is 1.75393e-05 + correction force for each atom along direction 3 is 1.78348e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.26031671 -0.36043109 -1.2941106 + H1 -0.22856480 -0.18812903 -0.55463739 + H2 +0.48888152 +0.54856012 +1.8487480 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3631649511196 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5059 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4970 1 6.5 1.e+02% + Potential init_pot 0.28240 2 0.14 4.3% + PW_Basis recip2real 0.25560 16 0.016 3.9% + PW_Basis gathers_scatterp 0.11236 16 0.0070 1.7% + Potential v_of_rho 0.90616 13 0.070 14.% + XC_Functional v_xc 0.28142 14 0.020 4.3% + H_Hartree_pw v_hartree 0.58406 13 0.045 9.0% + PW_Basis real2recip 0.66924 38 0.018 10.% + PW_Basis gatherp_scatters 0.26612 38 0.0070 4.1% + ORB_control set_orb_tables 1.0956 1 1.1 17.% + ORB_gen_tables gen_tables 1.0956 1 1.1 17.% + ORB_table_phi init_Table 0.47445 1 0.47 7.3% + ORB_table_phi cal_ST_Phi12_R 0.46914 126 0.0037 7.2% + ORB_table_beta init_Table_Beta 0.18511 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18359 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.24652 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24453 66 0.0037 3.8% + LOOP_ions opt_ions 4.8753 1 4.9 75.% + ESolver_KS_LCAO Run 4.3792 1 4.4 67.% + HSolverLCAO solve 2.0259 11 0.18 31.% + HamiltLCAO updateHk 1.0944 11 0.099 17.% + LCAO_Hamilt cal_Hgamma 1.0669 11 0.097 16.% + Gint_interface cal_gint 0.97190 23 0.042 15.% + Gint_Gamma distri_vl_value 0.31005 11 0.028 4.8% + Gint_Gamma distri_vl 2.1199 6 0.35 33.% + LCAO_Deepks cal_projected_DM 4.6412 13 0.36 71.% + LCAO_gen_fixedH add_v_delta 1.9743 6 0.33 30.% + LCAO_DESCRIPTOR add_v_delta 1.9744 6 0.33 30.% + ElecStateLCAO psiToRho 0.91239 11 0.083 14.% + Charge mix_rho 0.89426 10 0.089 14.% + LOOP_ions force_stress 0.49589 1 0.50 7.6% + Force_Stress_LCAO getForceStress 0.49586 1 0.50 7.6% + Force_LCAO_gamma ftable_gamma 0.29242 1 0.29 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.19107 1 0.19 2.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:35 2022 + Finish Time : Wed Sep 28 11:08:42 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..bddca4e6aa354285592e15e02bc4ba68b12ad314 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124283 ima = 3.6956e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122581994562 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111297172859 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111880046667 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112176040122 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112106217024 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112142730423 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112140648497 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112143915359 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112142900924 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112142823453 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112142813589 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/STRU new file mode 100644 index 0000000000000000000000000000000000000000..84aec3d05b013993e94f30fe2098b495158b8045 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.668669960153 16.942498834016 7.989586851916 0 0 0 +H +0.0 +2 +-17.324422376507 17.081812858465 6.736443233076 0 0 0 +-17.738534183814 17.528891292528 9.396300069981 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/conv new file mode 100644 index 0000000000000000000000000000000000000000..9aa427c1f8303947457e7442f187fb825a63d599 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/conv @@ -0,0 +1 @@ +183 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e9d83c5590c13c79b5d4c08e818d9df8dcbebe25 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754501177 0.01287204361 1.279467709 1.362460979 1.470344725 0.009666669839 0.01687066702 0.03916729493 +1.629955274e-18 0.000946257837 0.002964873562 0.0137637055 0.04845209644 -4.261302247e-19 3.094070261e-06 7.95404742e-06 +0.001590844047 0.006168849849 + +H atom_index 1 n_descriptor 18 +1.242071371 0.03522555492 0.1090159982 0.1458333532 0.3165850546 0.02303259544 0.02776129141 0.03830465283 +-9.770304203e-18 5.181663771e-05 0.1027792025 0.1147413355 0.1251151105 3.841006557e-18 3.422265794e-06 0.01353058549 +0.02710532148 0.03038621727 + +H atom_index 2 n_descriptor 18 +1.287204808 0.03376015897 0.1259079686 0.1677762316 0.3308497892 0.02529486659 0.03038970216 0.03718287161 +6.765402522e-17 5.609214097e-05 0.1085154835 0.1221299462 0.1438896897 8.8569113e-19 1.025070061e-06 0.01359240381 +0.02867994017 0.0323210364 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..2c0d940dbc312891a61809523c15ff1b555b792c Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..36ec0535c8c311eaba2b6621b363a63458d283ff Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..cba3f2cf4e770a513c7cd0855fd4def98a55a1fa Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..12acc64f36a5b065eb1b55af979400e764328e52 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:35 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0996203 SEC) : SETUP UNITCELL + DONE(0.100025 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118186 SEC) : INIT PLANEWAVE + DONE(0.162833 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444061 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651153e+02 0.000000e+00 2.156e-01 4.893e-01 + GE2 -4.663586e+02 -1.243262e+00 9.748e-02 4.479e-01 + GE3 -4.663638e+02 -5.161781e-03 6.254e-02 5.178e-01 + GE4 -4.663637e+02 3.700795e-05 1.980e-03 3.785e-01 + GE5 -4.663627e+02 1.001461e-03 9.988e-04 3.772e-01 + GE6 -4.663633e+02 -6.291840e-04 1.071e-04 3.727e-01 + GE7 -4.663632e+02 1.887929e-04 4.156e-05 3.685e-01 + GE8 -4.663632e+02 -3.069608e-05 2.331e-05 3.558e-01 + GE9 -4.663632e+02 2.348765e-05 1.819e-06 3.572e-01 + GE10 -4.663632e+02 -4.880341e-06 2.758e-07 3.566e-01 + GE11 -4.663632e+02 -4.009844e-07 9.594e-08 2.955e-01 +E_delta_band = -7.16824910e-02 Ry = -9.75290324e-01 eV +E_delta_NN= -1.95387084e-01 Ry = -2.65837766e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5059 11 0.59 1e+02 % + Run_lcao lcao_line 6.497 1 6.5 1e+02 % + Potential init_pot 0.2824 2 0.14 4.3 % + PW_Basis recip2real 0.2556 16 0.016 3.9 % + PW_Basis gathers_scatterp 0.11236 16 0.007 1.7 % + Potential v_of_rho 0.90616 13 0.07 14 % + XC_Functional v_xc 0.28142 14 0.02 4.3 % + H_Hartree_pw v_hartree 0.58406 13 0.045 9 % + PW_Basis real2recip 0.66924 38 0.018 10 % + PW_Basis gatherp_scatters 0.26612 38 0.007 4.1 % + ORB_control set_orb_tables 1.0956 1 1.1 17 % + ORB_gen_tables gen_tables 1.0956 1 1.1 17 % + ORB_table_phi init_Table 0.47445 1 0.47 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.46914 126 0.0037 7.2 % + ORB_table_beta init_Table_Beta 0.18511 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18359 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.24652 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24453 66 0.0037 3.8 % + LOOP_ions opt_ions 4.8753 1 4.9 75 % + ESolver_KS_LCAO Run 4.3792 1 4.4 67 % + HSolverLCAO solve 2.0259 11 0.18 31 % + HamiltLCAO updateHk 1.0944 11 0.099 17 % + LCAO_Hamilt cal_Hgamma 1.0669 11 0.097 16 % + Gint_interface cal_gint 0.9719 23 0.042 15 % + Gint_Gamma distri_vl_value 0.31005 11 0.028 4.8 % + Gint_Gamma distri_vl 2.1199 6 0.35 33 % + LCAO_Deepks cal_projected_DM 4.6412 13 0.36 71 % + LCAO_gen_fixedH add_v_delta 1.9743 6 0.33 30 % + LCAO_DESCRIPTOR add_v_delta 1.9744 6 0.33 30 % + ElecStateLCAO psiToRho 0.91239 11 0.083 14 % + Charge mix_rho 0.89426 10 0.089 14 % + LOOP_ions force_stress 0.49589 1 0.5 7.6 % + Force_Stress_LCAO getForceStress 0.49586 1 0.5 7.6 % + Force_LCAO_gamma ftable_gamma 0.29242 1 0.29 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.19107 1 0.19 2.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:35 2022 + FINISH Time : Wed Sep 28 11:08:42 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/183/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a63fbe37e0dcf17b41bc94ad6ddffda67701658e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.328752 0.61866 0.25574 +H 0.351986 0.670259 0.220756 +H 0.287426 0.64134 0.302301 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..053617816a672ff26524afc924bb57b8d6df1e4b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0459 2 + 2 -13.1318 2 + 3 -8.85607 2 + 4 -6.68658 2 + 5 1.18079 0 + 6 4.23421 0 + 7 11.1208 0 + 8 11.3511 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3ee94d7022e74c0ba18cda878cb0a83deba09a86 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:19 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.20505030857 17.3224772151 7.16072052446 0 0 0 0 + tauc_H1 9.85560190448 18.7672614031 6.18117027982 0 0 0 0 + tauc_H2 8.04793609057 17.9575092646 8.46443594748 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.073168172551 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0832285860886 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0996404137218 (SEC) + + DONE : INIT CHARGE Time : 0.141192281979 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388092 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000612 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126 + + Density error is 0.213969019278 + + Energy Rydberg eV + E_KohnSham -34.1914343473 -465.198329916 + E_Harris -34.3803897898 -467.769200603 + E_Fermi -0.394593570573 -5.36872095396 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000811139070341 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130611623336 + + Density error is 0.0985168191764 + + Energy Rydberg eV + E_KohnSham -34.2799084283 -466.402081544 + E_Harris -34.2867261207 -466.494841007 + E_Fermi -0.204290080691 -2.77950914228 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000779919898699 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123369330224 + + Density error is 0.063305669444 + + Energy Rydberg eV + E_KohnSham -34.2801934232 -466.405959097 + E_Harris -34.2845757458 -466.465583655 + E_Fermi -0.194778201669 -2.6500933889 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000744566524154 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111636593053 + + Density error is 0.00208239947021 + + Energy Rydberg eV + E_KohnSham -34.28015151 -466.40538884 + E_Harris -34.2801554794 -466.405442846 + E_Fermi -0.159701629654 -2.17285214319 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000745196907244 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111522944395 + + Density error is 0.000853259583393 + + Energy Rydberg eV + E_KohnSham -34.2801113882 -466.404842954 + E_Harris -34.2801118976 -466.404849885 + E_Fermi -0.159166985171 -2.16557793181 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000744732114778 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111370811204 + + Density error is 0.000195271419292 + + Energy Rydberg eV + E_KohnSham -34.2801345135 -466.40515759 + E_Harris -34.2801343883 -466.405155887 + E_Fermi -0.158964385505 -2.16282142194 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000744936989117 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111382611965 + + Density error is 3.22525370579e-05 + + Energy Rydberg eV + E_KohnSham -34.2801260277 -466.405042135 + E_Harris -34.2801260323 -466.405042198 + E_Fermi -0.158872052866 -2.16156517194 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000744895812739 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011137684411 + + Density error is 1.57013765055e-05 + + Energy Rydberg eV + E_KohnSham -34.2801301002 -466.405097544 + E_Harris -34.2801301013 -466.40509756 + E_Fermi -0.158901504779 -2.16196588577 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000744901769348 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011137596607 + + Density error is 2.05580699335e-06 + + Energy Rydberg eV + E_KohnSham -34.2801288486 -466.405080515 + E_Harris -34.2801288486 -466.405080515 + E_Fermi -0.158885825366 -2.16175255641 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000744900042978 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111375532791 + + Density error is 4.85938705211e-07 + + Energy Rydberg eV + E_KohnSham -34.2801290979 -466.405083906 + E_Harris -34.2801290979 -466.405083906 + E_Fermi -0.158884050657 -2.16172841025 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00074490068026 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111375602452 + + Density error is 1.55908821644e-07 + + Energy Rydberg eV + E_KohnSham -34.2801291114 -466.405084091 + E_Harris -34.2801291114 -466.405084091 + E_Fermi -0.15888381383 -2.16172518806 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000744900836123 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111375606122 + + Density error is 1.00887942623e-08 + + Energy Rydberg eV + E_KohnSham -34.2801291156 -466.405084148 + E_Harris -34.2801291156 -466.405084148 + E_band -7.89674059489 -107.440667718 + E_one_elec -68.9581775214 -938.224137986 + E_Hartree +35.8926162313 +488.344096873 + E_xc -8.18557712632 -111.370490336 + E_Ewald +7.09606983811 +96.5469832042 + E_demet -3.34173209568e-68 -4.54665976907e-67 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194074558208 -2.64051982847 + E_Fermi -0.158883661946 -2.16172312157 + + charge density convergence is achieved + final etot is -466.405084148 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0459 2.00000 + 2 -13.1318 2.00000 + 3 -8.85607 2.00000 + 4 -6.68658 2.00000 + 5 1.18079 0.00000 + 6 4.23421 0.00000 + 7 11.1208 0.00000 + 8 11.3511 0.00000 + + EFERMI = -2.161723121569553 eV + OUT.ABACUS/ final etot is -466.4050841480987 eV + correction force for each atom along direction 1 is -5.83146e-05 + correction force for each atom along direction 2 is 2.57137e-05 + correction force for each atom along direction 3 is 9.86264e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.091023318 +0.038743005 -0.11313736 + H1 -0.40305361 -0.23873182 +0.51622579 + H2 +0.31203029 +0.19998881 -0.40308843 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4050841480987 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9169 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9100 1 6.9 1.e+02% + Potential init_pot 0.24532 2 0.12 3.5% + PW_Basis recip2real 0.26191 17 0.015 3.8% + PW_Basis gathers_scatterp 0.11739 17 0.0069 1.7% + Potential v_of_rho 0.94784 14 0.068 14.% + XC_Functional v_xc 0.27862 15 0.019 4.0% + H_Hartree_pw v_hartree 0.63184 14 0.045 9.1% + PW_Basis real2recip 0.65379 41 0.016 9.5% + PW_Basis gatherp_scatters 0.25205 41 0.0061 3.6% + ORB_control set_orb_tables 0.89389 1 0.89 13.% + ORB_gen_tables gen_tables 0.89389 1 0.89 13.% + ORB_table_phi init_Table 0.37299 1 0.37 5.4% + ORB_table_phi cal_ST_Phi12_R 0.36880 126 0.0029 5.3% + ORB_table_beta init_Table_Beta 0.15562 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15434 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.20751 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20589 66 0.0031 3.0% + LOOP_ions opt_ions 5.5554 1 5.6 80.% + ESolver_KS_LCAO Run 5.0329 1 5.0 73.% + HSolverLCAO solve 2.6822 12 0.22 39.% + HamiltLCAO updateHk 1.3714 12 0.11 20.% + LCAO_Hamilt cal_Hgamma 1.3463 12 0.11 19.% + Gint_interface cal_gint 2.1622 25 0.086 31.% + Gint_Gamma distri_vl_value 0.15200 12 0.013 2.2% + Gint_Gamma distri_vl 2.6201 6 0.44 38.% + LCAO_Deepks cal_projected_DM 5.3799 14 0.38 78.% + LCAO_gen_fixedH add_v_delta 2.4927 6 0.42 36.% + LCAO_DESCRIPTOR add_v_delta 2.4929 6 0.42 36.% + ElecStateLCAO psiToRho 1.2926 12 0.11 19.% + Charge mix_rho 0.82423 11 0.075 12.% + LOOP_ions force_stress 0.52238 1 0.52 7.6% + Force_Stress_LCAO getForceStress 0.52236 1 0.52 7.6% + Force_LCAO_gamma ftable_gamma 0.32353 1 0.32 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.28798 1 0.29 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:19 2022 + Finish Time : Wed Sep 28 11:06:26 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..834f10b28e4df72a98b8f1e4b8053f799006d98d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123305 ima = 3.66056e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123734799585 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112751452243 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113338115833 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113534931729 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113507590984 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113525367185 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113518248294 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113520702901 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113519995449 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011351994491 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113519926113 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113519918262 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3b06e3ec860b061fe623e1d0b402057edc0b7b17 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.794949691444 17.322477215078 7.160720524439 0 0 0 +H +0.0 +2 +-18.144398095502 18.767261403102 6.181170279826 0 0 0 +-19.952063909449 17.957509264579 8.464435947483 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/conv new file mode 100644 index 0000000000000000000000000000000000000000..fbbd72ab5df8de47db064f670dac41738bf2d645 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/conv @@ -0,0 +1 @@ +184 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0ae16c56f4fd34f4569e75b6ddac1eee5b74b412 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745220449 0.01249311202 1.262785538 1.35787942 1.468233149 0.007734130156 0.01965115471 0.03891254091 +8.658152736e-19 0.001046731246 0.002313372651 0.01180080009 0.04137694397 9.949802363e-21 1.426402955e-06 4.562718391e-06 +0.00174060363 0.005678902678 + +H atom_index 1 n_descriptor 18 +1.217969989 0.03492834094 0.09734484042 0.1369953782 0.3125783084 0.02031984635 0.02662666071 0.03818070062 +-6.107209949e-18 3.481786597e-05 0.09211247837 0.1141729504 0.1173566587 -7.450936192e-18 5.362205259e-06 0.01338446308 +0.02452638447 0.02934143157 + +H atom_index 2 n_descriptor 18 +1.22404033 0.03471783354 0.09926303359 0.1396073036 0.3146561167 0.02058929425 0.02697942816 0.03794527542 +-7.533828952e-17 3.52924857e-05 0.09373343825 0.1143205652 0.1196394554 3.969580762e-19 5.143892775e-06 0.01326101143 +0.0247671868 0.02964054733 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5d2ac41e5eb8e4845f9e47d65055648c637189bd Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:19 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0731829 SEC) : SETUP UNITCELL + DONE(0.0832412 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.099655 SEC) : INIT PLANEWAVE + DONE(0.141295 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.388142 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651983e+02 0.000000e+00 2.140e-01 4.989e-01 + GE2 -4.664021e+02 -1.203752e+00 9.852e-02 4.732e-01 + GE3 -4.664060e+02 -3.877554e-03 6.331e-02 5.319e-01 + GE4 -4.664054e+02 5.702576e-04 2.082e-03 4.078e-01 + GE5 -4.664048e+02 5.458862e-04 8.533e-04 4.073e-01 + GE6 -4.664052e+02 -3.146364e-04 1.953e-04 4.036e-01 + GE7 -4.664050e+02 1.154553e-04 3.225e-05 3.896e-01 + GE8 -4.664051e+02 -5.540953e-05 1.570e-05 3.842e-01 + GE9 -4.664051e+02 1.702978e-05 2.056e-06 3.867e-01 + GE10 -4.664051e+02 -3.391773e-06 4.859e-07 3.879e-01 + GE11 -4.664051e+02 -1.848775e-07 1.559e-07 3.882e-01 + GE12 -4.664051e+02 -5.681452e-08 1.009e-08 3.204e-01 +E_delta_band = -6.90140209e-02 Ry = -9.38983926e-01 eV +E_delta_NN= -1.94074558e-01 Ry = -2.64051983e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9169 11 0.63 1e+02 % + Run_lcao lcao_line 6.91 1 6.9 1e+02 % + Potential init_pot 0.24532 2 0.12 3.5 % + PW_Basis recip2real 0.26191 17 0.015 3.8 % + PW_Basis gathers_scatterp 0.11739 17 0.0069 1.7 % + Potential v_of_rho 0.94784 14 0.068 14 % + XC_Functional v_xc 0.27862 15 0.019 4 % + H_Hartree_pw v_hartree 0.63184 14 0.045 9.1 % + PW_Basis real2recip 0.65379 41 0.016 9.5 % + PW_Basis gatherp_scatters 0.25205 41 0.0061 3.6 % + ORB_control set_orb_tables 0.89389 1 0.89 13 % + ORB_gen_tables gen_tables 0.89389 1 0.89 13 % + ORB_table_phi init_Table 0.37299 1 0.37 5.4 % + ORB_table_phi cal_ST_Phi12_R 0.3688 126 0.0029 5.3 % + ORB_table_beta init_Table_Beta 0.15562 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15434 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.20751 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20589 66 0.0031 3 % + LOOP_ions opt_ions 5.5554 1 5.6 80 % + ESolver_KS_LCAO Run 5.0329 1 5 73 % + HSolverLCAO solve 2.6822 12 0.22 39 % + HamiltLCAO updateHk 1.3714 12 0.11 20 % + LCAO_Hamilt cal_Hgamma 1.3463 12 0.11 19 % + Gint_interface cal_gint 2.1622 25 0.086 31 % + Gint_Gamma distri_vl_value 0.152 12 0.013 2.2 % + Gint_Gamma distri_vl 2.6201 6 0.44 38 % + LCAO_Deepks cal_projected_DM 5.3799 14 0.38 78 % + LCAO_gen_fixedH add_v_delta 2.4927 6 0.42 36 % + LCAO_DESCRIPTOR add_v_delta 2.4929 6 0.42 36 % + ElecStateLCAO psiToRho 1.2926 12 0.11 19 % + Charge mix_rho 0.82423 11 0.075 12 % + LOOP_ions force_stress 0.52238 1 0.52 7.6 % + Force_Stress_LCAO getForceStress 0.52236 1 0.52 7.6 % + Force_LCAO_gamma ftable_gamma 0.32353 1 0.32 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.28798 1 0.29 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:19 2022 + FINISH Time : Wed Sep 28 11:06:26 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/184/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..7e218d390e59628348cce35b280acc8086145e18 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.323737 0.634078 0.234521 +H 0.346981 0.649485 0.174441 +H 0.261118 0.631511 0.220287 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2539b75795eec929f6544845786ea1bc0adc0496 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4509 2 + 2 -12.8018 2 + 3 -9.40763 2 + 4 -6.78122 2 + 5 1.29354 0 + 6 4.46436 0 + 7 11.055 0 + 8 11.333 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4d5914449989d0277a7ea52861e9afe67fd51d5f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:42 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.06464006569 17.7541734285 6.56659702928 0 0 0 0 + tauc_H1 9.71547632771 18.1855911905 4.88435097709 0 0 0 0 + tauc_H2 7.31130854414 17.6823171911 6.16802598306 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.106554139388 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.106928342706 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124937499909 (SEC) + + DONE : INIT CHARGE Time : 0.167851554194 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446916 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 0 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00192 + + Density error is 0.215060949451 + + Energy Rydberg eV + E_KohnSham -34.1871248955 -465.139696816 + E_Harris -34.3801527848 -467.765975983 + E_Fermi -0.40996365915 -5.57784173737 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000920921672937 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00152277068488 + + Density error is 0.0978093716025 + + Energy Rydberg eV + E_KohnSham -34.2783730117 -466.381191129 + E_Harris -34.285260102 -466.474894799 + E_Fermi -0.217996155317 -2.96598985441 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000877195065782 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00139103419674 + + Density error is 0.0628482808271 + + Energy Rydberg eV + E_KohnSham -34.2788069073 -466.387094582 + E_Harris -34.283263647 -466.447731636 + E_Fermi -0.207554821591 -2.82392822101 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818373799495 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115016696711 + + Density error is 0.00195497524012 + + Energy Rydberg eV + E_KohnSham -34.2787847304 -466.386792849 + E_Harris -34.2787854855 -466.386803123 + E_Fermi -0.171574343359 -2.33438870029 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000820082210196 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114965195041 + + Density error is 0.00104334277435 + + Energy Rydberg eV + E_KohnSham -34.2787129208 -466.385815829 + E_Harris -34.2787148265 -466.385841758 + E_Fermi -0.171013862103 -2.32676296158 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818798976432 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114652390563 + + Density error is 0.000100065051858 + + Energy Rydberg eV + E_KohnSham -34.2787569451 -466.38641481 + E_Harris -34.278756953 -466.386414918 + E_Fermi -0.170955958739 -2.3259751459 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818693188759 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114609386262 + + Density error is 3.97199381613e-05 + + Energy Rydberg eV + E_KohnSham -34.2787437543 -466.38623534 + E_Harris -34.2787437631 -466.38623546 + E_Fermi -0.170849840841 -2.32453133783 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818637006989 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114613673645 + + Density error is 1.88966026485e-05 + + Energy Rydberg eV + E_KohnSham -34.2787458178 -466.386263415 + E_Harris -34.2787458194 -466.386263437 + E_Fermi -0.170899371249 -2.3252052336 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818645740597 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114610000935 + + Density error is 2.4199929852e-06 + + Energy Rydberg eV + E_KohnSham -34.2787442646 -466.386242284 + E_Harris -34.2787442646 -466.386242284 + E_Fermi -0.170880190687 -2.32494426867 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818649412358 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114609549463 + + Density error is 4.54550690826e-07 + + Energy Rydberg eV + E_KohnSham -34.2787445487 -466.386246148 + E_Harris -34.2787445487 -466.386246148 + E_Fermi -0.170878355292 -2.32491929683 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818649688679 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114609518132 + + Density error is 1.13442151587e-07 + + Energy Rydberg eV + E_KohnSham -34.2787445833 -466.38624662 + E_Harris -34.2787445833 -466.38624662 + E_Fermi -0.170878054882 -2.32491520956 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818649711606 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114609486065 + + Density error is 1.05792772275e-08 + + Energy Rydberg eV + E_KohnSham -34.2787445894 -466.386246702 + E_Harris -34.2787445894 -466.386246702 + E_band -8.00275379818 -108.883051346 + E_one_elec -69.4066646619 -944.326118576 + E_Hartree +36.084425832 +490.953800373 + E_xc -8.2167800716 -111.795028187 + E_Ewald +7.38432970687 +100.468959924 + E_demet -1.81215953054e-79 -2.46556953003e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195075154034 -2.65413363309 + E_Fermi -0.170877929413 -2.32491350245 + + charge density convergence is achieved + final etot is -466.386246702 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4509 2.00000 + 2 -12.8018 2.00000 + 3 -9.40763 2.00000 + 4 -6.78122 2.00000 + 5 1.29354 0.00000 + 6 4.46436 0.00000 + 7 11.0550 0.00000 + 8 11.3330 0.00000 + + EFERMI = -2.324913502452568 eV + OUT.ABACUS/ final etot is -466.3862467019525 eV + correction force for each atom along direction 1 is -9.53952e-05 + correction force for each atom along direction 2 is -0.000124983 + correction force for each atom along direction 3 is -8.20463e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.0855596 +0.18994702 -0.44161593 + H1 +0.39264254 -0.025652541 +0.29343370 + H2 -1.4782021 -0.16429448 +0.14818224 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3862467019525 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5064 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4967 1 6.5 1.e+02% + Potential init_pot 0.28076 2 0.14 4.3% + PW_Basis recip2real 0.29084 17 0.017 4.5% + PW_Basis gathers_scatterp 0.13157 17 0.0077 2.0% + Potential v_of_rho 1.0631 14 0.076 16.% + XC_Functional v_xc 0.31061 15 0.021 4.8% + H_Hartree_pw v_hartree 0.70498 14 0.050 11.% + PW_Basis real2recip 0.74681 41 0.018 11.% + PW_Basis gatherp_scatters 0.28160 41 0.0069 4.3% + ORB_control set_orb_tables 1.1065 1 1.1 17.% + ORB_gen_tables gen_tables 1.1065 1 1.1 17.% + ORB_table_phi init_Table 0.47508 1 0.48 7.3% + ORB_table_phi cal_ST_Phi12_R 0.46979 126 0.0037 7.2% + ORB_table_beta init_Table_Beta 0.18284 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18127 56 0.0032 2.8% + ORB_table_alpha init_Table_Alpha 0.26011 1 0.26 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25809 66 0.0039 4.0% + LOOP_ions opt_ions 4.8670 1 4.9 75.% + ESolver_KS_LCAO Run 4.3973 1 4.4 68.% + HSolverLCAO solve 1.7483 12 0.15 27.% + HamiltLCAO updateHk 0.97946 12 0.082 15.% + LCAO_Hamilt cal_Hgamma 0.94972 12 0.079 15.% + Gint_interface cal_gint 1.4602 25 0.058 22.% + Gint_Gamma distri_vl 2.3045 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.7285 14 0.34 73.% + LCAO_gen_fixedH add_v_delta 2.1570 6 0.36 33.% + LCAO_DESCRIPTOR add_v_delta 2.1570 6 0.36 33.% + ElecStateLCAO psiToRho 0.75100 12 0.063 12.% + Charge mix_rho 0.98474 11 0.090 15.% + LOOP_ions force_stress 0.46947 1 0.47 7.2% + Force_Stress_LCAO getForceStress 0.46943 1 0.47 7.2% + Force_LCAO_gamma ftable_gamma 0.25287 1 0.25 3.9% + Force_LCAO_gamma cal_fvl_dphi 0.24470 1 0.24 3.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:42 2022 + Finish Time : Wed Sep 28 11:06:48 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b625df85003a2df82e5452f3d5eedb99dff77ed5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123862 ima = 3.69115e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122800787062 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111452573994 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011208006106 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112365450337 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112300434688 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112335153836 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112333094567 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112336144489 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112335291982 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011233518989 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112335169377 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112335163783 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/STRU new file mode 100644 index 0000000000000000000000000000000000000000..28f6b4ee13dddc509d85a6e00672501e2b2bfb91 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.935359934302 17.754173428531 6.566597029299 0 0 0 +H +0.0 +2 +-18.284523672284 18.185591190462 4.884350977069 0 0 0 +-20.688691455867 17.682317191121 6.168025983064 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/conv new file mode 100644 index 0000000000000000000000000000000000000000..678d725c83ee45a69600d6e840f62c96080dd2c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/conv @@ -0,0 +1 @@ +185 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..1d8fbf1ba1d32d0cb37834629a01bd339eadf355 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753649972 0.01280764849 1.273665462 1.358221541 1.469928788 0.009411567449 0.01704325839 0.03915474708 +-3.275310938e-18 0.0009440855167 0.002856964616 0.01328631712 0.04727978626 7.018726759e-19 2.782299833e-06 7.381565776e-06 +0.001591491493 0.006137977558 + +H atom_index 1 n_descriptor 18 +1.232475785 0.0354081573 0.1047215124 0.1415428448 0.3136706288 0.02225534138 0.02720595385 0.03852444928 +-5.36075383e-17 4.897413043e-05 0.09906413409 0.1143462465 0.1213697424 9.449117664e-18 4.233383259e-06 0.0136172322 +0.02634981974 0.0299126287 + +H atom_index 2 n_descriptor 18 +1.275798897 0.03396805391 0.1202996011 0.161978555 0.3278006646 0.02439280268 0.02973800537 0.03725457232 +1.74673412e-19 5.309760895e-05 0.1074095701 0.1186345496 0.13895894 5.137096892e-18 1.82752927e-06 0.01338955281 +0.02792843354 0.03186024218 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..43bd3586a4225ecd0827cb87e401995019a5da72 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:42 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.106577 SEC) : SETUP UNITCELL + DONE(0.106944 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124958 SEC) : INIT PLANEWAVE + DONE(0.167984 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446977 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651397e+02 0.000000e+00 2.151e-01 4.740e-01 + GE2 -4.663812e+02 -1.241494e+00 9.781e-02 4.223e-01 + GE3 -4.663871e+02 -5.903453e-03 6.285e-02 4.914e-01 + GE4 -4.663868e+02 3.017323e-04 1.955e-03 3.518e-01 + GE5 -4.663858e+02 9.770205e-04 1.043e-03 3.509e-01 + GE6 -4.663864e+02 -5.989811e-04 1.001e-04 3.420e-01 + GE7 -4.663862e+02 1.794700e-04 3.972e-05 3.354e-01 + GE8 -4.663863e+02 -2.807545e-05 1.890e-05 3.282e-01 + GE9 -4.663862e+02 2.113171e-05 2.420e-06 3.284e-01 + GE10 -4.663862e+02 -3.864454e-06 4.546e-07 3.269e-01 + GE11 -4.663862e+02 -4.716750e-07 1.134e-07 3.272e-01 + GE12 -4.663862e+02 -8.203704e-08 1.058e-08 2.560e-01 +E_delta_band = -7.10197593e-02 Ry = -9.66273397e-01 eV +E_delta_NN= -1.95075154e-01 Ry = -2.65413363e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5064 11 0.59 1e+02 % + Run_lcao lcao_line 6.4967 1 6.5 1e+02 % + Potential init_pot 0.28076 2 0.14 4.3 % + PW_Basis recip2real 0.29084 17 0.017 4.5 % + PW_Basis gathers_scatterp 0.13157 17 0.0077 2 % + Potential v_of_rho 1.0631 14 0.076 16 % + XC_Functional v_xc 0.31061 15 0.021 4.8 % + H_Hartree_pw v_hartree 0.70498 14 0.05 11 % + PW_Basis real2recip 0.74681 41 0.018 11 % + PW_Basis gatherp_scatters 0.2816 41 0.0069 4.3 % + ORB_control set_orb_tables 1.1065 1 1.1 17 % + ORB_gen_tables gen_tables 1.1065 1 1.1 17 % + ORB_table_phi init_Table 0.47508 1 0.48 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.46979 126 0.0037 7.2 % + ORB_table_beta init_Table_Beta 0.18284 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18127 56 0.0032 2.8 % + ORB_table_alpha init_Table_Alpha 0.26011 1 0.26 4 % + ORB_table_alpha S_PhiAlpha_R 0.25809 66 0.0039 4 % + LOOP_ions opt_ions 4.867 1 4.9 75 % + ESolver_KS_LCAO Run 4.3973 1 4.4 68 % + HSolverLCAO solve 1.7483 12 0.15 27 % + HamiltLCAO updateHk 0.97946 12 0.082 15 % + LCAO_Hamilt cal_Hgamma 0.94972 12 0.079 15 % + Gint_interface cal_gint 1.4602 25 0.058 22 % + Gint_Gamma distri_vl 2.3045 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.7285 14 0.34 73 % + LCAO_gen_fixedH add_v_delta 2.157 6 0.36 33 % + LCAO_DESCRIPTOR add_v_delta 2.157 6 0.36 33 % + ElecStateLCAO psiToRho 0.751 12 0.063 12 % + Charge mix_rho 0.98474 11 0.09 15 % + LOOP_ions force_stress 0.46947 1 0.47 7.2 % + Force_Stress_LCAO getForceStress 0.46943 1 0.47 7.2 % + Force_LCAO_gamma ftable_gamma 0.25287 1 0.25 3.9 % + Force_LCAO_gamma cal_fvl_dphi 0.2447 1 0.24 3.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:42 2022 + FINISH Time : Wed Sep 28 11:06:48 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/185/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3974d98201dc3ec4dbfdb933eca5529eeb02d3b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.313175 0.644659 0.218567 +H 0.358846 0.663987 0.179976 +H 0.268483 0.61417 0.181719 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..cced5e7f20c27e89dd772b9f1c59ef5bf886cc04 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4685 2 + 2 -13.387 2 + 3 -9.00333 2 + 4 -6.78251 2 + 5 1.48665 0 + 6 4.77491 0 + 7 11.0222 0 + 8 11.2513 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3f1b240d37b30cd3717552eb07eff62ec79ea2fc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:59 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 8.76890947964 18.0504617708 6.11987745293 0 0 0 0 + tauc_H1 10.0476942076 18.5916413447 5.03933255246 0 0 0 0 + tauc_H2 7.51751028154 17.1967565918 5.08812469253 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.100067690054 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100418090481 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118353282089 (SEC) + + DONE : INIT CHARGE Time : 0.161075805218 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443862 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127 + + Density error is 0.218666650226 + + Energy Rydberg eV + E_KohnSham -34.18469208 -465.106596664 + E_Harris -34.3845864384 -467.826298936 + E_Fermi -0.419738032001 -5.71082890253 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00130140128722 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124159955947 + + Density error is 0.0977417808388 + + Energy Rydberg eV + E_KohnSham -34.2770295062 -466.362911798 + E_Harris -34.2836301905 -466.452718715 + E_Fermi -0.225639188212 -3.06997865178 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00124083988468 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116093558961 + + Density error is 0.0624547341833 + + Energy Rydberg eV + E_KohnSham -34.2773460189 -466.367218174 + E_Harris -34.2815685975 -466.424669304 + E_Fermi -0.211872745163 -2.88267658512 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114868054894 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102592479248 + + Density error is 0.00208788417581 + + Energy Rydberg eV + E_KohnSham -34.2773843262 -466.367739372 + E_Harris -34.277386999 -466.367775738 + E_Fermi -0.176174748618 -2.39698042492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114929851282 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102403712612 + + Density error is 0.00093122877232 + + Energy Rydberg eV + E_KohnSham -34.277307514 -466.366694288 + E_Harris -34.2773095151 -466.366721515 + E_Fermi -0.175029439829 -2.38139769943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114792501666 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102257035188 + + Density error is 0.000169019367828 + + Energy Rydberg eV + E_KohnSham -34.2773564688 -466.367360353 + E_Harris -34.2773565559 -466.367361538 + E_Fermi -0.175265207948 -2.38460548925 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114813924187 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102251137757 + + Density error is 4.89566901381e-05 + + Energy Rydberg eV + E_KohnSham -34.2773383434 -466.367113744 + E_Harris -34.2773383568 -466.367113927 + E_Fermi -0.175080409363 -2.38209117551 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114804625368 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102248228261 + + Density error is 1.80653134724e-05 + + Energy Rydberg eV + E_KohnSham -34.2773435206 -466.367184184 + E_Harris -34.2773435218 -466.3671842 + E_Fermi -0.175138985029 -2.38288813833 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114803180675 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102245734959 + + Density error is 2.88645502023e-06 + + Energy Rydberg eV + E_KohnSham -34.2773419257 -466.367162484 + E_Harris -34.2773419258 -466.367162485 + E_Fermi -0.175120849167 -2.38264138728 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114803295424 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102245511729 + + Density error is 2.69756633952e-07 + + Energy Rydberg eV + E_KohnSham -34.2773421064 -466.367164942 + E_Harris -34.2773421064 -466.367164942 + E_Fermi -0.175117694942 -2.38259847184 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114803345311 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102245557084 + + Density error is 1.31761629277e-07 + + Energy Rydberg eV + E_KohnSham -34.2773421577 -466.36716564 + E_Harris -34.2773421577 -466.36716564 + E_Fermi -0.175117687078 -2.38259836484 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114803355191 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102245557282 + + Density error is 9.94400155395e-09 + + Energy Rydberg eV + E_KohnSham -34.2773421576 -466.367165639 + E_Harris -34.2773421576 -466.367165639 + E_band -8.03212601438 -109.28268085 + E_one_elec -69.7539904874 -949.051728867 + E_Hartree +36.2624988138 +493.376607586 + E_xc -8.24570527676 -112.188575793 + E_Ewald +7.58326341625 +103.175591896 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195645539591 -2.66189412672 + E_Fermi -0.175117572892 -2.38259681126 + + charge density convergence is achieved + final etot is -466.367165639 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4685 2.00000 + 2 -13.3870 2.00000 + 3 -9.00333 2.00000 + 4 -6.78251 2.00000 + 5 1.48665 0.00000 + 6 4.77491 0.00000 + 7 11.0222 0.00000 + 8 11.2513 0.00000 + + EFERMI = -2.382596811258889 eV + OUT.ABACUS/ final etot is -466.3671656390816 eV + correction force for each atom along direction 1 is -2.70296e-05 + correction force for each atom along direction 2 is -1.37763e-05 + correction force for each atom along direction 3 is -6.61111e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.7103677 -0.65713073 +1.8707795 + H1 +1.7464330 +0.71116934 -1.6558196 + H2 -0.036065289 -0.054038610 -0.21495989 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3671656390816 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6542 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6444 1 6.6 1.e+02% + Potential init_pot 0.28368 2 0.14 4.3% + PW_Basis recip2real 0.30081 17 0.018 4.5% + PW_Basis gathers_scatterp 0.13100 17 0.0077 2.0% + Potential v_of_rho 1.0912 14 0.078 16.% + XC_Functional v_xc 0.31627 15 0.021 4.8% + H_Hartree_pw v_hartree 0.72844 14 0.052 11.% + PW_Basis real2recip 0.75552 41 0.018 11.% + PW_Basis gatherp_scatters 0.28773 41 0.0070 4.3% + ORB_control set_orb_tables 1.0959 1 1.1 16.% + ORB_gen_tables gen_tables 1.0959 1 1.1 16.% + ORB_table_phi init_Table 0.47432 1 0.47 7.1% + ORB_table_phi cal_ST_Phi12_R 0.46907 126 0.0037 7.0% + ORB_table_beta init_Table_Beta 0.18206 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18054 56 0.0032 2.7% + ORB_table_alpha init_Table_Alpha 0.25027 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24828 66 0.0038 3.7% + LOOP_ions opt_ions 5.0284 1 5.0 76.% + ESolver_KS_LCAO Run 4.5394 1 4.5 68.% + HSolverLCAO solve 1.8561 12 0.15 28.% + HamiltLCAO updateHk 1.0317 12 0.086 16.% + LCAO_Hamilt cal_Hgamma 1.0018 12 0.083 15.% + Gint_interface cal_gint 1.5800 25 0.063 24.% + Gint_Gamma distri_vl 2.3786 6 0.40 36.% + LCAO_Deepks cal_projected_DM 4.8861 14 0.35 73.% + LCAO_gen_fixedH add_v_delta 2.2285 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2285 6 0.37 33.% + ElecStateLCAO psiToRho 0.80705 12 0.067 12.% + Charge mix_rho 0.99298 11 0.090 15.% + LOOP_ions force_stress 0.48885 1 0.49 7.3% + Force_Stress_LCAO getForceStress 0.48882 1 0.49 7.3% + Force_LCAO_gamma ftable_gamma 0.26757 1 0.27 4.0% + Force_LCAO_gamma cal_fvl_dphi 0.25937 1 0.26 3.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:59 2022 + Finish Time : Wed Sep 28 11:05:05 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..390cf9dc90724b8b62a468d9c2b85ab8dde3c314 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123889 ima = 3.70134e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123285098194 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011236870585 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112798051282 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113081544514 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113013826982 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113053230495 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113044045515 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113047420742 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113046815904 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113046688462 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113046682416 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113046676759 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/STRU new file mode 100644 index 0000000000000000000000000000000000000000..aff77aa6141342d9a59d63e98ce5f6c6970590dc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-19.231090520333 18.050461770819 6.119877452904 0 0 0 +H +0.0 +2 +-17.952305792390 18.591641344675 5.039332552443 0 0 0 +-20.482489718437 17.196756591764 5.088124692518 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/conv new file mode 100644 index 0000000000000000000000000000000000000000..fedcfab38fa6f2d7cfd449d5ec53c1efcce9f4f9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/conv @@ -0,0 +1 @@ +186 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..cc76e72c5c973f69cf41d8bd0d856c42d409b6c6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746792834 0.01275059476 1.292003426 1.383323545 1.470281805 0.008285912687 0.0199164989 0.03896152594 +2.557496663e-18 0.001215338847 0.002615658069 0.01288722341 0.04627489496 -3.748120792e-19 1.967854676e-06 5.821335428e-06 +0.001708563195 0.005791285975 + +H atom_index 1 n_descriptor 18 +1.301353128 0.03222219894 0.1278030573 0.1760392464 0.3363290439 0.02442494939 0.0312962523 0.03617255378 +-5.356007347e-17 5.067143985e-05 0.1081414165 0.1245559069 0.151111849 -2.833129904e-18 1.592378801e-06 0.01364583729 +0.02828358551 0.03283310009 + +H atom_index 2 n_descriptor 18 +1.243113221 0.03413973808 0.106249221 0.1472489785 0.3194292502 0.02184925748 0.02797227292 0.03724187612 +-1.878353961e-17 4.532716051e-05 0.1016577287 0.1144041542 0.1265833478 4.277958534e-18 4.708511355e-06 0.01311388802 +0.02632560417 0.03052137619 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a48a69d23b01df7971a631bfae8160dc9fa5a9c6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:59 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.100091 SEC) : SETUP UNITCELL + DONE(0.100432 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118373 SEC) : INIT PLANEWAVE + DONE(0.161209 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443921 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651066e+02 0.000000e+00 2.187e-01 4.859e-01 + GE2 -4.663629e+02 -1.256315e+00 9.774e-02 4.349e-01 + GE3 -4.663672e+02 -4.306376e-03 6.245e-02 5.064e-01 + GE4 -4.663677e+02 -5.211976e-04 2.088e-03 3.618e-01 + GE5 -4.663667e+02 1.045084e-03 9.312e-04 3.625e-01 + GE6 -4.663674e+02 -6.660645e-04 1.690e-04 3.526e-01 + GE7 -4.663671e+02 2.466088e-04 4.896e-05 3.494e-01 + GE8 -4.663672e+02 -7.044036e-05 1.807e-05 3.403e-01 + GE9 -4.663672e+02 2.169968e-05 2.886e-06 3.379e-01 + GE10 -4.663672e+02 -2.457423e-06 2.698e-07 3.416e-01 + GE11 -4.663672e+02 -6.984014e-07 1.318e-07 3.390e-01 + GE12 -4.663672e+02 1.149651e-09 9.944e-09 2.644e-01 +E_delta_band = -7.22369161e-02 Ry = -9.82833665e-01 eV +E_delta_NN= -1.95645540e-01 Ry = -2.66189413e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6542 11 0.6 1e+02 % + Run_lcao lcao_line 6.6444 1 6.6 1e+02 % + Potential init_pot 0.28368 2 0.14 4.3 % + PW_Basis recip2real 0.30081 17 0.018 4.5 % + PW_Basis gathers_scatterp 0.131 17 0.0077 2 % + Potential v_of_rho 1.0912 14 0.078 16 % + XC_Functional v_xc 0.31627 15 0.021 4.8 % + H_Hartree_pw v_hartree 0.72844 14 0.052 11 % + PW_Basis real2recip 0.75552 41 0.018 11 % + PW_Basis gatherp_scatters 0.28773 41 0.007 4.3 % + ORB_control set_orb_tables 1.0959 1 1.1 16 % + ORB_gen_tables gen_tables 1.0959 1 1.1 16 % + ORB_table_phi init_Table 0.47432 1 0.47 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.46907 126 0.0037 7 % + ORB_table_beta init_Table_Beta 0.18206 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18054 56 0.0032 2.7 % + ORB_table_alpha init_Table_Alpha 0.25027 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24828 66 0.0038 3.7 % + LOOP_ions opt_ions 5.0284 1 5 76 % + ESolver_KS_LCAO Run 4.5394 1 4.5 68 % + HSolverLCAO solve 1.8561 12 0.15 28 % + HamiltLCAO updateHk 1.0317 12 0.086 16 % + LCAO_Hamilt cal_Hgamma 1.0018 12 0.083 15 % + Gint_interface cal_gint 1.58 25 0.063 24 % + Gint_Gamma distri_vl 2.3786 6 0.4 36 % + LCAO_Deepks cal_projected_DM 4.8861 14 0.35 73 % + LCAO_gen_fixedH add_v_delta 2.2285 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2285 6 0.37 33 % + ElecStateLCAO psiToRho 0.80705 12 0.067 12 % + Charge mix_rho 0.99298 11 0.09 15 % + LOOP_ions force_stress 0.48885 1 0.49 7.3 % + Force_Stress_LCAO getForceStress 0.48882 1 0.49 7.3 % + Force_LCAO_gamma ftable_gamma 0.26757 1 0.27 4 % + Force_LCAO_gamma cal_fvl_dphi 0.25937 1 0.26 3.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:59 2022 + FINISH Time : Wed Sep 28 11:05:05 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/186/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9cc1ce1b99245e1d42e8cee5d18f99e4b6ce8d8f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.30957 0.658204 0.223834 +H 0.322154 0.722714 0.214935 +H 0.316827 0.636737 0.161676 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f093ede2ddbdde2e6031e06cdabcfe6ebf935545 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2521 2 + 2 -12.7223 2 + 3 -9.32721 2 + 4 -6.73932 2 + 5 1.17751 0 + 6 4.21055 0 + 7 11.0976 0 + 8 11.3717 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fe5af79040eeaace33408e7714965d8fa3d87d80 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 8.6679468951 18.4297259571 6.26734433204 0 0 0 0 + tauc_H1 9.0203230843 20.2359882743 6.01818346667 0 0 0 0 + tauc_H2 8.87114961359 17.8286393845 4.5269323874 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.088041070998 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0973142966462 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115445369786 (SEC) + + DONE : INIT CHARGE Time : 0.164043046082 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.442016 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 144 0 25 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000678 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000899 + + Density error is 0.211726052097 + + Energy Rydberg eV + E_KohnSham -34.1933602561 -465.22453325 + E_Harris -34.3786675317 -467.745768079 + E_Fermi -0.397617245023 -5.40986015538 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000919167221901 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125173300095 + + Density error is 0.097837836262 + + Energy Rydberg eV + E_KohnSham -34.2803785494 -466.408477868 + E_Harris -34.2872461868 -466.501916869 + E_Fermi -0.209650434027 -2.85244049094 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000876445311396 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120340986262 + + Density error is 0.0627882827402 + + Energy Rydberg eV + E_KohnSham -34.2806046732 -466.411554441 + E_Harris -34.2850510912 -466.472051062 + E_Fermi -0.199756882443 -2.71783181594 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000818420504747 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115018544882 + + Density error is 0.0019134577879 + + Energy Rydberg eV + E_KohnSham -34.2805604431 -466.410952659 + E_Harris -34.2805604004 -466.410952079 + E_Fermi -0.16425369627 -2.23478618683 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000819090125933 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115321058918 + + Density error is 0.000793197696815 + + Energy Rydberg eV + E_KohnSham -34.2805193476 -466.410393526 + E_Harris -34.2805201717 -466.410404739 + E_Fermi -0.16386633433 -2.22951585726 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000818262026762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001152110737 + + Density error is 0.000115245004728 + + Energy Rydberg eV + E_KohnSham -34.2805456268 -466.410751074 + E_Harris -34.2805456314 -466.410751136 + E_Fermi -0.163684631338 -2.22704366123 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000818286511408 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115212792917 + + Density error is 2.84363722007e-05 + + Energy Rydberg eV + E_KohnSham -34.2805375634 -466.410641365 + E_Harris -34.280537567 -466.410641414 + E_Fermi -0.16361126362 -2.22604544221 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000818236229659 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011520554847 + + Density error is 1.40658839965e-05 + + Energy Rydberg eV + E_KohnSham -34.2805397924 -466.410671692 + E_Harris -34.2805397933 -466.410671704 + E_Fermi -0.163637848847 -2.22640715278 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000818242571487 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115207080137 + + Density error is 2.25295109243e-06 + + Energy Rydberg eV + E_KohnSham -34.2805386394 -466.410656005 + E_Harris -34.2805386394 -466.410656005 + E_Fermi -0.16362507109 -2.22623330248 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000818242803153 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115206982352 + + Density error is 3.02131783419e-07 + + Energy Rydberg eV + E_KohnSham -34.2805388621 -466.410659035 + E_Harris -34.2805388621 -466.410659035 + E_Fermi -0.163622838117 -2.22620292132 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000818243368253 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115207072184 + + Density error is 1.05279592094e-07 + + Energy Rydberg eV + E_KohnSham -34.280538893 -466.410659456 + E_Harris -34.280538893 -466.410659456 + E_Fermi -0.163622727297 -2.22620141354 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000818243553116 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115207094751 + + Density error is 1.07794026111e-08 + + Energy Rydberg eV + E_KohnSham -34.2805388961 -466.410659498 + E_Harris -34.2805388961 -466.410659498 + E_band -7.94386957167 -108.081890344 + E_one_elec -69.0550160366 -939.54169358 + E_Hartree +35.9205987553 +488.724818644 + E_xc -8.19033735747 -111.435256604 + E_Ewald +7.16900208126 +97.539277279 + E_demet -1.26693997815e-70 -1.72376027269e-69 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194420279007 -2.64522360125 + E_Fermi -0.163622644884 -2.22620029225 + + charge density convergence is achieved + final etot is -466.410659498 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2521 2.00000 + 2 -12.7223 2.00000 + 3 -9.32721 2.00000 + 4 -6.73932 2.00000 + 5 1.17751 0.00000 + 6 4.21055 0.00000 + 7 11.0976 0.00000 + 8 11.3717 0.00000 + + EFERMI = -2.226200292249604 eV + OUT.ABACUS/ final etot is -466.4106594975394 eV + correction force for each atom along direction 1 is 0.000146401 + correction force for each atom along direction 2 is 1.43756e-05 + correction force for each atom along direction 3 is -7.13671e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.17642461 +0.43348186 -0.54525825 + H1 -0.092180401 -0.15875801 +0.35193482 + H2 -0.084244208 -0.27472384 +0.19332343 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4106594975394 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9635 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9531 1 7.0 1.e+02% + Potential init_pot 0.28401 2 0.14 4.1% + PW_Basis recip2real 0.27956 17 0.016 4.0% + PW_Basis gathers_scatterp 0.11815 17 0.0069 1.7% + Potential v_of_rho 0.92836 14 0.066 13.% + XC_Functional v_xc 0.25413 15 0.017 3.6% + H_Hartree_pw v_hartree 0.63466 14 0.045 9.1% + PW_Basis real2recip 0.60492 41 0.015 8.7% + PW_Basis gatherp_scatters 0.23512 41 0.0057 3.4% + ORB_control set_orb_tables 1.1016 1 1.1 16.% + ORB_gen_tables gen_tables 1.1016 1 1.1 16.% + ORB_table_phi init_Table 0.48421 1 0.48 7.0% + ORB_table_phi cal_ST_Phi12_R 0.47924 126 0.0038 6.9% + ORB_table_beta init_Table_Beta 0.18722 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18574 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24924 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24738 66 0.0037 3.6% + LOOP_ions opt_ions 5.3335 1 5.3 77.% + ESolver_KS_LCAO Run 4.7716 1 4.8 69.% + HSolverLCAO solve 2.6409 12 0.22 38.% + HamiltLCAO updateHk 1.3527 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.3113 12 0.11 19.% + Gint_interface cal_gint 2.5120 25 0.10 36.% + Gint_Gamma distri_vl 2.4711 6 0.41 35.% + LCAO_Deepks cal_projected_DM 5.1626 14 0.37 74.% + LCAO_gen_fixedH add_v_delta 2.3405 6 0.39 34.% + LCAO_DESCRIPTOR add_v_delta 2.3405 6 0.39 34.% + ElecStateLCAO psiToRho 1.2731 12 0.11 18.% + Charge mix_rho 0.71248 11 0.065 10.% + LOOP_ions force_stress 0.56175 1 0.56 8.1% + Force_Stress_LCAO getForceStress 0.56172 1 0.56 8.1% + Force_LCAO_gamma ftable_gamma 0.34702 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.34042 1 0.34 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:48 2022 + Finish Time : Wed Sep 28 11:03:55 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..af61413e51b3dc873646251728fb72d1dc682299 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123915 ima = 3.71892e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122716882349 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111645703732 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112263401127 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112480369214 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112446420892 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112466054346 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112462642985 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112464897762 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011246422292 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112464137907 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112464125196 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112464120648 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0ad6cb80f9f9319120d34fcb3e162b48177f03f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-19.332053104884 18.429725957104 6.267344332032 0 0 0 +H +0.0 +2 +-18.979676915676 20.235988274293 6.018183466675 0 0 0 +-19.128850386436 17.828639384522 4.526932387423 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/conv new file mode 100644 index 0000000000000000000000000000000000000000..4fe9a441280e8a246f551c17283aa9ccee166fa0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/conv @@ -0,0 +1 @@ +187 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..22ce07c2f1f944350c5a3248e82c4f41c7822d7f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752914475 0.01268275996 1.262009315 1.34598883 1.469085443 0.009113427027 0.01703454284 0.03914446324 +9.839636188e-18 0.0009007097878 0.00268886711 0.01260321147 0.04504323 -1.683477983e-19 2.359658472e-06 6.564439468e-06 +0.001590967856 0.006086858242 + +H atom_index 1 n_descriptor 18 +1.230139978 0.03536510088 0.102889234 0.140630002 0.3134640228 0.02179305382 0.02708866465 0.03853051196 +1.603743213e-17 4.512202958e-05 0.09639556391 0.1145221887 0.1204826248 -2.209904793e-18 4.501372538e-06 0.013591215 +0.02570677805 0.02978285773 + +H atom_index 2 n_descriptor 18 +1.233790882 0.03524285281 0.1041071648 0.1422489887 0.3147368223 0.02196995864 0.02730320373 0.03839688083 +-8.601882271e-17 4.545614747e-05 0.09733054678 0.1146634577 0.1218915788 -4.606635847e-18 4.314309097e-06 0.01352749618 +0.02584979558 0.02996165495 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..8bcd0f16d4a9a0928c17c6a667216c3226a71dc4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0880659 SEC) : SETUP UNITCELL + DONE(0.0973358 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115466 SEC) : INIT PLANEWAVE + DONE(0.16418 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.442082 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652245e+02 0.000000e+00 2.117e-01 5.143e-01 + GE2 -4.664085e+02 -1.183945e+00 9.784e-02 4.393e-01 + GE3 -4.664116e+02 -3.076573e-03 6.279e-02 4.933e-01 + GE4 -4.664110e+02 6.017817e-04 1.913e-03 3.880e-01 + GE5 -4.664104e+02 5.591331e-04 7.932e-04 3.825e-01 + GE6 -4.664108e+02 -3.575474e-04 1.152e-04 3.748e-01 + GE7 -4.664106e+02 1.097090e-04 2.844e-05 3.670e-01 + GE8 -4.664107e+02 -3.032751e-05 1.407e-05 3.624e-01 + GE9 -4.664107e+02 1.568741e-05 2.253e-06 3.579e-01 + GE10 -4.664107e+02 -3.030550e-06 3.021e-07 3.644e-01 + GE11 -4.664107e+02 -4.205968e-07 1.053e-07 3.629e-01 + GE12 -4.664107e+02 -4.164207e-08 1.078e-08 3.037e-01 +E_delta_band = -6.96339405e-02 Ry = -9.47418364e-01 eV +E_delta_NN= -1.94420279e-01 Ry = -2.64522360e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9635 11 0.63 1e+02 % + Run_lcao lcao_line 6.9531 1 7 1e+02 % + Potential init_pot 0.28401 2 0.14 4.1 % + PW_Basis recip2real 0.27956 17 0.016 4 % + PW_Basis gathers_scatterp 0.11815 17 0.0069 1.7 % + Potential v_of_rho 0.92836 14 0.066 13 % + XC_Functional v_xc 0.25413 15 0.017 3.6 % + H_Hartree_pw v_hartree 0.63466 14 0.045 9.1 % + PW_Basis real2recip 0.60492 41 0.015 8.7 % + PW_Basis gatherp_scatters 0.23512 41 0.0057 3.4 % + ORB_control set_orb_tables 1.1016 1 1.1 16 % + ORB_gen_tables gen_tables 1.1016 1 1.1 16 % + ORB_table_phi init_Table 0.48421 1 0.48 7 % + ORB_table_phi cal_ST_Phi12_R 0.47924 126 0.0038 6.9 % + ORB_table_beta init_Table_Beta 0.18722 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18574 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24924 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24738 66 0.0037 3.6 % + LOOP_ions opt_ions 5.3335 1 5.3 77 % + ESolver_KS_LCAO Run 4.7716 1 4.8 69 % + HSolverLCAO solve 2.6409 12 0.22 38 % + HamiltLCAO updateHk 1.3527 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.3113 12 0.11 19 % + Gint_interface cal_gint 2.512 25 0.1 36 % + Gint_Gamma distri_vl 2.4711 6 0.41 35 % + LCAO_Deepks cal_projected_DM 5.1626 14 0.37 74 % + LCAO_gen_fixedH add_v_delta 2.3405 6 0.39 34 % + LCAO_DESCRIPTOR add_v_delta 2.3405 6 0.39 34 % + ElecStateLCAO psiToRho 1.2731 12 0.11 18 % + Charge mix_rho 0.71248 11 0.065 10 % + LOOP_ions force_stress 0.56175 1 0.56 8.1 % + Force_Stress_LCAO getForceStress 0.56172 1 0.56 8.1 % + Force_LCAO_gamma ftable_gamma 0.34702 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.34042 1 0.34 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:48 2022 + FINISH Time : Wed Sep 28 11:03:55 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/187/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..0126577d6817972a4862860b7bbcc62b665be823 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.318106 0.665809 0.226175 +H 0.29099 0.728184 0.227573 +H 0.360639 0.666401 0.179102 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..480ed7d91c80ed0032bf1e4f7d2666b8dd4976a7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2356 2 + 2 -13.0946 2 + 3 -9.01918 2 + 4 -6.72803 2 + 5 1.21307 0 + 6 4.41759 0 + 7 11.0836 0 + 8 11.3155 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f227f16dad9b740477cfb2021e48f77707222232 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:11 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 8.90697613274 18.6426501721 6.33288724751 0 0 0 0 + tauc_H1 8.14772086644 20.389140364 6.37205067567 0 0 0 0 + tauc_H2 10.0978828974 18.6592295568 5.01486995289 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0741469553664 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0866743381017 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.1030105573 (SEC) + + DONE : INIT CHARGE Time : 0.144426683022 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.390193 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000588 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00144 + + Density error is 0.214901721629 + + Energy Rydberg eV + E_KohnSham -34.1874337247 -465.143898654 + E_Harris -34.3793137598 -467.754560463 + E_Fermi -0.403873492203 -5.49498076512 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000871961620046 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00141833343973 + + Density error is 0.0982001893361 + + Energy Rydberg eV + E_KohnSham -34.2768409217 -466.360345975 + E_Harris -34.283611864 -466.452469371 + E_Fermi -0.212986479146 -2.89782971335 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000838001322632 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132682563774 + + Density error is 0.0629205939752 + + Energy Rydberg eV + E_KohnSham -34.2770966553 -466.363825409 + E_Harris -34.2814572505 -466.423154351 + E_Fermi -0.202050729246 -2.7490412028 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000797683763892 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117602245221 + + Density error is 0.00203646762943 + + Energy Rydberg eV + E_KohnSham -34.277077843 -466.363569454 + E_Harris -34.2770801537 -466.363600894 + E_Fermi -0.1665794134 -2.26642919174 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000799690891351 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117641880312 + + Density error is 0.000843437007169 + + Energy Rydberg eV + E_KohnSham -34.2770299007 -466.362917167 + E_Harris -34.2770306482 -466.362927337 + E_Fermi -0.165951276206 -2.25788294678 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000799083611164 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117449093439 + + Density error is 0.000184622118986 + + Energy Rydberg eV + E_KohnSham -34.2770580006 -466.363299485 + E_Harris -34.2770580601 -466.363300294 + E_Fermi -0.165844189047 -2.25642595123 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000799287386211 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117454810612 + + Density error is 3.5912992096e-05 + + Energy Rydberg eV + E_KohnSham -34.2770472146 -466.363152733 + E_Harris -34.2770472198 -466.363152804 + E_Fermi -0.165734999799 -2.2549403553 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000799252729811 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117450847538 + + Density error is 1.99735702543e-05 + + Energy Rydberg eV + E_KohnSham -34.2770517211 -466.363214048 + E_Harris -34.277051723 -466.363214073 + E_Fermi -0.16576875967 -2.2553996819 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000799263307662 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117450056754 + + Density error is 3.0166975387e-06 + + Energy Rydberg eV + E_KohnSham -34.2770502446 -466.363193959 + E_Harris -34.2770502446 -466.36319396 + E_Fermi -0.165750399338 -2.25514987677 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000799259955992 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117449093236 + + Density error is 5.02863956874e-07 + + Energy Rydberg eV + E_KohnSham -34.2770505691 -466.363198374 + E_Harris -34.2770505691 -466.363198374 + E_Fermi -0.165747389191 -2.25510892163 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000799260798493 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117449155292 + + Density error is 1.7999334188e-07 + + Energy Rydberg eV + E_KohnSham -34.2770505988 -466.363198778 + E_Harris -34.2770505988 -466.363198778 + E_Fermi -0.165747180784 -2.2551060861 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000799260986369 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117449146906 + + Density error is 1.03495043415e-08 + + Energy Rydberg eV + E_KohnSham -34.2770506016 -466.363198815 + E_Harris -34.2770506016 -466.363198815 + E_band -7.94923612396 -108.154906033 + E_one_elec -69.2148311449 -941.716089678 + E_Hartree +36.0073337384 +489.904908629 + E_xc -8.20473394391 -111.631132211 + E_Ewald +7.25968145979 +98.7730335181 + E_demet -3.19669091761e-73 -4.34932112243e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194700168743 -2.64903169646 + E_Fermi -0.165747005303 -2.25510369856 + + charge density convergence is achieved + final etot is -466.363198815 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2356 2.00000 + 2 -13.0946 2.00000 + 3 -9.01918 2.00000 + 4 -6.72803 2.00000 + 5 1.21307 0.00000 + 6 4.41759 0.00000 + 7 11.0836 0.00000 + 8 11.3155 0.00000 + + EFERMI = -2.255103698558961 eV + OUT.ABACUS/ final etot is -466.3631988154828 eV + correction force for each atom along direction 1 is 0.000120299 + correction force for each atom along direction 2 is 1.90852e-05 + correction force for each atom along direction 3 is -9.15714e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.9687457 +1.2010630 +1.6252197 + H1 +0.67494920 -1.3514952 -0.12975430 + H2 +1.2937965 +0.15043214 -1.4954654 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3631988154828 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2135 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2059 1 7.2 1.e+02% + Potential init_pot 0.24455 2 0.12 3.4% + PW_Basis recip2real 0.27614 17 0.016 3.8% + PW_Basis gathers_scatterp 0.11777 17 0.0069 1.6% + Potential v_of_rho 0.98298 14 0.070 14.% + XC_Functional v_xc 0.28799 15 0.019 4.0% + H_Hartree_pw v_hartree 0.65480 14 0.047 9.1% + PW_Basis real2recip 0.65722 41 0.016 9.1% + PW_Basis gatherp_scatters 0.24928 41 0.0061 3.5% + ORB_control set_orb_tables 0.89095 1 0.89 12.% + ORB_gen_tables gen_tables 0.89094 1 0.89 12.% + ORB_table_phi init_Table 0.37380 1 0.37 5.2% + ORB_table_phi cal_ST_Phi12_R 0.36961 126 0.0029 5.1% + ORB_table_beta init_Table_Beta 0.15214 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15086 56 0.0027 2.1% + ORB_table_alpha init_Table_Alpha 0.20722 1 0.21 2.9% + ORB_table_alpha S_PhiAlpha_R 0.20556 66 0.0031 2.8% + LOOP_ions opt_ions 5.8487 1 5.8 81.% + ESolver_KS_LCAO Run 5.3170 1 5.3 74.% + HSolverLCAO solve 2.9719 12 0.25 41.% + HamiltLCAO updateHk 1.4802 12 0.12 21.% + LCAO_Hamilt cal_Hgamma 1.4498 12 0.12 20.% + Gint_interface cal_gint 2.8416 25 0.11 39.% + Gint_Gamma distri_vl 2.7634 6 0.46 38.% + LCAO_Deepks cal_projected_DM 5.6941 14 0.41 79.% + LCAO_gen_fixedH add_v_delta 2.6372 6 0.44 37.% + LCAO_DESCRIPTOR add_v_delta 2.6374 6 0.44 37.% + ElecStateLCAO psiToRho 1.4746 12 0.12 20.% + Charge mix_rho 0.82416 11 0.075 11.% + LOOP_ions force_stress 0.53153 1 0.53 7.4% + Force_Stress_LCAO getForceStress 0.53151 1 0.53 7.4% + Force_LCAO_gamma ftable_gamma 0.33945 1 0.34 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.33220 1 0.33 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:11 2022 + Finish Time : Wed Sep 28 11:02:18 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d5d33e42c6335d302a909427bd81be89f2788ea8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012367 ima = 3.70243e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123369451315 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112388763644 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112938274338 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113166318778 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113129644783 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011315249958 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113144473099 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113147224595 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113146283981 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113146197848 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113146181501 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113146172344 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/STRU new file mode 100644 index 0000000000000000000000000000000000000000..aa3bdd0fbcc7cd3da270bf3be2e3bda804e0535f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-19.093023867249 18.642650172045 6.332887247495 0 0 0 +H +0.0 +2 +-19.852279133555 20.389140364042 6.372050675685 0 0 0 +-17.902117102568 18.659229556831 5.014869952896 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/conv new file mode 100644 index 0000000000000000000000000000000000000000..8d0097c9fb3ed75aef1c67e1e3f2f3ab22405225 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/conv @@ -0,0 +1 @@ +188 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4bc892e390129c8805726ba10f5813fa0c4b03b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747973062 0.01256868853 1.264247351 1.368602631 1.469168104 0.008297000073 0.0190988374 0.0390151899 +-2.156084757e-18 0.001062838285 0.002510867394 0.01205358968 0.04410192397 6.780342067e-20 1.738890814e-06 5.384934199e-06 +0.001662335228 0.005791948525 + +H atom_index 1 n_descriptor 18 +1.187421358 0.03614620138 0.08812057248 0.1236607991 0.2999627477 0.0191451949 0.02472812832 0.03963998415 +1.4987161e-17 3.725310196e-05 0.08471698821 0.1057106444 0.1128569796 1.072222568e-17 6.69225475e-06 0.01438974877 +0.02354727768 0.0276767022 + +H atom_index 2 n_descriptor 18 +1.289207642 0.0327492234 0.1221983721 0.1696952104 0.333515255 0.02374503625 0.03062393113 0.0364379999 +5.37705914e-17 4.611174746e-05 0.1074061756 0.119743008 0.1455650552 -5.880926623e-19 2.13659191e-06 0.01331294666 +0.02739529805 0.03239462721 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..afd9381968e299f37a8918af4e717f3d95600f4d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:11 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0741616 SEC) : SETUP UNITCELL + DONE(0.0866864 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103025 SEC) : INIT PLANEWAVE + DONE(0.144565 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.390237 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651439e+02 0.000000e+00 2.149e-01 5.189e-01 + GE2 -4.663603e+02 -1.216447e+00 9.820e-02 4.936e-01 + GE3 -4.663638e+02 -3.479434e-03 6.292e-02 5.503e-01 + GE4 -4.663636e+02 2.559557e-04 2.036e-03 4.297e-01 + GE5 -4.663629e+02 6.522872e-04 8.434e-04 4.295e-01 + GE6 -4.663633e+02 -3.823186e-04 1.846e-04 4.254e-01 + GE7 -4.663632e+02 1.467517e-04 3.591e-05 4.171e-01 + GE8 -4.663632e+02 -6.131457e-05 1.997e-05 4.065e-01 + GE9 -4.663632e+02 2.008879e-05 3.017e-06 4.104e-01 + GE10 -4.663632e+02 -4.414587e-06 5.029e-07 4.139e-01 + GE11 -4.663632e+02 -4.044335e-07 1.800e-07 4.202e-01 + GE12 -4.663632e+02 -3.726707e-08 1.035e-08 3.480e-01 +E_delta_band = -7.01994578e-02 Ry = -9.55112623e-01 eV +E_delta_NN= -1.94700169e-01 Ry = -2.64903170e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2135 11 0.66 1e+02 % + Run_lcao lcao_line 7.2059 1 7.2 1e+02 % + Potential init_pot 0.24455 2 0.12 3.4 % + PW_Basis recip2real 0.27614 17 0.016 3.8 % + PW_Basis gathers_scatterp 0.11777 17 0.0069 1.6 % + Potential v_of_rho 0.98298 14 0.07 14 % + XC_Functional v_xc 0.28799 15 0.019 4 % + H_Hartree_pw v_hartree 0.6548 14 0.047 9.1 % + PW_Basis real2recip 0.65722 41 0.016 9.1 % + PW_Basis gatherp_scatters 0.24928 41 0.0061 3.5 % + ORB_control set_orb_tables 0.89095 1 0.89 12 % + ORB_gen_tables gen_tables 0.89094 1 0.89 12 % + ORB_table_phi init_Table 0.3738 1 0.37 5.2 % + ORB_table_phi cal_ST_Phi12_R 0.36961 126 0.0029 5.1 % + ORB_table_beta init_Table_Beta 0.15214 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15086 56 0.0027 2.1 % + ORB_table_alpha init_Table_Alpha 0.20722 1 0.21 2.9 % + ORB_table_alpha S_PhiAlpha_R 0.20556 66 0.0031 2.8 % + LOOP_ions opt_ions 5.8487 1 5.8 81 % + ESolver_KS_LCAO Run 5.317 1 5.3 74 % + HSolverLCAO solve 2.9719 12 0.25 41 % + HamiltLCAO updateHk 1.4802 12 0.12 21 % + LCAO_Hamilt cal_Hgamma 1.4498 12 0.12 20 % + Gint_interface cal_gint 2.8416 25 0.11 39 % + Gint_Gamma distri_vl 2.7634 6 0.46 38 % + LCAO_Deepks cal_projected_DM 5.6941 14 0.41 79 % + LCAO_gen_fixedH add_v_delta 2.6372 6 0.44 37 % + LCAO_DESCRIPTOR add_v_delta 2.6374 6 0.44 37 % + ElecStateLCAO psiToRho 1.4746 12 0.12 20 % + Charge mix_rho 0.82416 11 0.075 11 % + LOOP_ions force_stress 0.53153 1 0.53 7.4 % + Force_Stress_LCAO getForceStress 0.53151 1 0.53 7.4 % + Force_LCAO_gamma ftable_gamma 0.33945 1 0.34 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.3322 1 0.33 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:11 2022 + FINISH Time : Wed Sep 28 11:02:18 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/188/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..732fa06e5f68f96cf066f77d0e307d717097f7ae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.33537 0.681675 0.217445 +H 0.288211 0.723013 0.241715 +H 0.389972 0.721953 0.216719 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c507dc4d7583702f064a07aff4a1d243bd2de098 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9962 2 + 2 -12.6464 2 + 3 -9.19001 2 + 4 -6.68268 2 + 5 1.00133 0 + 6 3.89948 0 + 7 11.1508 0 + 8 11.4107 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d92cb115232a6ccfd578e0d3120a136c6543bd70 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:43 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.39036390139 19.0869099556 6.08846668983 0 0 0 0 + tauc_H1 8.06992025608 20.2443745162 6.76801745199 0 0 0 0 + tauc_H2 10.9192080819 20.2146932278 6.06814566997 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.086862911514 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0872153892633 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.1053205011 (SEC) + + DONE : INIT CHARGE Time : 0.148261424123 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.428806 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000881 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00139 + + Density error is 0.210738838222 + + Energy Rydberg eV + E_KohnSham -34.1913706328 -465.197463036 + E_Harris -34.3744257635 -467.688055862 + E_Fermi -0.384895631621 -5.23677372535 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000973617697542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122776535941 + + Density error is 0.0987448294079 + + Energy Rydberg eV + E_KohnSham -34.2789440496 -466.388960498 + E_Harris -34.2861319171 -466.486756452 + E_Fermi -0.196711017696 -2.67639070005 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000919732470906 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114344234145 + + Density error is 0.0637632587838 + + Energy Rydberg eV + E_KohnSham -34.2793903384 -466.395032568 + E_Harris -34.2839874923 -466.457580056 + E_Fermi -0.190448138444 -2.59117985633 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000840463236521 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000981578118216 + + Density error is 0.0019377670505 + + Energy Rydberg eV + E_KohnSham -34.2792851655 -466.393601617 + E_Harris -34.2792867855 -466.393623658 + E_Fermi -0.155242622316 -2.11218423596 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000840736110376 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000979702547159 + + Density error is 0.000928691286974 + + Energy Rydberg eV + E_KohnSham -34.2792550641 -466.393192067 + E_Harris -34.2792553472 -466.393195918 + E_Fermi -0.155253763762 -2.11233582311 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000839693271383 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000977212073787 + + Density error is 0.000181051081057 + + Energy Rydberg eV + E_KohnSham -34.2792667133 -466.393350563 + E_Harris -34.279266719 -466.39335064 + E_Fermi -0.154783157281 -2.10593289346 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00083987215565 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000977289972513 + + Density error is 2.7311177876e-05 + + Energy Rydberg eV + E_KohnSham -34.2792636782 -466.393309268 + E_Harris -34.2792636802 -466.393309296 + E_Fermi -0.154773551172 -2.10580219564 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000839826141182 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000977230386867 + + Density error is 1.11390346382e-05 + + Energy Rydberg eV + E_KohnSham -34.2792659562 -466.393340261 + E_Harris -34.2792659567 -466.393340268 + E_Fermi -0.154785043655 -2.10595855889 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000839825095665 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00097721535807 + + Density error is 1.96275385088e-06 + + Energy Rydberg eV + E_KohnSham -34.2792650663 -466.393328153 + E_Harris -34.2792650663 -466.393328154 + E_Fermi -0.154774428131 -2.10581412728 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000839824173964 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000977212251196 + + Density error is 2.42302497878e-07 + + Energy Rydberg eV + E_KohnSham -34.2792652157 -466.393330186 + E_Harris -34.2792652157 -466.393330186 + E_Fermi -0.154772553985 -2.10578862821 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000839824420168 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000977212601607 + + Density error is 3.44398893419e-08 + + Energy Rydberg eV + E_KohnSham -34.2792652409 -466.393330529 + E_Harris -34.2792652409 -466.393330529 + E_band -7.86658870227 -107.030430173 + E_one_elec -68.6039098507 -933.404079047 + E_Hartree +35.7116853019 +485.882405289 + E_xc -8.15697859569 -110.981387365 + E_Ewald +6.89564522895 +93.8200665002 + E_demet -2.68522922714e-59 -3.65344179253e-58 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193620144773 -2.6343372165 + E_Fermi -0.15477242551 -2.10578688021 + + charge density convergence is achieved + final etot is -466.393330529 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9962 2.00000 + 2 -12.6464 2.00000 + 3 -9.19001 2.00000 + 4 -6.68268 2.00000 + 5 1.00133 0.00000 + 6 3.89948 0.00000 + 7 11.1508 0.00000 + 8 11.4107 0.00000 + + EFERMI = -2.105786880213352 eV + OUT.ABACUS/ final etot is -466.3933305293990 eV + correction force for each atom along direction 1 is 3.07858e-05 + correction force for each atom along direction 2 is 3.93397e-05 + correction force for each atom along direction 3 is 0.000151080 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.41212490 +1.4364448 +0.35371859 + H1 +0.54233618 -0.61383096 -0.32575671 + H2 -0.95446108 -0.82261380 -0.027961882 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3933305293990 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1203 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1107 1 6.1 1.e+02% + Potential init_pot 0.28206 2 0.14 4.6% + PW_Basis recip2real 0.27314 16 0.017 4.5% + PW_Basis gathers_scatterp 0.12099 16 0.0076 2.0% + Potential v_of_rho 0.99685 13 0.077 16.% + XC_Functional v_xc 0.29762 14 0.021 4.9% + H_Hartree_pw v_hartree 0.65636 13 0.050 11.% + PW_Basis real2recip 0.69851 38 0.018 11.% + PW_Basis gatherp_scatters 0.26634 38 0.0070 4.4% + ORB_control set_orb_tables 1.0920 1 1.1 18.% + ORB_gen_tables gen_tables 1.0920 1 1.1 18.% + ORB_table_phi init_Table 0.47230 1 0.47 7.7% + ORB_table_phi cal_ST_Phi12_R 0.46711 126 0.0037 7.6% + ORB_table_beta init_Table_Beta 0.18387 1 0.18 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18233 56 0.0033 3.0% + ORB_table_alpha init_Table_Alpha 0.24701 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.24501 66 0.0037 4.0% + LOOP_ions opt_ions 4.5135 1 4.5 74.% + ESolver_KS_LCAO Run 4.0441 1 4.0 66.% + HSolverLCAO solve 1.5876 11 0.14 26.% + HamiltLCAO updateHk 0.90627 11 0.082 15.% + LCAO_Hamilt cal_Hgamma 0.87859 11 0.080 14.% + Gint_interface cal_gint 1.3118 23 0.057 21.% + Gint_Gamma distri_vl 1.9592 6 0.33 32.% + LCAO_Deepks cal_projected_DM 4.3776 13 0.34 72.% + LCAO_gen_fixedH add_v_delta 1.8130 6 0.30 30.% + LCAO_DESCRIPTOR add_v_delta 1.8131 6 0.30 30.% + ElecStateLCAO psiToRho 0.66393 11 0.060 11.% + Charge mix_rho 0.91317 10 0.091 15.% + LOOP_ions force_stress 0.46929 1 0.47 7.7% + Force_Stress_LCAO getForceStress 0.46926 1 0.47 7.7% + Force_LCAO_gamma ftable_gamma 0.25122 1 0.25 4.1% + Force_LCAO_gamma cal_fvl_dphi 0.24303 1 0.24 4.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:43 2022 + Finish Time : Wed Sep 28 11:04:49 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d03206f2fc6308891ba88485854eb6070d055414 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123291 ima = 3.72868e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123436019242 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111993347912 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112783086168 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112976968471 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011296475227 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112973054054 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112969496785 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112971274024 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112970790925 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112970716795 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112970702018 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/STRU new file mode 100644 index 0000000000000000000000000000000000000000..68fc1cd110d5e94e3723edb2e0919e985749fd41 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.609636098613 19.086909955627 6.088466689823 0 0 0 +H +0.0 +2 +-19.930079743919 20.244374516195 6.768017451986 0 0 0 +-17.080791918053 20.214693227818 6.068145669987 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/conv new file mode 100644 index 0000000000000000000000000000000000000000..5592f994668cc7efd86130f3be5bda78f1b8cce9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/conv @@ -0,0 +1 @@ +189 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..aaa5624d100d98fe6cb82a1efc6c5bfa74180e2c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751706547 0.01245494205 1.244571298 1.333604584 1.468106817 0.008708291053 0.01728133201 0.03914785989 +4.745965643e-18 0.0008534393749 0.002462759858 0.01166620141 0.04202643403 -8.349891975e-20 1.799914667e-06 5.390797885e-06 +0.001586179972 0.005934085352 + +H atom_index 1 n_descriptor 18 +1.208791146 0.03588421101 0.0946394865 0.1317902531 0.3068540933 0.02028453882 0.02588506337 0.03924352819 +1.807966016e-17 3.825821582e-05 0.08843197151 0.1126573685 0.114063427 2.312339831e-18 5.518920921e-06 0.01396372352 +0.02415185685 0.02870441968 + +H atom_index 2 n_descriptor 18 +1.195388499 0.03630182401 0.09057991607 0.1262917366 0.3018072684 0.01965613532 0.025098091 0.03978875382 +4.282985665e-17 3.71242145e-05 0.0849897976 0.1078164024 0.1134751155 6.693519254e-18 5.978811207e-06 0.01434550017 +0.02359526197 0.02799284955 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..b947fcd179f0ad8fc58410194e57e1c2aa16f4ae Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..18773219c13af024492a17a4811cc118a9012fb7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..b6fbb1a8e87d144b599ab5dbe724d63bbe78629d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..92e378fb9de963465562fd382f1a2e2a0bfb7207 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:43 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0868858 SEC) : SETUP UNITCELL + DONE(0.0872306 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105344 SEC) : INIT PLANEWAVE + DONE(0.1484 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.428875 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651975e+02 0.000000e+00 2.107e-01 4.723e-01 + GE2 -4.663890e+02 -1.191497e+00 9.874e-02 4.211e-01 + GE3 -4.663950e+02 -6.072070e-03 6.376e-02 4.884e-01 + GE4 -4.663936e+02 1.430951e-03 1.938e-03 3.481e-01 + GE5 -4.663932e+02 4.095504e-04 9.287e-04 3.487e-01 + GE6 -4.663934e+02 -1.584960e-04 1.811e-04 3.426e-01 + GE7 -4.663933e+02 4.129465e-05 2.731e-05 3.273e-01 + GE8 -4.663933e+02 -3.099318e-05 1.114e-05 3.281e-01 + GE9 -4.663933e+02 1.210798e-05 1.963e-06 3.263e-01 + GE10 -4.663933e+02 -2.032713e-06 2.423e-07 3.274e-01 + GE11 -4.663933e+02 -3.433374e-07 3.444e-08 2.515e-01 +E_delta_band = -6.79128194e-02 Ry = -9.24001311e-01 eV +E_delta_NN= -1.93620145e-01 Ry = -2.63433722e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1203 11 0.56 1e+02 % + Run_lcao lcao_line 6.1107 1 6.1 1e+02 % + Potential init_pot 0.28206 2 0.14 4.6 % + PW_Basis recip2real 0.27314 16 0.017 4.5 % + PW_Basis gathers_scatterp 0.12099 16 0.0076 2 % + Potential v_of_rho 0.99685 13 0.077 16 % + XC_Functional v_xc 0.29762 14 0.021 4.9 % + H_Hartree_pw v_hartree 0.65636 13 0.05 11 % + PW_Basis real2recip 0.69851 38 0.018 11 % + PW_Basis gatherp_scatters 0.26634 38 0.007 4.4 % + ORB_control set_orb_tables 1.092 1 1.1 18 % + ORB_gen_tables gen_tables 1.092 1 1.1 18 % + ORB_table_phi init_Table 0.4723 1 0.47 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.46711 126 0.0037 7.6 % + ORB_table_beta init_Table_Beta 0.18387 1 0.18 3 % + ORB_table_beta VNL_PhiBeta_R 0.18233 56 0.0033 3 % + ORB_table_alpha init_Table_Alpha 0.24701 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.24501 66 0.0037 4 % + LOOP_ions opt_ions 4.5135 1 4.5 74 % + ESolver_KS_LCAO Run 4.0441 1 4 66 % + HSolverLCAO solve 1.5876 11 0.14 26 % + HamiltLCAO updateHk 0.90627 11 0.082 15 % + LCAO_Hamilt cal_Hgamma 0.87859 11 0.08 14 % + Gint_interface cal_gint 1.3118 23 0.057 21 % + Gint_Gamma distri_vl 1.9592 6 0.33 32 % + LCAO_Deepks cal_projected_DM 4.3776 13 0.34 72 % + LCAO_gen_fixedH add_v_delta 1.813 6 0.3 30 % + LCAO_DESCRIPTOR add_v_delta 1.8131 6 0.3 30 % + ElecStateLCAO psiToRho 0.66393 11 0.06 11 % + Charge mix_rho 0.91317 10 0.091 15 % + LOOP_ions force_stress 0.46929 1 0.47 7.7 % + Force_Stress_LCAO getForceStress 0.46926 1 0.47 7.7 % + Force_LCAO_gamma ftable_gamma 0.25122 1 0.25 4.1 % + Force_LCAO_gamma cal_fvl_dphi 0.24303 1 0.24 4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:43 2022 + FINISH Time : Wed Sep 28 11:04:49 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/189/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..cc07133901b540f5c9a655c9181b0cc341654b79 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.557347 0.302842 0.440749 +H 0.54035 0.32193 0.378384 +H 0.499022 0.294079 0.467801 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..072e03278602cc4beb2f221d78670b648a9d0090 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2413 2 + 2 -12.8196 2 + 3 -9.24222 2 + 4 -6.73504 2 + 5 1.18199 0 + 6 4.25938 0 + 7 11.095 0 + 8 11.3567 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1fda7ae196eec628f27f48356522c5670d7f2ff0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:05 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.6057059013 8.4795627835 12.340975152 0 0 0 0 + tauc_H1 15.1298063855 9.01404559735 10.5947601136 0 0 0 0 + tauc_H2 13.972622505 8.23422014213 13.0984196839 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0750009888792 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0753495001217 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0917248667252 (SEC) + + DONE : INIT CHARGE Time : 0.133230224328 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.378688 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000854 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00164 + + Density error is 0.213847012283 + + Energy Rydberg eV + E_KohnSham -34.1892150656 -465.168135039 + E_Harris -34.3791851618 -467.752810798 + E_Fermi -0.400630743354 -5.4508609036 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00128703103304 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132885390799 + + Density error is 0.0983397650691 + + Energy Rydberg eV + E_KohnSham -34.2795492933 -466.397195261 + E_Harris -34.2865229055 -466.492076123 + E_Fermi -0.208996094264 -2.84353774174 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00123341894137 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122562955102 + + Density error is 0.0633531589171 + + Energy Rydberg eV + E_KohnSham -34.2799931869 -466.403234743 + E_Harris -34.2844928501 -466.464455801 + E_Fermi -0.200285087095 -2.72501840892 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116973093306 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104070065081 + + Density error is 0.00194722801994 + + Energy Rydberg eV + E_KohnSham -34.2799383337 -466.402488427 + E_Harris -34.2799395203 -466.402504572 + E_Fermi -0.164649468685 -2.24017094679 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117319688232 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104126751331 + + Density error is 0.00100503353016 + + Energy Rydberg eV + E_KohnSham -34.2798800715 -466.401695729 + E_Harris -34.2798812456 -466.401711703 + E_Fermi -0.164302335967 -2.23544796386 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117184567843 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103853932017 + + Density error is 0.000138748881115 + + Energy Rydberg eV + E_KohnSham -34.2799115069 -466.40212343 + E_Harris -34.2799115243 -466.402123666 + E_Fermi -0.164083141037 -2.23246566384 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011719516313 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103843751412 + + Density error is 3.53071977203e-05 + + Energy Rydberg eV + E_KohnSham -34.2799012509 -466.40198389 + E_Harris -34.2799010964 -466.401981788 + E_Fermi -0.163997874257 -2.23130554978 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117187485039 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103843662528 + + Density error is 1.67990049064e-05 + + Energy Rydberg eV + E_KohnSham -34.2799044734 -466.402027734 + E_Harris -34.2799044746 -466.40202775 + E_Fermi -0.164031393499 -2.23176160246 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117188358862 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103841738205 + + Density error is 3.19983926123e-06 + + Energy Rydberg eV + E_KohnSham -34.2799031199 -466.402009319 + E_Harris -34.27990312 -466.40200932 + E_Fermi -0.164015934552 -2.2315512727 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117188163669 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103840842227 + + Density error is 3.95428652874e-07 + + Energy Rydberg eV + E_KohnSham -34.27990333 -466.402012177 + E_Harris -34.27990333 -466.402012177 + E_Fermi -0.164012553902 -2.23150527659 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117188271128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103840860345 + + Density error is 1.39492082832e-07 + + Energy Rydberg eV + E_KohnSham -34.2799033794 -466.402012849 + E_Harris -34.2799033794 -466.402012849 + E_Fermi -0.16401240559 -2.23150325871 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117188297727 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103840836161 + + Density error is 1.09596068509e-08 + + Energy Rydberg eV + E_KohnSham -34.2799033828 -466.402012896 + E_Harris -34.2799033828 -466.402012895 + E_band -7.94345679763 -108.076274265 + E_one_elec -69.0854075298 -939.955191058 + E_Hartree +35.9379718092 +488.961191169 + E_xc -8.19331860344 -111.475818536 + E_Ewald +7.18558438755 +97.7648911305 + E_demet -5.14620079803e-71 -7.00176539054e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19448502211 -2.64610447635 + E_Fermi -0.164012284585 -2.23150161235 + + charge density convergence is achieved + final etot is -466.402012896 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2413 2.00000 + 2 -12.8196 2.00000 + 3 -9.24222 2.00000 + 4 -6.73504 2.00000 + 5 1.18199 0.00000 + 6 4.25938 0.00000 + 7 11.0950 0.00000 + 8 11.3567 0.00000 + + EFERMI = -2.231501612351300 eV + OUT.ABACUS/ final etot is -466.4020128955049 eV + correction force for each atom along direction 1 is -0.000176923 + correction force for each atom along direction 2 is 0.000157665 + correction force for each atom along direction 3 is -8.75485e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.21036968 +0.43639965 -1.3899276 + H1 +0.44149141 -0.26766311 +0.86876953 + H2 -0.65186109 -0.16873654 +0.52115804 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4020128955049 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2002 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1920 1 6.2 1.e+02% + Potential init_pot 0.24360 2 0.12 3.9% + PW_Basis recip2real 0.23850 17 0.014 3.8% + PW_Basis gathers_scatterp 0.11431 17 0.0067 1.8% + Potential v_of_rho 0.94948 14 0.068 15.% + XC_Functional v_xc 0.30687 15 0.020 4.9% + H_Hartree_pw v_hartree 0.60591 14 0.043 9.8% + PW_Basis real2recip 0.64502 41 0.016 10.% + PW_Basis gatherp_scatters 0.27586 41 0.0067 4.4% + ORB_control set_orb_tables 0.90358 1 0.90 15.% + ORB_gen_tables gen_tables 0.90358 1 0.90 15.% + ORB_table_phi init_Table 0.37597 1 0.38 6.1% + ORB_table_phi cal_ST_Phi12_R 0.37176 126 0.0030 6.0% + ORB_table_beta init_Table_Beta 0.15860 1 0.16 2.6% + ORB_table_beta VNL_PhiBeta_R 0.15732 56 0.0028 2.5% + ORB_table_alpha init_Table_Alpha 0.21059 1 0.21 3.4% + ORB_table_alpha S_PhiAlpha_R 0.20892 66 0.0032 3.4% + LOOP_ions opt_ions 4.8415 1 4.8 78.% + ESolver_KS_LCAO Run 4.3607 1 4.4 70.% + HSolverLCAO solve 1.9960 12 0.17 32.% + HamiltLCAO updateHk 1.0668 12 0.089 17.% + LCAO_Hamilt cal_Hgamma 1.0415 12 0.087 17.% + Gint_interface cal_gint 0.14493 25 0.0058 2.3% + Gint_Gamma distri_vl_value 0.61047 12 0.051 9.8% + Gint_Gamma distri_vl 2.2790 6 0.38 37.% + LCAO_Deepks cal_projected_DM 4.5064 14 0.32 73.% + LCAO_gen_fixedH add_v_delta 2.1511 6 0.36 35.% + LCAO_DESCRIPTOR add_v_delta 2.1511 6 0.36 35.% + ElecStateLCAO psiToRho 0.91140 12 0.076 15.% + Charge mix_rho 0.81559 11 0.074 13.% + LOOP_ions force_stress 0.48069 1 0.48 7.8% + Force_Stress_LCAO getForceStress 0.48067 1 0.48 7.8% + Force_LCAO_gamma ftable_gamma 0.28623 1 0.29 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:05 2022 + Finish Time : Wed Sep 28 11:05:11 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b4ad36a20005fba8113cd4c55b96237e11a7584a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123791 ima = 3.68989e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123187096951 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111763381996 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112452168124 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112701966174 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112658027214 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011268310063 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112677854944 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112680573544 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112679873688 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112679738527 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112679722844 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112679716342 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/STRU new file mode 100644 index 0000000000000000000000000000000000000000..aa4094f646150088024f97754780dfe8f08f4535 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.394294098752 8.479562783512 12.340975152060 0 0 0 +H +0.0 +2 +-12.870193614459 9.014045597328 10.594760113635 0 0 0 +-14.027377494951 8.234220142104 13.098419683927 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/conv new file mode 100644 index 0000000000000000000000000000000000000000..ad4fd420dacabc7f6da83fcf5e4934b46457a0a0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/conv @@ -0,0 +1 @@ +19 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8e287bcfd9dbc5e1eeaa7dc2c244739dd11bb004 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751643509 0.01264535778 1.261360255 1.352332057 1.469094262 0.008877349434 0.01757901347 0.03911460906 +-3.335284586e-18 0.0009451897494 0.002638230526 0.01236697669 0.04482757053 3.403463582e-19 2.168318961e-06 6.202536588e-06 +0.001600838644 0.006018633687 + +H atom_index 1 n_descriptor 18 +1.205334731 0.03600923936 0.09422276014 0.1301702364 0.3049617338 0.02036481747 0.02565638857 0.03933850373 +-5.42956583e-17 4.19921966e-05 0.08957345691 0.1113715719 0.1135571568 5.257354936e-18 5.898739525e-06 0.01409580799 +0.02453562506 0.0285339547 + +H atom_index 2 n_descriptor 18 +1.260762332 0.03415670941 0.112675011 0.1548533197 0.3240866895 0.0230022909 0.02890454602 0.03737478154 +-6.186885277e-18 4.707685069e-05 0.1034581251 0.1159697091 0.1328304634 8.223645119e-18 3.161156214e-06 0.01321194887 +0.02669031268 0.03121911604 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..07511ec91b8e58a731626edb577caf7dd89ed63d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:05 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0750159 SEC) : SETUP UNITCELL + DONE(0.0753599 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0917377 SEC) : INIT PLANEWAVE + DONE(0.133331 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.378732 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651681e+02 0.000000e+00 2.138e-01 4.615e-01 + GE2 -4.663972e+02 -1.229060e+00 9.834e-02 4.122e-01 + GE3 -4.664032e+02 -6.039482e-03 6.335e-02 4.734e-01 + GE4 -4.664025e+02 7.463157e-04 1.947e-03 3.511e-01 + GE5 -4.664017e+02 7.926983e-04 1.005e-03 3.488e-01 + GE6 -4.664021e+02 -4.277012e-04 1.387e-04 3.466e-01 + GE7 -4.664020e+02 1.395399e-04 3.531e-05 3.320e-01 + GE8 -4.664020e+02 -4.384420e-05 1.680e-05 3.319e-01 + GE9 -4.664020e+02 1.841524e-05 3.200e-06 3.310e-01 + GE10 -4.664020e+02 -2.858324e-06 3.954e-07 3.298e-01 + GE11 -4.664020e+02 -6.716731e-07 1.395e-07 3.277e-01 + GE12 -4.664020e+02 -4.649299e-08 1.096e-08 2.611e-01 +E_delta_band = -6.97515758e-02 Ry = -9.49018875e-01 eV +E_delta_NN= -1.94485022e-01 Ry = -2.64610448e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2002 11 0.56 1e+02 % + Run_lcao lcao_line 6.192 1 6.2 1e+02 % + Potential init_pot 0.2436 2 0.12 3.9 % + PW_Basis recip2real 0.2385 17 0.014 3.8 % + PW_Basis gathers_scatterp 0.11431 17 0.0067 1.8 % + Potential v_of_rho 0.94948 14 0.068 15 % + XC_Functional v_xc 0.30687 15 0.02 4.9 % + H_Hartree_pw v_hartree 0.60591 14 0.043 9.8 % + PW_Basis real2recip 0.64502 41 0.016 10 % + PW_Basis gatherp_scatters 0.27586 41 0.0067 4.4 % + ORB_control set_orb_tables 0.90358 1 0.9 15 % + ORB_gen_tables gen_tables 0.90358 1 0.9 15 % + ORB_table_phi init_Table 0.37597 1 0.38 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.37176 126 0.003 6 % + ORB_table_beta init_Table_Beta 0.1586 1 0.16 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.15732 56 0.0028 2.5 % + ORB_table_alpha init_Table_Alpha 0.21059 1 0.21 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.20892 66 0.0032 3.4 % + LOOP_ions opt_ions 4.8415 1 4.8 78 % + ESolver_KS_LCAO Run 4.3607 1 4.4 70 % + HSolverLCAO solve 1.996 12 0.17 32 % + HamiltLCAO updateHk 1.0668 12 0.089 17 % + LCAO_Hamilt cal_Hgamma 1.0415 12 0.087 17 % + Gint_interface cal_gint 0.14493 25 0.0058 2.3 % + Gint_Gamma distri_vl_value 0.61047 12 0.051 9.8 % + Gint_Gamma distri_vl 2.279 6 0.38 37 % + LCAO_Deepks cal_projected_DM 4.5064 14 0.32 73 % + LCAO_gen_fixedH add_v_delta 2.1511 6 0.36 35 % + LCAO_DESCRIPTOR add_v_delta 2.1511 6 0.36 35 % + ElecStateLCAO psiToRho 0.9114 12 0.076 15 % + Charge mix_rho 0.81559 11 0.074 13 % + LOOP_ions force_stress 0.48069 1 0.48 7.8 % + Force_Stress_LCAO getForceStress 0.48067 1 0.48 7.8 % + Force_LCAO_gamma ftable_gamma 0.28623 1 0.29 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:05 2022 + FINISH Time : Wed Sep 28 11:05:11 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/19/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..06dc5fc75e5888a994bca2e24c8cf371bf8cf0f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.368646 0.701154 0.200218 +H 0.314794 0.68264 0.228901 +H 0.373007 0.76454 0.207757 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6d53bb3525680e568f692c0b43ae77bd227ab3b3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5109 2 + 2 -13.4253 2 + 3 -9.01656 2 + 4 -6.79374 2 + 5 1.54547 0 + 6 4.8295 0 + 7 11.0114 0 + 8 11.2438 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..8a8503ffbbd94025ec186b89de8acf8cc4df8ec7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:19 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 10.3220810813 19.6323141587 5.60610674547 0 0 0 0 + tauc_H1 8.81424224099 19.1139144213 6.40922334659 0 0 0 0 + tauc_H2 10.4442009333 21.4071339981 5.81719760012 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0869492263291 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877328433999 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105968662384 (SEC) + + DONE : INIT CHARGE Time : 0.155336770654 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445119 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00172 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000681 + + Density error is 0.218123220948 + + Energy Rydberg eV + E_KohnSham -34.1874516672 -465.144142773 + E_Harris -34.3858820998 -467.843927314 + E_Fermi -0.421712404445 -5.73769161774 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00153118336959 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092614490872 + + Density error is 0.0974361918949 + + Energy Rydberg eV + E_KohnSham -34.2779783389 -466.375821329 + E_Harris -34.2845252144 -466.46489614 + E_Fermi -0.228707500329 -3.11172517981 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00139538971277 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00089576794802 + + Density error is 0.062052615809 + + Energy Rydberg eV + E_KohnSham -34.2781533379 -466.378202313 + E_Harris -34.2823057785 -466.434699165 + E_Fermi -0.213319992248 -2.90236739189 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116536095852 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00085639971256 + + Density error is 0.0020924266647 + + Energy Rydberg eV + E_KohnSham -34.2782166677 -466.37906396 + E_Harris -34.2782195699 -466.379103445 + E_Fermi -0.177783317809 -2.41886613155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116049799027 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000857807377008 + + Density error is 0.000900641594987 + + Energy Rydberg eV + E_KohnSham -34.2781391318 -466.378009029 + E_Harris -34.2781419777 -466.378047749 + E_Fermi -0.176343125794 -2.39927131392 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115928566694 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856870480946 + + Density error is 0.000160375149252 + + Energy Rydberg eV + E_KohnSham -34.278195592 -466.37877721 + E_Harris -34.2781956726 -466.378778307 + E_Fermi -0.176783751019 -2.40526632768 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115891269809 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000857133015284 + + Density error is 4.79162529318e-05 + + Energy Rydberg eV + E_KohnSham -34.2781748375 -466.378494831 + E_Harris -34.2781748502 -466.378495002 + E_Fermi -0.176588111518 -2.40260451571 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115896430694 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000857053715772 + + Density error is 1.60542477227e-05 + + Energy Rydberg eV + E_KohnSham -34.2781796612 -466.378560459 + E_Harris -34.2781796622 -466.378560473 + E_Fermi -0.176646652326 -2.40340100425 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115892098034 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000857050609302 + + Density error is 2.41153612811e-06 + + Energy Rydberg eV + E_KohnSham -34.2781781384 -466.378539741 + E_Harris -34.2781781384 -466.378539741 + E_Fermi -0.176630334321 -2.40317898641 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115891355878 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000857052576831 + + Density error is 2.25534608332e-07 + + Energy Rydberg eV + E_KohnSham -34.2781783347 -466.378542412 + E_Harris -34.2781783347 -466.378542412 + E_Fermi -0.176627706243 -2.40314322958 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115891372302 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000857052893963 + + Density error is 1.05848669668e-07 + + Energy Rydberg eV + E_KohnSham -34.2781783733 -466.378542938 + E_Harris -34.2781783733 -466.378542938 + E_Fermi -0.176627689617 -2.40314300337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115891349101 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000857053065065 + + Density error is 9.62670204685e-09 + + Energy Rydberg eV + E_KohnSham -34.278178374 -466.378542947 + E_Harris -34.278178374 -466.378542947 + E_band -8.04757668308 -109.492897982 + E_one_elec -69.8476598137 -950.326165432 + E_Hartree +36.3062023656 +493.971224913 + E_xc -8.25267061104 -112.283344027 + E_Ewald +7.6391477553 +103.935937336 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195805914302 -2.66407613661 + E_Fermi -0.17662760767 -2.40314188843 + + charge density convergence is achieved + final etot is -466.378542947 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5109 2.00000 + 2 -13.4253 2.00000 + 3 -9.01656 2.00000 + 4 -6.79374 2.00000 + 5 1.54547 0.00000 + 6 4.82950 0.00000 + 7 11.0114 0.00000 + 8 11.2438 0.00000 + + EFERMI = -2.403141888426938 eV + OUT.ABACUS/ final etot is -466.3785429466413 eV + correction force for each atom along direction 1 is -0.000132831 + correction force for each atom along direction 2 is 0.000124041 + correction force for each atom along direction 3 is 0.000177967 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.3897955 -1.0414967 -0.97854670 + H1 -1.3783754 -0.34787426 +0.75242947 + H2 -0.011420110 +1.3893710 +0.22611723 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3785429466413 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6128 11 0.69 1.0e+02% + Run_lcao lcao_line 7.6029 1 7.6 1.e+02% + Potential init_pot 0.29485 2 0.15 3.9% + PW_Basis recip2real 0.30965 17 0.018 4.1% + PW_Basis gathers_scatterp 0.14078 17 0.0083 1.8% + Potential v_of_rho 1.0583 14 0.076 14.% + XC_Functional v_xc 0.29176 15 0.019 3.8% + H_Hartree_pw v_hartree 0.72115 14 0.052 9.5% + PW_Basis real2recip 0.74766 41 0.018 9.8% + PW_Basis gatherp_scatters 0.31293 41 0.0076 4.1% + ORB_control set_orb_tables 1.0921 1 1.1 14.% + ORB_gen_tables gen_tables 1.0921 1 1.1 14.% + ORB_table_phi init_Table 0.47407 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46893 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18401 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18239 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24912 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24716 66 0.0037 3.2% + LOOP_ions opt_ions 5.9871 1 6.0 79.% + ESolver_KS_LCAO Run 5.4040 1 5.4 71.% + HSolverLCAO solve 2.9282 12 0.24 38.% + HamiltLCAO updateHk 1.5042 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4745 12 0.12 19.% + Gint_interface cal_gint 2.7613 25 0.11 36.% + Gint_Gamma distri_vl 2.8149 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.8163 14 0.42 76.% + LCAO_gen_fixedH add_v_delta 2.6693 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6693 6 0.44 35.% + ElecStateLCAO psiToRho 1.4065 12 0.12 18.% + Charge mix_rho 0.85561 11 0.078 11.% + LOOP_ions force_stress 0.58295 1 0.58 7.7% + Force_Stress_LCAO getForceStress 0.58292 1 0.58 7.7% + Force_LCAO_gamma ftable_gamma 0.36381 1 0.36 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.35591 1 0.36 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:19 2022 + Finish Time : Wed Sep 28 11:02:27 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..cd870ec432e168642d1d96605f481dbe895acc80 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123977 ima = 3.68054e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122985844394 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112363604325 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112710193833 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112990175075 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112913632119 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112959104657 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112950573181 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112953754573 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112953155177 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112953059815 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112953053575 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112953049499 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b405ea8afe6ac647658ade9e3166e2161fea22a7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-17.677918918761 19.632314158688 5.606106745493 0 0 0 +H +0.0 +2 +-19.185757759011 19.113914421249 6.409223346568 0 0 0 +-17.555799066722 21.407133998090 5.817197600116 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/conv new file mode 100644 index 0000000000000000000000000000000000000000..eea62e547aa54fb929749df4ba10897d997f4aa3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/conv @@ -0,0 +1 @@ +190 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..84ca6eb203e0f72ab10fd5702b80ff871cac6626 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746828868 0.01279991726 1.29841092 1.383686827 1.470488913 0.008316578258 0.01994825347 0.03895806549 +-8.237144762e-19 0.001238721151 0.002644025408 0.01307961775 0.0467502266 5.872963314e-19 2.052547851e-06 5.974808326e-06 +0.001713321844 0.005818228116 + +H atom_index 1 n_descriptor 18 +1.280976515 0.03284910744 0.1200071498 0.1653388665 0.3306849058 0.02360782421 0.03013915993 0.03630055168 +3.083456086e-17 4.989144955e-05 0.108226908 0.1191509918 0.1421387048 -1.473373028e-17 2.622679073e-06 0.01319336687 +0.02777983297 0.03211604689 + +H atom_index 2 n_descriptor 18 +1.276065841 0.0330098945 0.1181555589 0.1628718099 0.3292920241 0.02339061091 0.02985935955 0.03637826514 +8.949510214e-18 4.943042136e-05 0.1079416945 0.1180370951 0.1400419087 7.698036502e-19 2.894208645e-06 0.01312982847 +0.02761896474 0.03192695737 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c0d185d9a9ae35f77a311a0d15ab654397d3e3bf Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:19 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0869754 SEC) : SETUP UNITCELL + DONE(0.0877483 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105985 SEC) : INIT PLANEWAVE + DONE(0.155464 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445178 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651441e+02 0.000000e+00 2.181e-01 5.508e-01 + GE2 -4.663758e+02 -1.231679e+00 9.744e-02 5.028e-01 + GE3 -4.663782e+02 -2.380984e-03 6.205e-02 5.724e-01 + GE4 -4.663791e+02 -8.616462e-04 2.092e-03 4.352e-01 + GE5 -4.663780e+02 1.054931e-03 9.006e-04 4.346e-01 + GE6 -4.663788e+02 -7.681811e-04 1.604e-04 4.213e-01 + GE7 -4.663785e+02 2.823793e-04 4.792e-05 4.246e-01 + GE8 -4.663786e+02 -6.562859e-05 1.605e-05 4.157e-01 + GE9 -4.663785e+02 2.071835e-05 2.412e-06 4.119e-01 + GE10 -4.663785e+02 -2.670746e-06 2.255e-07 4.140e-01 + GE11 -4.663785e+02 -5.259123e-07 1.058e-07 4.106e-01 + GE12 -4.663785e+02 -8.975145e-09 9.627e-09 3.479e-01 +E_delta_band = -7.26078442e-02 Ry = -9.87880401e-01 eV +E_delta_NN= -1.95805914e-01 Ry = -2.66407614e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6128 11 0.69 1e+02 % + Run_lcao lcao_line 7.6029 1 7.6 1e+02 % + Potential init_pot 0.29485 2 0.15 3.9 % + PW_Basis recip2real 0.30965 17 0.018 4.1 % + PW_Basis gathers_scatterp 0.14078 17 0.0083 1.8 % + Potential v_of_rho 1.0583 14 0.076 14 % + XC_Functional v_xc 0.29176 15 0.019 3.8 % + H_Hartree_pw v_hartree 0.72115 14 0.052 9.5 % + PW_Basis real2recip 0.74766 41 0.018 9.8 % + PW_Basis gatherp_scatters 0.31293 41 0.0076 4.1 % + ORB_control set_orb_tables 1.0921 1 1.1 14 % + ORB_gen_tables gen_tables 1.0921 1 1.1 14 % + ORB_table_phi init_Table 0.47407 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.46893 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18401 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18239 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24912 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24716 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9871 1 6 79 % + ESolver_KS_LCAO Run 5.404 1 5.4 71 % + HSolverLCAO solve 2.9282 12 0.24 38 % + HamiltLCAO updateHk 1.5042 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4745 12 0.12 19 % + Gint_interface cal_gint 2.7613 25 0.11 36 % + Gint_Gamma distri_vl 2.8149 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.8163 14 0.42 76 % + LCAO_gen_fixedH add_v_delta 2.6693 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6693 6 0.44 35 % + ElecStateLCAO psiToRho 1.4065 12 0.12 18 % + Charge mix_rho 0.85561 11 0.078 11 % + LOOP_ions force_stress 0.58295 1 0.58 7.7 % + Force_Stress_LCAO getForceStress 0.58292 1 0.58 7.7 % + Force_LCAO_gamma ftable_gamma 0.36381 1 0.36 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.35591 1 0.36 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:19 2022 + FINISH Time : Wed Sep 28 11:02:27 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/190/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ddbecb93ed8cb0f2f4c17c7bad0c7ecc916d2018 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.39413 0.716451 0.191763 +H 0.356974 0.666215 0.217705 +H 0.343112 0.760334 0.188109 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..598215593a26bd8bbc9371ff88fcb52733989afa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1358 2 + 2 -12.3166 2 + 3 -9.54175 2 + 4 -6.71822 2 + 5 0.961326 0 + 6 3.8667 0 + 7 11.1381 0 + 8 11.4309 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4a82c0be08ca9489ac12065a194d478309265edf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.0356506353 20.0606317058 5.36935176964 0 0 0 0 + tauc_H1 9.99526864575 18.6540183079 6.09574690642 0 0 0 0 + tauc_H2 9.6071407006 21.2893447395 5.26705993019 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0739282476358 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0869933374541 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103267793404 (SEC) + + DONE : INIT CHARGE Time : 0.144370522021 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.398746 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125 + + Density error is 0.209037387399 + + Energy Rydberg eV + E_KohnSham -34.1894471172 -465.171292264 + E_Harris -34.3699057895 -467.626558461 + E_Fermi -0.386880900211 -5.26378469024 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119455108353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112524768464 + + Density error is 0.098137892962 + + Energy Rydberg eV + E_KohnSham -34.2759400947 -466.348089595 + E_Harris -34.2831803405 -466.446598193 + E_Fermi -0.199735005348 -2.7175341628 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011197990538 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104808939162 + + Density error is 0.0633250373165 + + Energy Rydberg eV + E_KohnSham -34.2763461191 -466.35361384 + E_Harris -34.2809835105 -466.416708787 + E_Fermi -0.193447121368 -2.6319831123 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993098706226 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000917579041286 + + Density error is 0.00185241892937 + + Energy Rydberg eV + E_KohnSham -34.2762295696 -466.352028103 + E_Harris -34.2762289854 -466.352020154 + E_Fermi -0.158006067442 -2.14978283578 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993316229738 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000918611291267 + + Density error is 0.000916706473993 + + Energy Rydberg eV + E_KohnSham -34.276205253 -466.351697258 + E_Harris -34.2762058432 -466.351705288 + E_Fermi -0.158271471869 -2.15339384827 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000991462644242 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000916733058854 + + Density error is 9.98540380501e-05 + + Energy Rydberg eV + E_KohnSham -34.2762147881 -466.35182699 + E_Harris -34.2762147869 -466.351826974 + E_Fermi -0.157724668938 -2.14595421271 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000991430261365 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000916736198565 + + Density error is 2.08637632676e-05 + + Energy Rydberg eV + E_KohnSham -34.2762135607 -466.35181029 + E_Harris -34.2762135616 -466.351810303 + E_Fermi -0.157697036694 -2.14557825675 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00099137818599 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000916710114198 + + Density error is 7.44139109899e-06 + + Energy Rydberg eV + E_KohnSham -34.2762143811 -466.351821453 + E_Harris -34.2762143814 -466.351821456 + E_Fermi -0.157704302906 -2.14567711863 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000991373770953 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000916706493595 + + Density error is 1.37936087699e-06 + + Energy Rydberg eV + E_KohnSham -34.2762137495 -466.35181286 + E_Harris -34.2762137495 -466.35181286 + E_Fermi -0.15769705328 -2.14557848242 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000991373787627 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000916704246633 + + Density error is 2.05129441376e-07 + + Energy Rydberg eV + E_KohnSham -34.2762138661 -466.351814446 + E_Harris -34.2762138661 -466.351814446 + E_Fermi -0.157696164236 -2.14556638635 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0009913741945 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00091670448103 + + Density error is 5.41901622944e-08 + + Energy Rydberg eV + E_KohnSham -34.2762138841 -466.351814691 + E_Harris -34.2762138841 -466.351814691 + E_band -7.89556667131 -107.424695669 + E_one_elec -68.6474124388 -933.995962123 + E_Hartree +35.7196187271 +485.990345076 + E_xc -8.15800987751 -110.995418674 + E_Ewald +6.93516428174 +94.3577507977 + E_demet -2.73544664808e-59 -3.72176609889e-58 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193728476532 -2.6358111457 + E_Fermi -0.157696068698 -2.14556508649 + + charge density convergence is achieved + final etot is -466.351814691 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1358 2.00000 + 2 -12.3166 2.00000 + 3 -9.54175 2.00000 + 4 -6.71822 2.00000 + 5 0.961326 0.00000 + 6 3.86670 0.00000 + 7 11.1381 0.00000 + 8 11.4309 0.00000 + + EFERMI = -2.145565086489765 eV + OUT.ABACUS/ final etot is -466.3518146910782 eV + correction force for each atom along direction 1 is -0.000163403 + correction force for each atom along direction 2 is 3.65699e-05 + correction force for each atom along direction 3 is 8.35324e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -2.0290090 -0.25568818 +0.55383296 + H1 +1.0382909 +0.32271719 -0.34992679 + H2 +0.99071810 -0.067029006 -0.20390617 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3518146910782 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7189 11 0.61 1.0e+02% + Run_lcao lcao_line 6.7112 1 6.7 1.e+02% + Potential init_pot 0.25352 2 0.13 3.8% + PW_Basis recip2real 0.25159 16 0.016 3.7% + PW_Basis gathers_scatterp 0.10452 16 0.0065 1.6% + Potential v_of_rho 0.91059 13 0.070 14.% + XC_Functional v_xc 0.27859 14 0.020 4.1% + H_Hartree_pw v_hartree 0.59537 13 0.046 8.9% + PW_Basis real2recip 0.59903 38 0.016 8.9% + PW_Basis gatherp_scatters 0.22340 38 0.0059 3.3% + ORB_control set_orb_tables 0.89926 1 0.90 13.% + ORB_gen_tables gen_tables 0.89925 1 0.90 13.% + ORB_table_phi init_Table 0.37585 1 0.38 5.6% + ORB_table_phi cal_ST_Phi12_R 0.37156 126 0.0029 5.5% + ORB_table_beta init_Table_Beta 0.15565 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15433 56 0.0028 2.3% + ORB_table_alpha init_Table_Alpha 0.21004 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20843 66 0.0032 3.1% + LOOP_ions opt_ions 5.3420 1 5.3 80.% + ESolver_KS_LCAO Run 4.8010 1 4.8 71.% + HSolverLCAO solve 2.6593 11 0.24 40.% + HamiltLCAO updateHk 1.3608 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3292 11 0.12 20.% + Gint_interface cal_gint 2.5409 23 0.11 38.% + Gint_Gamma distri_vl 2.3001 6 0.38 34.% + LCAO_Deepks cal_projected_DM 5.1874 13 0.40 77.% + LCAO_gen_fixedH add_v_delta 2.1699 6 0.36 32.% + LCAO_DESCRIPTOR add_v_delta 2.1697 6 0.36 32.% + ElecStateLCAO psiToRho 1.2817 11 0.12 19.% + Charge mix_rho 0.75431 10 0.075 11.% + LOOP_ions force_stress 0.54085 1 0.54 8.0% + Force_Stress_LCAO getForceStress 0.54083 1 0.54 8.0% + Force_LCAO_gamma ftable_gamma 0.34671 1 0.35 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.33936 1 0.34 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:48 2022 + Finish Time : Wed Sep 28 11:06:55 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..bf52795309d454b56bcb8b522c340a25b5597643 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123877 ima = 3.68946e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122768138992 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111289054553 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112118351834 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112322850994 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112313467407 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318483652 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112317367269 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318639493 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318278717 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318227057 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318215734 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/STRU new file mode 100644 index 0000000000000000000000000000000000000000..cd2e51e4562f52d62b33d39270eb48562449ce83 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.964349364729 20.060631705859 5.369351769628 0 0 0 +H +0.0 +2 +-18.004731354239 18.654018307852 6.095746906394 0 0 0 +-18.392859299399 21.289344739570 5.267059930178 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/conv new file mode 100644 index 0000000000000000000000000000000000000000..057730c757bcb81da6b72a752468d0fd39c7d8f9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/conv @@ -0,0 +1 @@ +191 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b3fde79dde9993217c9d76bcf8d2577dc7130d46 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.756809973 0.01260199437 1.245247801 1.322177071 1.468649165 0.009846650591 0.01538301306 0.03930138098 +-2.068790325e-19 0.0007116325874 0.002711068013 0.01287906081 0.04351413392 -1.789580106e-19 2.49402231e-06 7.010270278e-06 +0.001569747829 0.00608073158 + +H atom_index 1 n_descriptor 18 +1.20375736 0.03664727701 0.09698615595 0.1293424175 0.3030611757 0.02117484814 0.02550049872 0.04001754045 +7.749214662e-18 4.011726689e-05 0.08939012971 0.110347775 0.1136858118 -4.015735662e-18 4.381632653e-06 0.01435964394 +0.02479688286 0.02839211176 + +H atom_index 2 n_descriptor 18 +1.209470192 0.03647304704 0.09880872292 0.1317241228 0.3052418823 0.02146118701 0.02583854814 0.03978947028 +5.382253748e-18 4.059112981e-05 0.09083071402 0.1124389042 0.1139844228 9.86828637e-18 4.141152712e-06 0.01420059678 +0.02503441289 0.02869610389 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c312eda203385c73882c3b6470c0827a7a6ea9f9 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0739441 SEC) : SETUP UNITCELL + DONE(0.0870047 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103278 SEC) : INIT PLANEWAVE + DONE(0.14447 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.398788 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651713e+02 0.000000e+00 2.090e-01 5.141e-01 + GE2 -4.663481e+02 -1.176797e+00 9.814e-02 4.871e-01 + GE3 -4.663536e+02 -5.524245e-03 6.333e-02 5.497e-01 + GE4 -4.663520e+02 1.585737e-03 1.852e-03 4.200e-01 + GE5 -4.663517e+02 3.308446e-04 9.167e-04 4.197e-01 + GE6 -4.663518e+02 -1.297324e-04 9.985e-05 4.137e-01 + GE7 -4.663518e+02 1.670012e-05 2.086e-05 3.999e-01 + GE8 -4.663518e+02 -1.116235e-05 7.441e-06 4.038e-01 + GE9 -4.663518e+02 8.593081e-06 1.379e-06 4.003e-01 + GE10 -4.663518e+02 -1.585910e-06 2.051e-07 4.042e-01 + GE11 -4.663518e+02 -2.455431e-07 5.419e-08 3.354e-01 +E_delta_band = -6.81538998e-02 Ry = -9.27281378e-01 eV +E_delta_NN= -1.93728477e-01 Ry = -2.63581115e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7189 11 0.61 1e+02 % + Run_lcao lcao_line 6.7112 1 6.7 1e+02 % + Potential init_pot 0.25352 2 0.13 3.8 % + PW_Basis recip2real 0.25159 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.10452 16 0.0065 1.6 % + Potential v_of_rho 0.91059 13 0.07 14 % + XC_Functional v_xc 0.27859 14 0.02 4.1 % + H_Hartree_pw v_hartree 0.59537 13 0.046 8.9 % + PW_Basis real2recip 0.59903 38 0.016 8.9 % + PW_Basis gatherp_scatters 0.2234 38 0.0059 3.3 % + ORB_control set_orb_tables 0.89926 1 0.9 13 % + ORB_gen_tables gen_tables 0.89925 1 0.9 13 % + ORB_table_phi init_Table 0.37585 1 0.38 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.37156 126 0.0029 5.5 % + ORB_table_beta init_Table_Beta 0.15565 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15433 56 0.0028 2.3 % + ORB_table_alpha init_Table_Alpha 0.21004 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20843 66 0.0032 3.1 % + LOOP_ions opt_ions 5.342 1 5.3 80 % + ESolver_KS_LCAO Run 4.801 1 4.8 71 % + HSolverLCAO solve 2.6593 11 0.24 40 % + HamiltLCAO updateHk 1.3608 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3292 11 0.12 20 % + Gint_interface cal_gint 2.5409 23 0.11 38 % + Gint_Gamma distri_vl 2.3001 6 0.38 34 % + LCAO_Deepks cal_projected_DM 5.1874 13 0.4 77 % + LCAO_gen_fixedH add_v_delta 2.1699 6 0.36 32 % + LCAO_DESCRIPTOR add_v_delta 2.1697 6 0.36 32 % + ElecStateLCAO psiToRho 1.2817 11 0.12 19 % + Charge mix_rho 0.75431 10 0.075 11 % + LOOP_ions force_stress 0.54085 1 0.54 8 % + Force_Stress_LCAO getForceStress 0.54083 1 0.54 8 % + Force_LCAO_gamma ftable_gamma 0.34671 1 0.35 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.33936 1 0.34 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:48 2022 + FINISH Time : Wed Sep 28 11:06:55 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/191/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5be63bc55533b360ace6a1ee257858e377ee7c3b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.406735 0.726606 0.187024 +H 0.421346 0.681636 0.230683 +H 0.344831 0.727925 0.16933 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d70c9453c195dcf1a5554b85b757615d7f73cfb6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2664 2 + 2 -13.6997 2 + 3 -8.6151 2 + 4 -6.73506 2 + 5 1.47436 0 + 6 4.74979 0 + 7 11.0485 0 + 8 11.243 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..dd1a858c98f101804de9ee249e843a1e8b1d2048 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:53 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.3885910642 20.3449680969 5.23667152218 0 0 0 0 + tauc_H1 11.7976912247 19.0858088617 6.4591359308 0 0 0 0 + tauc_H2 9.65526905323 20.3819065616 4.74123836083 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0867225532002 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0985027735085 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116821300824 (SEC) + + DONE : INIT CHARGE Time : 0.166205940628 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447772 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000647 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00182 + + Density error is 0.219366506938 + + Energy Rydberg eV + E_KohnSham -34.1832323678 -465.08673626 + E_Harris -34.3839688843 -467.817896681 + E_Fermi -0.414811081563 -5.6437943028 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000994678102312 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0014609535366 + + Density error is 0.0979544888927 + + Energy Rydberg eV + E_KohnSham -34.2752615344 -466.338857308 + E_Harris -34.2817568811 -466.427231034 + E_Fermi -0.219969396244 -2.99283717454 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000962573681928 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134161140193 + + Density error is 0.0625688998255 + + Energy Rydberg eV + E_KohnSham -34.2755518798 -466.34280766 + E_Harris -34.2796708715 -466.398849417 + E_Fermi -0.206234817718 -2.80596864696 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000920470792788 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113866432026 + + Density error is 0.00223071029112 + + Energy Rydberg eV + E_KohnSham -34.2755898863 -466.343324765 + E_Harris -34.2755954862 -466.343400956 + E_Fermi -0.171133588278 -2.32839191977 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00092152601118 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113517442423 + + Density error is 0.000889022490929 + + Energy Rydberg eV + E_KohnSham -34.275522565 -466.342408812 + E_Harris -34.2755239517 -466.342427679 + E_Fermi -0.169905910103 -2.31168850128 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000920738393599 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113337346484 + + Density error is 0.0002447648945 + + Energy Rydberg eV + E_KohnSham -34.2755662962 -466.343003805 + E_Harris -34.2755664641 -466.343006089 + E_Fermi -0.170130755771 -2.31474768353 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000921073400046 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113297035423 + + Density error is 4.59438786237e-05 + + Energy Rydberg eV + E_KohnSham -34.2755484579 -466.342761103 + E_Harris -34.2755484694 -466.342761259 + E_Fermi -0.169893504034 -2.31151970805 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000921003688604 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113300158338 + + Density error is 1.94371910371e-05 + + Energy Rydberg eV + E_KohnSham -34.2755550111 -466.342850263 + E_Harris -34.2755550126 -466.342850284 + E_Fermi -0.169949393197 -2.31228011912 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000921003752169 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113295985694 + + Density error is 1.9155556357e-06 + + Energy Rydberg eV + E_KohnSham -34.2755534432 -466.342828931 + E_Harris -34.2755534432 -466.342828931 + E_Fermi -0.169928675747 -2.31199824375 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000921002763016 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113295296998 + + Density error is 3.05595731408e-07 + + Energy Rydberg eV + E_KohnSham -34.2755537031 -466.342832468 + E_Harris -34.2755537031 -466.342832468 + E_Fermi -0.16992680873 -2.31197284169 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000921003481079 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113295315811 + + Density error is 1.41391362033e-07 + + Energy Rydberg eV + E_KohnSham -34.2755537265 -466.342832786 + E_Harris -34.2755537265 -466.342832786 + E_Fermi -0.169926757331 -2.31197214237 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000921003722629 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113295291482 + + Density error is 9.00093555165e-09 + + Energy Rydberg eV + E_KohnSham -34.2755537265 -466.342832785 + E_Harris -34.2755537265 -466.342832785 + E_band -7.9843483744 -108.632632709 + E_one_elec -69.6302948002 -947.368762702 + E_Hartree +36.2193168415 +492.789086712 + E_xc -8.23777724731 -112.080709418 + E_Ewald +7.49692219411 +102.000859303 + E_demet -9.384944562e-87 -1.27688721457e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195123173486 -2.65478697125 + E_Fermi -0.169926623514 -2.31197032169 + + charge density convergence is achieved + final etot is -466.342832785 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2664 2.00000 + 2 -13.6997 2.00000 + 3 -8.61510 2.00000 + 4 -6.73506 2.00000 + 5 1.47436 0.00000 + 6 4.74979 0.00000 + 7 11.0485 0.00000 + 8 11.2430 0.00000 + + EFERMI = -2.311970321688798 eV + OUT.ABACUS/ final etot is -466.3428327849196 eV + correction force for each atom along direction 1 is -7.88103e-05 + correction force for each atom along direction 2 is -3.85780e-05 + correction force for each atom along direction 3 is 6.47277e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.4057640 +1.3309607 -0.79883627 + H1 -0.45182302 -0.82725658 +0.60946088 + H2 -0.95394098 -0.50370415 +0.18937539 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3428327849196 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5103 11 0.68 1.0e+02% + Run_lcao lcao_line 7.5005 1 7.5 1.e+02% + Potential init_pot 0.28416 2 0.14 3.8% + PW_Basis recip2real 0.30149 17 0.018 4.0% + PW_Basis gathers_scatterp 0.12649 17 0.0074 1.7% + Potential v_of_rho 1.0651 14 0.076 14.% + XC_Functional v_xc 0.30296 15 0.020 4.0% + H_Hartree_pw v_hartree 0.71708 14 0.051 9.5% + PW_Basis real2recip 0.70212 41 0.017 9.3% + PW_Basis gatherp_scatters 0.26513 41 0.0065 3.5% + ORB_control set_orb_tables 1.0912 1 1.1 15.% + ORB_gen_tables gen_tables 1.0912 1 1.1 15.% + ORB_table_phi init_Table 0.47352 1 0.47 6.3% + ORB_table_phi cal_ST_Phi12_R 0.46848 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18335 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18187 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24781 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24589 66 0.0037 3.3% + LOOP_ions opt_ions 5.8821 1 5.9 78.% + ESolver_KS_LCAO Run 5.2921 1 5.3 70.% + HSolverLCAO solve 2.8065 12 0.23 37.% + HamiltLCAO updateHk 1.4440 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4111 12 0.12 19.% + Gint_interface cal_gint 2.6381 25 0.11 35.% + Gint_Gamma distri_vl 2.7567 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.7136 14 0.41 76.% + LCAO_gen_fixedH add_v_delta 2.6102 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6103 6 0.44 35.% + ElecStateLCAO psiToRho 1.3454 12 0.11 18.% + Charge mix_rho 0.85879 11 0.078 11.% + LOOP_ions force_stress 0.58986 1 0.59 7.9% + Force_Stress_LCAO getForceStress 0.58983 1 0.59 7.9% + Force_LCAO_gamma ftable_gamma 0.36890 1 0.37 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.36103 1 0.36 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:53 2022 + Finish Time : Wed Sep 28 11:03:00 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e11ac292387fdf0ccc770105f28c0bcea4a43b4d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123397 ima = 3.70122e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012403117316 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113367957277 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113749095888 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113996676195 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113939630092 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113974532446 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113962313949 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113965486795 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011396476256 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113964701666 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113964695039 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113964688695 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b44c800d6a19e0974b4ba75a356d227b00228da7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.611408935803 20.344968096949 5.236671522158 0 0 0 +H +0.0 +2 +-16.202308775342 19.085808861725 6.459135930774 0 0 0 +-18.344730946790 20.381906561601 4.741238360847 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/conv new file mode 100644 index 0000000000000000000000000000000000000000..71ac5c2f25474c364a814f300909247cd7564002 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/conv @@ -0,0 +1 @@ +192 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d1bcf2cd58002991d8acb51fb428e405e12f118c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.739365325 0.01263545795 1.296418547 1.3876072 1.469447057 0.007210251077 0.02211286547 0.03874140744 +2.490014627e-18 0.001250404304 0.002244404223 0.01308349235 0.04141279477 4.263096686e-19 1.302177805e-06 4.287664462e-06 +0.001930893147 0.005300714995 + +H atom_index 1 n_descriptor 18 +1.259361924 0.03276199778 0.1140413619 0.1573853219 0.3276165562 0.02225490893 0.02922184412 0.03607514783 +3.299524555e-17 3.464266379e-05 0.1057909891 0.1156591651 0.1352138292 2.556717099e-18 3.429504215e-06 0.01264270074 +0.02670898762 0.03141884981 + +H atom_index 2 n_descriptor 18 +1.258479403 0.03279350082 0.113725032 0.1569631586 0.3273608414 0.02221904907 0.0291715743 0.03609588972 +1.258512084e-19 3.45788882e-05 0.1056347965 0.1155634388 0.1348516617 7.552693808e-19 3.467160341e-06 0.01264057716 +0.02667806535 0.03138256568 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a077748dac92c5abacd7450ad27658676d68a22d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:53 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.086745 SEC) : SETUP UNITCELL + DONE(0.0985225 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116843 SEC) : INIT PLANEWAVE + DONE(0.166337 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447835 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650867e+02 0.000000e+00 2.194e-01 5.474e-01 + GE2 -4.663389e+02 -1.252121e+00 9.795e-02 4.986e-01 + GE3 -4.663428e+02 -3.950352e-03 6.257e-02 5.615e-01 + GE4 -4.663433e+02 -5.171048e-04 2.231e-03 4.266e-01 + GE5 -4.663424e+02 9.159527e-04 8.890e-04 4.262e-01 + GE6 -4.663430e+02 -5.949932e-04 2.448e-04 4.170e-01 + GE7 -4.663428e+02 2.427022e-04 4.594e-05 4.120e-01 + GE8 -4.663429e+02 -8.916005e-05 1.944e-05 3.985e-01 + GE9 -4.663428e+02 2.133237e-05 1.916e-06 4.018e-01 + GE10 -4.663428e+02 -3.536709e-06 3.056e-07 4.028e-01 + GE11 -4.663428e+02 -3.183226e-07 1.414e-07 4.002e-01 + GE12 -4.663428e+02 1.016917e-09 9.001e-09 3.368e-01 +E_delta_band = -7.14024589e-02 Ry = -9.71480292e-01 eV +E_delta_NN= -1.95123173e-01 Ry = -2.65478697e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5103 11 0.68 1e+02 % + Run_lcao lcao_line 7.5005 1 7.5 1e+02 % + Potential init_pot 0.28416 2 0.14 3.8 % + PW_Basis recip2real 0.30149 17 0.018 4 % + PW_Basis gathers_scatterp 0.12649 17 0.0074 1.7 % + Potential v_of_rho 1.0651 14 0.076 14 % + XC_Functional v_xc 0.30296 15 0.02 4 % + H_Hartree_pw v_hartree 0.71708 14 0.051 9.5 % + PW_Basis real2recip 0.70212 41 0.017 9.3 % + PW_Basis gatherp_scatters 0.26513 41 0.0065 3.5 % + ORB_control set_orb_tables 1.0912 1 1.1 15 % + ORB_gen_tables gen_tables 1.0912 1 1.1 15 % + ORB_table_phi init_Table 0.47352 1 0.47 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.46848 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18335 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18187 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24781 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24589 66 0.0037 3.3 % + LOOP_ions opt_ions 5.8821 1 5.9 78 % + ESolver_KS_LCAO Run 5.2921 1 5.3 70 % + HSolverLCAO solve 2.8065 12 0.23 37 % + HamiltLCAO updateHk 1.444 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.4111 12 0.12 19 % + Gint_interface cal_gint 2.6381 25 0.11 35 % + Gint_Gamma distri_vl 2.7567 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.7136 14 0.41 76 % + LCAO_gen_fixedH add_v_delta 2.6102 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6103 6 0.44 35 % + ElecStateLCAO psiToRho 1.3454 12 0.11 18 % + Charge mix_rho 0.85879 11 0.078 11 % + LOOP_ions force_stress 0.58986 1 0.59 7.9 % + Force_Stress_LCAO getForceStress 0.58983 1 0.59 7.9 % + Force_LCAO_gamma ftable_gamma 0.3689 1 0.37 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.36103 1 0.36 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:53 2022 + FINISH Time : Wed Sep 28 11:03:00 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/192/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..bb9f1f60e4bbd50c367cc7131b7845acf4f09bd3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.415051 0.732705 0.173882 +H 0.451815 0.685936 0.199366 +H 0.355968 0.706968 0.188515 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8ddaad02e7e36a285868deccf48b6c9740e21a0f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4366 2 + 2 -12.7477 2 + 3 -9.43751 2 + 4 -6.77859 2 + 5 1.2736 0 + 6 4.41956 0 + 7 11.0606 0 + 8 11.3441 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ce935a156f314af0f20ad2fc0ce25e2ea6abe185 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:31 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.6214343531 20.5157496116 4.86869083031 0 0 0 0 + tauc_H1 12.6508112996 19.2062047174 5.5822427426 0 0 0 0 + tauc_H2 9.96711005786 19.7951077744 5.2784138857 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105575876468 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105936808321 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124040908865 (SEC) + + DONE : INIT CHARGE Time : 0.167115382707 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446621 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000731 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00165 + + Density error is 0.213988422627 + + Energy Rydberg eV + E_KohnSham -34.1890126262 -465.165380711 + E_Harris -34.3795909482 -467.758331804 + E_Fermi -0.407479160597 -5.54403840038 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000984716396039 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138386898441 + + Density error is 0.097630740601 + + Energy Rydberg eV + E_KohnSham -34.2786523326 -466.384991484 + E_Harris -34.2855135943 -466.478343739 + E_Fermi -0.217282189507 -2.95627585122 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000938214523363 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127308683945 + + Density error is 0.0627014012482 + + Energy Rydberg eV + E_KohnSham -34.2790019295 -466.389747995 + E_Harris -34.2834486485 -466.45024871 + E_Fermi -0.2065562299 -2.81034168404 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000881187042183 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107276675384 + + Density error is 0.00193306746363 + + Energy Rydberg eV + E_KohnSham -34.2789805773 -466.389457482 + E_Harris -34.2789808596 -466.389461323 + E_Fermi -0.170652975387 -2.32185284591 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00088413164481 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107180886563 + + Density error is 0.000962704991523 + + Energy Rydberg eV + E_KohnSham -34.278916604 -466.388587082 + E_Harris -34.2789183082 -466.388610268 + E_Fermi -0.170101928937 -2.31435547434 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882841551308 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106934799789 + + Density error is 9.42801260949e-05 + + Energy Rydberg eV + E_KohnSham -34.2789584374 -466.389156254 + E_Harris -34.2789584421 -466.389156317 + E_Fermi -0.170047247568 -2.31361149614 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882725820965 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106894390994 + + Density error is 4.09074415373e-05 + + Energy Rydberg eV + E_KohnSham -34.2789461003 -466.388988399 + E_Harris -34.2789461091 -466.388988518 + E_Fermi -0.169937177759 -2.31211391957 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00088269307612 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106898808105 + + Density error is 9.80903933817e-06 + + Energy Rydberg eV + E_KohnSham -34.2789476144 -466.389008999 + E_Harris -34.2789476148 -466.389009004 + E_Fermi -0.169984462094 -2.31275725594 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882708330904 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106898676771 + + Density error is 2.09542556984e-06 + + Energy Rydberg eV + E_KohnSham -34.2789464448 -466.388993086 + E_Harris -34.2789464448 -466.388993087 + E_Fermi -0.169977392648 -2.3126610712 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882707755519 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106898078744 + + Density error is 2.96766390477e-07 + + Energy Rydberg eV + E_KohnSham -34.2789465903 -466.388995066 + E_Harris -34.2789465903 -466.388995066 + E_Fermi -0.169975056371 -2.31262928451 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882708670971 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106898155132 + + Density error is 3.58869369285e-08 + + Energy Rydberg eV + E_KohnSham -34.2789466185 -466.38899545 + E_Harris -34.2789466185 -466.38899545 + E_band -7.99671403576 -108.800876163 + E_one_elec -69.3563617521 -943.641712377 + E_Hartree +36.0595902689 +490.615895202 + E_xc -8.21268255841 -111.73927866 + E_Ewald +7.35465868906 +100.065265016 + E_demet -4.16739990626e-78 -5.67003845697e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194975407194 -2.65277650771 + E_Fermi -0.169974979081 -2.31262823293 + + charge density convergence is achieved + final etot is -466.38899545 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4366 2.00000 + 2 -12.7477 2.00000 + 3 -9.43751 2.00000 + 4 -6.77859 2.00000 + 5 1.27360 0.00000 + 6 4.41956 0.00000 + 7 11.0606 0.00000 + 8 11.3441 0.00000 + + EFERMI = -2.312628232926778 eV + OUT.ABACUS/ final etot is -466.3889954498515 eV + correction force for each atom along direction 1 is -5.66618e-05 + correction force for each atom along direction 2 is -1.34097e-05 + correction force for each atom along direction 3 is -7.90866e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.80879934 +0.093788005 -0.049927302 + H1 +1.0356105 -0.50135869 +0.27051025 + H2 -0.22681118 +0.40757069 -0.22058294 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3889954498515 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0697 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0599 1 7.1 1.e+02% + Potential init_pot 0.28165 2 0.14 4.0% + PW_Basis recip2real 0.26545 16 0.017 3.8% + PW_Basis gathers_scatterp 0.11626 16 0.0073 1.6% + Potential v_of_rho 0.95518 13 0.073 14.% + XC_Functional v_xc 0.28261 14 0.020 4.0% + H_Hartree_pw v_hartree 0.63059 13 0.049 8.9% + PW_Basis real2recip 0.68527 38 0.018 9.7% + PW_Basis gatherp_scatters 0.26431 38 0.0070 3.7% + ORB_control set_orb_tables 1.0936 1 1.1 15.% + ORB_gen_tables gen_tables 1.0936 1 1.1 15.% + ORB_table_phi init_Table 0.47552 1 0.48 6.7% + ORB_table_phi cal_ST_Phi12_R 0.47037 126 0.0037 6.7% + ORB_table_beta init_Table_Beta 0.18404 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18254 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.24689 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24495 66 0.0037 3.5% + LOOP_ions opt_ions 5.4355 1 5.4 77.% + ESolver_KS_LCAO Run 4.8517 1 4.9 69.% + HSolverLCAO solve 2.4319 11 0.22 34.% + HamiltLCAO updateHk 1.2726 11 0.12 18.% + LCAO_Hamilt cal_Hgamma 1.2451 11 0.11 18.% + Gint_interface cal_gint 2.2737 23 0.099 32.% + Gint_Gamma distri_vl 2.3326 6 0.39 33.% + LCAO_Deepks cal_projected_DM 5.2741 13 0.41 75.% + LCAO_gen_fixedH add_v_delta 2.1870 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1870 6 0.36 31.% + ElecStateLCAO psiToRho 1.1428 11 0.10 16.% + Charge mix_rho 0.90596 10 0.091 13.% + LOOP_ions force_stress 0.58360 1 0.58 8.3% + Force_Stress_LCAO getForceStress 0.58357 1 0.58 8.3% + Force_LCAO_gamma ftable_gamma 0.36936 1 0.37 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.36123 1 0.36 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:31 2022 + Finish Time : Wed Sep 28 11:07:39 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1e30725953a50751ec3da4ca9aac81e4c893ba52 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123755 ima = 3.69819e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012264648481 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111419518558 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112025193205 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112291954115 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112231550268 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112264213525 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011226279118 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112265329594 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112264869834 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112264786847 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001122647695 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1ffef2e3bc237f6fc4e94a4d0a402f0ec80027f4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.378565646906 20.515749611601 4.868690830281 0 0 0 +H +0.0 +2 +-15.349188700471 19.206204717377 5.582242742586 0 0 0 +-18.032889942123 19.795107774366 5.278413885670 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/conv new file mode 100644 index 0000000000000000000000000000000000000000..6a7d53bbf158f7f970acf1c8363550a10f9f7121 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/conv @@ -0,0 +1 @@ +193 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e65696825221aea5a5e9131dc24e7d03e9d312b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754129722 0.01281086513 1.272341829 1.354532557 1.469830001 0.009495890274 0.01679743029 0.03916455777 +2.355345382e-18 0.0009168698768 0.002863947186 0.01334830984 0.04712130315 5.368523615e-20 2.83324393e-06 7.486386965e-06 +0.001590724261 0.006156187902 + +H atom_index 1 n_descriptor 18 +1.266269617 0.03434962146 0.1171115431 0.1572831364 0.3248137911 0.02403356305 0.02918381605 0.03753610554 +-2.14892957e-17 5.193452403e-05 0.1062479932 0.117133025 0.1349111851 -7.678464805e-18 2.189890214e-06 0.0133562021 +0.02764022948 0.03146328096 + +H atom_index 2 n_descriptor 18 +1.236199035 0.03535251567 0.1063531945 0.1432025234 0.314865412 0.02253858364 0.02742125064 0.03846042982 +-2.908144853e-17 4.909317346e-05 0.1000045995 0.1145751515 0.1227730085 -4.205330727e-18 3.859704073e-06 0.01357625005 +0.02653139432 0.03008972689 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..959f343ece387f0eb9ee5e7cedc6004d823bbe49 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:31 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105599 SEC) : SETUP UNITCELL + DONE(0.105951 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124063 SEC) : INIT PLANEWAVE + DONE(0.167254 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446688 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651654e+02 0.000000e+00 2.140e-01 5.395e-01 + GE2 -4.663850e+02 -1.219611e+00 9.763e-02 4.953e-01 + GE3 -4.663897e+02 -4.756510e-03 6.270e-02 5.628e-01 + GE4 -4.663895e+02 2.905127e-04 1.933e-03 4.225e-01 + GE5 -4.663886e+02 8.704005e-04 9.627e-04 4.209e-01 + GE6 -4.663892e+02 -5.691720e-04 9.428e-05 4.043e-01 + GE7 -4.663890e+02 1.678543e-04 4.091e-05 4.043e-01 + GE8 -4.663890e+02 -2.059954e-05 9.809e-06 4.042e-01 + GE9 -4.663890e+02 1.591252e-05 2.095e-06 3.989e-01 + GE10 -4.663890e+02 -1.979872e-06 2.968e-07 4.051e-01 + GE11 -4.663890e+02 -3.836613e-07 3.589e-08 3.317e-01 +E_delta_band = -7.08241412e-02 Ry = -9.63611876e-01 eV +E_delta_NN= -1.94975407e-01 Ry = -2.65277651e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0697 11 0.64 1e+02 % + Run_lcao lcao_line 7.0599 1 7.1 1e+02 % + Potential init_pot 0.28165 2 0.14 4 % + PW_Basis recip2real 0.26545 16 0.017 3.8 % + PW_Basis gathers_scatterp 0.11626 16 0.0073 1.6 % + Potential v_of_rho 0.95518 13 0.073 14 % + XC_Functional v_xc 0.28261 14 0.02 4 % + H_Hartree_pw v_hartree 0.63059 13 0.049 8.9 % + PW_Basis real2recip 0.68527 38 0.018 9.7 % + PW_Basis gatherp_scatters 0.26431 38 0.007 3.7 % + ORB_control set_orb_tables 1.0936 1 1.1 15 % + ORB_gen_tables gen_tables 1.0936 1 1.1 15 % + ORB_table_phi init_Table 0.47552 1 0.48 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.47037 126 0.0037 6.7 % + ORB_table_beta init_Table_Beta 0.18404 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18254 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.24689 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24495 66 0.0037 3.5 % + LOOP_ions opt_ions 5.4355 1 5.4 77 % + ESolver_KS_LCAO Run 4.8517 1 4.9 69 % + HSolverLCAO solve 2.4319 11 0.22 34 % + HamiltLCAO updateHk 1.2726 11 0.12 18 % + LCAO_Hamilt cal_Hgamma 1.2451 11 0.11 18 % + Gint_interface cal_gint 2.2737 23 0.099 32 % + Gint_Gamma distri_vl 2.3326 6 0.39 33 % + LCAO_Deepks cal_projected_DM 5.2741 13 0.41 75 % + LCAO_gen_fixedH add_v_delta 2.187 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.187 6 0.36 31 % + ElecStateLCAO psiToRho 1.1428 11 0.1 16 % + Charge mix_rho 0.90596 10 0.091 13 % + LOOP_ions force_stress 0.5836 1 0.58 8.3 % + Force_Stress_LCAO getForceStress 0.58357 1 0.58 8.3 % + Force_LCAO_gamma ftable_gamma 0.36936 1 0.37 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.36123 1 0.36 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:31 2022 + FINISH Time : Wed Sep 28 11:07:39 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/193/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4f33583c124f5db18b7c2b4f4c6186b04c27bad0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.42731 0.743072 0.168628 +H 0.474821 0.697397 0.174711 +H 0.383525 0.737334 0.215321 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ba61f52d6e6aacbc72c91396eb4858231b9cf1d5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1975 2 + 2 -13.4099 2 + 3 -8.76896 2 + 4 -6.71941 2 + 5 1.34229 0 + 6 4.53614 0 + 7 11.077 0 + 8 11.2922 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c3cc2378306ff123789f983d5eeb555213f5806c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:51 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.9646915478 20.8060213847 4.72159719909 0 0 0 0 + tauc_H1 13.2949917035 19.5271072323 4.89190769516 0 0 0 0 + tauc_H2 10.7386892863 20.645340589 6.02899336076 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.100517972764 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100886826434 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118943757979 (SEC) + + DONE : INIT CHARGE Time : 0.163539520201 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447703 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000656 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134 + + Density error is 0.217075116993 + + Energy Rydberg eV + E_KohnSham -34.1872544857 -465.141459981 + E_Harris -34.3830653046 -467.805602849 + E_Fermi -0.406675187365 -5.53309978339 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000987919136361 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128204160867 + + Density error is 0.0982422776522 + + Energy Rydberg eV + E_KohnSham -34.2781186047 -466.377729744 + E_Harris -34.2847611037 -466.46810558 + E_Fermi -0.21372662425 -2.9078999041 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000954080774664 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119771227551 + + Density error is 0.0629412965609 + + Energy Rydberg eV + E_KohnSham -34.2784248929 -466.381897008 + E_Harris -34.2826822212 -466.439820932 + E_Fermi -0.201999935468 -2.748350118 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000913231037678 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105195658898 + + Density error is 0.00213591596916 + + Energy Rydberg eV + E_KohnSham -34.2784267014 -466.381921615 + E_Harris -34.2784310065 -466.381980188 + E_Fermi -0.166779632718 -2.26915331532 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914666649498 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104966713047 + + Density error is 0.000890495798557 + + Energy Rydberg eV + E_KohnSham -34.2783681122 -466.381124467 + E_Harris -34.2783691594 -466.381138716 + E_Fermi -0.165892920363 -2.2570889748 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000913954385827 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104801528196 + + Density error is 0.000216223981299 + + Energy Rydberg eV + E_KohnSham -34.2784036679 -466.381608227 + E_Harris -34.2784037745 -466.381609678 + E_Fermi -0.165915446412 -2.25739545741 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914262191967 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104798917623 + + Density error is 4.08323370024e-05 + + Energy Rydberg eV + E_KohnSham -34.2783894126 -466.381414274 + E_Harris -34.2783894213 -466.381414392 + E_Fermi -0.165745257621 -2.25507992012 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914203858676 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010479650095 + + Density error is 1.84626116124e-05 + + Energy Rydberg eV + E_KohnSham -34.2783950613 -466.381491128 + E_Harris -34.2783950626 -466.381491147 + E_Fermi -0.165790817065 -2.25569978816 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00091420801192 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104794107996 + + Density error is 2.62500780708e-06 + + Energy Rydberg eV + E_KohnSham -34.2783935867 -466.381471065 + E_Harris -34.2783935867 -466.381471066 + E_Fermi -0.165772279592 -2.2554475729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914205266901 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104793502338 + + Density error is 4.34621989567e-07 + + Energy Rydberg eV + E_KohnSham -34.2783938256 -466.381474316 + E_Harris -34.2783938256 -466.381474316 + E_Fermi -0.165769623706 -2.25541143772 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0009142060441 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104793550502 + + Density error is 1.82530007539e-07 + + Energy Rydberg eV + E_KohnSham -34.2783938567 -466.381474739 + E_Harris -34.2783938567 -466.381474739 + E_Fermi -0.165769487897 -2.25540958994 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914206279944 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104793543415 + + Density error is 9.52114758066e-09 + + Energy Rydberg eV + E_KohnSham -34.2783938574 -466.381474749 + E_Harris -34.2783938574 -466.381474749 + E_band -7.95193330619 -108.19160308 + E_one_elec -69.3517658713 -943.579182212 + E_Hartree +36.0818646269 +490.91895339 + E_xc -8.21596588996 -111.783950677 + E_Ewald +7.3317415246 +99.7534609978 + E_demet -1.37055384112e-78 -1.8647341655e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194738240184 -2.649549685 + E_Fermi -0.165769309079 -2.25540715699 + + charge density convergence is achieved + final etot is -466.381474749 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1975 2.00000 + 2 -13.4099 2.00000 + 3 -8.76896 2.00000 + 4 -6.71941 2.00000 + 5 1.34229 0.00000 + 6 4.53614 0.00000 + 7 11.0770 0.00000 + 8 11.2922 0.00000 + + EFERMI = -2.255407156991257 eV + OUT.ABACUS/ final etot is -466.3814747488436 eV + correction force for each atom along direction 1 is 6.53337e-05 + correction force for each atom along direction 2 is -0.000110096 + correction force for each atom along direction 3 is 0.000159595 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.0322003 +0.33309603 -1.3124176 + H1 -0.53877789 +0.13995911 +0.34176280 + H2 -0.49342245 -0.47305514 +0.97065481 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3814747488436 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7057 11 0.70 1.0e+02% + Run_lcao lcao_line 7.6956 1 7.7 1.e+02% + Potential init_pot 0.28588 2 0.14 3.7% + PW_Basis recip2real 0.29558 17 0.017 3.8% + PW_Basis gathers_scatterp 0.12631 17 0.0074 1.6% + Potential v_of_rho 1.0935 14 0.078 14.% + XC_Functional v_xc 0.32155 15 0.021 4.2% + H_Hartree_pw v_hartree 0.72490 14 0.052 9.4% + PW_Basis real2recip 0.75612 41 0.018 9.8% + PW_Basis gatherp_scatters 0.28668 41 0.0070 3.7% + ORB_control set_orb_tables 1.0898 1 1.1 14.% + ORB_gen_tables gen_tables 1.0898 1 1.1 14.% + ORB_table_phi init_Table 0.47236 1 0.47 6.1% + ORB_table_phi cal_ST_Phi12_R 0.46719 126 0.0037 6.1% + ORB_table_beta init_Table_Beta 0.18202 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18053 56 0.0032 2.3% + ORB_table_alpha init_Table_Alpha 0.24649 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24452 66 0.0037 3.2% + LOOP_ions opt_ions 6.0827 1 6.1 79.% + ESolver_KS_LCAO Run 5.4834 1 5.5 71.% + HSolverLCAO solve 2.8057 12 0.23 36.% + HamiltLCAO updateHk 1.4505 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4209 12 0.12 18.% + Gint_interface cal_gint 2.6404 25 0.11 34.% + Gint_Gamma distri_vl 2.8564 6 0.48 37.% + LCAO_Deepks cal_projected_DM 5.9177 14 0.42 77.% + LCAO_gen_fixedH add_v_delta 2.7076 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.7077 6 0.45 35.% + ElecStateLCAO psiToRho 1.3381 12 0.11 17.% + Charge mix_rho 0.98856 11 0.090 13.% + LOOP_ions force_stress 0.59907 1 0.60 7.8% + Force_Stress_LCAO getForceStress 0.59904 1 0.60 7.8% + Force_LCAO_gamma ftable_gamma 0.37749 1 0.38 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.36933 1 0.37 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:51 2022 + Finish Time : Wed Sep 28 11:08:58 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..235ca977128dbe87231536b7811fbbb5bfbc501c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123679 ima = 3.70572e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123801833871 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112899971823 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113385398019 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113618433518 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011357221636 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113600942398 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113590499308 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011359349023 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113592775918 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113592689747 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113592678718 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113592669761 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/STRU new file mode 100644 index 0000000000000000000000000000000000000000..6ca62058af90b3f014827885c600761a4a227e7f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.035308452243 20.806021384705 4.721597199086 0 0 0 +H +0.0 +2 +-14.705008296505 19.527107232254 4.891907695155 0 0 0 +-17.261310713701 20.645340589037 6.028993360756 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/conv new file mode 100644 index 0000000000000000000000000000000000000000..190905159a2942bbcecd5b4f3a5e286761b59753 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/conv @@ -0,0 +1 @@ +194 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..126e82c3b55be393af04aa6c09c7218510e04cab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742916388 0.01259078172 1.279961422 1.375240759 1.46899226 0.007556779669 0.02073686346 0.03884019051 +1.570500878e-18 0.0011648897 0.002329273011 0.0123853442 0.04222439007 -9.405043565e-20 1.425727383e-06 4.608141865e-06 +0.001813762077 0.005552696585 + +H atom_index 1 n_descriptor 18 +1.222773484 0.03448884604 0.09981915201 0.1395836314 0.3149074011 0.02061684117 0.02697720336 0.03766548109 +9.456512684e-18 3.500374776e-05 0.09512412867 0.11405924 0.119742859 -1.30581866e-17 5.190047296e-06 0.01315601287 +0.02504525663 0.02965757036 + +H atom_index 2 n_descriptor 18 +1.265815634 0.03296102964 0.1144264671 0.1593054197 0.3283412733 0.0224625732 0.02945258745 0.03633326064 +4.179797605e-17 3.836162547e-05 0.1055399452 0.1159958529 0.1367850513 -1.782079012e-18 3.346979738e-06 0.01282544828 +0.02664510107 0.03158155469 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e1a9aefbb269d81e654da32406af4df7c4518a40 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:51 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.100553 SEC) : SETUP UNITCELL + DONE(0.100901 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118965 SEC) : INIT PLANEWAVE + DONE(0.163674 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447764 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651415e+02 0.000000e+00 2.171e-01 5.504e-01 + GE2 -4.663777e+02 -1.236270e+00 9.824e-02 5.132e-01 + GE3 -4.663819e+02 -4.167265e-03 6.294e-02 5.852e-01 + GE4 -4.663819e+02 -2.460645e-05 2.136e-03 4.446e-01 + GE5 -4.663811e+02 7.971474e-04 8.905e-04 4.424e-01 + GE6 -4.663816e+02 -4.837596e-04 2.162e-04 4.354e-01 + GE7 -4.663814e+02 1.939529e-04 4.083e-05 4.281e-01 + GE8 -4.663815e+02 -7.685396e-05 1.846e-05 4.184e-01 + GE9 -4.663815e+02 2.006260e-05 2.625e-06 4.201e-01 + GE10 -4.663815e+02 -3.250639e-06 4.346e-07 4.203e-01 + GE11 -4.663815e+02 -4.233381e-07 1.825e-07 4.212e-01 + GE12 -4.663815e+02 -9.370156e-09 9.521e-09 3.419e-01 +E_delta_band = -7.04699925e-02 Ry = -9.58793437e-01 eV +E_delta_NN= -1.94738240e-01 Ry = -2.64954969e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7057 11 0.7 1e+02 % + Run_lcao lcao_line 7.6956 1 7.7 1e+02 % + Potential init_pot 0.28588 2 0.14 3.7 % + PW_Basis recip2real 0.29558 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.12631 17 0.0074 1.6 % + Potential v_of_rho 1.0935 14 0.078 14 % + XC_Functional v_xc 0.32155 15 0.021 4.2 % + H_Hartree_pw v_hartree 0.7249 14 0.052 9.4 % + PW_Basis real2recip 0.75612 41 0.018 9.8 % + PW_Basis gatherp_scatters 0.28668 41 0.007 3.7 % + ORB_control set_orb_tables 1.0898 1 1.1 14 % + ORB_gen_tables gen_tables 1.0898 1 1.1 14 % + ORB_table_phi init_Table 0.47236 1 0.47 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.46719 126 0.0037 6.1 % + ORB_table_beta init_Table_Beta 0.18202 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18053 56 0.0032 2.3 % + ORB_table_alpha init_Table_Alpha 0.24649 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24452 66 0.0037 3.2 % + LOOP_ions opt_ions 6.0827 1 6.1 79 % + ESolver_KS_LCAO Run 5.4834 1 5.5 71 % + HSolverLCAO solve 2.8057 12 0.23 36 % + HamiltLCAO updateHk 1.4505 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.4209 12 0.12 18 % + Gint_interface cal_gint 2.6404 25 0.11 34 % + Gint_Gamma distri_vl 2.8564 6 0.48 37 % + LCAO_Deepks cal_projected_DM 5.9177 14 0.42 77 % + LCAO_gen_fixedH add_v_delta 2.7076 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.7077 6 0.45 35 % + ElecStateLCAO psiToRho 1.3381 12 0.11 17 % + Charge mix_rho 0.98856 11 0.09 13 % + LOOP_ions force_stress 0.59907 1 0.6 7.8 % + Force_Stress_LCAO getForceStress 0.59904 1 0.6 7.8 % + Force_LCAO_gamma ftable_gamma 0.37749 1 0.38 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.36933 1 0.37 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:51 2022 + FINISH Time : Wed Sep 28 11:08:58 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/194/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b9d939d18e07aa5f83474dcb61d8541dcbff3a9c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.436813 0.737012 0.165242 +H 0.488995 0.714588 0.130727 +H 0.46985 0.756673 0.217397 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..28a05b3746a4921ab10990fa83b29bb67b9add11 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4225 2 + 2 -12.6583 2 + 3 -9.49018 2 + 4 -6.77577 2 + 5 1.22998 0 + 6 4.36134 0 + 7 11.0678 0 + 8 11.356 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a81b0e067bad0c5eda3cda9da44f0b6e655983e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:11 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.2307624484 20.6363307409 4.62677923118 0 0 0 0 + tauc_H1 13.6918567317 20.0084607292 3.66034611456 0 0 0 0 + tauc_H2 13.1558032818 21.1868536258 6.08711770979 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0862284814264 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0927353829485 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.110691657508 (SEC) + + DONE : INIT CHARGE Time : 0.159098294669 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438006 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00093 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000925 + + Density error is 0.213742187972 + + Energy Rydberg eV + E_KohnSham -34.1876094646 -465.146289718 + E_Harris -34.3780091004 -467.736809661 + E_Fermi -0.40656645486 -5.53162040176 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00132508316896 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000984806270283 + + Density error is 0.0977453295501 + + Energy Rydberg eV + E_KohnSham -34.2778748627 -466.374413463 + E_Harris -34.2848245177 -466.468968371 + E_Fermi -0.215315769147 -2.92952132965 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00126330511945 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000930210142888 + + Density error is 0.0628657794655 + + Energy Rydberg eV + E_KohnSham -34.2782894531 -466.380054255 + E_Harris -34.2827875688 -466.441254259 + E_Fermi -0.205586507576 -2.79714793496 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118341007559 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000855329630301 + + Density error is 0.00192603734883 + + Energy Rydberg eV + E_KohnSham -34.2782504567 -466.379523683 + E_Harris -34.2782508734 -466.379529352 + E_Fermi -0.169649947638 -2.30820595328 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118782958206 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000857922277799 + + Density error is 0.00102202607154 + + Energy Rydberg eV + E_KohnSham -34.278185518 -466.378640146 + E_Harris -34.2781873223 -466.378664695 + E_Fermi -0.169245718219 -2.30270612989 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011859434499 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856558270765 + + Density error is 0.000101682659096 + + Energy Rydberg eV + E_KohnSham -34.2782253715 -466.37918238 + E_Harris -34.2782253786 -466.379182477 + E_Fermi -0.169113478209 -2.30090691224 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118560251546 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856406813482 + + Density error is 3.80235350338e-05 + + Energy Rydberg eV + E_KohnSham -34.278214068 -466.379028588 + E_Harris -34.2782140761 -466.379028699 + E_Fermi -0.169004004155 -2.29941744132 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118558181972 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856401208171 + + Density error is 1.55802743321e-05 + + Energy Rydberg eV + E_KohnSham -34.2782154568 -466.379047485 + E_Harris -34.2782154579 -466.379047499 + E_Fermi -0.169055287643 -2.30011518897 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118559465333 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856407779411 + + Density error is 2.0523128864e-06 + + Energy Rydberg eV + E_KohnSham -34.2782141145 -466.379029222 + E_Harris -34.2782141145 -466.379029222 + E_Fermi -0.169039567309 -2.29990130286 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118559599051 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856407522369 + + Density error is 3.75486573072e-07 + + Energy Rydberg eV + E_KohnSham -34.2782143575 -466.379032528 + E_Harris -34.2782143575 -466.379032528 + E_Fermi -0.169038075049 -2.29988099962 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118559699759 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856408124067 + + Density error is 8.65036715802e-08 + + Energy Rydberg eV + E_KohnSham -34.2782143876 -466.379032937 + E_Harris -34.2782143876 -466.379032937 + E_band -7.98883428828 -108.693666698 + E_one_elec -69.2849659887 -942.670323182 + E_Hartree +36.0240281185 +490.132047324 + E_xc -8.20691835904 -111.660852704 + E_Ewald +7.31393438463 +99.5111824291 + E_demet -9.39367062927e-76 -1.27807445693e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194848555786 -2.65105060576 + E_Fermi -0.169037863797 -2.29987812539 + + charge density convergence is achieved + final etot is -466.379032937 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4225 2.00000 + 2 -12.6583 2.00000 + 3 -9.49018 2.00000 + 4 -6.77577 2.00000 + 5 1.22998 0.00000 + 6 4.36134 0.00000 + 7 11.0678 0.00000 + 8 11.3560 0.00000 + + EFERMI = -2.299878125385773 eV + OUT.ABACUS/ final etot is -466.3790329374535 eV + correction force for each atom along direction 1 is 0.000118797 + correction force for each atom along direction 2 is -0.000128393 + correction force for each atom along direction 3 is -2.60496e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.54829138 -0.42444499 -0.76439181 + H1 -0.54813982 -0.076810336 -0.32518105 + H2 -0.00015156509 +0.50125533 +1.0895729 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3790329374535 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9455 11 0.54 1.0e+02% + Run_lcao lcao_line 5.9365 1 5.9 1.e+02% + Potential init_pot 0.28514 2 0.14 4.8% + PW_Basis recip2real 0.26492 16 0.017 4.5% + PW_Basis gathers_scatterp 0.11383 16 0.0071 1.9% + Potential v_of_rho 0.86615 13 0.067 15.% + XC_Functional v_xc 0.23853 14 0.017 4.0% + H_Hartree_pw v_hartree 0.59064 13 0.045 9.9% + PW_Basis real2recip 0.55167 38 0.015 9.3% + PW_Basis gatherp_scatters 0.21278 38 0.0056 3.6% + ORB_control set_orb_tables 1.1062 1 1.1 19.% + ORB_gen_tables gen_tables 1.1062 1 1.1 19.% + ORB_table_phi init_Table 0.48477 1 0.48 8.2% + ORB_table_phi cal_ST_Phi12_R 0.47986 126 0.0038 8.1% + ORB_table_beta init_Table_Beta 0.18772 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18624 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25606 1 0.26 4.3% + ORB_table_alpha S_PhiAlpha_R 0.25414 66 0.0039 4.3% + LOOP_ions opt_ions 4.3162 1 4.3 73.% + ESolver_KS_LCAO Run 3.8010 1 3.8 64.% + HSolverLCAO solve 1.8461 11 0.17 31.% + HamiltLCAO updateHk 0.99687 11 0.091 17.% + LCAO_Hamilt cal_Hgamma 0.95887 11 0.087 16.% + Gint_interface cal_gint 1.6827 23 0.073 28.% + Gint_Gamma distri_vl 1.8498 6 0.31 31.% + LCAO_Deepks cal_projected_DM 4.1690 13 0.32 70.% + LCAO_gen_fixedH add_v_delta 1.7157 6 0.29 29.% + LCAO_DESCRIPTOR add_v_delta 1.7156 6 0.29 29.% + ElecStateLCAO psiToRho 0.83562 11 0.076 14.% + Charge mix_rho 0.65508 10 0.066 11.% + LOOP_ions force_stress 0.51504 1 0.52 8.7% + Force_Stress_LCAO getForceStress 0.51501 1 0.52 8.7% + Force_LCAO_gamma ftable_gamma 0.30074 1 0.30 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.29397 1 0.29 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:11 2022 + Finish Time : Wed Sep 28 11:10:17 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..13612a0db1a1ca3428b705ccca56a8af4f3a4db8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123703 ima = 3.70991e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122671343285 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111286647462 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111953465001 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112227288825 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112168124482 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112199216563 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112198417807 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112201077462 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112200348587 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112200259644 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112200240772 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/STRU new file mode 100644 index 0000000000000000000000000000000000000000..2ac967ef39bb0f6dbc7d3ddbc1751cb2fb8b34d1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.769237551618 20.636330740915 4.626779231183 0 0 0 +H +0.0 +2 +-14.308143268370 20.008460729237 3.660346114551 0 0 0 +-14.844196718229 21.186853625855 6.087117709774 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/conv new file mode 100644 index 0000000000000000000000000000000000000000..382a1f074cf8ee4551e8c18c80675abfa6b75a3f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/conv @@ -0,0 +1 @@ +195 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9e38babe07a3fa4db8ffb22a1ca29edc91752b95 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754993956 0.01280643827 1.268764951 1.350491823 1.46974454 0.009665861164 0.0164176994 0.03919251016 +-2.847884792e-19 0.0008722837805 0.002883001648 0.01346125385 0.04692980386 6.226023035e-20 2.906860857e-06 7.6690365e-06 +0.001587839608 0.006166967455 + +H atom_index 1 n_descriptor 18 +1.228572098 0.03572072274 0.1044565775 0.1398264258 0.3120304746 0.02234103057 0.02696768824 0.03885732602 +2.179219657e-17 4.790773938e-05 0.09816234395 0.1143040706 0.1197752403 1.680931487e-17 3.958241051e-06 0.01374227105 +0.02630858984 0.02971154283 + +H atom_index 2 n_descriptor 18 +1.26517323 0.03450710783 0.1174716142 0.1567842673 0.3243691377 0.02418013243 0.0291186025 0.03768091469 +-8.785956597e-18 5.129713295e-05 0.1060234242 0.1172109379 0.1344191905 1.429343357e-17 1.98230381e-06 0.01338255617 +0.02767768824 0.03141666422 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f6572421dd4939c89c0f84344c0c52c3a0fd76f2 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..9af754a793837958be7012f61c7223d9705c556c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:11 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0862619 SEC) : SETUP UNITCELL + DONE(0.0927541 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.110712 SEC) : INIT PLANEWAVE + DONE(0.159248 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438068 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651463e+02 0.000000e+00 2.137e-01 4.606e-01 + GE2 -4.663744e+02 -1.228124e+00 9.775e-02 3.842e-01 + GE3 -4.663801e+02 -5.640792e-03 6.287e-02 4.437e-01 + GE4 -4.663795e+02 5.305722e-04 1.926e-03 3.272e-01 + GE5 -4.663786e+02 8.835364e-04 1.022e-03 3.303e-01 + GE6 -4.663792e+02 -5.422340e-04 1.017e-04 3.120e-01 + GE7 -4.663790e+02 1.537921e-04 3.802e-05 3.138e-01 + GE8 -4.663790e+02 -1.889652e-05 1.558e-05 3.070e-01 + GE9 -4.663790e+02 1.826304e-05 2.052e-06 3.076e-01 + GE10 -4.663790e+02 -3.306064e-06 3.755e-07 3.068e-01 + GE11 -4.663790e+02 -4.097637e-07 8.650e-08 2.464e-01 +E_delta_band = -7.05560127e-02 Ry = -9.59963801e-01 eV +E_delta_NN= -1.94848556e-01 Ry = -2.65105061e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9455 11 0.54 1e+02 % + Run_lcao lcao_line 5.9365 1 5.9 1e+02 % + Potential init_pot 0.28514 2 0.14 4.8 % + PW_Basis recip2real 0.26492 16 0.017 4.5 % + PW_Basis gathers_scatterp 0.11383 16 0.0071 1.9 % + Potential v_of_rho 0.86615 13 0.067 15 % + XC_Functional v_xc 0.23853 14 0.017 4 % + H_Hartree_pw v_hartree 0.59064 13 0.045 9.9 % + PW_Basis real2recip 0.55167 38 0.015 9.3 % + PW_Basis gatherp_scatters 0.21278 38 0.0056 3.6 % + ORB_control set_orb_tables 1.1062 1 1.1 19 % + ORB_gen_tables gen_tables 1.1062 1 1.1 19 % + ORB_table_phi init_Table 0.48477 1 0.48 8.2 % + ORB_table_phi cal_ST_Phi12_R 0.47986 126 0.0038 8.1 % + ORB_table_beta init_Table_Beta 0.18772 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18624 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.25606 1 0.26 4.3 % + ORB_table_alpha S_PhiAlpha_R 0.25414 66 0.0039 4.3 % + LOOP_ions opt_ions 4.3162 1 4.3 73 % + ESolver_KS_LCAO Run 3.801 1 3.8 64 % + HSolverLCAO solve 1.8461 11 0.17 31 % + HamiltLCAO updateHk 0.99687 11 0.091 17 % + LCAO_Hamilt cal_Hgamma 0.95887 11 0.087 16 % + Gint_interface cal_gint 1.6827 23 0.073 28 % + Gint_Gamma distri_vl 1.8498 6 0.31 31 % + LCAO_Deepks cal_projected_DM 4.169 13 0.32 70 % + LCAO_gen_fixedH add_v_delta 1.7157 6 0.29 29 % + LCAO_DESCRIPTOR add_v_delta 1.7156 6 0.29 29 % + ElecStateLCAO psiToRho 0.83562 11 0.076 14 % + Charge mix_rho 0.65508 10 0.066 11 % + LOOP_ions force_stress 0.51504 1 0.52 8.7 % + Force_Stress_LCAO getForceStress 0.51501 1 0.52 8.7 % + Force_LCAO_gamma ftable_gamma 0.30074 1 0.3 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.29397 1 0.29 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:11 2022 + FINISH Time : Wed Sep 28 11:10:17 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/195/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..1797966acf5db73119e8954be38c36168c57f375 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.444962 0.736863 0.177533 +H 0.446027 0.764355 0.11934 +H 0.496678 0.756 0.214011 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e83e0fc72ac3eb659a1fe011d0645ead81fae505 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1923 2 + 2 -13.4118 2 + 3 -8.76372 2 + 4 -6.71815 2 + 5 1.34142 0 + 6 4.53159 0 + 7 11.0782 0 + 8 11.2931 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..6b5b5b161926345bd6f4f63616093927ffe5e80e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:05 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.4589321515 20.6321619868 4.97092877627 0 0 0 0 + tauc_H1 12.4887509781 21.4019330632 3.34152180994 0 0 0 0 + tauc_H2 13.906980077 21.1680033615 5.99230623593 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0888276633146 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0985572326128 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11688180237 (SEC) + + DONE : INIT CHARGE Time : 0.165693941743 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445618 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000751 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00141 + + Density error is 0.217223553605 + + Energy Rydberg eV + E_KohnSham -34.1870111882 -465.13814975 + E_Harris -34.3831277033 -467.806451826 + E_Fermi -0.406821734404 -5.53509365814 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107969719333 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129710755956 + + Density error is 0.0982856152741 + + Energy Rydberg eV + E_KohnSham -34.278190532 -466.378708365 + E_Harris -34.2848431185 -466.469221448 + E_Fermi -0.213331596564 -2.90252527671 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104136229352 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121233396384 + + Density error is 0.0630041378904 + + Energy Rydberg eV + E_KohnSham -34.2785141231 -466.383111048 + E_Harris -34.2827812994 -466.44116896 + E_Fermi -0.201814111278 -2.74582185018 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993333671669 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107266417202 + + Density error is 0.00213681438737 + + Energy Rydberg eV + E_KohnSham -34.2785130172 -466.383096001 + E_Harris -34.2785174636 -466.383156498 + E_Fermi -0.166587378496 -2.26653756243 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000994047624082 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107132062821 + + Density error is 0.00090599307119 + + Energy Rydberg eV + E_KohnSham -34.2784532904 -466.382283376 + E_Harris -34.2784541766 -466.382295434 + E_Fermi -0.16571911481 -2.25472422893 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993247495717 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010696588001 + + Density error is 0.000212348365069 + + Energy Rydberg eV + E_KohnSham -34.2784888417 -466.382767076 + E_Harris -34.2784889341 -466.382768334 + E_Fermi -0.165726936814 -2.25483065276 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993591377383 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106967237462 + + Density error is 4.08559428127e-05 + + Energy Rydberg eV + E_KohnSham -34.2784749249 -466.382577729 + E_Harris -34.2784749336 -466.382577848 + E_Fermi -0.165560239646 -2.25256262144 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993501836677 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106963846602 + + Density error is 1.76696193909e-05 + + Energy Rydberg eV + E_KohnSham -34.2784803824 -466.382651982 + E_Harris -34.2784803837 -466.382651999 + E_Fermi -0.165605816037 -2.25318272004 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993499469042 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106961356518 + + Density error is 1.6060506632e-06 + + Energy Rydberg eV + E_KohnSham -34.2784789426 -466.382632393 + E_Harris -34.2784789426 -466.382632393 + E_Fermi -0.165586650445 -2.25292195878 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993501657933 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106961250825 + + Density error is 2.54296694083e-07 + + Energy Rydberg eV + E_KohnSham -34.2784791771 -466.382635583 + E_Harris -34.2784791771 -466.382635583 + E_Fermi -0.165585262624 -2.25290307652 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993501943116 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106961255355 + + Density error is 1.1098391521e-07 + + Energy Rydberg eV + E_KohnSham -34.278479201 -466.382635908 + E_Harris -34.278479201 -466.382635908 + E_Fermi -0.165585255317 -2.2529029771 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993501979915 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001069612403 + + Density error is 9.72043576543e-09 + + Energy Rydberg eV + E_KohnSham -34.2784792007 -466.382635903 + E_Harris -34.2784792007 -466.382635903 + E_band -7.950486282 -108.171915306 + E_one_elec -69.3451685976 -943.489421698 + E_Hartree +36.0789583727 +490.879411774 + E_xc -8.21546483821 -111.777133518 + E_Ewald +7.3274783823 +99.6954579711 + E_demet -1.90201044753e-78 -2.58781797419e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194719754431 -2.64929817342 + E_Fermi -0.165585151855 -2.25290156942 + + charge density convergence is achieved + final etot is -466.382635903 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1923 2.00000 + 2 -13.4118 2.00000 + 3 -8.76372 2.00000 + 4 -6.71815 2.00000 + 5 1.34142 0.00000 + 6 4.53159 0.00000 + 7 11.0782 0.00000 + 8 11.2931 0.00000 + + EFERMI = -2.252901569417046 eV + OUT.ABACUS/ final etot is -466.3826359034810 eV + correction force for each atom along direction 1 is 7.36490e-05 + correction force for each atom along direction 2 is -2.98763e-05 + correction force for each atom along direction 3 is 1.92678e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.27405906 -0.82255628 +1.3668173 + H1 +0.43366944 +0.66215434 -0.78088914 + H2 -0.15961038 +0.16040195 -0.58592821 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3826359034810 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2839 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2734 1 6.3 1.e+02% + Potential init_pot 0.28408 2 0.14 4.5% + PW_Basis recip2real 0.28323 17 0.017 4.5% + PW_Basis gathers_scatterp 0.12145 17 0.0071 1.9% + Charge atomic_rho 0.10006 1 0.10 1.6% + Potential v_of_rho 0.94302 14 0.067 15.% + XC_Functional v_xc 0.25899 15 0.017 4.1% + H_Hartree_pw v_hartree 0.64280 14 0.046 10.% + PW_Basis real2recip 0.59723 41 0.015 9.5% + PW_Basis gatherp_scatters 0.23033 41 0.0056 3.7% + ORB_control set_orb_tables 1.1085 1 1.1 18.% + ORB_gen_tables gen_tables 1.1085 1 1.1 18.% + ORB_table_phi init_Table 0.48626 1 0.49 7.7% + ORB_table_phi cal_ST_Phi12_R 0.48135 126 0.0038 7.7% + ORB_table_beta init_Table_Beta 0.18776 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18625 56 0.0033 3.0% + ORB_table_alpha init_Table_Alpha 0.25611 1 0.26 4.1% + ORB_table_alpha S_PhiAlpha_R 0.25419 66 0.0039 4.0% + LOOP_ions opt_ions 4.6428 1 4.6 74.% + ESolver_KS_LCAO Run 4.1322 1 4.1 66.% + HSolverLCAO solve 1.9920 12 0.17 32.% + HamiltLCAO updateHk 1.0608 12 0.088 17.% + LCAO_Hamilt cal_Hgamma 1.0190 12 0.085 16.% + Gint_interface cal_gint 1.8139 25 0.073 29.% + Gint_Gamma distri_vl 2.1567 6 0.36 34.% + LCAO_Deepks cal_projected_DM 4.4948 14 0.32 72.% + LCAO_gen_fixedH add_v_delta 2.0242 6 0.34 32.% + LCAO_DESCRIPTOR add_v_delta 2.0242 6 0.34 32.% + ElecStateLCAO psiToRho 0.91656 12 0.076 15.% + Charge mix_rho 0.71392 11 0.065 11.% + LOOP_ions force_stress 0.51046 1 0.51 8.1% + Force_Stress_LCAO getForceStress 0.51043 1 0.51 8.1% + Force_LCAO_gamma ftable_gamma 0.29820 1 0.30 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.29137 1 0.29 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:05 2022 + Finish Time : Wed Sep 28 11:03:11 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..fe115cbcf177904e099078231a82b6985582acb4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123589 ima = 3.68454e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123855286409 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112914481407 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113410530663 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113646064466 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113599482262 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113627839434 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113617844542 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011362078599 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113620114875 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113620054973 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011362005062 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113620045485 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5525a149fbaa16fd0772d92e25ba32397d66395d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.541067848523 20.632161986754 4.970928776254 0 0 0 +H +0.0 +2 +-15.511249021910 21.401933063236 3.341521809917 0 0 0 +-14.093019923013 21.168003361531 5.992306235915 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/conv new file mode 100644 index 0000000000000000000000000000000000000000..bf38dafde5af10aadbca9d47b962747c1bb09ca3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/conv @@ -0,0 +1 @@ +196 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..848a843c6d12e489f016d7b99f541dec79f6c0cb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742817765 0.01258856172 1.279974818 1.374980012 1.4689617 0.007539593956 0.02075705891 0.03883553034 +-3.944112888e-18 0.00116406604 0.002323097051 0.01238547694 0.04213558984 8.908058906e-20 1.418307226e-06 4.586991384e-06 +0.001816973989 0.005548150789 + +H atom_index 1 n_descriptor 18 +1.263440049 0.03303501085 0.1136008031 0.1581943219 0.3276968111 0.02235866181 0.02932170484 0.03637941025 +-1.301297349e-17 3.799501793e-05 0.1051188755 0.115750731 0.1358299743 -5.540428323e-18 3.451402116e-06 0.0128106279 +0.02655805101 0.03148702347 + +H atom_index 2 n_descriptor 18 +1.224208901 0.03443013005 0.1003054759 0.1402426718 0.3154401306 0.02067711111 0.02706520299 0.03760353296 +-2.239815771e-19 3.494710565e-05 0.09551308335 0.1140965832 0.1203135099 2.857792904e-18 5.122731286e-06 0.01312365554 +0.02509749692 0.02973010455 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..eeb82def514d14da6e763623da5905f734591d90 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:05 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0888487 SEC) : SETUP UNITCELL + DONE(0.0985743 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116902 SEC) : INIT PLANEWAVE + DONE(0.165823 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445689 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651381e+02 0.000000e+00 2.172e-01 4.612e-01 + GE2 -4.663787e+02 -1.240559e+00 9.829e-02 3.894e-01 + GE3 -4.663831e+02 -4.402683e-03 6.300e-02 4.397e-01 + GE4 -4.663831e+02 1.504650e-05 2.137e-03 3.292e-01 + GE5 -4.663823e+02 8.126249e-04 9.060e-04 3.316e-01 + GE6 -4.663828e+02 -4.836997e-04 2.123e-04 3.248e-01 + GE7 -4.663826e+02 1.893474e-04 4.086e-05 3.152e-01 + GE8 -4.663827e+02 -7.425362e-05 1.767e-05 3.085e-01 + GE9 -4.663826e+02 1.958981e-05 1.606e-06 3.055e-01 + GE10 -4.663826e+02 -3.190355e-06 2.543e-07 3.069e-01 + GE11 -4.663826e+02 -3.254183e-07 1.110e-07 3.067e-01 + GE12 -4.663826e+02 4.890269e-09 9.720e-09 2.511e-01 +E_delta_band = -7.04372345e-02 Ry = -9.58347741e-01 eV +E_delta_NN= -1.94719754e-01 Ry = -2.64929817e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2839 11 0.57 1e+02 % + Run_lcao lcao_line 6.2734 1 6.3 1e+02 % + Potential init_pot 0.28408 2 0.14 4.5 % + PW_Basis recip2real 0.28323 17 0.017 4.5 % + PW_Basis gathers_scatterp 0.12145 17 0.0071 1.9 % + Charge atomic_rho 0.10006 1 0.1 1.6 % + Potential v_of_rho 0.94302 14 0.067 15 % + XC_Functional v_xc 0.25899 15 0.017 4.1 % + H_Hartree_pw v_hartree 0.6428 14 0.046 10 % + PW_Basis real2recip 0.59723 41 0.015 9.5 % + PW_Basis gatherp_scatters 0.23033 41 0.0056 3.7 % + ORB_control set_orb_tables 1.1085 1 1.1 18 % + ORB_gen_tables gen_tables 1.1085 1 1.1 18 % + ORB_table_phi init_Table 0.48626 1 0.49 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.48135 126 0.0038 7.7 % + ORB_table_beta init_Table_Beta 0.18776 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18625 56 0.0033 3 % + ORB_table_alpha init_Table_Alpha 0.25611 1 0.26 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.25419 66 0.0039 4 % + LOOP_ions opt_ions 4.6428 1 4.6 74 % + ESolver_KS_LCAO Run 4.1322 1 4.1 66 % + HSolverLCAO solve 1.992 12 0.17 32 % + HamiltLCAO updateHk 1.0608 12 0.088 17 % + LCAO_Hamilt cal_Hgamma 1.019 12 0.085 16 % + Gint_interface cal_gint 1.8139 25 0.073 29 % + Gint_Gamma distri_vl 2.1567 6 0.36 34 % + LCAO_Deepks cal_projected_DM 4.4948 14 0.32 72 % + LCAO_gen_fixedH add_v_delta 2.0242 6 0.34 32 % + LCAO_DESCRIPTOR add_v_delta 2.0242 6 0.34 32 % + ElecStateLCAO psiToRho 0.91656 12 0.076 15 % + Charge mix_rho 0.71392 11 0.065 11 % + LOOP_ions force_stress 0.51046 1 0.51 8.1 % + Force_Stress_LCAO getForceStress 0.51043 1 0.51 8.1 % + Force_LCAO_gamma ftable_gamma 0.2982 1 0.3 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.29137 1 0.29 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:05 2022 + FINISH Time : Wed Sep 28 11:03:11 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/196/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..998af5bf7195f5727cd88daa1b1b4fc3b10bd16e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.452079 0.746947 0.186388 +H 0.431853 0.811051 0.192983 +H 0.504299 0.759514 0.152171 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2a019e2047a0f893034dceaaa257fd3f72aa4301 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4515 2 + 2 -12.6318 2 + 3 -9.51758 2 + 4 -6.78003 2 + 5 1.18953 0 + 6 4.39222 0 + 7 11.0632 0 + 8 11.3441 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..06a709c4997eda98ba163389d7a1d65b482c7f57 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:18 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.6582012856 20.9145227826 5.2188623926 0 0 0 0 + tauc_H1 12.0918908165 22.7094266826 5.40351999857 0 0 0 0 + tauc_H2 14.1203733871 21.2663829571 4.26079665181 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0856148201862 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0859638103321 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103957981209 (SEC) + + DONE : INIT CHARGE Time : 0.151983296481 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.432918 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000623 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00168 + + Density error is 0.213085619383 + + Energy Rydberg eV + E_KohnSham -34.1863015385 -465.12849447 + E_Harris -34.3754867526 -467.702491359 + E_Fermi -0.406769306018 -5.53438033336 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00091200048152 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00150073055008 + + Density error is 0.0975246989177 + + Energy Rydberg eV + E_KohnSham -34.2750604013 -466.336120752 + E_Harris -34.2819630724 -466.43003641 + E_Fermi -0.217752353575 -2.96267276153 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000872000846254 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013855239718 + + Density error is 0.0626172192211 + + Energy Rydberg eV + E_KohnSham -34.2753450205 -466.339993194 + E_Harris -34.2798155477 -466.400817838 + E_Fermi -0.20701960939 -2.81664628544 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00082890886698 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118893173911 + + Density error is 0.00193178489028 + + Energy Rydberg eV + E_KohnSham -34.2753167882 -466.339609074 + E_Harris -34.2753174197 -466.339617666 + E_Fermi -0.171011823493 -2.32673522487 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000833328855327 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119051255357 + + Density error is 0.000858493607401 + + Energy Rydberg eV + E_KohnSham -34.2752658752 -466.338916368 + E_Harris -34.2752669865 -466.338931488 + E_Fermi -0.170588412349 -2.32097442073 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000832098015893 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118777915865 + + Density error is 0.000116984409644 + + Energy Rydberg eV + E_KohnSham -34.2752989925 -466.339366952 + E_Harris -34.2752990082 -466.339367165 + E_Fermi -0.170458521496 -2.319207165 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000832000643455 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118748945676 + + Density error is 3.54750137556e-05 + + Energy Rydberg eV + E_KohnSham -34.2752883767 -466.339222516 + E_Harris -34.2752883812 -466.339222577 + E_Fermi -0.17037608038 -2.31808549608 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000831945486796 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118742915891 + + Density error is 1.946602275e-05 + + Energy Rydberg eV + E_KohnSham -34.2752908942 -466.339256768 + E_Harris -34.275290896 -466.339256793 + E_Fermi -0.170404308707 -2.31846956217 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000831959170807 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118741153225 + + Density error is 2.39834998968e-06 + + Energy Rydberg eV + E_KohnSham -34.2752894065 -466.339236528 + E_Harris -34.2752894065 -466.339236528 + E_Fermi -0.170385704654 -2.31821644104 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000831962113712 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118741067774 + + Density error is 6.64315907547e-07 + + Energy Rydberg eV + E_KohnSham -34.275289736 -466.339241011 + E_Harris -34.275289736 -466.339241011 + E_Fermi -0.170384375574 -2.31819835798 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000831962984074 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118741033799 + + Density error is 1.49500112301e-07 + + Energy Rydberg eV + E_KohnSham -34.2752897601 -466.339241339 + E_Harris -34.2752897601 -466.339241339 + E_Fermi -0.170383870467 -2.31819148565 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000831963055933 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118741005504 + + Density error is 1.14502774377e-08 + + Energy Rydberg eV + E_KohnSham -34.2752897695 -466.339241466 + E_Harris -34.2752897695 -466.339241466 + E_band -7.99383430202 -108.761695375 + E_one_elec -69.3033502663 -942.920454111 + E_Hartree +36.0317082665 +490.236541098 + E_xc -8.20841133845 -111.681165731 + E_Ewald +7.32902715237 +99.7165300689 + E_demet -7.70261885436e-75 -1.04799505941e-73 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.1949299338 -2.65215781045 + E_Fermi -0.170383707079 -2.31818926264 + + charge density convergence is achieved + final etot is -466.339241466 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4515 2.00000 + 2 -12.6318 2.00000 + 3 -9.51758 2.00000 + 4 -6.78003 2.00000 + 5 1.18953 0.00000 + 6 4.39222 0.00000 + 7 11.0632 0.00000 + 8 11.3441 0.00000 + + EFERMI = -2.318189262635246 eV + OUT.ABACUS/ final etot is -466.3392414657070 eV + correction force for each atom along direction 1 is 9.52084e-05 + correction force for each atom along direction 2 is 0.000164828 + correction force for each atom along direction 3 is 7.34331e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.5619357 +1.3334584 +0.86594987 + H1 -0.22570936 -1.0721168 +0.24247859 + H2 +1.7876451 -0.26134156 -1.1084285 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3392414657070 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2566 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2481 1 6.2 1.e+02% + Potential init_pot 0.28677 2 0.14 4.6% + PW_Basis recip2real 0.28784 17 0.017 4.6% + PW_Basis gathers_scatterp 0.12719 17 0.0075 2.0% + Charge atomic_rho 0.10073 1 0.10 1.6% + Potential v_of_rho 0.93730 14 0.067 15.% + XC_Functional v_xc 0.25951 15 0.017 4.1% + H_Hartree_pw v_hartree 0.63552 14 0.045 10.% + PW_Basis real2recip 0.59683 41 0.015 9.5% + PW_Basis gatherp_scatters 0.23218 41 0.0057 3.7% + ORB_control set_orb_tables 1.1027 1 1.1 18.% + ORB_gen_tables gen_tables 1.1027 1 1.1 18.% + ORB_table_phi init_Table 0.48047 1 0.48 7.7% + ORB_table_phi cal_ST_Phi12_R 0.47556 126 0.0038 7.6% + ORB_table_beta init_Table_Beta 0.18810 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18659 56 0.0033 3.0% + ORB_table_alpha init_Table_Alpha 0.25514 1 0.26 4.1% + ORB_table_alpha S_PhiAlpha_R 0.25319 66 0.0038 4.0% + LOOP_ions opt_ions 4.6361 1 4.6 74.% + ESolver_KS_LCAO Run 4.1284 1 4.1 66.% + HSolverLCAO solve 1.9931 12 0.17 32.% + HamiltLCAO updateHk 1.0635 12 0.089 17.% + LCAO_Hamilt cal_Hgamma 1.0268 12 0.086 16.% + Gint_interface cal_gint 1.8206 25 0.073 29.% + Gint_Gamma distri_vl 2.1543 6 0.36 34.% + LCAO_Deepks cal_projected_DM 4.4871 14 0.32 72.% + LCAO_gen_fixedH add_v_delta 2.0240 6 0.34 32.% + LCAO_DESCRIPTOR add_v_delta 2.0239 6 0.34 32.% + ElecStateLCAO psiToRho 0.91529 12 0.076 15.% + Charge mix_rho 0.71784 11 0.065 11.% + LOOP_ions force_stress 0.50749 1 0.51 8.1% + Force_Stress_LCAO getForceStress 0.50746 1 0.51 8.1% + Force_LCAO_gamma ftable_gamma 0.29753 1 0.30 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.29099 1 0.29 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:18 2022 + Finish Time : Wed Sep 28 11:10:24 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..5fc82ffa5e031f87b97a27004b22aca7aed0d56d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123868 ima = 3.69125e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122522766654 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111384008989 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112001227943 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112261657618 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112213916803 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011224040502 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112237201508 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112239953546 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112238996807 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112238908382 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112238877968 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112238870077 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b4a3a2a82baab1fe190e1969eb800a89ffecbf64 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.341798714434 20.914522782564 5.218862392616 0 0 0 +H +0.0 +2 +-15.908109183433 22.709426682618 5.403519998582 0 0 0 +-13.879626612852 21.266382957110 4.260796651806 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/conv new file mode 100644 index 0000000000000000000000000000000000000000..4a17d539c7d494a289f0fe3d3660af79b320a004 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/conv @@ -0,0 +1 @@ +197 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..082c24b038ead57d3e37aa31aecd1c75f43d3c55 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755547413 0.01278100575 1.26401232 1.355213385 1.469915836 0.00981054767 0.01634145631 0.03922518662 +3.632501723e-20 0.0008582554066 0.00291654849 0.01352131615 0.04719668527 -1.30229004e-19 2.935261791e-06 7.793587235e-06 +0.00157778541 0.006131051026 + +H atom_index 1 n_descriptor 18 +1.205140221 0.03651822564 0.09712954652 0.1298357348 0.3033247387 0.02126199579 0.02558337186 0.03982664809 +1.383567294e-17 4.576101241e-05 0.09233787882 0.1110220508 0.1132238556 -2.69006824e-18 4.974412036e-06 0.01432196527 +0.02542215518 0.0285073339 + +H atom_index 2 n_descriptor 18 +1.289639488 0.0337982335 0.1273914911 0.1691503119 0.3317388541 0.02551949683 0.03053561876 0.03727720413 +-8.886155478e-18 5.34401153e-05 0.1079633754 0.1224795655 0.1449128259 1.121742829e-17 7.518692142e-07 0.01363683983 +0.02855345255 0.03240597366 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..6c26b03bd102eb6a70d3ae17a3448fccfda95b18 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/dm_eig.npy differ diff --git 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mode 100644 index 0000000000000000000000000000000000000000..fa7ed0cbb4e31c70edb34630d02cd18a36547c07 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..ba0ef07c9548505addfd3221d37a6c61093214b3 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..ae43839bd8f757f0a2da1c0d4a199f41c43d7e41 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:18 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0856384 SEC) : SETUP UNITCELL + DONE(0.0859966 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103978 SEC) : INIT PLANEWAVE + DONE(0.152121 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.432985 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651285e+02 0.000000e+00 2.131e-01 4.597e-01 + GE2 -4.663361e+02 -1.207626e+00 9.752e-02 3.853e-01 + GE3 -4.663400e+02 -3.872442e-03 6.262e-02 4.397e-01 + GE4 -4.663396e+02 3.841201e-04 1.932e-03 3.281e-01 + GE5 -4.663389e+02 6.927062e-04 8.585e-04 3.314e-01 + GE6 -4.663394e+02 -4.505844e-04 1.170e-04 3.277e-01 + GE7 -4.663392e+02 1.444362e-04 3.548e-05 3.129e-01 + GE8 -4.663393e+02 -3.425218e-05 1.947e-05 3.065e-01 + GE9 -4.663392e+02 2.024048e-05 2.398e-06 3.079e-01 + GE10 -4.663392e+02 -4.483459e-06 6.643e-07 3.093e-01 + GE11 -4.663392e+02 -3.278440e-07 1.495e-07 3.066e-01 + GE12 -4.663392e+02 -1.266771e-07 1.145e-08 2.507e-01 +E_delta_band = -7.06663502e-02 Ry = -9.61465020e-01 eV +E_delta_NN= -1.94929934e-01 Ry = -2.65215781e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2566 11 0.57 1e+02 % + Run_lcao lcao_line 6.2481 1 6.2 1e+02 % + Potential init_pot 0.28677 2 0.14 4.6 % + PW_Basis recip2real 0.28784 17 0.017 4.6 % + PW_Basis gathers_scatterp 0.12719 17 0.0075 2 % + Charge atomic_rho 0.10073 1 0.1 1.6 % + Potential v_of_rho 0.9373 14 0.067 15 % + XC_Functional v_xc 0.25951 15 0.017 4.1 % + H_Hartree_pw v_hartree 0.63552 14 0.045 10 % + PW_Basis real2recip 0.59683 41 0.015 9.5 % + PW_Basis gatherp_scatters 0.23218 41 0.0057 3.7 % + ORB_control set_orb_tables 1.1027 1 1.1 18 % + ORB_gen_tables gen_tables 1.1027 1 1.1 18 % + ORB_table_phi init_Table 0.48047 1 0.48 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.47556 126 0.0038 7.6 % + ORB_table_beta init_Table_Beta 0.1881 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18659 56 0.0033 3 % + ORB_table_alpha init_Table_Alpha 0.25514 1 0.26 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.25319 66 0.0038 4 % + LOOP_ions opt_ions 4.6361 1 4.6 74 % + ESolver_KS_LCAO Run 4.1284 1 4.1 66 % + HSolverLCAO solve 1.9931 12 0.17 32 % + HamiltLCAO updateHk 1.0635 12 0.089 17 % + LCAO_Hamilt cal_Hgamma 1.0268 12 0.086 16 % + Gint_interface cal_gint 1.8206 25 0.073 29 % + Gint_Gamma distri_vl 2.1543 6 0.36 34 % + LCAO_Deepks cal_projected_DM 4.4871 14 0.32 72 % + LCAO_gen_fixedH add_v_delta 2.024 6 0.34 32 % + LCAO_DESCRIPTOR add_v_delta 2.0239 6 0.34 32 % + ElecStateLCAO psiToRho 0.91529 12 0.076 15 % + Charge mix_rho 0.71784 11 0.065 11 % + LOOP_ions force_stress 0.50749 1 0.51 8.1 % + Force_Stress_LCAO getForceStress 0.50746 1 0.51 8.1 % + Force_LCAO_gamma ftable_gamma 0.29753 1 0.3 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.29099 1 0.29 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:18 2022 + FINISH Time : Wed Sep 28 11:10:24 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/197/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..26b371763390c708b9fc130eb0910c1a62d116d1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.452586 0.766462 0.190933 +H 0.421854 0.807767 0.228404 +H 0.484805 0.792484 0.137844 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d9f404e4373d77b18429f799da2cffc7354146cd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0649 2 + 2 -13.5854 2 + 3 -8.50234 2 + 4 -6.6811 2 + 5 1.25229 0 + 6 4.52887 0 + 7 11.0976 0 + 8 11.2843 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..284a7853559c16080928753446f54cfc04afb16e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:58 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.6724207806 21.4609455943 5.34612781789 0 0 0 0 + tauc_H1 11.8119250251 22.6174667862 6.39532480855 0 0 0 0 + tauc_H2 13.5745486992 22.1895486566 3.85962104028 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871749558145 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0975612767483 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115713516303 (SEC) + + DONE : INIT CHARGE Time : 0.164888896846 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44443 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000606 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103 + + Density error is 0.217769913174 + + Energy Rydberg eV + E_KohnSham -34.1811085772 -465.057840606 + E_Harris -34.3783808827 -467.741868019 + E_Fermi -0.40319114183 -5.48569691202 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000802245116185 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119580531511 + + Density error is 0.0985006016201 + + Energy Rydberg eV + E_KohnSham -34.271931917 -466.29355554 + E_Harris -34.2785609933 -466.38374875 + E_Fermi -0.209985982713 -2.85700586502 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000775358095978 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011450360671 + + Density error is 0.0630896247675 + + Energy Rydberg eV + E_KohnSham -34.2721956545 -466.297143872 + E_Harris -34.2764074139 -466.354447799 + E_Fermi -0.19842999169 -2.69977854108 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000744270773825 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106595854087 + + Density error is 0.00229324556225 + + Energy Rydberg eV + E_KohnSham -34.2721948346 -466.297132716 + E_Harris -34.2722024402 -466.297236196 + E_Fermi -0.163593802384 -2.22580786992 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000743741126616 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106322007401 + + Density error is 0.000844973497191 + + Energy Rydberg eV + E_KohnSham -34.2721474175 -466.296487574 + E_Harris -34.272147943 -466.296494724 + E_Fermi -0.162639185086 -2.21281963524 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000743297184451 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106220939167 + + Density error is 0.000224935308263 + + Energy Rydberg eV + E_KohnSham -34.272178216 -466.29690661 + E_Harris -34.2721783194 -466.296908016 + E_Fermi -0.162622536718 -2.21259312258 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00074355801103 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106240034285 + + Density error is 4.20700962922e-05 + + Energy Rydberg eV + E_KohnSham -34.2721657595 -466.29673713 + E_Harris -34.2721657693 -466.296737263 + E_Fermi -0.162451358249 -2.21026412003 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000743480420697 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106230798873 + + Density error is 1.80699570366e-05 + + Energy Rydberg eV + E_KohnSham -34.2721714872 -466.296815059 + E_Harris -34.2721714885 -466.296815077 + E_Fermi -0.162497011043 -2.21088525815 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000743483250722 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106229884646 + + Density error is 2.5533841593e-06 + + Energy Rydberg eV + E_KohnSham -34.2721699815 -466.296794573 + E_Harris -34.2721699815 -466.296794573 + E_Fermi -0.16247881487 -2.21063768652 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000743485326504 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106229943165 + + Density error is 4.84928750332e-07 + + Energy Rydberg eV + E_KohnSham -34.27217022 -466.296797818 + E_Harris -34.27217022 -466.296797818 + E_Fermi -0.162476436652 -2.2106053292 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000743485625195 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106229994094 + + Density error is 1.85948295634e-07 + + Energy Rydberg eV + E_KohnSham -34.2721702475 -466.296798192 + E_Harris -34.2721702475 -466.296798192 + E_Fermi -0.162476241665 -2.21060267627 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000743485773642 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010623000599 + + Density error is 9.92206694655e-09 + + Energy Rydberg eV + E_KohnSham -34.272170249 -466.296798213 + E_Harris -34.272170249 -466.296798213 + E_band -7.9134127405 -107.667503897 + E_one_elec -69.2413167226 -942.07644445 + E_Hartree +36.0411824867 +490.365444477 + E_xc -8.20880139178 -111.686472678 + E_Ewald +7.2613149994 +98.7952589646 + E_demet -5.24189616808e-73 -7.13196562102e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194345022248 -2.64419968051 + E_Fermi -0.162476060254 -2.21060020804 + + charge density convergence is achieved + final etot is -466.296798213 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0649 2.00000 + 2 -13.5854 2.00000 + 3 -8.50234 2.00000 + 4 -6.68110 2.00000 + 5 1.25229 0.00000 + 6 4.52887 0.00000 + 7 11.0976 0.00000 + 8 11.2843 0.00000 + + EFERMI = -2.210600208040581 eV + OUT.ABACUS/ final etot is -466.2967982127348 eV + correction force for each atom along direction 1 is 4.02759e-05 + correction force for each atom along direction 2 is 2.37360e-05 + correction force for each atom along direction 3 is -5.78852e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.3717644 -1.8222658 -1.6764376 + H1 -0.48433654 +1.6162737 +0.39823168 + H2 -0.88742789 +0.20599209 +1.2782060 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2967982127348 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8446 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8347 1 6.8 1.e+02% + Potential init_pot 0.28141 2 0.14 4.1% + PW_Basis recip2real 0.29987 17 0.018 4.4% + PW_Basis gathers_scatterp 0.12732 17 0.0075 1.9% + Potential v_of_rho 1.0606 14 0.076 15.% + XC_Functional v_xc 0.30255 15 0.020 4.4% + H_Hartree_pw v_hartree 0.71226 14 0.051 10.% + PW_Basis real2recip 0.69682 41 0.017 10.% + PW_Basis gatherp_scatters 0.26548 41 0.0065 3.9% + ORB_control set_orb_tables 1.0958 1 1.1 16.% + ORB_gen_tables gen_tables 1.0958 1 1.1 16.% + ORB_table_phi init_Table 0.47577 1 0.48 7.0% + ORB_table_phi cal_ST_Phi12_R 0.47066 126 0.0037 6.9% + ORB_table_beta init_Table_Beta 0.18748 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18595 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24648 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24456 66 0.0037 3.6% + LOOP_ions opt_ions 5.2173 1 5.2 76.% + ESolver_KS_LCAO Run 4.6836 1 4.7 68.% + HSolverLCAO solve 2.2046 12 0.18 32.% + HamiltLCAO updateHk 1.1737 12 0.098 17.% + LCAO_Hamilt cal_Hgamma 1.1408 12 0.095 17.% + Gint_interface cal_gint 1.9905 25 0.080 29.% + Gint_Gamma distri_vl 2.4538 6 0.41 36.% + LCAO_Deepks cal_projected_DM 5.0659 14 0.36 74.% + LCAO_gen_fixedH add_v_delta 2.3079 6 0.38 34.% + LCAO_DESCRIPTOR add_v_delta 2.3079 6 0.38 34.% + ElecStateLCAO psiToRho 1.0129 12 0.084 15.% + Charge mix_rho 0.85733 11 0.078 13.% + LOOP_ions force_stress 0.53345 1 0.53 7.8% + Force_Stress_LCAO getForceStress 0.53342 1 0.53 7.8% + Force_LCAO_gamma ftable_gamma 0.31544 1 0.32 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.30760 1 0.31 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:58 2022 + Finish Time : Wed Sep 28 11:05:05 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..16b68212385b215c48c1eafcba74447a76692e8d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123506 ima = 3.68829e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124397729654 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113625575894 + charge after normalized = 8.00000000000004 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114089986177 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114293616199 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114255700348 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011428002545 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114269564646 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114272653372 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114271945589 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011427186519 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114271851859 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114271842664 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/STRU new file mode 100644 index 0000000000000000000000000000000000000000..dbab6f695c684e4623b909433fa4c7e9970854f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.327579219443 21.460945594305 5.346127817904 0 0 0 +H +0.0 +2 +-16.188074974935 22.617466786206 6.395324808520 0 0 0 +-14.425451300763 22.189548656651 3.859621040273 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/conv new file mode 100644 index 0000000000000000000000000000000000000000..f5753de335aac0750ea8742c78caaeb08a9f7e9a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/conv @@ -0,0 +1 @@ +198 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..62c82b9158b2b90899626c66b38f560257cf58d2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.737801163 0.01244264524 1.276995616 1.382196738 1.468382691 0.00692487889 0.022286231 0.03869439412 +-2.019743902e-18 0.001153973301 0.002093694198 0.01251880412 0.03878208061 2.647063328e-19 1.053052109e-06 3.662443137e-06 +0.001961018325 0.005122832042 + +H atom_index 1 n_descriptor 18 +1.272813618 0.03218859712 0.1194291236 0.1650045607 0.3324605948 0.0226494972 0.03010678808 0.03581933001 +-8.542324628e-18 3.068382731e-05 0.1071145244 0.1175121841 0.1415146963 2.060701807e-18 2.614848911e-06 0.01265386334 +0.0268801088 0.03199589779 + +H atom_index 2 n_descriptor 18 +1.19001793 0.03514216061 0.09200769624 0.1281307747 0.3066562107 0.01926824741 0.02538727093 0.03852643985 +7.441755208e-19 2.553345504e-05 0.08747054601 0.1095625049 0.1133647731 -3.104073095e-18 5.107342362e-06 0.01358125622 +0.02373976946 0.02824193655 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3c3fa2aad58004d0443d71471ed9f853ab28636d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/e_base.npy new file mode 100644 index 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TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:58 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871982 SEC) : SETUP UNITCELL + DONE(0.0975779 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115733 SEC) : INIT PLANEWAVE + DONE(0.165018 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444494 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650578e+02 0.000000e+00 2.178e-01 5.030e-01 + GE2 -4.662936e+02 -1.235715e+00 9.850e-02 4.445e-01 + GE3 -4.662971e+02 -3.588332e-03 6.309e-02 5.142e-01 + GE4 -4.662971e+02 1.115595e-05 2.293e-03 3.713e-01 + GE5 -4.662965e+02 6.451424e-04 8.450e-04 3.720e-01 + GE6 -4.662969e+02 -4.190360e-04 2.249e-04 3.661e-01 + GE7 -4.662967e+02 1.694795e-04 4.207e-05 3.610e-01 + GE8 -4.662968e+02 -7.792900e-05 1.807e-05 3.505e-01 + GE9 -4.662968e+02 2.048605e-05 2.553e-06 3.520e-01 + GE10 -4.662968e+02 -3.244619e-06 4.849e-07 3.510e-01 + GE11 -4.662968e+02 -3.743946e-07 1.859e-07 3.512e-01 + GE12 -4.662968e+02 -2.058070e-08 9.922e-09 2.839e-01 +E_delta_band = -6.97954015e-02 Ry = -9.49615154e-01 eV +E_delta_NN= -1.94345022e-01 Ry = -2.64419968e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8446 11 0.62 1e+02 % + Run_lcao lcao_line 6.8347 1 6.8 1e+02 % + Potential init_pot 0.28141 2 0.14 4.1 % + PW_Basis recip2real 0.29987 17 0.018 4.4 % + PW_Basis gathers_scatterp 0.12732 17 0.0075 1.9 % + Potential v_of_rho 1.0606 14 0.076 15 % + XC_Functional v_xc 0.30255 15 0.02 4.4 % + H_Hartree_pw v_hartree 0.71226 14 0.051 10 % + PW_Basis real2recip 0.69682 41 0.017 10 % + PW_Basis gatherp_scatters 0.26548 41 0.0065 3.9 % + ORB_control set_orb_tables 1.0958 1 1.1 16 % + ORB_gen_tables gen_tables 1.0958 1 1.1 16 % + ORB_table_phi init_Table 0.47577 1 0.48 7 % + ORB_table_phi cal_ST_Phi12_R 0.47066 126 0.0037 6.9 % + ORB_table_beta init_Table_Beta 0.18748 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18595 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24648 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24456 66 0.0037 3.6 % + LOOP_ions opt_ions 5.2173 1 5.2 76 % + ESolver_KS_LCAO Run 4.6836 1 4.7 68 % + HSolverLCAO solve 2.2046 12 0.18 32 % + HamiltLCAO updateHk 1.1737 12 0.098 17 % + LCAO_Hamilt cal_Hgamma 1.1408 12 0.095 17 % + Gint_interface cal_gint 1.9905 25 0.08 29 % + Gint_Gamma distri_vl 2.4538 6 0.41 36 % + LCAO_Deepks cal_projected_DM 5.0659 14 0.36 74 % + LCAO_gen_fixedH add_v_delta 2.3079 6 0.38 34 % + LCAO_DESCRIPTOR add_v_delta 2.3079 6 0.38 34 % + ElecStateLCAO psiToRho 1.0129 12 0.084 15 % + Charge mix_rho 0.85733 11 0.078 13 % + LOOP_ions force_stress 0.53345 1 0.53 7.8 % + Force_Stress_LCAO getForceStress 0.53342 1 0.53 7.8 % + Force_LCAO_gamma ftable_gamma 0.31544 1 0.32 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.3076 1 0.31 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:58 2022 + FINISH Time : Wed Sep 28 11:05:05 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/198/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..69c2e47e1df4e1c227f67db81410eed6f31a3a33 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.459025 0.767918 0.201825 +H 0.442167 0.820327 0.237364 +H 0.490036 0.797381 0.155482 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1f7a4496018865877759dd2d62d562a3d1e89e62 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.624 2 + 2 -12.9379 2 + 3 -9.4287 2 + 4 -6.81683 2 + 5 1.41604 0 + 6 4.70972 0 + 7 11.0144 0 + 8 11.2893 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1a2703912b5c873c91f2a7a1ab370ece8d013d11 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:21 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.8526865069 21.5017072807 5.65109568364 0 0 0 0 + tauc_H1 12.3806725812 22.9691657051 6.64618200049 0 0 0 0 + tauc_H2 13.7210180019 22.3266572928 4.35350186489 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870219532229 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0987038787268 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11676577632 (SEC) + + DONE : INIT CHARGE Time : 0.165249990953 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445245 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000811 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124 + + Density error is 0.215921898454 + + Energy Rydberg eV + E_KohnSham -34.1860806177 -465.125488688 + E_Harris -34.3808524279 -467.775495116 + E_Fermi -0.419352306191 -5.70558083364 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000984967118555 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00142690551989 + + Density error is 0.0971372811385 + + Energy Rydberg eV + E_KohnSham -34.2759129573 -466.347720371 + E_Harris -34.2826282146 -466.439086135 + E_Fermi -0.228507184286 -3.10899974022 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000931880154595 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134732080031 + + Density error is 0.0620349790976 + + Energy Rydberg eV + E_KohnSham -34.2761261182 -466.350620574 + E_Harris -34.2804426361 -466.409349814 + E_Fermi -0.214580537893 -2.91951799526 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00085991767736 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122929830424 + + Density error is 0.00200775997998 + + Energy Rydberg eV + E_KohnSham -34.2761617351 -466.351105167 + E_Harris -34.2761633478 -466.351127108 + E_Fermi -0.178567632933 -2.42953728627 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00086327198925 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123357074687 + + Density error is 0.00088442382721 + + Energy Rydberg eV + E_KohnSham -34.2760907321 -466.350139122 + E_Harris -34.2760932039 -466.350172752 + E_Fermi -0.177513791524 -2.41519903831 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000861802269724 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123132625492 + + Density error is 0.000125507797734 + + Energy Rydberg eV + E_KohnSham -34.2761430737 -466.350851266 + E_Harris -34.2761431207 -466.350851905 + E_Fermi -0.177765835149 -2.41862826775 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000861745148346 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123110360185 + + Density error is 4.36599238237e-05 + + Energy Rydberg eV + E_KohnSham -34.2761247086 -466.350601396 + E_Harris -34.2761247182 -466.350601526 + E_Fermi -0.177627826444 -2.41675056299 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000861723671121 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123106270042 + + Density error is 1.91176370236e-05 + + Energy Rydberg eV + E_KohnSham -34.2761282723 -466.350649883 + E_Harris -34.2761282736 -466.3506499 + E_Fermi -0.177678984231 -2.41744660039 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000861720114207 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123104482344 + + Density error is 2.46389776291e-06 + + Energy Rydberg eV + E_KohnSham -34.2761267765 -466.350629531 + E_Harris -34.2761267766 -466.350629532 + E_Fermi -0.177658427257 -2.41716690841 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000861720126343 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123104563611 + + Density error is 6.04802042554e-07 + + Energy Rydberg eV + E_KohnSham -34.2761269857 -466.350632377 + E_Harris -34.2761269857 -466.350632377 + E_Fermi -0.177656713475 -2.41714359121 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000861720686846 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123104630583 + + Density error is 1.64471560416e-07 + + Energy Rydberg eV + E_KohnSham -34.2761270159 -466.350632788 + E_Harris -34.2761270159 -466.350632788 + E_Fermi -0.177656313402 -2.41713814795 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00086172071479 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123104628641 + + Density error is 1.08554241796e-08 + + Energy Rydberg eV + E_KohnSham -34.2761270222 -466.350632874 + E_Harris -34.2761270222 -466.350632874 + E_band -8.05654009783 -109.614851496 + E_one_elec -69.7454824671 -948.935971312 + E_Hartree +36.244000379 +493.124923469 + E_xc -8.24263515456 -112.146804637 + E_Ewald +7.59135588058 +103.285695522 + E_demet -1.84107627266e-88 -2.50491277607e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195718420408 -2.66288572111 + E_Fermi -0.177656129397 -2.41713564443 + + charge density convergence is achieved + final etot is -466.350632874 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6240 2.00000 + 2 -12.9379 2.00000 + 3 -9.42870 2.00000 + 4 -6.81683 2.00000 + 5 1.41604 0.00000 + 6 4.70972 0.00000 + 7 11.0144 0.00000 + 8 11.2893 0.00000 + + EFERMI = -2.417135644431005 eV + OUT.ABACUS/ final etot is -466.3506328742653 eV + correction force for each atom along direction 1 is 0.000138731 + correction force for each atom along direction 2 is 6.04284e-05 + correction force for each atom along direction 3 is 4.44182e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.99497777 -0.68771627 +1.5390028 + H1 -0.33921331 -0.0097305364 +0.54731930 + H2 +1.3341911 +0.69744681 -2.0863221 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3506328742653 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1156 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1058 1 6.1 1.e+02% + Potential init_pot 0.28345 2 0.14 4.6% + PW_Basis recip2real 0.29213 17 0.017 4.8% + PW_Basis gathers_scatterp 0.13019 17 0.0077 2.1% + Potential v_of_rho 0.94617 14 0.068 15.% + XC_Functional v_xc 0.26027 15 0.017 4.3% + H_Hartree_pw v_hartree 0.64286 14 0.046 11.% + PW_Basis real2recip 0.60335 41 0.015 9.9% + PW_Basis gatherp_scatters 0.23370 41 0.0057 3.8% + ORB_control set_orb_tables 1.1049 1 1.1 18.% + ORB_gen_tables gen_tables 1.1049 1 1.1 18.% + ORB_table_phi init_Table 0.48716 1 0.49 8.0% + ORB_table_phi cal_ST_Phi12_R 0.48221 126 0.0038 7.9% + ORB_table_beta init_Table_Beta 0.18890 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18729 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.24996 1 0.25 4.1% + ORB_table_alpha S_PhiAlpha_R 0.24807 66 0.0038 4.1% + LOOP_ions opt_ions 4.4800 1 4.5 73.% + ESolver_KS_LCAO Run 3.9940 1 4.0 65.% + HSolverLCAO solve 1.8379 12 0.15 30.% + HamiltLCAO updateHk 0.99304 12 0.083 16.% + LCAO_Hamilt cal_Hgamma 0.95688 12 0.080 16.% + Gint_interface cal_gint 1.6433 25 0.066 27.% + Gint_Gamma distri_vl 2.0854 6 0.35 34.% + LCAO_Deepks cal_projected_DM 4.3369 14 0.31 71.% + LCAO_gen_fixedH add_v_delta 1.9539 6 0.33 32.% + LCAO_DESCRIPTOR add_v_delta 1.9539 6 0.33 32.% + ElecStateLCAO psiToRho 0.82869 12 0.069 14.% + Charge mix_rho 0.72646 11 0.066 12.% + LOOP_ions force_stress 0.48574 1 0.49 7.9% + Force_Stress_LCAO getForceStress 0.48571 1 0.49 7.9% + Force_LCAO_gamma ftable_gamma 0.27440 1 0.27 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.26769 1 0.27 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:21 2022 + Finish Time : Wed Sep 28 11:06:27 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..93f59c3ad9ac4d77f659bdc91172385afeba94f4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124052 ima = 3.6824e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122399499334 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111493786327 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111950184581 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112238798453 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112164213065 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112207493705 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112201943074 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112205002798 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112204346365 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112204249066 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112204225555 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112204216949 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5de1ce08c90a5ed5687c5b7a6335536f43484920 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.147313493082 21.501707280664 5.651095683620 0 0 0 +H +0.0 +2 +-15.619327418749 22.969165705130 6.646182000516 0 0 0 +-14.278981998041 22.326657292856 4.353501864895 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/conv new file mode 100644 index 0000000000000000000000000000000000000000..42841b523512a1d1e091091b1ff43b0529e4bff2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/conv @@ -0,0 +1 @@ +199 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ab873e1fc99a621bcfc2b4338993441bb7f58788 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753651771 0.01288357317 1.285860778 1.371019628 1.470704565 0.009550018328 0.0173965886 0.03914728011 +2.93075885e-18 0.001015516761 0.002977367951 0.01376863496 0.04915714953 -1.436793889e-19 3.068427186e-06 7.857136423e-06 +0.001591916934 0.006135394859 + +H atom_index 1 n_descriptor 18 +1.24780402 0.03490705201 0.110429474 0.1484356305 0.3185795321 0.02316816119 0.02809983467 0.0379787365 +-2.793905685e-17 5.368318783e-05 0.1045166261 0.1149381089 0.1274736437 -3.909939472e-18 3.403194011e-06 0.01344280355 +0.02735475766 0.03066474459 + +H atom_index 2 n_descriptor 18 +1.301824596 0.03320612674 0.1311688298 0.1754395856 0.3349265673 0.02583904752 0.03121992113 0.03694207889 +-2.182706021e-17 5.890371289e-05 0.1085381929 0.1265296603 0.1504453845 4.735200059e-18 6.220162652e-07 0.01392570543 +0.02915163496 0.03284691203 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..33edd2c9ac1926ee6255c6ee918a8b477a3fb95d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:21 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870476 SEC) : SETUP UNITCELL + DONE(0.0987229 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116785 SEC) : INIT PLANEWAVE + DONE(0.165383 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445308 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651255e+02 0.000000e+00 2.159e-01 4.438e-01 + GE2 -4.663477e+02 -1.222232e+00 9.714e-02 3.740e-01 + GE3 -4.663506e+02 -2.900203e-03 6.203e-02 4.272e-01 + GE4 -4.663511e+02 -4.845927e-04 2.008e-03 3.171e-01 + GE5 -4.663501e+02 9.660451e-04 8.844e-04 3.171e-01 + GE6 -4.663509e+02 -7.121441e-04 1.255e-04 3.151e-01 + GE7 -4.663506e+02 2.498704e-04 4.366e-05 3.070e-01 + GE8 -4.663506e+02 -4.848693e-05 1.912e-05 3.005e-01 + GE9 -4.663506e+02 2.035112e-05 2.464e-06 2.957e-01 + GE10 -4.663506e+02 -2.845053e-06 6.048e-07 2.957e-01 + GE11 -4.663506e+02 -4.110560e-07 1.645e-07 2.984e-01 + GE12 -4.663506e+02 -8.670921e-08 1.086e-08 2.395e-01 +E_delta_band = -7.23527602e-02 Ry = -9.84409805e-01 eV +E_delta_NN= -1.95718420e-01 Ry = -2.66288572e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1156 11 0.56 1e+02 % + Run_lcao lcao_line 6.1058 1 6.1 1e+02 % + Potential init_pot 0.28345 2 0.14 4.6 % + PW_Basis recip2real 0.29213 17 0.017 4.8 % + PW_Basis gathers_scatterp 0.13019 17 0.0077 2.1 % + Potential v_of_rho 0.94617 14 0.068 15 % + XC_Functional v_xc 0.26027 15 0.017 4.3 % + H_Hartree_pw v_hartree 0.64286 14 0.046 11 % + PW_Basis real2recip 0.60335 41 0.015 9.9 % + PW_Basis gatherp_scatters 0.2337 41 0.0057 3.8 % + ORB_control set_orb_tables 1.1049 1 1.1 18 % + ORB_gen_tables gen_tables 1.1049 1 1.1 18 % + ORB_table_phi init_Table 0.48716 1 0.49 8 % + ORB_table_phi cal_ST_Phi12_R 0.48221 126 0.0038 7.9 % + ORB_table_beta init_Table_Beta 0.1889 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18729 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.24996 1 0.25 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.24807 66 0.0038 4.1 % + LOOP_ions opt_ions 4.48 1 4.5 73 % + ESolver_KS_LCAO Run 3.994 1 4 65 % + HSolverLCAO solve 1.8379 12 0.15 30 % + HamiltLCAO updateHk 0.99304 12 0.083 16 % + LCAO_Hamilt cal_Hgamma 0.95688 12 0.08 16 % + Gint_interface cal_gint 1.6433 25 0.066 27 % + Gint_Gamma distri_vl 2.0854 6 0.35 34 % + LCAO_Deepks cal_projected_DM 4.3369 14 0.31 71 % + LCAO_gen_fixedH add_v_delta 1.9539 6 0.33 32 % + LCAO_DESCRIPTOR add_v_delta 1.9539 6 0.33 32 % + ElecStateLCAO psiToRho 0.82869 12 0.069 14 % + Charge mix_rho 0.72646 11 0.066 12 % + LOOP_ions force_stress 0.48574 1 0.49 7.9 % + Force_Stress_LCAO getForceStress 0.48571 1 0.49 7.9 % + Force_LCAO_gamma ftable_gamma 0.2744 1 0.27 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.26769 1 0.27 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:21 2022 + FINISH Time : Wed Sep 28 11:06:27 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/199/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e69992db63870e3022a2a016a89f76ef8dd0cd31 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.663383 0.0272931 0.258249 +H 0.609399 0.044515 0.22597 +H 0.708157 0.0471058 0.215941 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2a6c2b941f6ed4104bda175f99ab27ce05f1e819 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4751 2 + 2 -12.8973 2 + 3 -9.36106 2 + 4 -6.78644 2 + 5 1.3527 0 + 6 4.53275 0 + 7 11.0458 0 + 8 11.3208 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..49c0e4819536d78cb06b8dbe67428b72f086f189 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:06 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.5747264189 0.76420612388 7.23096387513 0 0 0 0 + tauc_H1 17.0631850985 1.2464210202 6.3271582406 0 0 0 0 + tauc_H2 19.8283892863 1.3189634028 6.04633744722 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0886908957499 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0898203929225 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107947354449 (SEC) + + DONE : INIT CHARGE Time : 0.157632443983 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.436962 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000897 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128 + + Density error is 0.215625827088 + + Energy Rydberg eV + E_KohnSham -34.1879783753 -465.151309005 + E_Harris -34.3820313308 -467.791534913 + E_Fermi -0.412220057174 -5.60854160745 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00128102823446 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121214515626 + + Density error is 0.097700430614 + + Energy Rydberg eV + E_KohnSham -34.2792724833 -466.393429068 + E_Harris -34.2860843336 -466.486109045 + E_Fermi -0.220070270517 -2.99420963943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00122466955636 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112634427861 + + Density error is 0.062731063375 + + Energy Rydberg eV + E_KohnSham -34.2796741986 -466.398894685 + E_Harris -34.2840868177 -466.458931448 + E_Fermi -0.208821836445 -2.84116684248 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00115197098103 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000979843073088 + + Density error is 0.0019679414844 + + Energy Rydberg eV + E_KohnSham -34.2796670222 -466.398797045 + E_Harris -34.2796682352 -466.398813548 + E_Fermi -0.172872146647 -2.35204621989 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00115613980818 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980257404102 + + Density error is 0.00102823035169 + + Energy Rydberg eV + E_KohnSham -34.2795915891 -466.397770724 + E_Harris -34.2795938177 -466.397801046 + E_Fermi -0.172147021379 -2.34218038448 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00115435360112 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000978207868852 + + Density error is 9.73301675689e-05 + + Energy Rydberg eV + E_KohnSham -34.2796399209 -466.398428313 + E_Harris -34.2796399249 -466.398428366 + E_Fermi -0.172180598866 -2.34263722963 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00115414771927 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000977844368803 + + Density error is 4.71822287213e-05 + + Energy Rydberg eV + E_KohnSham -34.2796255197 -466.398232374 + E_Harris -34.279625531 -466.398232527 + E_Fermi -0.172059077661 -2.34098384882 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00115411150791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009778758565 + + Density error is 9.41131210632e-06 + + Energy Rydberg eV + E_KohnSham -34.2796271886 -466.398255081 + E_Harris -34.279627189 -466.398255085 + E_Fermi -0.172114578956 -2.34173898267 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00115412776478 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000977882311327 + + Density error is 2.07819431372e-06 + + Energy Rydberg eV + E_KohnSham -34.2796259684 -466.398238479 + E_Harris -34.2796259685 -466.39823848 + E_Fermi -0.172107955606 -2.34164886737 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0011541265072 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000977878865755 + + Density error is 2.80740352949e-07 + + Energy Rydberg eV + E_KohnSham -34.2796261 -466.398240269 + E_Harris -34.2796261 -466.398240269 + E_Fermi -0.172105579269 -2.34161653565 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0011541277343 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000977879693101 + + Density error is 2.86300353044e-08 + + Energy Rydberg eV + E_KohnSham -34.2796261295 -466.398240672 + E_Harris -34.2796261295 -466.398240672 + E_band -8.01427624758 -109.039822313 + E_one_elec -69.4998436869 -945.593884251 + E_Hartree +36.1300819207 +491.574983329 + E_xc -8.22409769251 -111.894589527 + E_Ewald +7.43809550008 +101.200481069 + E_demet -1.0107244447e-82 -1.37516115558e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19523038121 -2.65624560717 + E_Fermi -0.172105521746 -2.341615753 + + charge density convergence is achieved + final etot is -466.398240672 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4751 2.00000 + 2 -12.8973 2.00000 + 3 -9.36106 2.00000 + 4 -6.78644 2.00000 + 5 1.35270 0.00000 + 6 4.53275 0.00000 + 7 11.0458 0.00000 + 8 11.3208 0.00000 + + EFERMI = -2.341615753002473 eV + OUT.ABACUS/ final etot is -466.3982406715474 eV + correction force for each atom along direction 1 is 1.54039e-05 + correction force for each atom along direction 2 is 8.11975e-05 + correction force for each atom along direction 3 is -9.55333e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.26829112 -0.18861263 +0.39777199 + H1 -0.72160705 +0.012415528 +0.0084416590 + H2 +0.98989817 +0.17619710 -0.40621365 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3982406715474 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9235 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9126 1 6.9 1.e+02% + Potential init_pot 0.28051 2 0.14 4.1% + PW_Basis recip2real 0.28058 16 0.018 4.1% + PW_Basis gathers_scatterp 0.11974 16 0.0075 1.7% + Potential v_of_rho 0.96213 13 0.074 14.% + XC_Functional v_xc 0.25918 14 0.019 3.7% + H_Hartree_pw v_hartree 0.65956 13 0.051 9.5% + PW_Basis real2recip 0.64423 38 0.017 9.3% + PW_Basis gatherp_scatters 0.24476 38 0.0064 3.5% + ORB_control set_orb_tables 1.0933 1 1.1 16.% + ORB_gen_tables gen_tables 1.0933 1 1.1 16.% + ORB_table_phi init_Table 0.47299 1 0.47 6.8% + ORB_table_phi cal_ST_Phi12_R 0.46790 126 0.0037 6.8% + ORB_table_beta init_Table_Beta 0.18517 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18362 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24835 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24637 66 0.0037 3.6% + LOOP_ions opt_ions 5.3054 1 5.3 77.% + ESolver_KS_LCAO Run 4.7525 1 4.8 69.% + HSolverLCAO solve 2.4999 11 0.23 36.% + HamiltLCAO updateHk 1.3032 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2685 11 0.12 18.% + Gint_interface cal_gint 2.3148 23 0.10 33.% + Gint_Gamma distri_vl 2.2962 6 0.38 33.% + LCAO_Deepks cal_projected_DM 5.1438 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1500 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1500 6 0.36 31.% + ElecStateLCAO psiToRho 1.1807 11 0.11 17.% + Charge mix_rho 0.77857 10 0.078 11.% + LOOP_ions force_stress 0.55276 1 0.55 8.0% + Force_Stress_LCAO getForceStress 0.55273 1 0.55 8.0% + Force_LCAO_gamma ftable_gamma 0.33350 1 0.33 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.32563 1 0.33 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:06 2022 + Finish Time : Wed Sep 28 11:05:13 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..50e5b13223d51c641415248f87a3ca13c59d2a88 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123837 ima = 3.63481e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122770589764 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111487127409 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112069418315 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112355788157 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112285205083 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112323116311 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112321505794 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112324209603 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112323786894 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112323701721 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112323685425 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/STRU new file mode 100644 index 0000000000000000000000000000000000000000..685cbec5e602e43043e3e68dce2a04c16a264af0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.425273581092 0.764206123875 7.230963875121 0 0 0 +H +0.0 +2 +-10.936814901455 1.246421020197 6.327158240581 0 0 0 +-8.171610713700 1.318963402801 6.046337447218 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/conv new file mode 100644 index 0000000000000000000000000000000000000000..8db0d358f38c074733148ce3c41218256a270a2f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/conv @@ -0,0 +1 @@ +2 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e64afbcfbe6c66f68ab4897888ca42558b57f04e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752788129 0.01282866504 1.279413226 1.361654107 1.470028936 0.009261110475 0.01741787216 0.03911756172 +1.200015668e-17 0.0009926077593 0.002845533536 0.01327034621 0.04752796505 1.428276981e-18 2.739171298e-06 7.265073821e-06 +0.001601890142 0.006129977786 + +H atom_index 1 n_descriptor 18 +1.254374032 0.03456203368 0.1118648405 0.1515732083 0.3211705704 0.02319755285 0.02849663996 0.03767684732 +-3.495976856e-17 5.153263995e-05 0.1044066633 0.1155040588 0.130110939 -5.617375094e-18 3.235898053e-06 0.01333364414 +0.02716388943 0.03094801385 + +H atom_index 2 n_descriptor 18 +1.265487793 0.03419020983 0.1159095752 0.1568924045 0.3247108204 0.02374074531 0.02914441454 0.03737197331 +-3.231529882e-17 5.2605419e-05 0.1064001885 0.1167350658 0.1346780658 -4.07674582e-18 2.597531312e-06 0.01331208838 +0.02756086771 0.03143468336 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..97c5d6bffaf586b08ccccc7eccaf5e0a4b404821 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/dm_eig.npy differ diff --git 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@@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:06 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0887153 SEC) : SETUP UNITCELL + DONE(0.0898367 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107969 SEC) : INIT PLANEWAVE + DONE(0.15776 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.437028 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651513e+02 0.000000e+00 2.156e-01 5.350e-01 + GE2 -4.663934e+02 -1.242120e+00 9.770e-02 4.846e-01 + GE3 -4.663989e+02 -5.465617e-03 6.273e-02 5.539e-01 + GE4 -4.663988e+02 9.763988e-05 1.968e-03 4.179e-01 + GE5 -4.663978e+02 1.026321e-03 1.028e-03 4.148e-01 + GE6 -4.663984e+02 -6.575889e-04 9.733e-05 3.888e-01 + GE7 -4.663982e+02 1.959384e-04 4.718e-05 3.933e-01 + GE8 -4.663983e+02 -2.270628e-05 9.411e-06 3.931e-01 + GE9 -4.663982e+02 1.660134e-05 2.078e-06 3.912e-01 + GE10 -4.663982e+02 -1.790042e-06 2.807e-07 3.922e-01 + GE11 -4.663982e+02 -4.020799e-07 2.863e-08 3.255e-01 +E_delta_band = -7.13682102e-02 Ry = -9.71014315e-01 eV +E_delta_NN= -1.95230381e-01 Ry = -2.65624561e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9235 11 0.63 1e+02 % + Run_lcao lcao_line 6.9126 1 6.9 1e+02 % + Potential init_pot 0.28051 2 0.14 4.1 % + PW_Basis recip2real 0.28058 16 0.018 4.1 % + PW_Basis gathers_scatterp 0.11974 16 0.0075 1.7 % + Potential v_of_rho 0.96213 13 0.074 14 % + XC_Functional v_xc 0.25918 14 0.019 3.7 % + H_Hartree_pw v_hartree 0.65956 13 0.051 9.5 % + PW_Basis real2recip 0.64423 38 0.017 9.3 % + PW_Basis gatherp_scatters 0.24476 38 0.0064 3.5 % + ORB_control set_orb_tables 1.0933 1 1.1 16 % + ORB_gen_tables gen_tables 1.0933 1 1.1 16 % + ORB_table_phi init_Table 0.47299 1 0.47 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.4679 126 0.0037 6.8 % + ORB_table_beta init_Table_Beta 0.18517 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18362 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24835 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24637 66 0.0037 3.6 % + LOOP_ions opt_ions 5.3054 1 5.3 77 % + ESolver_KS_LCAO Run 4.7525 1 4.8 69 % + HSolverLCAO solve 2.4999 11 0.23 36 % + HamiltLCAO updateHk 1.3032 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2685 11 0.12 18 % + Gint_interface cal_gint 2.3148 23 0.1 33 % + Gint_Gamma distri_vl 2.2962 6 0.38 33 % + LCAO_Deepks cal_projected_DM 5.1438 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.15 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.15 6 0.36 31 % + ElecStateLCAO psiToRho 1.1807 11 0.11 17 % + Charge mix_rho 0.77857 10 0.078 11 % + LOOP_ions force_stress 0.55276 1 0.55 8 % + Force_Stress_LCAO getForceStress 0.55273 1 0.55 8 % + Force_LCAO_gamma ftable_gamma 0.3335 1 0.33 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.32563 1 0.33 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:06 2022 + FINISH Time : Wed Sep 28 11:05:13 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/2/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..136b0d63a4858b723b42d8e73c5e487a37c50ea8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.546629 0.30605 0.435384 +H 0.589334 0.353398 0.42939 +H 0.495102 0.334867 0.463247 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..cf26f04bf2325fd06050fefaa2885e03c7155593 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4384 2 + 2 -13.1541 2 + 3 -9.1521 2 + 4 -6.77769 2 + 5 1.41722 0 + 6 4.62624 0 + 7 11.0399 0 + 8 11.291 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a4142445c5cd7d3e972d0b6c08e7240132415daa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/running_scf.log @@ -0,0 +1,777 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:03 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.3056033287 8.56939000723 12.1907653292 0 0 0 0 + tauc_H1 16.5013534058 9.89513064671 12.0229107074 0 0 0 0 + tauc_H2 13.8628654564 9.37626836818 12.9709076318 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874531223077 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877982098347 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105749365467 (SEC) + + DONE : INIT CHARGE Time : 0.153364451923 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.432979 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000718 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00146 + + Density error is 0.216401188238 + + Energy Rydberg eV + E_KohnSham -34.1893340446 -465.169753832 + E_Harris -34.3843448175 -467.823011515 + E_Fermi -0.413893519829 -5.63131023495 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000905737507556 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132360307527 + + Density error is 0.0976304468252 + + Energy Rydberg eV + E_KohnSham -34.2797530152 -466.39996704 + E_Harris -34.2864167098 -466.490631255 + E_Fermi -0.222003042823 -3.02050635573 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000862439486165 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122637668134 + + Density error is 0.0624641468563 + + Energy Rydberg eV + E_KohnSham -34.280036105 -466.403818674 + E_Harris -34.2843274712 -466.462205707 + E_Fermi -0.209100815339 -2.84496254506 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000805704143671 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105841744443 + + Density error is 0.0020118981929 + + Energy Rydberg eV + E_KohnSham -34.2800561977 -466.404092049 + E_Harris -34.2800578841 -466.404114994 + E_Fermi -0.173396462407 -2.35917990178 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000807512531555 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105642005927 + + Density error is 0.000910018995047 + + Energy Rydberg eV + E_KohnSham -34.279985278 -466.403127137 + E_Harris -34.2799872718 -466.403154264 + E_Fermi -0.172397233576 -2.34558469608 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000806475442854 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105472510931 + + Density error is 0.000130435433248 + + Energy Rydberg eV + E_KohnSham -34.2800331737 -466.403778791 + E_Harris -34.2800332077 -466.403779254 + E_Fermi -0.172573474536 -2.34798257735 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000806599741681 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105454684965 + + Density error is 4.45775716474e-05 + + Energy Rydberg eV + E_KohnSham -34.2800164163 -466.403550795 + E_Harris -34.2800164274 -466.403550947 + E_Fermi -0.172429327037 -2.34602135002 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000806548421359 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105454029265 + + Density error is 1.41345658885e-05 + + Energy Rydberg eV + E_KohnSham -34.2800202528 -466.403602994 + E_Harris -34.2800202537 -466.403603005 + E_Fermi -0.172480628697 -2.34671934491 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000806549399365 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105451529451 + + Density error is 1.57715202858e-06 + + Energy Rydberg eV + E_KohnSham -34.280018798 -466.403583199 + E_Harris -34.280018798 -466.403583199 + E_Fermi -0.172465456552 -2.34651291727 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000806550307035 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105451419817 + + Density error is 1.44381357474e-07 + + Energy Rydberg eV + E_KohnSham -34.2800189929 -466.403585851 + E_Harris -34.2800189929 -466.403585851 + E_Fermi -0.172464002681 -2.34649313635 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000806550589444 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105451466684 + + Density error is 3.17030245091e-08 + + Energy Rydberg eV + E_KohnSham -34.2800190203 -466.403586225 + E_Harris -34.2800190203 -466.403586225 + E_band -8.01462539208 -109.044572668 + E_one_elec -69.5834575036 -946.73150859 + E_Hartree +36.1767723618 +492.21023937 + E_xc -8.23175555743 -111.998780124 + E_Ewald +7.48214383731 +101.799789443 + E_demet -9.31798921534e-86 -1.26777747231e-84 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195354194616 -2.65793017497 + E_Fermi -0.172464007459 -2.34649320136 + + charge density convergence is achieved + final etot is -466.403586225 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4384 2.00000 + 2 -13.1541 2.00000 + 3 -9.15210 2.00000 + 4 -6.77769 2.00000 + 5 1.41722 0.00000 + 6 4.62624 0.00000 + 7 11.0399 0.00000 + 8 11.2910 0.00000 + + EFERMI = -2.346493201361598 eV + OUT.ABACUS/ final etot is -466.4035862245200 eV + correction force for each atom along direction 1 is 6.71754e-06 + correction force for each atom along direction 2 is 2.37625e-05 + correction force for each atom along direction 3 is 0.000174409 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.65562664 -1.1436090 +0.00058919904 + H1 +1.0192302 +1.0265557 -0.17241898 + H2 -0.36360353 +0.11705335 +0.17182978 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4035862245200 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9132 11 0.54 1.0e+02% + Run_lcao lcao_line 5.9038 1 5.9 1.e+02% + Potential init_pot 0.28518 2 0.14 4.8% + PW_Basis recip2real 0.25859 16 0.016 4.4% + PW_Basis gathers_scatterp 0.11853 16 0.0074 2.0% + Potential v_of_rho 0.85862 13 0.066 15.% + XC_Functional v_xc 0.24580 14 0.018 4.2% + H_Hartree_pw v_hartree 0.57892 13 0.045 9.8% + PW_Basis real2recip 0.55788 38 0.015 9.4% + PW_Basis gatherp_scatters 0.22691 38 0.0060 3.8% + ORB_control set_orb_tables 1.1057 1 1.1 19.% + ORB_gen_tables gen_tables 1.1057 1 1.1 19.% + ORB_table_phi init_Table 0.48899 1 0.49 8.3% + ORB_table_phi cal_ST_Phi12_R 0.48400 126 0.0038 8.2% + ORB_table_beta init_Table_Beta 0.18837 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18683 56 0.0033 3.2% + ORB_table_alpha init_Table_Alpha 0.24912 1 0.25 4.2% + ORB_table_alpha S_PhiAlpha_R 0.24723 66 0.0037 4.2% + LOOP_ions opt_ions 4.2873 1 4.3 73.% + ESolver_KS_LCAO Run 3.7844 1 3.8 64.% + HSolverLCAO solve 1.8320 11 0.17 31.% + HamiltLCAO updateHk 0.98497 11 0.090 17.% + LCAO_Hamilt cal_Hgamma 0.95633 11 0.087 16.% + Gint_Gamma distri_vl_value 0.57849 11 0.053 9.8% + Gint_Gamma distri_vl 1.8393 6 0.31 31.% + LCAO_Deepks cal_projected_DM 3.9372 13 0.30 67.% + LCAO_gen_fixedH add_v_delta 1.7083 6 0.28 29.% + LCAO_DESCRIPTOR add_v_delta 1.7082 6 0.28 29.% + ElecStateLCAO psiToRho 0.82866 11 0.075 14.% + Charge mix_rho 0.64873 10 0.065 11.% + LOOP_ions force_stress 0.50274 1 0.50 8.5% + Force_Stress_LCAO getForceStress 0.50271 1 0.50 8.5% + Force_LCAO_gamma ftable_gamma 0.29616 1 0.30 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:03 2022 + Finish Time : Wed Sep 28 11:04:09 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0962a7fc6256e12064e71dda3f2d3de4d1551956 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123721 ima = 3.67084e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122934862028 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111982680526 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112455833913 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112724924808 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112659092058 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112697429001 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112690995365 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112694092396 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112693522344 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112693452782 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112693446158 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/STRU new file mode 100644 index 0000000000000000000000000000000000000000..61a3016799c2e828f8c391c25b431862e5cdb607 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.694396671242 8.569390007208 12.190765329226 0 0 0 +H +0.0 +2 +-11.498646594250 9.895130646682 12.022910707434 0 0 0 +-14.137134543632 9.376268368159 12.970907631806 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/conv new file mode 100644 index 0000000000000000000000000000000000000000..e693c2adb64a8b0aae79eef5f5c852232d0bcb88 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/conv @@ -0,0 +1 @@ +20 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..546b0846e1d2dd7acc3f48e4a75f23a0f458e291 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749417789 0.01277754813 1.28468451 1.371399894 1.470009167 0.008645663613 0.01875111694 0.03902770351 +7.723055967e-19 0.001113702147 0.002698218023 0.01286085368 0.04668165923 1.544529694e-20 2.251979954e-06 6.342690948e-06 +0.001650906511 0.005975202065 + +H atom_index 1 n_descriptor 18 +1.277378856 0.03332735546 0.1186752534 0.1630999125 0.329150758 0.02367647104 0.02988245311 0.0366939235 +4.975840635e-17 5.097676678e-05 0.1075641121 0.1181273897 0.1400967126 -8.094938592e-18 2.578273618e-06 0.0132388786 +0.02759916982 0.03194064701 + +H atom_index 2 n_descriptor 18 +1.249941746 0.03425322392 0.1087370053 0.1498588803 0.3207266229 0.02240303008 0.02829662321 0.03737367762 +-2.237444964e-17 4.835877335e-05 0.1029149169 0.1148838597 0.1287499003 -5.908800905e-20 4.141739664e-06 0.0131965797 +0.02663543475 0.03077789153 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3ea4279488f9273d083a3d66279275edda6e1a6f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/log.scf @@ -0,0 +1,100 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:03 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874766 SEC) : SETUP UNITCELL + DONE(0.087814 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105771 SEC) : INIT PLANEWAVE + DONE(0.1535 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.433044 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651698e+02 0.000000e+00 2.164e-01 4.554e-01 + GE2 -4.664000e+02 -1.230213e+00 9.763e-02 3.807e-01 + GE3 -4.664038e+02 -3.851634e-03 6.246e-02 4.388e-01 + GE4 -4.664041e+02 -2.733756e-04 2.012e-03 3.268e-01 + GE5 -4.664031e+02 9.649121e-04 9.100e-04 3.299e-01 + GE6 -4.664038e+02 -6.516537e-04 1.304e-04 3.184e-01 + GE7 -4.664036e+02 2.279954e-04 4.458e-05 3.136e-01 + GE8 -4.664036e+02 -5.219862e-05 1.413e-05 3.013e-01 + GE9 -4.664036e+02 1.979468e-05 1.577e-06 3.066e-01 + GE10 -4.664036e+02 -2.651746e-06 1.444e-07 3.039e-01 + GE11 -4.664036e+02 -3.734089e-07 3.170e-08 2.479e-01 +E_delta_band = -7.16320362e-02 Ry = -9.74603852e-01 eV +E_delta_NN= -1.95354195e-01 Ry = -2.65793017e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9132 11 0.54 1e+02 % + Run_lcao lcao_line 5.9038 1 5.9 1e+02 % + Potential init_pot 0.28518 2 0.14 4.8 % + PW_Basis recip2real 0.25859 16 0.016 4.4 % + PW_Basis gathers_scatterp 0.11853 16 0.0074 2 % + Potential v_of_rho 0.85862 13 0.066 15 % + XC_Functional v_xc 0.2458 14 0.018 4.2 % + H_Hartree_pw v_hartree 0.57892 13 0.045 9.8 % + PW_Basis real2recip 0.55788 38 0.015 9.4 % + PW_Basis gatherp_scatters 0.22691 38 0.006 3.8 % + ORB_control set_orb_tables 1.1057 1 1.1 19 % + ORB_gen_tables gen_tables 1.1057 1 1.1 19 % + ORB_table_phi init_Table 0.48899 1 0.49 8.3 % + ORB_table_phi cal_ST_Phi12_R 0.484 126 0.0038 8.2 % + ORB_table_beta init_Table_Beta 0.18837 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18683 56 0.0033 3.2 % + ORB_table_alpha init_Table_Alpha 0.24912 1 0.25 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.24723 66 0.0037 4.2 % + LOOP_ions opt_ions 4.2873 1 4.3 73 % + ESolver_KS_LCAO Run 3.7844 1 3.8 64 % + HSolverLCAO solve 1.832 11 0.17 31 % + HamiltLCAO updateHk 0.98497 11 0.09 17 % + LCAO_Hamilt cal_Hgamma 0.95633 11 0.087 16 % + Gint_Gamma distri_vl_value 0.57849 11 0.053 9.8 % + Gint_Gamma distri_vl 1.8393 6 0.31 31 % + LCAO_Deepks cal_projected_DM 3.9372 13 0.3 67 % + LCAO_gen_fixedH add_v_delta 1.7083 6 0.28 29 % + LCAO_DESCRIPTOR add_v_delta 1.7082 6 0.28 29 % + ElecStateLCAO psiToRho 0.82866 11 0.075 14 % + Charge mix_rho 0.64873 10 0.065 11 % + LOOP_ions force_stress 0.50274 1 0.5 8.5 % + Force_Stress_LCAO getForceStress 0.50271 1 0.5 8.5 % + Force_LCAO_gamma ftable_gamma 0.29616 1 0.3 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:03 2022 + FINISH Time : Wed Sep 28 11:04:09 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/20/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..024cf9d602131811365d38c4c96bcb438effe01b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.460961 0.775896 0.222039 +H 0.466488 0.823792 0.264904 +H 0.500646 0.792902 0.172811 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..03aafde5237041499aea65397680a2005e1282e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.361 2 + 2 -13.1485 2 + 3 -9.09804 2 + 4 -6.76062 2 + 5 1.37613 0 + 6 4.54749 0 + 7 11.0555 0 + 8 11.3035 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..26cedf72dddff9afac7c2a31303f5a845118e3fd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:10 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.9069015056 21.7250961242 6.21709170353 0 0 0 0 + tauc_H1 13.0616669615 23.0661830316 7.41730273658 0 0 0 0 + tauc_H2 14.0180900785 22.2012617049 4.83871501713 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0729261264399 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.086152970857 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.102501605367 (SEC) + + DONE : INIT CHARGE Time : 0.144724171248 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.385962 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00063 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123 + + Density error is 0.215796820322 + + Energy Rydberg eV + E_KohnSham -34.190654666 -465.187721808 + E_Harris -34.3841180468 -467.819926141 + E_Fermi -0.410137974838 -5.58021342398 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000917840245448 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130532144563 + + Density error is 0.0977892307528 + + Energy Rydberg eV + E_KohnSham -34.2805156135 -466.410342722 + E_Harris -34.28719116 -466.501168191 + E_Fermi -0.218551138497 -2.97354078795 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00088322117361 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123190975481 + + Density error is 0.0625999632353 + + Energy Rydberg eV + E_KohnSham -34.2807769438 -466.413898303 + E_Harris -34.2850817876 -466.472468707 + E_Fermi -0.206234535465 -2.8059648067 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000842932368512 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112004647577 + + Density error is 0.00201428632257 + + Energy Rydberg eV + E_KohnSham -34.2807858184 -466.414019048 + E_Harris -34.2807872125 -466.414038015 + E_Fermi -0.170665756184 -2.32202673758 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000845039199573 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112104170835 + + Density error is 0.000883954159363 + + Energy Rydberg eV + E_KohnSham -34.2807213652 -466.413142118 + E_Harris -34.2807228728 -466.413162629 + E_Fermi -0.169766071659 -2.30978590164 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000844134427199 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111949811042 + + Density error is 0.000149418298834 + + Energy Rydberg eV + E_KohnSham -34.2807638502 -466.413720156 + E_Harris -34.280763893 -466.413720738 + E_Fermi -0.169869281658 -2.31119014572 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000844322374609 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111955054917 + + Density error is 4.06214328198e-05 + + Energy Rydberg eV + E_KohnSham -34.2807486171 -466.413512898 + E_Harris -34.280748626 -466.413513019 + E_Fermi -0.169727381988 -2.30925950166 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00084425792609 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111950073544 + + Density error is 1.5053576795e-05 + + Energy Rydberg eV + E_KohnSham -34.2807527114 -466.413568604 + E_Harris -34.2807527123 -466.413568616 + E_Fermi -0.169773201546 -2.30988290872 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000844262220877 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111948974829 + + Density error is 1.66151990828e-06 + + Energy Rydberg eV + E_KohnSham -34.2807513245 -466.413549734 + E_Harris -34.2807513245 -466.413549734 + E_Fermi -0.169757069947 -2.30966342706 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000844263112172 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111948836785 + + Density error is 1.37442865981e-07 + + Energy Rydberg eV + E_KohnSham -34.2807515253 -466.413552466 + E_Harris -34.2807515253 -466.413552466 + E_Fermi -0.169755439378 -2.30964124203 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00084426348665 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111948889889 + + Density error is 4.85765743856e-08 + + Energy Rydberg eV + E_KohnSham -34.2807515542 -466.41355286 + E_Harris -34.2807515542 -466.41355286 + E_band -7.99198062934 -108.736474865 + E_one_elec -69.4608645494 -945.063545878 + E_Hartree +36.1207912801 +491.448577678 + E_xc -8.22264909574 -111.874880357 + E_Ewald +7.40595311998 +100.763161553 + E_demet -2.36613263567e-82 -3.21928860689e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195104765672 -2.65453652009 + E_Fermi -0.169755487452 -2.30964189611 + + charge density convergence is achieved + final etot is -466.41355286 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3610 2.00000 + 2 -13.1485 2.00000 + 3 -9.09804 2.00000 + 4 -6.76062 2.00000 + 5 1.37613 0.00000 + 6 4.54749 0.00000 + 7 11.0555 0.00000 + 8 11.3035 0.00000 + + EFERMI = -2.309641896109195 eV + OUT.ABACUS/ final etot is -466.4135528596979 eV + correction force for each atom along direction 1 is 3.39199e-05 + correction force for each atom along direction 2 is 2.89509e-05 + correction force for each atom along direction 3 is -4.06590e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.24212598 -0.83757752 -0.50126702 + H1 +0.093760135 +0.76695965 +0.67734370 + H2 +0.14836584 +0.070617867 -0.17607668 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4135528596979 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.4861 11 0.50 1.0e+02% + Run_lcao lcao_line 5.4783 1 5.5 1.e+02% + Potential init_pot 0.23830 2 0.12 4.3% + PW_Basis recip2real 0.24713 16 0.015 4.5% + PW_Basis gathers_scatterp 0.10260 16 0.0064 1.9% + Potential v_of_rho 0.91087 13 0.070 17.% + XC_Functional v_xc 0.27549 14 0.020 5.0% + H_Hartree_pw v_hartree 0.59697 13 0.046 11.% + PW_Basis real2recip 0.60215 38 0.016 11.% + PW_Basis gatherp_scatters 0.22619 38 0.0060 4.1% + ORB_control set_orb_tables 0.89200 1 0.89 16.% + ORB_gen_tables gen_tables 0.89200 1 0.89 16.% + ORB_table_phi init_Table 0.36929 1 0.37 6.7% + ORB_table_phi cal_ST_Phi12_R 0.36512 126 0.0029 6.7% + ORB_table_beta init_Table_Beta 0.15589 1 0.16 2.8% + ORB_table_beta VNL_PhiBeta_R 0.15460 56 0.0028 2.8% + ORB_table_alpha init_Table_Alpha 0.20831 1 0.21 3.8% + ORB_table_alpha S_PhiAlpha_R 0.20672 66 0.0031 3.8% + LOOP_ions opt_ions 4.1294 1 4.1 75.% + ESolver_KS_LCAO Run 3.6999 1 3.7 67.% + HSolverLCAO solve 1.5462 11 0.14 28.% + HamiltLCAO updateHk 0.86585 11 0.079 16.% + LCAO_Hamilt cal_Hgamma 0.83646 11 0.076 15.% + Gint_interface cal_gint 1.3209 23 0.057 24.% + Gint_Gamma distri_vl 1.8000 6 0.30 33.% + LCAO_Deepks cal_projected_DM 4.0076 13 0.31 73.% + LCAO_gen_fixedH add_v_delta 1.6715 6 0.28 30.% + LCAO_DESCRIPTOR add_v_delta 1.6716 6 0.28 30.% + ElecStateLCAO psiToRho 0.66339 11 0.060 12.% + Charge mix_rho 0.75588 10 0.076 14.% + LOOP_ions force_stress 0.42936 1 0.43 7.8% + Force_Stress_LCAO getForceStress 0.42933 1 0.43 7.8% + Force_LCAO_gamma ftable_gamma 0.23524 1 0.24 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.22774 1 0.23 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:10 2022 + Finish Time : Wed Sep 28 11:09:16 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8095b536784071aaf7eac7855c8b8a1d6bb6e011 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123874 ima = 3.7117e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123063349704 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112133131871 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112623300462 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112877590452 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112820131544 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112854042775 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112846886582 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112849782215 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112849192254 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112849121831 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112849117971 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d18401ae6a2371dc10d920a33524eb57d4966cfa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.093098494386 21.725096124251 6.217091703515 0 0 0 +H +0.0 +2 +-14.938333038486 23.066183031539 7.417302736594 0 0 0 +-13.981909921511 22.201261704892 4.838715017127 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/conv new file mode 100644 index 0000000000000000000000000000000000000000..e0cb9b2ddce0c271a5d30466f0b3747f127bd623 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/conv @@ -0,0 +1 @@ +200 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..11be244c4e00eb06cac67b4809f3f41044a24f88 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748657498 0.01273120016 1.28056312 1.368433972 1.469664857 0.008461571159 0.01889431076 0.03900711685 +2.403380847e-18 0.001103132868 0.002622092321 0.01262605641 0.04569499329 1.3214566e-19 2.073171173e-06 5.989276945e-06 +0.001665687652 0.005934967887 + +H atom_index 1 n_descriptor 18 +1.266366639 0.03360209843 0.1142508889 0.1578515014 0.3262534166 0.02300360995 0.02927350116 0.03686006731 +-1.418056649e-17 4.77991378e-05 0.1057130862 0.1162140144 0.1355837104 -3.0433348e-18 3.275766655e-06 0.01311464227 +0.02702147136 0.03149701758 + +H atom_index 2 n_descriptor 18 +1.244925857 0.03433924463 0.1066949455 0.1477340531 0.3195168514 0.02201758533 0.02803099178 0.03746711492 +3.314730182e-17 4.580217551e-05 0.1010687776 0.1146796406 0.1268761959 1.683689121e-18 4.457817182e-06 0.0131886864 +0.02624496005 0.0305554671 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..88b129cb0adec0fe633d56b979fb2c65f4c149c2 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..17a346781174d42f2186c8afd3e25275965c0536 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..fabfa8b5eba79d2866a8f1454be7496d2ed8cd0d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..27097bf5451e87fca6803700ba684a37a4750648 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..b4a9a5425f185e4f097b9ea3abfd9fb943dd4956 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:10 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0729416 SEC) : SETUP UNITCELL + DONE(0.0861655 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.102514 SEC) : INIT PLANEWAVE + DONE(0.144828 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.386005 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651877e+02 0.000000e+00 2.158e-01 4.235e-01 + GE2 -4.664103e+02 -1.222621e+00 9.779e-02 3.838e-01 + GE3 -4.664139e+02 -3.555581e-03 6.260e-02 4.461e-01 + GE4 -4.664140e+02 -1.207456e-04 2.014e-03 3.183e-01 + GE5 -4.664131e+02 8.769309e-04 8.840e-04 3.198e-01 + GE6 -4.664137e+02 -5.780379e-04 1.494e-04 3.124e-01 + GE7 -4.664135e+02 2.072575e-04 4.062e-05 3.099e-01 + GE8 -4.664136e+02 -5.570593e-05 1.505e-05 2.961e-01 + GE9 -4.664135e+02 1.886989e-05 1.662e-06 3.022e-01 + GE10 -4.664136e+02 -2.731874e-06 1.374e-07 3.012e-01 + GE11 -4.664136e+02 -3.937532e-07 4.858e-08 2.334e-01 +E_delta_band = -7.11224565e-02 Ry = -9.67670665e-01 eV +E_delta_NN= -1.95104766e-01 Ry = -2.65453652e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.4861 11 0.5 1e+02 % + Run_lcao lcao_line 5.4783 1 5.5 1e+02 % + Potential init_pot 0.2383 2 0.12 4.3 % + PW_Basis recip2real 0.24713 16 0.015 4.5 % + PW_Basis gathers_scatterp 0.1026 16 0.0064 1.9 % + Potential v_of_rho 0.91087 13 0.07 17 % + XC_Functional v_xc 0.27549 14 0.02 5 % + H_Hartree_pw v_hartree 0.59697 13 0.046 11 % + PW_Basis real2recip 0.60215 38 0.016 11 % + PW_Basis gatherp_scatters 0.22619 38 0.006 4.1 % + ORB_control set_orb_tables 0.892 1 0.89 16 % + ORB_gen_tables gen_tables 0.892 1 0.89 16 % + ORB_table_phi init_Table 0.36929 1 0.37 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.36512 126 0.0029 6.7 % + ORB_table_beta init_Table_Beta 0.15589 1 0.16 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.1546 56 0.0028 2.8 % + ORB_table_alpha init_Table_Alpha 0.20831 1 0.21 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.20672 66 0.0031 3.8 % + LOOP_ions opt_ions 4.1294 1 4.1 75 % + ESolver_KS_LCAO Run 3.6999 1 3.7 67 % + HSolverLCAO solve 1.5462 11 0.14 28 % + HamiltLCAO updateHk 0.86585 11 0.079 16 % + LCAO_Hamilt cal_Hgamma 0.83646 11 0.076 15 % + Gint_interface cal_gint 1.3209 23 0.057 24 % + Gint_Gamma distri_vl 1.8 6 0.3 33 % + LCAO_Deepks cal_projected_DM 4.0076 13 0.31 73 % + LCAO_gen_fixedH add_v_delta 1.6715 6 0.28 30 % + LCAO_DESCRIPTOR add_v_delta 1.6716 6 0.28 30 % + ElecStateLCAO psiToRho 0.66339 11 0.06 12 % + Charge mix_rho 0.75588 10 0.076 14 % + LOOP_ions force_stress 0.42936 1 0.43 7.8 % + Force_Stress_LCAO getForceStress 0.42933 1 0.43 7.8 % + Force_LCAO_gamma ftable_gamma 0.23524 1 0.24 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.22774 1 0.23 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:10 2022 + FINISH Time : Wed Sep 28 11:09:16 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/200/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..90e60e7b5921d997bfea2629e93db831cc54cfb5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.469924 0.785286 0.248627 +H 0.502715 0.833136 0.283321 +H 0.492194 0.798594 0.186693 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bcef86a582de60e26a1e1a8a48587788760b7120 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.061 2 + 2 -12.5822 2 + 3 -9.28915 2 + 4 -6.69844 2 + 5 1.01945 0 + 6 3.93106 0 + 7 11.1407 0 + 8 11.4101 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f42b38db7aec58093acf8b7a08c4b5df2b489b5c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:26 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.1578733754 21.9880169195 6.96155729797 0 0 0 0 + tauc_H1 14.0760202007 23.3278194685 7.932983027 0 0 0 0 + tauc_H2 13.781429194 22.3606327148 5.22740827102 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0740508034856 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0743317962671 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0900229342607 (SEC) + + DONE : INIT CHARGE Time : 0.13130982598 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.376734 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 144 4 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000652 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000874 + + Density error is 0.210543047659 + + Energy Rydberg eV + E_KohnSham -34.1914807722 -465.19896156 + E_Harris -34.3744074226 -467.687806321 + E_Fermi -0.387206155175 -5.26821001105 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00097350989196 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110255161713 + + Density error is 0.0985294711394 + + Energy Rydberg eV + E_KohnSham -34.2789601255 -466.389179222 + E_Harris -34.2861230772 -466.486636179 + E_Fermi -0.198969992704 -2.7071256318 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000935389241147 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105424797308 + + Density error is 0.06361819099 + + Energy Rydberg eV + E_KohnSham -34.2793834301 -466.394938576 + E_Harris -34.2839740459 -466.457397108 + E_Fermi -0.192348074316 -2.61702981002 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000898830798294 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100031123449 + + Density error is 0.00190908732862 + + Energy Rydberg eV + E_KohnSham -34.2792819538 -466.393557921 + E_Harris -34.2792826577 -466.393567497 + E_Fermi -0.157042762661 -2.13667640186 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000899924455605 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100155284891 + + Density error is 0.000911793826706 + + Energy Rydberg eV + E_KohnSham -34.2792500792 -466.393124244 + E_Harris -34.279250494 -466.393129887 + E_Fermi -0.157056838192 -2.13686790927 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000899483863544 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100081675751 + + Density error is 0.000157703109731 + + Energy Rydberg eV + E_KohnSham -34.2792638641 -466.393311797 + E_Harris -34.2792638706 -466.393311885 + E_Fermi -0.156603141138 -2.13069504417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00089965443566 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100098845249 + + Density error is 2.69217966133e-05 + + Energy Rydberg eV + E_KohnSham -34.2792601487 -466.393261247 + E_Harris -34.2792601506 -466.393261272 + E_Fermi -0.156588693733 -2.13049847715 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000899602142422 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100093062232 + + Density error is 1.09855791109e-05 + + Energy Rydberg eV + E_KohnSham -34.2792622392 -466.39328969 + E_Harris -34.2792622398 -466.393289697 + E_Fermi -0.156600790618 -2.13066306371 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000899607854584 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100093478513 + + Density error is 2.10046609114e-06 + + Energy Rydberg eV + E_KohnSham -34.2792613578 -466.393277698 + E_Harris -34.2792613578 -466.393277698 + E_Fermi -0.156590423131 -2.13052200681 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000899607186721 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100093317841 + + Density error is 3.69192701745e-07 + + Energy Rydberg eV + E_KohnSham -34.2792615141 -466.393279824 + E_Harris -34.2792615141 -466.393279824 + E_Fermi -0.156588507347 -2.13049594124 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000899607894776 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100093389866 + + Density error is 1.28848894756e-07 + + Energy Rydberg eV + E_KohnSham -34.2792615363 -466.393280126 + E_Harris -34.2792615363 -466.393280126 + E_Fermi -0.156588357532 -2.13049390289 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000899608125347 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010009341038 + + Density error is 1.10046901134e-08 + + Energy Rydberg eV + E_KohnSham -34.2792615394 -466.393280167 + E_Harris -34.2792615394 -466.393280167 + E_band -7.88358251793 -107.261642897 + E_one_elec -68.6729555346 -934.343493771 + E_Hartree +35.7407492143 +486.277840103 + E_xc -8.16159040316 -111.044134225 + E_Ewald +6.94009529839 +94.4248407212 + E_demet -7.19626323403e-61 -9.79101842907e-60 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193757754971 -2.63620949929 + E_Fermi -0.156588242629 -2.13049233957 + + charge density convergence is achieved + final etot is -466.393280167 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0610 2.00000 + 2 -12.5822 2.00000 + 3 -9.28915 2.00000 + 4 -6.69844 2.00000 + 5 1.01945 0.00000 + 6 3.93106 0.00000 + 7 11.1407 0.00000 + 8 11.4101 0.00000 + + EFERMI = -2.130492339565048 eV + OUT.ABACUS/ final etot is -466.3932801674770 eV + correction force for each atom along direction 1 is -3.21296e-05 + correction force for each atom along direction 2 is 0.000126072 + correction force for each atom along direction 3 is 6.67497e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.0056290 +1.1714262 -0.29022980 + H1 -0.61309477 -0.82567065 -0.32450972 + H2 -0.39253420 -0.34575557 +0.61473952 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3932801674770 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5815 11 0.51 1.0e+02% + Run_lcao lcao_line 5.5737 1 5.6 1.e+02% + Potential init_pot 0.24249 2 0.12 4.3% + PW_Basis recip2real 0.28168 17 0.017 5.0% + PW_Basis gathers_scatterp 0.11520 17 0.0068 2.1% + Potential v_of_rho 0.99245 14 0.071 18.% + XC_Functional v_xc 0.28294 15 0.019 5.1% + H_Hartree_pw v_hartree 0.66551 14 0.048 12.% + PW_Basis real2recip 0.65525 41 0.016 12.% + PW_Basis gatherp_scatters 0.25516 41 0.0062 4.6% + ORB_control set_orb_tables 0.89885 1 0.90 16.% + ORB_gen_tables gen_tables 0.89885 1 0.90 16.% + ORB_table_phi init_Table 0.37411 1 0.37 6.7% + ORB_table_phi cal_ST_Phi12_R 0.36984 126 0.0029 6.6% + ORB_table_beta init_Table_Beta 0.15684 1 0.16 2.8% + ORB_table_beta VNL_PhiBeta_R 0.15547 56 0.0028 2.8% + ORB_table_alpha init_Table_Alpha 0.20985 1 0.21 3.8% + ORB_table_alpha S_PhiAlpha_R 0.20810 66 0.0032 3.7% + LOOP_ions opt_ions 4.2246 1 4.2 76.% + ESolver_KS_LCAO Run 3.8199 1 3.8 68.% + HSolverLCAO solve 1.4524 12 0.12 26.% + HamiltLCAO updateHk 0.82745 12 0.069 15.% + LCAO_Hamilt cal_Hgamma 0.79198 12 0.066 14.% + Gint_interface cal_gint 1.1789 25 0.047 21.% + Gint_Gamma distri_vl 1.9979 6 0.33 36.% + LCAO_Deepks cal_projected_DM 4.1088 14 0.29 74.% + LCAO_gen_fixedH add_v_delta 1.8689 6 0.31 33.% + LCAO_DESCRIPTOR add_v_delta 1.8689 6 0.31 33.% + ElecStateLCAO psiToRho 0.60582 12 0.050 11.% + Charge mix_rho 0.83125 11 0.076 15.% + LOOP_ions force_stress 0.40456 1 0.40 7.2% + Force_Stress_LCAO getForceStress 0.40453 1 0.40 7.2% + Force_LCAO_gamma ftable_gamma 0.20463 1 0.20 3.7% + Force_LCAO_gamma cal_fvl_dphi 0.19710 1 0.20 3.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:26 2022 + Finish Time : Wed Sep 28 11:07:32 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..deed33fe4871b7a625d969fcbba10b487b446a89 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/OUT.ABACUS/warning.log @@ -0,0 +1,77 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123596 ima = 3.66888e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 3 + 3 1 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123187096342 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111752622589 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112535780376 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112736775296 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112721523868 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112731263332 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112727903748 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011272965806 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112729168519 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112729101916 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112729087502 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112729081241 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/STRU new file mode 100644 index 0000000000000000000000000000000000000000..cc94242b26e7d0b39382298991eabd82fbb29eb1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.842126624548 21.988016919457 6.961557297971 0 0 0 +H +0.0 +2 +-13.923979799300 23.327819468526 7.932983026993 0 0 0 +-14.218570806023 22.360632714754 5.227408271023 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/conv new file mode 100644 index 0000000000000000000000000000000000000000..ebbf30473a4a2d63ee037f05847a60f3b65f4599 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/conv @@ -0,0 +1 @@ +201 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7503e4878b4bc70c61b39e20c57dce8114a17daa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753089427 0.01251947155 1.246871238 1.332671537 1.468356043 0.009008635711 0.0168022802 0.03918319357 +6.81470127e-19 0.0008292557238 0.002549301525 0.01200063771 0.04285833167 3.705668705e-19 2.024518431e-06 5.888908968e-06 +0.001573300089 0.006005386838 + +H atom_index 1 n_descriptor 18 +1.202428827 0.03624094083 0.09347274221 0.1289376901 0.3038004148 0.02025108031 0.02547210403 0.03964389674 +6.631439568e-18 3.934718858e-05 0.08744505865 0.1101363667 0.1137050925 -1.214810368e-18 5.587047507e-06 0.014222363 +0.02413052837 0.0283461015 + +H atom_index 2 n_descriptor 18 +1.212142183 0.03593559704 0.09648608706 0.1329824829 0.3074423465 0.02071549042 0.02604427455 0.03925329255 +-2.051832113e-17 4.019245639e-05 0.08994456331 0.1136900346 0.1141305143 2.838093398e-18 5.208323136e-06 0.01395852386 +0.02453183083 0.02885785781 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c927c0e182040361807a9aa1def1e56f1adf04e9 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:26 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0740662 SEC) : SETUP UNITCELL + DONE(0.0743403 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0900362 SEC) : INIT PLANEWAVE + DONE(0.131413 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.376777 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651990e+02 0.000000e+00 2.105e-01 4.086e-01 + GE2 -4.663892e+02 -1.190218e+00 9.853e-02 3.683e-01 + GE3 -4.663949e+02 -5.759354e-03 6.362e-02 4.289e-01 + GE4 -4.663936e+02 1.380655e-03 1.909e-03 3.066e-01 + GE5 -4.663931e+02 4.336766e-04 9.118e-04 3.073e-01 + GE6 -4.663933e+02 -1.875525e-04 1.577e-04 3.041e-01 + GE7 -4.663933e+02 5.054997e-05 2.692e-05 2.841e-01 + GE8 -4.663933e+02 -2.844332e-05 1.099e-05 2.866e-01 + GE9 -4.663933e+02 1.199238e-05 2.100e-06 2.825e-01 + GE10 -4.663933e+02 -2.126289e-06 3.692e-07 2.878e-01 + GE11 -4.663933e+02 -3.016214e-07 1.288e-07 2.861e-01 + GE12 -4.663933e+02 -4.194601e-08 1.100e-08 2.143e-01 +E_delta_band = -6.81976407e-02 Ry = -9.27876504e-01 eV +E_delta_NN= -1.93757755e-01 Ry = -2.63620950e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5815 11 0.51 1e+02 % + Run_lcao lcao_line 5.5737 1 5.6 1e+02 % + Potential init_pot 0.24249 2 0.12 4.3 % + PW_Basis recip2real 0.28168 17 0.017 5 % + PW_Basis gathers_scatterp 0.1152 17 0.0068 2.1 % + Potential v_of_rho 0.99245 14 0.071 18 % + XC_Functional v_xc 0.28294 15 0.019 5.1 % + H_Hartree_pw v_hartree 0.66551 14 0.048 12 % + PW_Basis real2recip 0.65525 41 0.016 12 % + PW_Basis gatherp_scatters 0.25516 41 0.0062 4.6 % + ORB_control set_orb_tables 0.89885 1 0.9 16 % + ORB_gen_tables gen_tables 0.89885 1 0.9 16 % + ORB_table_phi init_Table 0.37411 1 0.37 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.36984 126 0.0029 6.6 % + ORB_table_beta init_Table_Beta 0.15684 1 0.16 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.15547 56 0.0028 2.8 % + ORB_table_alpha init_Table_Alpha 0.20985 1 0.21 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.2081 66 0.0032 3.7 % + LOOP_ions opt_ions 4.2246 1 4.2 76 % + ESolver_KS_LCAO Run 3.8199 1 3.8 68 % + HSolverLCAO solve 1.4524 12 0.12 26 % + HamiltLCAO updateHk 0.82745 12 0.069 15 % + LCAO_Hamilt cal_Hgamma 0.79198 12 0.066 14 % + Gint_interface cal_gint 1.1789 25 0.047 21 % + Gint_Gamma distri_vl 1.9979 6 0.33 36 % + LCAO_Deepks cal_projected_DM 4.1088 14 0.29 74 % + LCAO_gen_fixedH add_v_delta 1.8689 6 0.31 33 % + LCAO_DESCRIPTOR add_v_delta 1.8689 6 0.31 33 % + ElecStateLCAO psiToRho 0.60582 12 0.05 11 % + Charge mix_rho 0.83125 11 0.076 15 % + LOOP_ions force_stress 0.40456 1 0.4 7.2 % + Force_Stress_LCAO getForceStress 0.40453 1 0.4 7.2 % + Force_LCAO_gamma ftable_gamma 0.20463 1 0.2 3.7 % + Force_LCAO_gamma cal_fvl_dphi 0.1971 1 0.2 3.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:26 2022 + FINISH Time : Wed Sep 28 11:07:32 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/201/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d8f39b4eedb238a78de2aabb8986225123a3067a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.481758 0.783942 0.263071 +H 0.511882 0.810251 0.312236 +H 0.482594 0.827875 0.217839 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6369707c424c583a9cee2026b7cf9f3a309925b2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6694 2 + 2 -13.432 2 + 3 -9.12968 2 + 4 -6.82878 2 + 5 1.62608 0 + 6 4.98097 0 + 7 10.9789 0 + 8 11.2182 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e14fb58f41335506f2e24a3445a7e4e44d29f939 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:00 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.4892224455 21.9503815412 7.3660008471 0 0 0 0 + tauc_H1 14.3327027912 22.6870281425 8.74261315194 0 0 0 0 + tauc_H2 13.5126373362 23.1805083609 6.09948894432 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0869651696739 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.087403216098 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105636753994 (SEC) + + DONE : INIT CHARGE Time : 0.154262578368 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.434818 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 144 4 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00117 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000883 + + Density error is 0.219527417548 + + Energy Rydberg eV + E_KohnSham -34.1837306086 -465.093515175 + E_Harris -34.3854306225 -467.837784649 + E_Fermi -0.42948230818 -5.84340658143 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00121569501193 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121824933857 + + Density error is 0.097078065816 + + Energy Rydberg eV + E_KohnSham -34.2753864401 -466.340556737 + E_Harris -34.2819540321 -466.429913411 + E_Fermi -0.235698525603 -3.2068429584 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00113473154511 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011745656606 + + Density error is 0.0617092583694 + + Energy Rydberg eV + E_KohnSham -34.2756044305 -466.343522648 + E_Harris -34.2797367801 -466.39974615 + E_Fermi -0.219153032626 -2.98172997769 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0010102611398 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111470742067 + + Density error is 0.00211429136029 + + Energy Rydberg eV + E_KohnSham -34.2756898335 -466.344684616 + E_Harris -34.2756927044 -466.344723677 + E_Fermi -0.18338958785 -2.49514334863 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00101032268392 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111879464317 + + Density error is 0.000948189864469 + + Energy Rydberg eV + E_KohnSham -34.2756021028 -466.343490979 + E_Harris -34.2756061968 -466.343546681 + E_Fermi -0.181716705534 -2.47238261706 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100920980982 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111717457296 + + Density error is 0.000108155907848 + + Energy Rydberg eV + E_KohnSham -34.2756664756 -466.344366816 + E_Harris -34.2756665016 -466.34436717 + E_Fermi -0.182286417824 -2.48013395042 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100909661392 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111716288448 + + Density error is 5.28183790224e-05 + + Energy Rydberg eV + E_KohnSham -34.2756452078 -466.344077453 + E_Harris -34.2756452208 -466.344077629 + E_Fermi -0.182121506037 -2.47789021045 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0010091116222 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111710776253 + + Density error is 8.0125651178e-06 + + Energy Rydberg eV + E_KohnSham -34.275648174 -466.34411781 + E_Harris -34.2756481743 -466.344117813 + E_Fermi -0.182182631481 -2.47872186477 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0010091041881 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111711308605 + + Density error is 1.38247765895e-06 + + Energy Rydberg eV + E_KohnSham -34.2756469718 -466.344101453 + E_Harris -34.2756469718 -466.344101453 + E_Fermi -0.182175703089 -2.47862759917 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100910264164 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111711434952 + + Density error is 1.58177320801e-07 + + Energy Rydberg eV + E_KohnSham -34.2756470854 -466.344102999 + E_Harris -34.2756470854 -466.344102999 + E_Fermi -0.182174002738 -2.47860446471 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0010091028429 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111711424944 + + Density error is 3.98435839821e-08 + + Energy Rydberg eV + E_KohnSham -34.2756471123 -466.344103364 + E_Harris -34.2756471123 -466.344103364 + E_band -8.0936590577 -110.119880854 + E_one_elec -70.0929519994 -953.663536832 + E_Hartree +36.4178579934 +495.490377665 + E_xc -8.27093675383 -112.53186765 + E_Ewald +7.79307158536 +106.030178483 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196330646675 -2.67121548681 + E_Fermi -0.182174174177 -2.47860679725 + + charge density convergence is achieved + final etot is -466.344103364 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6694 2.00000 + 2 -13.4320 2.00000 + 3 -9.12968 2.00000 + 4 -6.82878 2.00000 + 5 1.62608 0.00000 + 6 4.98097 0.00000 + 7 10.9789 0.00000 + 8 11.2182 0.00000 + + EFERMI = -2.478606797253557 eV + OUT.ABACUS/ final etot is -466.3441033641503 eV + correction force for each atom along direction 1 is 0.000163573 + correction force for each atom along direction 2 is 5.95342e-05 + correction force for each atom along direction 3 is 5.22621e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.94273335 -2.3664496 +0.11048864 + H1 +0.94167968 +0.78814429 +1.5809244 + H2 +0.0010536618 +1.5783053 -1.6914131 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3441033641503 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.3939 11 0.49 1.0e+02% + Run_lcao lcao_line 5.3843 1 5.4 1.e+02% + Potential init_pot 0.28605 2 0.14 5.3% + PW_Basis recip2real 0.26586 16 0.017 4.9% + PW_Basis gathers_scatterp 0.11418 16 0.0071 2.1% + Potential v_of_rho 0.85812 13 0.066 16.% + XC_Functional v_xc 0.22373 14 0.016 4.1% + H_Hartree_pw v_hartree 0.59438 13 0.046 11.% + PW_Basis real2recip 0.55849 38 0.015 10.% + PW_Basis gatherp_scatters 0.22238 38 0.0059 4.1% + ORB_control set_orb_tables 1.1130 1 1.1 21.% + ORB_gen_tables gen_tables 1.1130 1 1.1 21.% + ORB_table_phi init_Table 0.48570 1 0.49 9.0% + ORB_table_phi cal_ST_Phi12_R 0.48076 126 0.0038 8.9% + ORB_table_beta init_Table_Beta 0.19026 1 0.19 3.5% + ORB_table_beta VNL_PhiBeta_R 0.18877 56 0.0034 3.5% + ORB_table_alpha init_Table_Alpha 0.25733 1 0.26 4.8% + ORB_table_alpha S_PhiAlpha_R 0.25543 66 0.0039 4.7% + LOOP_ions opt_ions 3.7580 1 3.8 70.% + ESolver_KS_LCAO Run 3.3183 1 3.3 62.% + HSolverLCAO solve 1.3719 11 0.12 25.% + HamiltLCAO updateHk 0.77764 11 0.071 14.% + LCAO_Hamilt cal_Hgamma 0.74245 11 0.067 14.% + Gint_interface cal_gint 0.97765 23 0.043 18.% + Gint_Gamma distri_vl 1.6327 6 0.27 30.% + LCAO_Deepks cal_projected_DM 3.6089 13 0.28 67.% + LCAO_gen_fixedH add_v_delta 1.4990 6 0.25 28.% + LCAO_DESCRIPTOR add_v_delta 1.4990 6 0.25 28.% + ElecStateLCAO psiToRho 0.57522 11 0.052 11.% + Charge mix_rho 0.65525 10 0.066 12.% + LOOP_ions force_stress 0.43951 1 0.44 8.1% + Force_Stress_LCAO getForceStress 0.43948 1 0.44 8.1% + Force_LCAO_gamma ftable_gamma 0.22929 1 0.23 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.20076 1 0.20 3.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:00 2022 + Finish Time : Wed Sep 28 11:13:05 2022 + Total Time : 0 h 0 mins 5 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..93234d88c3b9544f536df2b7f1617621734b3241 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/OUT.ABACUS/warning.log @@ -0,0 +1,73 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124373 ima = 3.66659e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 3 + 3 1 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122774824575 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112113255254 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112428862327 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112734900622 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011264494658 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112695647685 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112691014031 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112693693573 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112693358587 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112693302783 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112693308131 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/STRU new file mode 100644 index 0000000000000000000000000000000000000000..515694ada65bf606bb64c4e6af0a8ccde168af57 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.510777554555 21.950381541196 7.366000847095 0 0 0 +H +0.0 +2 +-13.667297208861 22.687028142478 8.742613151947 0 0 0 +-14.487362663769 23.180508360846 6.099488944334 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/conv new file mode 100644 index 0000000000000000000000000000000000000000..83e5bf028494b7193c812d054cf0221b3ca828df --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/conv @@ -0,0 +1 @@ +202 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f62dd6f93621286c81956c10133f564453af2ba0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748627706 0.01286917397 1.306731117 1.388928032 1.471239581 0.008718140722 0.01964531428 0.03901669322 +1.885181781e-18 0.001264328762 0.002803501625 0.01350284856 0.04884605045 4.867001285e-22 2.421558614e-06 6.668083006e-06 +0.001670011382 0.005894545986 + +H atom_index 1 n_descriptor 18 +1.290851931 0.03274647765 0.1243211123 0.1699296336 0.3326261727 0.02438571557 0.03064305789 0.03632059848 +7.689911431e-17 5.584935836e-05 0.1088426384 0.1226235154 0.146117951 -3.068931313e-18 1.924335141e-06 0.01347961186 +0.02850132775 0.03247590876 + +H atom_index 2 n_descriptor 18 +1.297825583 0.03253990927 0.1270974145 0.1735966914 0.3345053268 0.02469972327 0.03103618977 0.03628126026 +3.59576256e-17 5.652824068e-05 0.1086753929 0.1247829854 0.1492030062 -3.659461086e-18 1.564854028e-06 0.01365550015 +0.0287109815 0.03271893641 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..183c12ac7925863cf079e0bd27c652276d43758f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:00 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870068 SEC) : SETUP UNITCELL + DONE(0.0874181 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105662 SEC) : INIT PLANEWAVE + DONE(0.15439 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.434893 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650935e+02 0.000000e+00 2.195e-01 4.223e-01 + GE2 -4.663406e+02 -1.247042e+00 9.708e-02 3.426e-01 + GE3 -4.663435e+02 -2.965911e-03 6.171e-02 4.036e-01 + GE4 -4.663447e+02 -1.161968e-03 2.114e-03 2.813e-01 + GE5 -4.663435e+02 1.193637e-03 9.482e-04 2.853e-01 + GE6 -4.663444e+02 -8.758371e-04 1.082e-04 2.615e-01 + GE7 -4.663441e+02 2.893627e-04 5.282e-05 2.644e-01 + GE8 -4.663441e+02 -4.035721e-05 8.013e-06 2.625e-01 + GE9 -4.663441e+02 1.635782e-05 1.382e-06 2.640e-01 + GE10 -4.663441e+02 -1.546346e-06 1.582e-07 2.643e-01 + GE11 -4.663441e+02 -3.652965e-07 3.984e-08 2.049e-01 +E_delta_band = -7.36427089e-02 Ry = -1.00196046e+00 eV +E_delta_NN= -1.96330647e-01 Ry = -2.67121549e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.3939 11 0.49 1e+02 % + Run_lcao lcao_line 5.3843 1 5.4 1e+02 % + Potential init_pot 0.28605 2 0.14 5.3 % + PW_Basis recip2real 0.26586 16 0.017 4.9 % + PW_Basis gathers_scatterp 0.11418 16 0.0071 2.1 % + Potential v_of_rho 0.85812 13 0.066 16 % + XC_Functional v_xc 0.22373 14 0.016 4.1 % + H_Hartree_pw v_hartree 0.59438 13 0.046 11 % + PW_Basis real2recip 0.55849 38 0.015 10 % + PW_Basis gatherp_scatters 0.22238 38 0.0059 4.1 % + ORB_control set_orb_tables 1.113 1 1.1 21 % + ORB_gen_tables gen_tables 1.113 1 1.1 21 % + ORB_table_phi init_Table 0.4857 1 0.49 9 % + ORB_table_phi cal_ST_Phi12_R 0.48076 126 0.0038 8.9 % + ORB_table_beta init_Table_Beta 0.19026 1 0.19 3.5 % + ORB_table_beta VNL_PhiBeta_R 0.18877 56 0.0034 3.5 % + ORB_table_alpha init_Table_Alpha 0.25733 1 0.26 4.8 % + ORB_table_alpha S_PhiAlpha_R 0.25543 66 0.0039 4.7 % + LOOP_ions opt_ions 3.758 1 3.8 70 % + ESolver_KS_LCAO Run 3.3183 1 3.3 62 % + HSolverLCAO solve 1.3719 11 0.12 25 % + HamiltLCAO updateHk 0.77764 11 0.071 14 % + LCAO_Hamilt cal_Hgamma 0.74245 11 0.067 14 % + Gint_interface cal_gint 0.97765 23 0.043 18 % + Gint_Gamma distri_vl 1.6327 6 0.27 30 % + LCAO_Deepks cal_projected_DM 3.6089 13 0.28 67 % + LCAO_gen_fixedH add_v_delta 1.499 6 0.25 28 % + LCAO_DESCRIPTOR add_v_delta 1.499 6 0.25 28 % + ElecStateLCAO psiToRho 0.57522 11 0.052 11 % + Charge mix_rho 0.65525 10 0.066 12 % + LOOP_ions force_stress 0.43951 1 0.44 8.1 % + Force_Stress_LCAO getForceStress 0.43948 1 0.44 8.1 % + Force_LCAO_gamma ftable_gamma 0.22929 1 0.23 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.20076 1 0.2 3.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:00 2022 + FINISH Time : Wed Sep 28 11:13:05 2022 + TOTAL Time : 5 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/202/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9e2e7b0666034d20d50038cc1dc8b56a82055258 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.490319 0.788139 0.26525 +H 0.539569 0.800394 0.305584 +H 0.476959 0.848953 0.240881 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b8c3352a2311915da512d86d39e48a314ca52f5b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2776 2 + 2 -12.8877 2 + 3 -9.22164 2 + 4 -6.743 2 + 5 1.23372 0 + 6 4.33073 0 + 7 11.0845 0 + 8 11.3453 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..5a7b5e9df415e090bf3cc91702c9a6ba960f00c6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:16 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.7289329486 22.0678786116 7.42700468899 0 0 0 0 + tauc_H1 15.10793245 22.4110216439 8.55635333527 0 0 0 0 + tauc_H2 13.354863984 23.7706925064 6.74465540794 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871145403473 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0973868039797 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115599371929 (SEC) + + DONE : INIT CHARGE Time : 0.165094610142 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443765 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 4 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00151 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000738 + + Density error is 0.213386518623 + + Energy Rydberg eV + E_KohnSham -34.1917852741 -465.20310452 + E_Harris -34.38057062 -467.771660924 + E_Fermi -0.402063709937 -5.47035741417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00142286271618 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000997510872515 + + Density error is 0.0978909644294 + + Energy Rydberg eV + E_KohnSham -34.2802642493 -466.406922736 + E_Harris -34.2870806604 -466.499664767 + E_Fermi -0.212303074934 -2.88853152202 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00132548124721 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000961456115988 + + Density error is 0.0628275683199 + + Energy Rydberg eV + E_KohnSham -34.2805378924 -466.410645842 + E_Harris -34.2849485551 -466.470655986 + E_Fermi -0.201821702281 -2.74592513109 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116228505912 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000919305190871 + + Density error is 0.00195796352574 + + Energy Rydberg eV + E_KohnSham -34.2805094409 -466.41025874 + E_Harris -34.2805105147 -466.410273348 + E_Fermi -0.166259769544 -2.26208021396 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116283478156 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000919283503993 + + Density error is 0.00085563948092 + + Energy Rydberg eV + E_KohnSham -34.2804592807 -466.409576275 + E_Harris -34.2804601473 -466.409588066 + E_Fermi -0.165725545062 -2.254811717 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116069583521 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000918670867254 + + Density error is 0.000142508267379 + + Energy Rydberg eV + E_KohnSham -34.2804903766 -466.409999356 + E_Harris -34.2804903941 -466.409999593 + E_Fermi -0.165615842729 -2.25331914018 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116058553431 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000918902199244 + + Density error is 3.3648644872e-05 + + Energy Rydberg eV + E_KohnSham -34.2804798105 -466.409855597 + E_Harris -34.2804798154 -466.409855663 + E_Fermi -0.165521350284 -2.25203350452 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116055047909 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000918808183398 + + Density error is 1.82292761434e-05 + + Energy Rydberg eV + E_KohnSham -34.2804830578 -466.409899778 + E_Harris -34.2804830593 -466.409899799 + E_Fermi -0.165553997604 -2.25247769409 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116054359013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000918819898141 + + Density error is 2.79449500001e-06 + + Energy Rydberg eV + E_KohnSham -34.2804816611 -466.409880776 + E_Harris -34.2804816611 -466.409880776 + E_Fermi -0.165537500175 -2.25225323505 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116053613343 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000918821454155 + + Density error is 3.75408879543e-07 + + Energy Rydberg eV + E_KohnSham -34.2804819476 -466.409884673 + E_Harris -34.2804819476 -466.409884673 + E_Fermi -0.165534586602 -2.25221359387 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116053672438 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00091882199715 + + Density error is 1.37958389373e-07 + + Energy Rydberg eV + E_KohnSham -34.2804819854 -466.409885188 + E_Harris -34.2804819854 -466.409885188 + E_Fermi -0.165534453547 -2.25221178356 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116053664629 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000918822225625 + + Density error is 1.08411535529e-08 + + Energy Rydberg eV + E_KohnSham -34.2804819882 -466.409885226 + E_Harris -34.2804819882 -466.409885226 + E_band -7.95694809224 -108.259832745 + E_one_elec -69.1829904774 -941.282875172 + E_Hartree +35.9849909555 +489.600919473 + E_xc -8.20085503764 -111.578356984 + E_Ewald +7.24291240923 +98.5448788805 + E_demet -6.03015068212e-74 -8.20444090754e-73 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194645548727 -2.64828855302 + E_Fermi -0.165534334319 -2.25221016138 + + charge density convergence is achieved + final etot is -466.409885226 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2776 2.00000 + 2 -12.8877 2.00000 + 3 -9.22164 2.00000 + 4 -6.74300 2.00000 + 5 1.23372 0.00000 + 6 4.33073 0.00000 + 7 11.0845 0.00000 + 8 11.3453 0.00000 + + EFERMI = -2.252210161377975 eV + OUT.ABACUS/ final etot is -466.4098852256797 eV + correction force for each atom along direction 1 is 0.000149286 + correction force for each atom along direction 2 is 0.000124031 + correction force for each atom along direction 3 is 3.98687e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.65995669 +0.67627425 -0.71958727 + H1 +0.65539664 -0.0090458055 +0.57424221 + H2 +0.0045600486 -0.66722844 +0.14534506 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4098852256797 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1712 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1611 1 6.2 1.e+02% + Potential init_pot 0.28166 2 0.14 4.6% + PW_Basis recip2real 0.29116 17 0.017 4.7% + PW_Basis gathers_scatterp 0.12637 17 0.0074 2.0% + Potential v_of_rho 1.0470 14 0.075 17.% + XC_Functional v_xc 0.30246 15 0.020 4.9% + H_Hartree_pw v_hartree 0.70084 14 0.050 11.% + PW_Basis real2recip 0.70290 41 0.017 11.% + PW_Basis gatherp_scatters 0.27614 41 0.0067 4.5% + ORB_control set_orb_tables 1.0906 1 1.1 18.% + ORB_gen_tables gen_tables 1.0906 1 1.1 18.% + ORB_table_phi init_Table 0.47582 1 0.48 7.7% + ORB_table_phi cal_ST_Phi12_R 0.47071 126 0.0037 7.6% + ORB_table_beta init_Table_Beta 0.17993 1 0.18 2.9% + ORB_table_beta VNL_PhiBeta_R 0.17835 56 0.0032 2.9% + ORB_table_alpha init_Table_Alpha 0.24847 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.24654 66 0.0037 4.0% + LOOP_ions opt_ions 4.5492 1 4.5 74.% + ESolver_KS_LCAO Run 4.0981 1 4.1 66.% + HSolverLCAO solve 1.6310 12 0.14 26.% + HamiltLCAO updateHk 0.91464 12 0.076 15.% + LCAO_Hamilt cal_Hgamma 0.88494 12 0.074 14.% + Gint_interface cal_gint 0.96888 25 0.039 16.% + Gint_Gamma distri_vl_value 0.13592 12 0.011 2.2% + Gint_Gamma distri_vl 2.1504 6 0.36 35.% + LCAO_Deepks cal_projected_DM 4.3768 14 0.31 71.% + LCAO_gen_fixedH add_v_delta 2.0061 6 0.33 33.% + LCAO_DESCRIPTOR add_v_delta 2.0062 6 0.33 33.% + ElecStateLCAO psiToRho 0.69708 12 0.058 11.% + Charge mix_rho 0.85120 11 0.077 14.% + LOOP_ions force_stress 0.45093 1 0.45 7.3% + Force_Stress_LCAO getForceStress 0.45090 1 0.45 7.3% + Force_LCAO_gamma ftable_gamma 0.23613 1 0.24 3.8% + Force_LCAO_gamma cal_fvl_dphi 0.18864 1 0.19 3.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:16 2022 + Finish Time : Wed Sep 28 11:13:22 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..bad47aef950e7b60293f93beda20c3cdb0850e4d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123444 ima = 3.65381e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122971441565 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111927168206 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011251160801 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112745734142 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112704226312 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112728516283 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112723299304 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112725945817 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112725085739 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112724982855 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112724969032 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112724962704 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d943775c9de5af6adb51bc584197800556791014 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.271067051377 22.067878611586 7.427004688972 0 0 0 +H +0.0 +2 +-12.892067549998 22.411021643925 8.556353335262 0 0 0 +-14.645136016017 23.770692506450 6.744655407959 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/conv new file mode 100644 index 0000000000000000000000000000000000000000..34e5af45ac586b8135d405d2495ba9cc8bf71607 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/conv @@ -0,0 +1 @@ +203 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..44ff5fd9066575fc8b20244766b93b0a3c9aa197 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751118761 0.01267828251 1.26638913 1.355823609 1.469242106 0.008811534662 0.01781378329 0.03909061033 +3.972571442e-19 0.0009788889423 0.002648711225 0.01245984966 0.04518976302 -2.051719979e-19 2.188932228e-06 6.227616776e-06 +0.001612421294 0.006019476412 + +H atom_index 1 n_descriptor 18 +1.261664 0.03406850775 0.1129309368 0.155303604 0.324383431 0.02301567995 0.02896134556 0.03728608253 +3.226973578e-17 4.763649823e-05 0.1039956666 0.1159722805 0.1332601126 -4.764167658e-18 3.199975622e-06 0.01319796819 +0.02678440591 0.03126451823 + +H atom_index 2 n_descriptor 18 +1.216653148 0.03559228878 0.09770710153 0.1349490966 0.3091930282 0.02088158486 0.02632831638 0.0388200421 +1.119667207e-18 4.346261282e-05 0.09287715674 0.1139299021 0.1156073887 -7.835995653e-18 5.527173157e-06 0.01378606047 +0.02506328206 0.0291321838 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..aec72b7d7992ff4a76a296e7b83fc4313e6626f4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:16 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871364 SEC) : SETUP UNITCELL + DONE(0.0974055 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115619 SEC) : INIT PLANEWAVE + DONE(0.165225 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443833 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652031e+02 0.000000e+00 2.134e-01 4.564e-01 + GE2 -4.664069e+02 -1.203818e+00 9.789e-02 3.939e-01 + GE3 -4.664106e+02 -3.723106e-03 6.283e-02 4.653e-01 + GE4 -4.664103e+02 3.871025e-04 1.958e-03 3.289e-01 + GE5 -4.664096e+02 6.824647e-04 8.556e-04 3.253e-01 + GE6 -4.664100e+02 -4.230807e-04 1.425e-04 3.234e-01 + GE7 -4.664099e+02 1.437585e-04 3.365e-05 3.066e-01 + GE8 -4.664099e+02 -4.418102e-05 1.823e-05 3.023e-01 + GE9 -4.664099e+02 1.900231e-05 2.794e-06 3.001e-01 + GE10 -4.664099e+02 -3.897547e-06 3.754e-07 2.989e-01 + GE11 -4.664099e+02 -5.143727e-07 1.380e-07 2.998e-01 + GE12 -4.664099e+02 -3.805506e-08 1.084e-08 2.350e-01 +E_delta_band = -7.01057109e-02 Ry = -9.53837131e-01 eV +E_delta_NN= -1.94645549e-01 Ry = -2.64828855e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1712 11 0.56 1e+02 % + Run_lcao lcao_line 6.1611 1 6.2 1e+02 % + Potential init_pot 0.28166 2 0.14 4.6 % + PW_Basis recip2real 0.29116 17 0.017 4.7 % + PW_Basis gathers_scatterp 0.12637 17 0.0074 2 % + Potential v_of_rho 1.047 14 0.075 17 % + XC_Functional v_xc 0.30246 15 0.02 4.9 % + H_Hartree_pw v_hartree 0.70084 14 0.05 11 % + PW_Basis real2recip 0.7029 41 0.017 11 % + PW_Basis gatherp_scatters 0.27614 41 0.0067 4.5 % + ORB_control set_orb_tables 1.0906 1 1.1 18 % + ORB_gen_tables gen_tables 1.0906 1 1.1 18 % + ORB_table_phi init_Table 0.47582 1 0.48 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.47071 126 0.0037 7.6 % + ORB_table_beta init_Table_Beta 0.17993 1 0.18 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.17835 56 0.0032 2.9 % + ORB_table_alpha init_Table_Alpha 0.24847 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.24654 66 0.0037 4 % + LOOP_ions opt_ions 4.5492 1 4.5 74 % + ESolver_KS_LCAO Run 4.0981 1 4.1 66 % + HSolverLCAO solve 1.631 12 0.14 26 % + HamiltLCAO updateHk 0.91464 12 0.076 15 % + LCAO_Hamilt cal_Hgamma 0.88494 12 0.074 14 % + Gint_interface cal_gint 0.96888 25 0.039 16 % + Gint_Gamma distri_vl_value 0.13592 12 0.011 2.2 % + Gint_Gamma distri_vl 2.1504 6 0.36 35 % + LCAO_Deepks cal_projected_DM 4.3768 14 0.31 71 % + LCAO_gen_fixedH add_v_delta 2.0061 6 0.33 33 % + LCAO_DESCRIPTOR add_v_delta 2.0062 6 0.33 33 % + ElecStateLCAO psiToRho 0.69708 12 0.058 11 % + Charge mix_rho 0.8512 11 0.077 14 % + LOOP_ions force_stress 0.45093 1 0.45 7.3 % + Force_Stress_LCAO getForceStress 0.4509 1 0.45 7.3 % + Force_LCAO_gamma ftable_gamma 0.23613 1 0.24 3.8 % + Force_LCAO_gamma cal_fvl_dphi 0.18864 1 0.19 3.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:16 2022 + FINISH Time : Wed Sep 28 11:13:22 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/203/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..18576df8173f70d9adf689e7a663fcf1904fe9b7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.50291 0.786401 0.259745 +H 0.557507 0.804196 0.293959 +H 0.492368 0.838176 0.222051 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bbd73324b3f0450c34a436494ff03ea9f6499280 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2593 2 + 2 -12.9155 2 + 3 -9.18771 2 + 4 -6.73871 2 + 5 1.23407 0 + 6 4.3264 0 + 7 11.0869 0 + 8 11.3449 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..75a1ec33726d6a65cea17c3750a517a56fc9eb42 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.0814847469 22.0192388496 7.27286285593 0 0 0 0 + tauc_H1 15.6101958743 22.5174960605 8.23084941457 0 0 0 0 + tauc_H2 13.7863057556 23.4689227758 6.21743510209 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0877353712148 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0881315322773 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106239554482 (SEC) + + DONE : INIT CHARGE Time : 0.155642543759 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.435694 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 4 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00151 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000764 + + Density error is 0.213725851911 + + Energy Rydberg eV + E_KohnSham -34.1913496544 -465.197177611 + E_Harris -34.3808212894 -467.775071456 + E_Fermi -0.401660561629 -5.46487230004 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00136491988311 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100276239175 + + Density error is 0.0980467327788 + + Energy Rydberg eV + E_KohnSham -34.2803994548 -466.408762302 + E_Harris -34.287232867 -466.501735644 + E_Fermi -0.211495269254 -2.8775407619 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00126974134196 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000963207691417 + + Density error is 0.0629707677776 + + Energy Rydberg eV + E_KohnSham -34.2807145935 -466.413049984 + E_Harris -34.2851351431 -466.473194646 + E_Fermi -0.201339081054 -2.73935873242 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00110642763024 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914620890306 + + Density error is 0.00196258375649 + + Energy Rydberg eV + E_KohnSham -34.2806828371 -466.412617915 + E_Harris -34.2806832639 -466.412623722 + E_Fermi -0.165774591129 -2.25547902297 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00110572320181 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000915532009148 + + Density error is 0.000892594048881 + + Energy Rydberg eV + E_KohnSham -34.280629758 -466.411895737 + E_Harris -34.2806309013 -466.411911293 + E_Fermi -0.16526898405 -2.24859988575 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00110364486538 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914799146227 + + Density error is 0.000139897110936 + + Energy Rydberg eV + E_KohnSham -34.2806606598 -466.412316178 + E_Harris -34.2806606759 -466.412316397 + E_Fermi -0.165133004899 -2.24674979448 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011035860597 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914994734785 + + Density error is 3.55460670603e-05 + + Energy Rydberg eV + E_KohnSham -34.2806503887 -466.412176432 + E_Harris -34.280650395 -466.412176519 + E_Fermi -0.165034477107 -2.24540925511 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011035497496 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914921525481 + + Density error is 1.44033861774e-05 + + Energy Rydberg eV + E_KohnSham -34.2806536746 -466.412221139 + E_Harris -34.2806536755 -466.412221151 + E_Fermi -0.165069217122 -2.24588191726 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00110353064557 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914921178411 + + Density error is 1.67216698389e-06 + + Energy Rydberg eV + E_KohnSham -34.2806523722 -466.412203419 + E_Harris -34.2806523722 -466.412203419 + E_Fermi -0.165054101002 -2.2456762519 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00110352821026 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914922870818 + + Density error is 1.62513562736e-07 + + Energy Rydberg eV + E_KohnSham -34.2806525835 -466.412206294 + E_Harris -34.2806525835 -466.412206294 + E_Fermi -0.165052574756 -2.24565548625 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00110352862906 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009149233996 + + Density error is 4.16913715841e-08 + + Energy Rydberg eV + E_KohnSham -34.280652611 -466.412206668 + E_Harris -34.280652611 -466.412206668 + E_band -7.95273188649 -108.202468323 + E_one_elec -69.1694847005 -941.099119651 + E_Hartree +35.9797667915 +489.529841075 + E_xc -8.19997679655 -111.566407901 + E_Ewald +7.23361426024 +98.4183710734 + E_demet -1.08112697967e-73 -1.4709487185e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194611688562 -2.64782786184 + E_Fermi -0.16505256581 -2.24565536454 + + charge density convergence is achieved + final etot is -466.412206668 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2593 2.00000 + 2 -12.9155 2.00000 + 3 -9.18771 2.00000 + 4 -6.73871 2.00000 + 5 1.23407 0.00000 + 6 4.32640 0.00000 + 7 11.0869 0.00000 + 8 11.3449 0.00000 + + EFERMI = -2.245655364535997 eV + OUT.ABACUS/ final etot is -466.4122066683605 eV + correction force for each atom along direction 1 is 1.91713e-05 + correction force for each atom along direction 2 is 0.000179232 + correction force for each atom along direction 3 is -8.76024e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.76663526 -0.27858691 +0.77800904 + H1 -0.54382883 -0.28320163 -0.28131542 + H2 -0.22280643 +0.56178854 -0.49669362 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4122066683605 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5098 11 0.50 1.0e+02% + Run_lcao lcao_line 5.4998 1 5.5 1.e+02% + Potential init_pot 0.28518 2 0.14 5.2% + PW_Basis recip2real 0.26636 16 0.017 4.8% + PW_Basis gathers_scatterp 0.11476 16 0.0072 2.1% + Potential v_of_rho 0.88192 13 0.068 16.% + XC_Functional v_xc 0.24675 14 0.018 4.5% + H_Hartree_pw v_hartree 0.59585 13 0.046 11.% + PW_Basis real2recip 0.56049 38 0.015 10.% + PW_Basis gatherp_scatters 0.21810 38 0.0057 4.0% + ORB_control set_orb_tables 1.1095 1 1.1 20.% + ORB_gen_tables gen_tables 1.1095 1 1.1 20.% + ORB_table_phi init_Table 0.49122 1 0.49 8.9% + ORB_table_phi cal_ST_Phi12_R 0.48622 126 0.0039 8.8% + ORB_table_beta init_Table_Beta 0.18605 1 0.19 3.4% + ORB_table_beta VNL_PhiBeta_R 0.18457 56 0.0033 3.3% + ORB_table_alpha init_Table_Alpha 0.25291 1 0.25 4.6% + ORB_table_alpha S_PhiAlpha_R 0.25100 66 0.0038 4.6% + LOOP_ions opt_ions 3.8778 1 3.9 70.% + ESolver_KS_LCAO Run 3.4284 1 3.4 62.% + HSolverLCAO solve 1.4547 11 0.13 26.% + HamiltLCAO updateHk 0.82036 11 0.075 15.% + LCAO_Hamilt cal_Hgamma 0.78306 11 0.071 14.% + Gint_interface cal_gint 1.0400 23 0.045 19.% + Gint_Gamma distri_vl 1.6764 6 0.28 30.% + LCAO_Deepks cal_projected_DM 3.7243 13 0.29 68.% + LCAO_gen_fixedH add_v_delta 1.5374 6 0.26 28.% + LCAO_DESCRIPTOR add_v_delta 1.5374 6 0.26 28.% + ElecStateLCAO psiToRho 0.61967 11 0.056 11.% + Charge mix_rho 0.65237 10 0.065 12.% + LOOP_ions force_stress 0.44917 1 0.45 8.2% + Force_Stress_LCAO getForceStress 0.44915 1 0.45 8.2% + Force_LCAO_gamma ftable_gamma 0.23656 1 0.24 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.20444 1 0.20 3.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:48 2022 + Finish Time : Wed Sep 28 11:11:53 2022 + Total Time : 0 h 0 mins 5 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..f18e0f109f7b871d9950738694a718dc54a0eeef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123793 ima = 3.62019e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123052648007 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111895880965 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112497500124 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112733330343 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112691457545 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112715454225 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112710001008 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112712678676 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112712051621 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112711980149 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112711972822 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/STRU new file mode 100644 index 0000000000000000000000000000000000000000..71554575003e82778da0434e401d54022b08fe07 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.918515253132 22.019238849576 7.272862855921 0 0 0 +H +0.0 +2 +-12.389804125732 22.517496060505 8.230849414561 0 0 0 +-14.213694244360 23.468922775810 6.217435102090 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/conv new file mode 100644 index 0000000000000000000000000000000000000000..3e4759d87f479effb3d7654031be25338166540a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/conv @@ -0,0 +1 @@ +204 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..91ecd0e51eef4c09f61aed9d98b70482d722990d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750600037 0.01266337512 1.266341322 1.356246669 1.469165149 0.008705035675 0.01798961277 0.03907419923 +-1.717918859e-18 0.0009902525354 0.002618834384 0.0123726688 0.04491703961 4.595788666e-19 2.10903956e-06 6.064890594e-06 +0.00162074953 0.005995996501 + +H atom_index 1 n_descriptor 18 +1.216630383 0.03553217003 0.09748951026 0.1350208206 0.3094106334 0.0207977338 0.02634059772 0.03876254796 +-4.793669812e-17 4.281718137e-05 0.09268895775 0.1139472332 0.115674493 -2.271635738e-18 5.582908625e-06 0.01375571458 +0.02498944457 0.02913874574 + +H atom_index 2 n_descriptor 18 +1.259526247 0.03407476013 0.1119176174 0.1543588715 0.3238912472 0.02281776618 0.02884883384 0.03728631866 +-4.247240922e-17 4.676351099e-05 0.1034279158 0.1157425868 0.1324545166 -2.047415006e-18 3.401587598e-06 0.01317486563 +0.02663406874 0.03117584659 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..31c05593601ac69696242971851b8502de046cbe Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..8905c291423f8e120cdf7f34ff457d7f9d77e986 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..5e7a9f5345a5d2334e13a8afef62cd599008f2d7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..373654e12b62225b5e39463c8d4b6315d696d14b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..40d72342d19ddd93e2048417ca4ea82b03d778dc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0877574 SEC) : SETUP UNITCELL + DONE(0.088149 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.10626 SEC) : INIT PLANEWAVE + DONE(0.155773 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.435757 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651972e+02 0.000000e+00 2.137e-01 4.344e-01 + GE2 -4.664088e+02 -1.211585e+00 9.805e-02 3.490e-01 + GE3 -4.664130e+02 -4.287682e-03 6.297e-02 4.061e-01 + GE4 -4.664126e+02 4.320691e-04 1.963e-03 2.963e-01 + GE5 -4.664119e+02 7.221780e-04 8.926e-04 2.952e-01 + GE6 -4.664123e+02 -4.204413e-04 1.399e-04 2.900e-01 + GE7 -4.664122e+02 1.397458e-04 3.555e-05 2.769e-01 + GE8 -4.664122e+02 -4.470635e-05 1.440e-05 2.670e-01 + GE9 -4.664122e+02 1.772016e-05 1.672e-06 2.692e-01 + GE10 -4.664122e+02 -2.875009e-06 1.625e-07 2.689e-01 + GE11 -4.664122e+02 -3.747973e-07 4.169e-08 2.138e-01 +E_delta_band = -7.00395229e-02 Ry = -9.52936597e-01 eV +E_delta_NN= -1.94611689e-01 Ry = -2.64782786e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5098 11 0.5 1e+02 % + Run_lcao lcao_line 5.4998 1 5.5 1e+02 % + Potential init_pot 0.28518 2 0.14 5.2 % + PW_Basis recip2real 0.26636 16 0.017 4.8 % + PW_Basis gathers_scatterp 0.11476 16 0.0072 2.1 % + Potential v_of_rho 0.88192 13 0.068 16 % + XC_Functional v_xc 0.24675 14 0.018 4.5 % + H_Hartree_pw v_hartree 0.59585 13 0.046 11 % + PW_Basis real2recip 0.56049 38 0.015 10 % + PW_Basis gatherp_scatters 0.2181 38 0.0057 4 % + ORB_control set_orb_tables 1.1095 1 1.1 20 % + ORB_gen_tables gen_tables 1.1095 1 1.1 20 % + ORB_table_phi init_Table 0.49122 1 0.49 8.9 % + ORB_table_phi cal_ST_Phi12_R 0.48622 126 0.0039 8.8 % + ORB_table_beta init_Table_Beta 0.18605 1 0.19 3.4 % + ORB_table_beta VNL_PhiBeta_R 0.18457 56 0.0033 3.3 % + ORB_table_alpha init_Table_Alpha 0.25291 1 0.25 4.6 % + ORB_table_alpha S_PhiAlpha_R 0.251 66 0.0038 4.6 % + LOOP_ions opt_ions 3.8778 1 3.9 70 % + ESolver_KS_LCAO Run 3.4284 1 3.4 62 % + HSolverLCAO solve 1.4547 11 0.13 26 % + HamiltLCAO updateHk 0.82036 11 0.075 15 % + LCAO_Hamilt cal_Hgamma 0.78306 11 0.071 14 % + Gint_interface cal_gint 1.04 23 0.045 19 % + Gint_Gamma distri_vl 1.6764 6 0.28 30 % + LCAO_Deepks cal_projected_DM 3.7243 13 0.29 68 % + LCAO_gen_fixedH add_v_delta 1.5374 6 0.26 28 % + LCAO_DESCRIPTOR add_v_delta 1.5374 6 0.26 28 % + ElecStateLCAO psiToRho 0.61967 11 0.056 11 % + Charge mix_rho 0.65237 10 0.065 12 % + LOOP_ions force_stress 0.44917 1 0.45 8.2 % + Force_Stress_LCAO getForceStress 0.44915 1 0.45 8.2 % + Force_LCAO_gamma ftable_gamma 0.23656 1 0.24 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.20444 1 0.2 3.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:48 2022 + FINISH Time : Wed Sep 28 11:11:53 2022 + TOTAL Time : 5 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/204/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..1914d8a7bfae625d80dca8ddd8660c08d42e99a8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.51888 0.777448 0.250403 +H 0.577906 0.784974 0.276862 +H 0.529025 0.782782 0.186843 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ac068ae3baea839934e4955e8a191845d6df9f71 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3937 2 + 2 -13.1499 2 + 3 -9.12284 2 + 4 -6.76773 2 + 5 1.39653 0 + 6 4.57909 0 + 7 11.0494 0 + 8 11.2988 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..455f0533f8d686799076a3b7bb2f4d2d28b2dcd1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:06 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.5286497689 21.7685406894 7.01127942481 0 0 0 0 + tauc_H1 16.1813788787 21.9792797229 7.75214561353 0 0 0 0 + tauc_H2 14.8126872849 21.9178823518 5.23161738143 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.113212264589 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.113753110753 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.138861611835 (SEC) + + DONE : INIT CHARGE Time : 0.182077921418 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.468964 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000843 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000608 + + Density error is 0.216726492075 + + Energy Rydberg eV + E_KohnSham -34.1885382162 -465.158926031 + E_Harris -34.384448293 -467.824419371 + E_Fermi -0.412887793082 -5.61762662056 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00129637315307 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00081291405416 + + Density error is 0.0979739811253 + + Energy Rydberg eV + E_KohnSham -34.2803173166 -466.407644754 + E_Harris -34.2870360244 -466.499057463 + E_Fermi -0.219179019714 -2.98208355016 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00124783493813 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783525411149 + + Density error is 0.062832533579 + + Energy Rydberg eV + E_KohnSham -34.2806969962 -466.41281056 + E_Harris -34.285036121 -466.471847381 + E_Fermi -0.207477197916 -2.82287209673 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00118781245479 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000752759871171 + + Density error is 0.00201682862788 + + Energy Rydberg eV + E_KohnSham -34.2806998225 -466.412849014 + E_Harris -34.2807013221 -466.412869417 + E_Fermi -0.171754791742 -2.3368438265 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00119093848843 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000754698063918 + + Density error is 0.000987359936438 + + Energy Rydberg eV + E_KohnSham -34.2806255215 -466.411838097 + E_Harris -34.2806273317 -466.411862725 + E_Fermi -0.170906148229 -2.32529743914 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00118957042486 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000753937167625 + + Density error is 0.000131230742249 + + Energy Rydberg eV + E_KohnSham -34.2806710268 -466.412457228 + E_Harris -34.2806710497 -466.41245754 + E_Fermi -0.170975967032 -2.32624737269 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00118975440022 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000754112057561 + + Density error is 4.31327982703e-05 + + Energy Rydberg eV + E_KohnSham -34.2806557445 -466.412249301 + E_Harris -34.2806557553 -466.412249448 + E_Fermi -0.170840435924 -2.32440337738 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00118964907995 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000754045830634 + + Density error is 1.65811303076e-05 + + Energy Rydberg eV + E_KohnSham -34.2806594176 -466.412299277 + E_Harris -34.2806594189 -466.412299294 + E_Fermi -0.170892510087 -2.3251118827 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00118965098354 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000754052510033 + + Density error is 1.23708007888e-06 + + Energy Rydberg eV + E_KohnSham -34.2806578583 -466.412278061 + E_Harris -34.2806578583 -466.412278061 + E_Fermi -0.170873999489 -2.32486003309 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0011896526785 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000754053982181 + + Density error is 1.83348323087e-07 + + Energy Rydberg eV + E_KohnSham -34.2806581289 -466.412281743 + E_Harris -34.2806581289 -466.412281743 + E_Fermi -0.170873173875 -2.32484880004 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00118965347159 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000754054411693 + + Density error is 3.18201543543e-08 + + Energy Rydberg eV + E_KohnSham -34.2806581436 -466.412281943 + E_Harris -34.2806581436 -466.412281943 + E_band -8.00167847673 -108.868420847 + E_one_elec -69.5126732108 -945.768438879 + E_Hartree +36.1443426517 +491.769010527 + E_xc -8.22643391173 -111.92637542 + E_Ewald +7.43797624093 +101.198858465 + E_demet -6.72301165639e-84 -9.14712662473e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195207186022 -2.65593002045 + E_Fermi -0.170873142256 -2.32484836984 + + charge density convergence is achieved + final etot is -466.412281943 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3937 2.00000 + 2 -13.1499 2.00000 + 3 -9.12284 2.00000 + 4 -6.76773 2.00000 + 5 1.39653 0.00000 + 6 4.57909 0.00000 + 7 11.0494 0.00000 + 8 11.2988 0.00000 + + EFERMI = -2.324848369842681 eV + OUT.ABACUS/ final etot is -466.4122819427720 eV + correction force for each atom along direction 1 is 9.55626e-05 + correction force for each atom along direction 2 is 4.37026e-05 + correction force for each atom along direction 3 is -5.70382e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.59139936 -0.13258987 +0.71906075 + H1 +0.46876877 +0.057176866 +0.24334658 + H2 +0.12263059 +0.075413005 -0.96240733 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4122819427720 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9499 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9399 1 6.9 1.e+02% + Potential init_pot 0.28734 2 0.14 4.1% + PW_Basis recip2real 0.27684 16 0.017 4.0% + PW_Basis gathers_scatterp 0.12117 16 0.0076 1.7% + Charge atomic_rho 0.10163 1 0.10 1.5% + Potential v_of_rho 1.0073 13 0.077 14.% + XC_Functional v_xc 0.29386 14 0.021 4.2% + H_Hartree_pw v_hartree 0.67060 13 0.052 9.6% + PW_Basis real2recip 0.71292 38 0.019 10.% + PW_Basis gatherp_scatters 0.28400 38 0.0075 4.1% + ORB_control set_orb_tables 1.0881 1 1.1 16.% + ORB_gen_tables gen_tables 1.0881 1 1.1 16.% + ORB_table_phi init_Table 0.46706 1 0.47 6.7% + ORB_table_phi cal_ST_Phi12_R 0.46199 126 0.0037 6.6% + ORB_table_beta init_Table_Beta 0.18142 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.17993 56 0.0032 2.6% + ORB_table_alpha init_Table_Alpha 0.24776 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24583 66 0.0037 3.5% + LOOP_ions opt_ions 5.3063 1 5.3 76.% + ESolver_KS_LCAO Run 4.7630 1 4.8 69.% + HSolverLCAO solve 2.3071 11 0.21 33.% + HamiltLCAO updateHk 1.2187 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1911 11 0.11 17.% + Gint_interface cal_gint 2.0982 23 0.091 30.% + Gint_Gamma distri_vl 2.2990 6 0.38 33.% + LCAO_Deepks cal_projected_DM 5.1486 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1520 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1521 6 0.36 31.% + ElecStateLCAO psiToRho 1.0720 11 0.097 15.% + Charge mix_rho 0.90802 10 0.091 13.% + LOOP_ions force_stress 0.54312 1 0.54 7.8% + Force_Stress_LCAO getForceStress 0.54308 1 0.54 7.8% + Force_LCAO_gamma ftable_gamma 0.32300 1 0.32 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.30956 1 0.31 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:06 2022 + Finish Time : Wed Sep 28 11:02:13 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..fc72aa18608d330a6e1cfc5a58e6a7a8ad2dbbe4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124034 ima = 3.66598e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123151496937 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111968016088 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112501612925 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112775085295 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112710860139 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011274679275 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112740904758 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112744094371 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112743359714 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112743319016 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112743308835 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d2064f0f559f39e39c3d86ab34c1ff1ce76abaae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.471350231062 21.768540689371 7.011279424807 0 0 0 +H +0.0 +2 +-11.818621121319 21.979279722910 7.752145613504 0 0 0 +-13.187312715088 21.917882351803 5.231617381419 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/conv new file mode 100644 index 0000000000000000000000000000000000000000..cec26e98dd7ab0f0c74944521e1a1502e3c7efac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/conv @@ -0,0 +1 @@ +205 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..3ca17b0f1a9fb77e585c7628b94f9bec2aa95659 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748997915 0.01275477312 1.282664273 1.369292057 1.469790583 0.008540734518 0.01881830628 0.03901121341 +-1.641770226e-18 0.00110729752 0.002655002561 0.01273311982 0.04611869781 5.637666008e-19 2.154129297e-06 6.150457546e-06 +0.001659695617 0.005957438198 + +H atom_index 1 n_descriptor 18 +1.253161088 0.0340946939 0.1096816003 0.1514628562 0.321979128 0.02246737399 0.02849759101 0.03724101096 +-1.975356908e-17 4.750252423e-05 0.103304796 0.1150897441 0.1301080544 -3.436975322e-18 3.988590029e-06 0.01314987043 +0.02663975724 0.03092436918 + +H atom_index 2 n_descriptor 18 +1.265068918 0.03368698972 0.1139317889 0.1571401157 0.3256906208 0.02301784035 0.02918763026 0.03691915755 +-2.625740929e-18 4.862618697e-05 0.1057131928 0.1161123066 0.1349853159 4.012995711e-18 3.317142663e-06 0.01313241196 +0.02706556344 0.03144030844 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f42df15c39143f1712ece12d312d1ba8700894a1 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..dd2a42838ed3fadb087d5ee7a1905be8ef539ba5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:06 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.113251 SEC) : SETUP UNITCELL + DONE(0.113772 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.138887 SEC) : INIT PLANEWAVE + DONE(0.182214 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.469028 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651589e+02 0.000000e+00 2.167e-01 5.232e-01 + GE2 -4.664076e+02 -1.248719e+00 9.797e-02 4.875e-01 + GE3 -4.664128e+02 -5.165806e-03 6.283e-02 5.577e-01 + GE4 -4.664128e+02 -3.845388e-05 2.017e-03 4.144e-01 + GE5 -4.664118e+02 1.010917e-03 9.874e-04 4.155e-01 + GE6 -4.664125e+02 -6.191310e-04 1.312e-04 4.063e-01 + GE7 -4.664122e+02 2.079268e-04 4.313e-05 3.999e-01 + GE8 -4.664123e+02 -4.997631e-05 1.658e-05 3.930e-01 + GE9 -4.664123e+02 2.121630e-05 1.237e-06 3.910e-01 + GE10 -4.664123e+02 -3.682048e-06 1.833e-07 3.952e-01 + GE11 -4.664123e+02 -1.996715e-07 3.182e-08 3.157e-01 +E_delta_band = -7.13372724e-02 Ry = -9.70593385e-01 eV +E_delta_NN= -1.95207186e-01 Ry = -2.65593002e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9499 11 0.63 1e+02 % + Run_lcao lcao_line 6.9399 1 6.9 1e+02 % + Potential init_pot 0.28734 2 0.14 4.1 % + PW_Basis recip2real 0.27684 16 0.017 4 % + PW_Basis gathers_scatterp 0.12117 16 0.0076 1.7 % + Charge atomic_rho 0.10163 1 0.1 1.5 % + Potential v_of_rho 1.0073 13 0.077 14 % + XC_Functional v_xc 0.29386 14 0.021 4.2 % + H_Hartree_pw v_hartree 0.6706 13 0.052 9.6 % + PW_Basis real2recip 0.71292 38 0.019 10 % + PW_Basis gatherp_scatters 0.284 38 0.0075 4.1 % + ORB_control set_orb_tables 1.0881 1 1.1 16 % + ORB_gen_tables gen_tables 1.0881 1 1.1 16 % + ORB_table_phi init_Table 0.46706 1 0.47 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.46199 126 0.0037 6.6 % + ORB_table_beta init_Table_Beta 0.18142 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.17993 56 0.0032 2.6 % + ORB_table_alpha init_Table_Alpha 0.24776 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24583 66 0.0037 3.5 % + LOOP_ions opt_ions 5.3063 1 5.3 76 % + ESolver_KS_LCAO Run 4.763 1 4.8 69 % + HSolverLCAO solve 2.3071 11 0.21 33 % + HamiltLCAO updateHk 1.2187 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1911 11 0.11 17 % + Gint_interface cal_gint 2.0982 23 0.091 30 % + Gint_Gamma distri_vl 2.299 6 0.38 33 % + LCAO_Deepks cal_projected_DM 5.1486 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.152 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1521 6 0.36 31 % + ElecStateLCAO psiToRho 1.072 11 0.097 15 % + Charge mix_rho 0.90802 10 0.091 13 % + LOOP_ions force_stress 0.54312 1 0.54 7.8 % + Force_Stress_LCAO getForceStress 0.54308 1 0.54 7.8 % + Force_LCAO_gamma ftable_gamma 0.323 1 0.32 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.30956 1 0.31 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:06 2022 + FINISH Time : Wed Sep 28 11:02:13 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/205/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ce6ac8dc255614a78df1cb5ba9b913eca2894b0b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.541546 0.771752 0.238751 +H 0.589681 0.728456 0.245966 +H 0.499118 0.736476 0.197949 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f6b69f156c8e4244dd4b4ee6905e7605841a7998 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.144 2 + 2 -12.6722 2 + 3 -9.27306 2 + 4 -6.71381 2 + 5 1.05331 0 + 6 4.08591 0 + 7 11.1207 0 + 8 11.3819 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..80b52120370c70337c07bf20979d16996ff4e37d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.163301982 21.6090663281 6.68502164853 0 0 0 0 + tauc_H1 16.5110630157 20.3967713618 6.88704980977 0 0 0 0 + tauc_H2 13.9753036043 20.6213224952 5.54257472503 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.086850610028 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0900505858027 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.108121861358 (SEC) + + DONE : INIT CHARGE Time : 0.157949397599 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.435326 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108 + + Density error is 0.21195836954 + + Energy Rydberg eV + E_KohnSham -34.1892921313 -465.169183572 + E_Harris -34.3751665077 -467.698134203 + E_Fermi -0.392563094598 -5.34109491104 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000924783996073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111345008267 + + Density error is 0.0984432565664 + + Energy Rydberg eV + E_KohnSham -34.2777391867 -466.372567496 + E_Harris -34.2848193851 -466.468898539 + E_Fermi -0.203884243562 -2.77398744486 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000877380629196 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105085880343 + + Density error is 0.0634202571694 + + Energy Rydberg eV + E_KohnSham -34.278151483 -466.378177076 + E_Harris -34.2827070399 -466.440158608 + E_Fermi -0.196214989769 -2.66964189388 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000814702047482 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946033741244 + + Density error is 0.00192064737395 + + Energy Rydberg eV + E_KohnSham -34.2780707157 -466.377078181 + E_Harris -34.2780712162 -466.37708499 + E_Fermi -0.160688997879 -2.18628597706 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000814880042589 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000944808309887 + + Density error is 0.000923702373418 + + Energy Rydberg eV + E_KohnSham -34.2780312129 -466.376540717 + E_Harris -34.278031704 -466.3765474 + E_Fermi -0.160583332944 -2.18484833188 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000814098227337 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943270924133 + + Density error is 0.00015743185117 + + Energy Rydberg eV + E_KohnSham -34.2780501479 -466.376798341 + E_Harris -34.2780501621 -466.376798534 + E_Fermi -0.160201610323 -2.17965472917 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000814318451967 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943377001709 + + Density error is 3.19786499866e-05 + + Energy Rydberg eV + E_KohnSham -34.2780441073 -466.376716155 + E_Harris -34.2780441108 -466.376716202 + E_Fermi -0.160166916043 -2.17918268928 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000814250497201 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943307455244 + + Density error is 1.26773608759e-05 + + Energy Rydberg eV + E_KohnSham -34.2780468703 -466.376753747 + E_Harris -34.2780468709 -466.376753756 + E_Fermi -0.1601845745 -2.1794229449 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00081425288636 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943302032294 + + Density error is 2.70441138388e-06 + + Energy Rydberg eV + E_KohnSham -34.2780458086 -466.376739302 + E_Harris -34.2780458086 -466.376739303 + E_Fermi -0.160173200472 -2.17926819331 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000814253842072 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943300337716 + + Density error is 4.72619725182e-07 + + Energy Rydberg eV + E_KohnSham -34.2780459654 -466.376741435 + E_Harris -34.2780459654 -466.376741435 + E_Fermi -0.160170573951 -2.17923245767 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000814254113903 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943300838091 + + Density error is 1.66976278276e-07 + + Energy Rydberg eV + E_KohnSham -34.2780459978 -466.376741876 + E_Harris -34.2780459978 -466.376741876 + E_Fermi -0.160170371792 -2.17922970715 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000814254161346 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943300897499 + + Density error is 1.15531245397e-08 + + Energy Rydberg eV + E_KohnSham -34.2780460012 -466.376741922 + E_Harris -34.2780460012 -466.376741922 + E_band -7.90889443234 -107.60602916 + E_one_elec -68.8430506211 -936.657756149 + E_Hartree +35.8218705844 +487.381552966 + E_xc -8.17481995008 -111.224131445 + E_Ewald +7.04316054827 +95.8271153853 + E_demet -5.82674989933e-64 -7.92769994519e-63 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194090977381 -2.64074322276 + E_Fermi -0.160170215975 -2.17922758715 + + charge density convergence is achieved + final etot is -466.376741922 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1440 2.00000 + 2 -12.6722 2.00000 + 3 -9.27306 2.00000 + 4 -6.71381 2.00000 + 5 1.05331 0.00000 + 6 4.08591 0.00000 + 7 11.1207 0.00000 + 8 11.3819 0.00000 + + EFERMI = -2.179227587153302 eV + OUT.ABACUS/ final etot is -466.3767419224874 eV + correction force for each atom along direction 1 is -3.53272e-05 + correction force for each atom along direction 2 is -3.64980e-05 + correction force for each atom along direction 3 is -2.87031e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.4990565 -0.75753493 -1.2117104 + H1 +0.60655324 -0.28193239 +0.21452666 + H2 +0.89250330 +1.0394673 +0.99718372 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3767419224874 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9618 11 0.54 1.0e+02% + Run_lcao lcao_line 5.9523 1 6.0 1.e+02% + Potential init_pot 0.28305 2 0.14 4.7% + PW_Basis recip2real 0.28001 17 0.016 4.7% + PW_Basis gathers_scatterp 0.11789 17 0.0069 2.0% + Potential v_of_rho 0.92934 14 0.066 16.% + XC_Functional v_xc 0.25332 15 0.017 4.2% + H_Hartree_pw v_hartree 0.63408 14 0.045 11.% + PW_Basis real2recip 0.59634 41 0.015 10.% + PW_Basis gatherp_scatters 0.22771 41 0.0056 3.8% + ORB_control set_orb_tables 1.1063 1 1.1 19.% + ORB_gen_tables gen_tables 1.1063 1 1.1 19.% + ORB_table_phi init_Table 0.48345 1 0.48 8.1% + ORB_table_phi cal_ST_Phi12_R 0.47858 126 0.0038 8.0% + ORB_table_beta init_Table_Beta 0.18853 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18705 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25626 1 0.26 4.3% + ORB_table_alpha S_PhiAlpha_R 0.25436 66 0.0039 4.3% + LOOP_ions opt_ions 4.3340 1 4.3 73.% + ESolver_KS_LCAO Run 3.8593 1 3.9 65.% + HSolverLCAO solve 1.7258 12 0.14 29.% + HamiltLCAO updateHk 0.94214 12 0.079 16.% + LCAO_Hamilt cal_Hgamma 0.90087 12 0.075 15.% + Gint_interface cal_gint 1.5107 25 0.060 25.% + Gint_Gamma distri_vl 2.0192 6 0.34 34.% + LCAO_Deepks cal_projected_DM 4.1971 14 0.30 70.% + LCAO_gen_fixedH add_v_delta 1.8860 6 0.31 32.% + LCAO_DESCRIPTOR add_v_delta 1.8860 6 0.31 32.% + ElecStateLCAO psiToRho 0.76916 12 0.064 13.% + Charge mix_rho 0.71172 11 0.065 12.% + LOOP_ions force_stress 0.47454 1 0.47 8.0% + Force_Stress_LCAO getForceStress 0.47451 1 0.47 8.0% + Force_LCAO_gamma ftable_gamma 0.25988 1 0.26 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.25320 1 0.25 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:48 2022 + Finish Time : Wed Sep 28 11:04:54 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..cd633ecce56ed90ea8414d644f3ff1a9d5a93441 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123829 ima = 3.66041e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123182624678 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111798903684 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112536720045 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756732685 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112732843817 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011274746139 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112742862523 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112745025099 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112744501955 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112744406583 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112744389072 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112744380525 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/STRU new file mode 100644 index 0000000000000000000000000000000000000000..27518a745a955c960ea71508ead3cf766b794209 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.836698018024 21.609066328120 6.685021648513 0 0 0 +H +0.0 +2 +-11.488936984324 20.396771361781 6.887049809768 0 0 0 +-14.024696395745 20.621322495216 5.542574725017 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/conv new file mode 100644 index 0000000000000000000000000000000000000000..b5fbe2561a03705ae05220460681a5ab77c3c5dd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/conv @@ -0,0 +1 @@ +206 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a316e41e9e876e246cc50bcdaaa1564942e3dbf3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752664567 0.01254943007 1.249115381 1.344221732 1.468716495 0.008999099542 0.01712897371 0.03916698058 +-2.397620774e-18 0.0008724526923 0.002595091886 0.01209354045 0.04378252757 -3.67327749e-19 2.064290061e-06 6.031505748e-06 +0.001575619117 0.005989030686 + +H atom_index 1 n_descriptor 18 +1.255856722 0.03442052086 0.1109774592 0.1525205779 0.322587335 0.02278815679 0.02861513098 0.03763264204 +-1.701885522e-17 4.506944199e-05 0.1014507424 0.1158038097 0.1307299744 1.744266509e-18 3.244635859e-06 0.01324486484 +0.0263250827 0.03099069315 + +H atom_index 2 n_descriptor 18 +1.179304365 0.03686546072 0.08653085437 0.1197437368 0.2948511525 0.01913917412 0.02412179167 0.04051619624 +2.808944028e-17 3.828876005e-05 0.08206777126 0.1020712606 0.1123814066 3.720230721e-18 6.513089204e-06 0.01493684249 +0.0232446235 0.02710029176 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e8454b4918463385274e9721fd3f698f956d3d8f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0868725 SEC) : SETUP UNITCELL + DONE(0.0900667 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.108143 SEC) : INIT PLANEWAVE + DONE(0.158079 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.435396 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651692e+02 0.000000e+00 2.120e-01 4.376e-01 + GE2 -4.663726e+02 -1.203384e+00 9.844e-02 3.620e-01 + GE3 -4.663782e+02 -5.609579e-03 6.342e-02 4.211e-01 + GE4 -4.663771e+02 1.098894e-03 1.921e-03 3.111e-01 + GE5 -4.663765e+02 5.374641e-04 9.237e-04 3.090e-01 + GE6 -4.663768e+02 -2.576239e-04 1.574e-04 3.063e-01 + GE7 -4.663767e+02 8.218582e-05 3.198e-05 2.872e-01 + GE8 -4.663768e+02 -3.759183e-05 1.268e-05 2.832e-01 + GE9 -4.663767e+02 1.444464e-05 2.704e-06 2.849e-01 + GE10 -4.663767e+02 -2.132969e-06 4.726e-07 2.853e-01 + GE11 -4.663767e+02 -4.408486e-07 1.670e-07 2.831e-01 + GE12 -4.663767e+02 -4.632690e-08 1.155e-08 2.269e-01 +E_delta_band = -6.88844147e-02 Ry = -9.37220543e-01 eV +E_delta_NN= -1.94090977e-01 Ry = -2.64074322e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9618 11 0.54 1e+02 % + Run_lcao lcao_line 5.9523 1 6 1e+02 % + Potential init_pot 0.28305 2 0.14 4.7 % + PW_Basis recip2real 0.28001 17 0.016 4.7 % + PW_Basis gathers_scatterp 0.11789 17 0.0069 2 % + Potential v_of_rho 0.92934 14 0.066 16 % + XC_Functional v_xc 0.25332 15 0.017 4.2 % + H_Hartree_pw v_hartree 0.63408 14 0.045 11 % + PW_Basis real2recip 0.59634 41 0.015 10 % + PW_Basis gatherp_scatters 0.22771 41 0.0056 3.8 % + ORB_control set_orb_tables 1.1063 1 1.1 19 % + ORB_gen_tables gen_tables 1.1063 1 1.1 19 % + ORB_table_phi init_Table 0.48345 1 0.48 8.1 % + ORB_table_phi cal_ST_Phi12_R 0.47858 126 0.0038 8 % + ORB_table_beta init_Table_Beta 0.18853 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18705 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.25626 1 0.26 4.3 % + ORB_table_alpha S_PhiAlpha_R 0.25436 66 0.0039 4.3 % + LOOP_ions opt_ions 4.334 1 4.3 73 % + ESolver_KS_LCAO Run 3.8593 1 3.9 65 % + HSolverLCAO solve 1.7258 12 0.14 29 % + HamiltLCAO updateHk 0.94214 12 0.079 16 % + LCAO_Hamilt cal_Hgamma 0.90087 12 0.075 15 % + Gint_interface cal_gint 1.5107 25 0.06 25 % + Gint_Gamma distri_vl 2.0192 6 0.34 34 % + LCAO_Deepks cal_projected_DM 4.1971 14 0.3 70 % + LCAO_gen_fixedH add_v_delta 1.886 6 0.31 32 % + LCAO_DESCRIPTOR add_v_delta 1.886 6 0.31 32 % + ElecStateLCAO psiToRho 0.76916 12 0.064 13 % + Charge mix_rho 0.71172 11 0.065 12 % + LOOP_ions force_stress 0.47454 1 0.47 8 % + Force_Stress_LCAO getForceStress 0.47451 1 0.47 8 % + Force_LCAO_gamma ftable_gamma 0.25988 1 0.26 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.2532 1 0.25 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:48 2022 + FINISH Time : Wed Sep 28 11:04:54 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/206/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..38d36a113576148f9b9feac7525c3e16348791a9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.564399 0.772308 0.226108 +H 0.593971 0.716138 0.21495 +H 0.502531 0.758242 0.238914 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..36900f94f0aeacef91c15bc3bd7932d7b45d54b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3951 2 + 2 -13.2912 2 + 3 -9.02246 2 + 4 -6.76799 2 + 5 1.44226 0 + 6 4.65346 0 + 7 11.0417 0 + 8 11.28 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a19583d67eaa6deb129ca2702591144a525a1ddf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:32 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.8031845769 21.6246160571 6.33101281435 0 0 0 0 + tauc_H1 16.6311953974 20.0518551788 6.01860059482 0 0 0 0 + tauc_H2 14.0708593606 21.2307782183 6.68959972016 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0733601451661 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0869977430904 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.102610175634 (SEC) + + DONE : INIT CHARGE Time : 0.143990249695 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388947 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 0 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000893 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00184 + + Density error is 0.216981383938 + + Energy Rydberg eV + E_KohnSham -34.1893968915 -465.170608908 + E_Harris -34.3852683009 -467.835576151 + E_Fermi -0.414018608361 -5.63301215174 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000993475661321 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00148088436442 + + Density error is 0.0977383062306 + + Energy Rydberg eV + E_KohnSham -34.2798959648 -466.401911969 + E_Harris -34.2865075039 -466.491866573 + E_Fermi -0.221596387815 -3.01497353051 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00093957977873 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00135522072444 + + Density error is 0.0624954326282 + + Energy Rydberg eV + E_KohnSham -34.2801547865 -466.405433418 + E_Harris -34.2844015537 -466.463213651 + E_Fermi -0.208325389441 -2.83441233447 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000853288632927 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113497278873 + + Density error is 0.00205507249931 + + Energy Rydberg eV + E_KohnSham -34.2801820576 -466.405804461 + E_Harris -34.2801844331 -466.405836782 + E_Fermi -0.172781186574 -2.35080864461 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000852356592896 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113142045161 + + Density error is 0.000897110282858 + + Energy Rydberg eV + E_KohnSham -34.2801123637 -466.404856227 + E_Harris -34.2801141706 -466.404880811 + E_Fermi -0.171712998572 -2.33627520124 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000851360479207 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112951386038 + + Density error is 0.000166118416802 + + Energy Rydberg eV + E_KohnSham -34.280158853 -466.405488746 + E_Harris -34.2801589162 -466.405489606 + E_Fermi -0.171912746953 -2.33899291739 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000851431552039 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112917142576 + + Density error is 4.53234513337e-05 + + Energy Rydberg eV + E_KohnSham -34.280141728 -466.405255748 + E_Harris -34.2801417394 -466.405255903 + E_Fermi -0.171743542964 -2.33669077902 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000851383583761 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112919708287 + + Density error is 1.76543072054e-05 + + Energy Rydberg eV + E_KohnSham -34.2801465139 -466.405320865 + E_Harris -34.2801465153 -466.405320883 + E_Fermi -0.171796565205 -2.33741218362 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000851372231393 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112916066788 + + Density error is 2.29991244649e-06 + + Energy Rydberg eV + E_KohnSham -34.2801449212 -466.405299194 + E_Harris -34.2801449212 -466.405299194 + E_Fermi -0.171778594898 -2.33716768505 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000851372056919 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112915334075 + + Density error is 3.3461968241e-07 + + Energy Rydberg eV + E_KohnSham -34.2801451675 -466.405302545 + E_Harris -34.2801451675 -466.405302545 + E_Fermi -0.171776241849 -2.33713567018 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000851372557386 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112915369082 + + Density error is 1.29324412895e-07 + + Energy Rydberg eV + E_KohnSham -34.2801451984 -466.405302966 + E_Harris -34.2801451984 -466.405302966 + E_Fermi -0.171776142043 -2.33713431224 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000851372646011 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112915346162 + + Density error is 1.00635453922e-08 + + Energy Rydberg eV + E_KohnSham -34.2801452007 -466.405302997 + E_Harris -34.2801452007 -466.405302997 + E_band -8.00793482138 -108.953542783 + E_one_elec -69.5946714921 -946.884082731 + E_Hartree +36.1867338589 +492.345772491 + E_xc -8.23327945779 -112.019513852 + E_Ewald +7.48478770438 +101.8357611 + E_demet -1.89526934429e-86 -2.57864623271e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195322229438 -2.65749526642 + E_Fermi -0.171776026091 -2.33713273463 + + charge density convergence is achieved + final etot is -466.405302997 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3951 2.00000 + 2 -13.2912 2.00000 + 3 -9.02246 2.00000 + 4 -6.76799 2.00000 + 5 1.44226 0.00000 + 6 4.65346 0.00000 + 7 11.0417 0.00000 + 8 11.2800 0.00000 + + EFERMI = -2.337132734632673 eV + OUT.ABACUS/ final etot is -466.4053029971139 eV + correction force for each atom along direction 1 is -0.000106524 + correction force for each atom along direction 2 is -2.17191e-05 + correction force for each atom along direction 3 is 5.52497e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.36205431 +1.2408398 +0.019500354 + H1 +0.36743647 -0.95136094 -0.15978617 + H2 -0.72949077 -0.28947884 +0.14028582 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4053029971139 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2203 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2132 1 6.2 1.e+02% + Potential init_pot 0.24400 2 0.12 3.9% + PW_Basis recip2real 0.28440 17 0.017 4.6% + PW_Basis gathers_scatterp 0.11512 17 0.0068 1.9% + Potential v_of_rho 0.99535 14 0.071 16.% + XC_Functional v_xc 0.28833 15 0.019 4.6% + H_Hartree_pw v_hartree 0.66452 14 0.047 11.% + PW_Basis real2recip 0.64959 41 0.016 10.% + PW_Basis gatherp_scatters 0.24449 41 0.0060 3.9% + ORB_control set_orb_tables 0.90118 1 0.90 14.% + ORB_gen_tables gen_tables 0.90118 1 0.90 14.% + ORB_table_phi init_Table 0.37750 1 0.38 6.1% + ORB_table_phi cal_ST_Phi12_R 0.37326 126 0.0030 6.0% + ORB_table_beta init_Table_Beta 0.15596 1 0.16 2.5% + ORB_table_beta VNL_PhiBeta_R 0.15463 56 0.0028 2.5% + ORB_table_alpha init_Table_Alpha 0.20964 1 0.21 3.4% + ORB_table_alpha S_PhiAlpha_R 0.20800 66 0.0032 3.3% + LOOP_ions opt_ions 4.8538 1 4.9 78.% + ESolver_KS_LCAO Run 4.3720 1 4.4 70.% + HSolverLCAO solve 2.0012 12 0.17 32.% + HamiltLCAO updateHk 1.0616 12 0.088 17.% + LCAO_Hamilt cal_Hgamma 1.0277 12 0.086 17.% + Gint_interface cal_gint 1.8085 25 0.072 29.% + Gint_Gamma distri_vl 2.2870 6 0.38 37.% + LCAO_Deepks cal_projected_DM 4.7243 14 0.34 76.% + LCAO_gen_fixedH add_v_delta 2.1580 6 0.36 35.% + LCAO_DESCRIPTOR add_v_delta 2.1579 6 0.36 35.% + ElecStateLCAO psiToRho 0.92283 12 0.077 15.% + Charge mix_rho 0.83435 11 0.076 13.% + LOOP_ions force_stress 0.48166 1 0.48 7.7% + Force_Stress_LCAO getForceStress 0.48164 1 0.48 7.7% + Force_LCAO_gamma ftable_gamma 0.28529 1 0.29 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.27798 1 0.28 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:32 2022 + Finish Time : Wed Sep 28 11:08:38 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..9f9a8e95d36383515d3e03fdd2a443bb6de6f3c3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123631 ima = 3.68755e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123160517853 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112331341351 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112771280557 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113034052825 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112971216005 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113008358499 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113000032889 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113003302437 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113002582346 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113002498076 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113002485989 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113002480258 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0016fadf794f524b5421c5184cd19129e0cac165 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.196815423096 21.624616057077 6.331012814357 0 0 0 +H +0.0 +2 +-11.368804602603 20.051855178821 6.018600594804 0 0 0 +-13.929140639456 21.230778218260 6.689599720187 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/conv new file mode 100644 index 0000000000000000000000000000000000000000..f96247de49abc561bab01540e9ba6a8e28da830b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/conv @@ -0,0 +1 @@ +207 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..6c5815a75c95e38674539484f46ebe784ef1b0f4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747181278 0.01274637171 1.287599587 1.374955671 1.469891335 0.008268406593 0.01953124092 0.03896701227 +6.911788772e-19 0.001166980034 0.002591190717 0.0127376897 0.04568805213 1.646629691e-19 1.971059245e-06 5.79356685e-06 +0.001702204923 0.005855042089 + +H atom_index 1 n_descriptor 18 +1.266217954 0.03341618543 0.1142111039 0.1580432027 0.3265574779 0.02288428167 0.02929842446 0.03667867576 +-1.0141779e-17 4.69032171e-05 0.1060828692 0.1161551298 0.1358157835 -1.213542734e-17 3.402545116e-06 0.01305373151 +0.02704816635 0.03151601028 + +H atom_index 2 n_descriptor 18 +1.260104659 0.03362531868 0.1120107701 0.1550964278 0.3247027007 0.02260920536 0.02894599857 0.03682857278 +-1.658127967e-17 4.633954578e-05 0.1049784257 0.1155037008 0.1332898919 2.722948118e-18 3.74026051e-06 0.01304283523 +0.02683315428 0.03125850199 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ea813af8f1e981fb3ea057346c6607d3521eca47 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:32 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733756 SEC) : SETUP UNITCELL + DONE(0.0870101 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.102622 SEC) : INIT PLANEWAVE + DONE(0.144092 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.388991 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651706e+02 0.000000e+00 2.170e-01 4.505e-01 + GE2 -4.664019e+02 -1.231303e+00 9.774e-02 4.127e-01 + GE3 -4.664054e+02 -3.521449e-03 6.250e-02 4.758e-01 + GE4 -4.664058e+02 -3.710428e-04 2.055e-03 3.519e-01 + GE5 -4.664049e+02 9.482333e-04 8.971e-04 3.504e-01 + GE6 -4.664055e+02 -6.325191e-04 1.661e-04 3.468e-01 + GE7 -4.664053e+02 2.329985e-04 4.532e-05 3.389e-01 + GE8 -4.664053e+02 -6.511677e-05 1.765e-05 3.347e-01 + GE9 -4.664053e+02 2.167038e-05 2.300e-06 3.327e-01 + GE10 -4.664053e+02 -3.351160e-06 3.346e-07 3.299e-01 + GE11 -4.664053e+02 -4.204697e-07 1.293e-07 3.301e-01 + GE12 -4.664053e+02 -3.132392e-08 1.006e-08 2.641e-01 +E_delta_band = -7.16064153e-02 Ry = -9.74255262e-01 eV +E_delta_NN= -1.95322229e-01 Ry = -2.65749527e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2203 11 0.57 1e+02 % + Run_lcao lcao_line 6.2132 1 6.2 1e+02 % + Potential init_pot 0.244 2 0.12 3.9 % + PW_Basis recip2real 0.2844 17 0.017 4.6 % + PW_Basis gathers_scatterp 0.11512 17 0.0068 1.9 % + Potential v_of_rho 0.99535 14 0.071 16 % + XC_Functional v_xc 0.28833 15 0.019 4.6 % + H_Hartree_pw v_hartree 0.66452 14 0.047 11 % + PW_Basis real2recip 0.64959 41 0.016 10 % + PW_Basis gatherp_scatters 0.24449 41 0.006 3.9 % + ORB_control set_orb_tables 0.90118 1 0.9 14 % + ORB_gen_tables gen_tables 0.90118 1 0.9 14 % + ORB_table_phi init_Table 0.3775 1 0.38 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.37326 126 0.003 6 % + ORB_table_beta init_Table_Beta 0.15596 1 0.16 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.15463 56 0.0028 2.5 % + ORB_table_alpha init_Table_Alpha 0.20964 1 0.21 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.208 66 0.0032 3.3 % + LOOP_ions opt_ions 4.8538 1 4.9 78 % + ESolver_KS_LCAO Run 4.372 1 4.4 70 % + HSolverLCAO solve 2.0012 12 0.17 32 % + HamiltLCAO updateHk 1.0616 12 0.088 17 % + LCAO_Hamilt cal_Hgamma 1.0277 12 0.086 17 % + Gint_interface cal_gint 1.8085 25 0.072 29 % + Gint_Gamma distri_vl 2.287 6 0.38 37 % + LCAO_Deepks cal_projected_DM 4.7243 14 0.34 76 % + LCAO_gen_fixedH add_v_delta 2.158 6 0.36 35 % + LCAO_DESCRIPTOR add_v_delta 2.1579 6 0.36 35 % + ElecStateLCAO psiToRho 0.92283 12 0.077 15 % + Charge mix_rho 0.83435 11 0.076 13 % + LOOP_ions force_stress 0.48166 1 0.48 7.7 % + Force_Stress_LCAO getForceStress 0.48164 1 0.48 7.7 % + Force_LCAO_gamma ftable_gamma 0.28529 1 0.29 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.27798 1 0.28 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:32 2022 + FINISH Time : Wed Sep 28 11:08:38 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/207/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..496f80a24dbec08ca0902c5950a461f58a74be9f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.588357 0.759896 0.218157 +H 0.621502 0.700065 0.209793 +H 0.53184 0.737399 0.245876 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..5b17ed19061ef1dcfe53b664df274ad42855e300 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9921 2 + 2 -12.4948 2 + 3 -9.29973 2 + 4 -6.68383 2 + 5 0.931658 0 + 6 3.81445 0 + 7 11.1575 0 + 8 11.4236 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e46f211d7867b8d82b4d294aa4072d8b337ceaaa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:33 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.4739846695 21.2770764919 6.10839713107 0 0 0 0 + tauc_H1 17.402051432 19.6018246753 5.87420934961 0 0 0 0 + tauc_H2 14.8915166201 20.6471590782 6.88454059946 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.085293551698 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101192513803 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119359855646 (SEC) + + DONE : INIT CHARGE Time : 0.166804778437 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446574 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 0 81 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000879 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00156 + + Density error is 0.209652553868 + + Energy Rydberg eV + E_KohnSham -34.1901369527 -465.180677957 + E_Harris -34.3711832196 -467.643938788 + E_Fermi -0.382503166305 -5.20422256479 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000997278693565 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00135413674707 + + Density error is 0.0986442520136 + + Energy Rydberg eV + E_KohnSham -34.2769946 -466.362436875 + E_Harris -34.2842797635 -466.461556609 + E_Fermi -0.195309395013 -2.65732064511 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000948575299663 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125738268684 + + Density error is 0.0637497956132 + + Energy Rydberg eV + E_KohnSham -34.2774448917 -466.368563408 + E_Harris -34.2820880236 -466.431736459 + E_Fermi -0.189668967193 -2.5805786876 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000874945136752 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107363083803 + + Density error is 0.00191361250386 + + Energy Rydberg eV + E_KohnSham -34.27732262 -466.366899816 + E_Harris -34.2773239076 -466.366917335 + E_Fermi -0.154438900432 -2.10124903873 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000873301030637 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107304080583 + + Density error is 0.00091122028102 + + Energy Rydberg eV + E_KohnSham -34.2773003941 -466.366597417 + E_Harris -34.2773011318 -466.366607454 + E_Fermi -0.154608451329 -2.10355589702 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000872367080715 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107029392067 + + Density error is 0.000171649511833 + + Energy Rydberg eV + E_KohnSham -34.2773058703 -466.366671925 + E_Harris -34.2773058626 -466.36667182 + E_Fermi -0.154080522889 -2.09637306211 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000872455421179 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107026501563 + + Density error is 2.41860568558e-05 + + Energy Rydberg eV + E_KohnSham -34.277305809 -466.366671091 + E_Harris -34.2773058096 -466.366671099 + E_Fermi -0.154071803962 -2.09625443502 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000872400225774 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107021721031 + + Density error is 7.95134149946e-06 + + Energy Rydberg eV + E_KohnSham -34.2773070533 -466.36668802 + E_Harris -34.2773070536 -466.366688024 + E_Fermi -0.154076388641 -2.09631681278 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000872400896886 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107020937099 + + Density error is 2.5391589621e-06 + + Energy Rydberg eV + E_KohnSham -34.277306454 -466.366679867 + E_Harris -34.277306454 -466.366679867 + E_Fermi -0.154069749937 -2.09622648858 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000872398564807 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107019997694 + + Density error is 4.95808484662e-07 + + Energy Rydberg eV + E_KohnSham -34.2773065813 -466.366681598 + E_Harris -34.2773065813 -466.366681598 + E_Fermi -0.154067809676 -2.09620008998 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000872398990094 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107020004191 + + Density error is 1.99098303724e-07 + + Energy Rydberg eV + E_KohnSham -34.2773065828 -466.366681618 + E_Harris -34.2773065828 -466.366681618 + E_Fermi -0.154067575966 -2.09619691019 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000872399165135 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107019982997 + + Density error is 1.14599565646e-08 + + Energy Rydberg eV + E_KohnSham -34.2773065855 -466.366681656 + E_Harris -34.2773065855 -466.366681656 + E_band -7.85999983153 -106.940783988 + E_one_elec -68.5096032748 -932.120972257 + E_Hartree +35.6627477097 +485.216575188 + E_xc -8.14928195667 -110.876669219 + E_Ewald +6.8447002702 +93.1269247768 + E_demet -1.90962659279e-56 -2.59818027142e-55 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193503515161 -2.63275038922 + E_Fermi -0.154067401579 -2.09619453753 + + charge density convergence is achieved + final etot is -466.366681656 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9921 2.00000 + 2 -12.4948 2.00000 + 3 -9.29973 2.00000 + 4 -6.68383 2.00000 + 5 0.931658 0.00000 + 6 3.81445 0.00000 + 7 11.1575 0.00000 + 8 11.4236 0.00000 + + EFERMI = -2.096194537528456 eV + OUT.ABACUS/ final etot is -466.3666816561940 eV + correction force for each atom along direction 1 is -0.000100091 + correction force for each atom along direction 2 is -0.000178757 + correction force for each atom along direction 3 is 7.19346e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.28468093 -2.1212388 +0.10238177 + H1 -0.66014983 +1.6843991 +0.11306697 + H2 +0.37546890 +0.43683973 -0.21544874 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3666816561940 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2912 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2820 1 6.3 1.e+02% + Potential init_pot 0.28665 2 0.14 4.6% + PW_Basis recip2real 0.28688 17 0.017 4.6% + PW_Basis gathers_scatterp 0.12532 17 0.0074 2.0% + Potential v_of_rho 0.92385 14 0.066 15.% + XC_Functional v_xc 0.25021 15 0.017 4.0% + H_Hartree_pw v_hartree 0.63234 14 0.045 10.% + PW_Basis real2recip 0.59436 41 0.014 9.4% + PW_Basis gatherp_scatters 0.23027 41 0.0056 3.7% + ORB_control set_orb_tables 1.1110 1 1.1 18.% + ORB_gen_tables gen_tables 1.1110 1 1.1 18.% + ORB_table_phi init_Table 0.48999 1 0.49 7.8% + ORB_table_phi cal_ST_Phi12_R 0.48511 126 0.0039 7.7% + ORB_table_beta init_Table_Beta 0.19025 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18874 56 0.0034 3.0% + ORB_table_alpha init_Table_Alpha 0.25326 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25140 66 0.0038 4.0% + LOOP_ions opt_ions 4.6468 1 4.6 74.% + ESolver_KS_LCAO Run 4.1312 1 4.1 66.% + HSolverLCAO solve 2.0145 12 0.17 32.% + HamiltLCAO updateHk 1.0752 12 0.090 17.% + LCAO_Hamilt cal_Hgamma 1.0384 12 0.087 17.% + Gint_interface cal_gint 1.8470 25 0.074 29.% + Gint_Gamma distri_vl 2.1459 6 0.36 34.% + LCAO_Deepks cal_projected_DM 4.4964 14 0.32 71.% + LCAO_gen_fixedH add_v_delta 2.0142 6 0.34 32.% + LCAO_DESCRIPTOR add_v_delta 2.0142 6 0.34 32.% + ElecStateLCAO psiToRho 0.92495 12 0.077 15.% + Charge mix_rho 0.71631 11 0.065 11.% + LOOP_ions force_stress 0.51532 1 0.52 8.2% + Force_Stress_LCAO getForceStress 0.51529 1 0.52 8.2% + Force_LCAO_gamma ftable_gamma 0.30354 1 0.30 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.29674 1 0.30 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:33 2022 + Finish Time : Wed Sep 28 11:03:39 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..fbe1673f3a6f803d3fa7d93186424a128404ad3b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123416 ima = 3.70247e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123259443718 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111780375079 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112616079211 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112805088943 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112801746324 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112804351194 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112802847845 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112803989012 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112803625678 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112803608414 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112803591188 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112803581628 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c334eec3505d551e630b7b4126a85c83f47d4e76 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.526015330471 21.277076491871 6.108397131049 0 0 0 +H +0.0 +2 +-10.597948568023 19.601824675266 5.874209349635 0 0 0 +-13.108483379963 20.647159078156 6.884540599483 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/conv new file mode 100644 index 0000000000000000000000000000000000000000..8b5119bd7d61580b12cb1d86c802f0ab715b59be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/conv @@ -0,0 +1 @@ +208 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..3f6016f41fa0d4be38004b5f0cebe0e308356c11 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753677174 0.01244088323 1.238665843 1.327429682 1.468153749 0.009078744184 0.01657853107 0.0392279693 +-8.476362404e-19 0.0007877836169 0.00251071907 0.01179064044 0.04207042935 2.534791537e-19 1.922315802e-06 5.701930749e-06 +0.001556094758 0.005961335291 + +H atom_index 1 n_descriptor 18 +1.174071521 0.03709001188 0.08510867204 0.1177120456 0.2927029196 0.01888841364 0.02380613425 0.04084655043 +-2.459713865e-17 3.587350451e-05 0.07972643192 0.1001639306 0.1122259828 2.135654048e-18 6.28611678e-06 0.01514264836 +0.02278507686 0.02678046998 + +H atom_index 2 n_descriptor 18 +1.21911272 0.03574919394 0.09867107845 0.1359559964 0.3100491968 0.02103236632 0.0264530965 0.03903747294 +5.506832511e-17 3.965992046e-05 0.0910931721 0.1145335455 0.116246874 -3.368584826e-18 4.766436915e-06 0.01379789339 +0.02467255302 0.0292089024 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..aef0681501c724da757695179c69968257f30d79 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:33 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0853151 SEC) : SETUP UNITCELL + DONE(0.10121 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119382 SEC) : INIT PLANEWAVE + DONE(0.166929 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446706 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651807e+02 0.000000e+00 2.097e-01 4.628e-01 + GE2 -4.663624e+02 -1.181759e+00 9.864e-02 3.816e-01 + GE3 -4.663686e+02 -6.126533e-03 6.375e-02 4.436e-01 + GE4 -4.663669e+02 1.663593e-03 1.914e-03 3.323e-01 + GE5 -4.663666e+02 3.023987e-04 9.112e-04 3.314e-01 + GE6 -4.663667e+02 -7.450795e-05 1.716e-04 3.292e-01 + GE7 -4.663667e+02 8.337929e-07 2.419e-05 3.071e-01 + GE8 -4.663667e+02 -1.692933e-05 7.951e-06 3.096e-01 + GE9 -4.663667e+02 8.153919e-06 2.539e-06 3.053e-01 + GE10 -4.663667e+02 -1.731678e-06 4.958e-07 3.102e-01 + GE11 -4.663667e+02 -2.024640e-08 1.991e-07 3.056e-01 + GE12 -4.663667e+02 -3.774194e-08 1.146e-08 2.512e-01 +E_delta_band = -6.76341812e-02 Ry = -9.20210244e-01 eV +E_delta_NN= -1.93503515e-01 Ry = -2.63275039e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2912 11 0.57 1e+02 % + Run_lcao lcao_line 6.282 1 6.3 1e+02 % + Potential init_pot 0.28665 2 0.14 4.6 % + PW_Basis recip2real 0.28688 17 0.017 4.6 % + PW_Basis gathers_scatterp 0.12532 17 0.0074 2 % + Potential v_of_rho 0.92385 14 0.066 15 % + XC_Functional v_xc 0.25021 15 0.017 4 % + H_Hartree_pw v_hartree 0.63234 14 0.045 10 % + PW_Basis real2recip 0.59436 41 0.014 9.4 % + PW_Basis gatherp_scatters 0.23027 41 0.0056 3.7 % + ORB_control set_orb_tables 1.111 1 1.1 18 % + ORB_gen_tables gen_tables 1.111 1 1.1 18 % + ORB_table_phi init_Table 0.48999 1 0.49 7.8 % + ORB_table_phi cal_ST_Phi12_R 0.48511 126 0.0039 7.7 % + ORB_table_beta init_Table_Beta 0.19025 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18874 56 0.0034 3 % + ORB_table_alpha init_Table_Alpha 0.25326 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.2514 66 0.0038 4 % + LOOP_ions opt_ions 4.6468 1 4.6 74 % + ESolver_KS_LCAO Run 4.1312 1 4.1 66 % + HSolverLCAO solve 2.0145 12 0.17 32 % + HamiltLCAO updateHk 1.0752 12 0.09 17 % + LCAO_Hamilt cal_Hgamma 1.0384 12 0.087 17 % + Gint_interface cal_gint 1.847 25 0.074 29 % + Gint_Gamma distri_vl 2.1459 6 0.36 34 % + LCAO_Deepks cal_projected_DM 4.4964 14 0.32 71 % + LCAO_gen_fixedH add_v_delta 2.0142 6 0.34 32 % + LCAO_DESCRIPTOR add_v_delta 2.0142 6 0.34 32 % + ElecStateLCAO psiToRho 0.92495 12 0.077 15 % + Charge mix_rho 0.71631 11 0.065 11 % + LOOP_ions force_stress 0.51532 1 0.52 8.2 % + Force_Stress_LCAO getForceStress 0.51529 1 0.52 8.2 % + Force_LCAO_gamma ftable_gamma 0.30354 1 0.3 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.29674 1 0.3 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:33 2022 + FINISH Time : Wed Sep 28 11:03:39 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/208/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5a758d9ce089d33160a1c28447ff713098b5c0d0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.604705 0.743833 0.22388 +H 0.653719 0.726528 0.185957 +H 0.56139 0.695438 0.226541 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..eb502ed9f623f3bff9afb3c336c55321b3829783 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3226 2 + 2 -13.4146 2 + 3 -8.87422 2 + 4 -6.75019 2 + 5 1.43452 0 + 6 4.64958 0 + 7 11.0507 0 + 8 11.2742 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..158a58f9777abef2a5107b701d81a599f9401292 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:52 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.931734387 20.8273353538 6.26863231113 0 0 0 0 + tauc_H1 18.304143121 20.342792402 5.20679006889 0 0 0 0 + tauc_H2 15.7189309211 19.4722535092 6.34314327929 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0872673336623 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0974372923041 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115648592234 (SEC) + + DONE : INIT CHARGE Time : 0.164896376001 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44691 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 0 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00147 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124 + + Density error is 0.217632698972 + + Energy Rydberg eV + E_KohnSham -34.1882075835 -465.154427542 + E_Harris -34.385063802 -467.832793801 + E_Fermi -0.41249059539 -5.61222246871 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00134495965104 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122688982775 + + Density error is 0.0978023075693 + + Energy Rydberg eV + E_KohnSham -34.279096471 -466.391034297 + E_Harris -34.2856828684 -466.480646831 + E_Fermi -0.219534298234 -2.98691736241 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00124898700346 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114811758471 + + Density error is 0.0625568713914 + + Energy Rydberg eV + E_KohnSham -34.2793772507 -466.394854501 + E_Harris -34.2835944591 -466.452232565 + E_Fermi -0.206474154761 -2.80922499449 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00108351731951 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101409082472 + + Density error is 0.00210169835282 + + Energy Rydberg eV + E_KohnSham -34.2794017375 -466.395187661 + E_Harris -34.2794050328 -466.395232497 + E_Fermi -0.171094884936 -2.32786533379 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00108093653467 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101145992518 + + Density error is 0.000890532656684 + + Energy Rydberg eV + E_KohnSham -34.279334993 -466.394279556 + E_Harris -34.2793364584 -466.394299493 + E_Fermi -0.170035843521 -2.31345633612 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107928929201 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101010395027 + + Density error is 0.000209517847616 + + Energy Rydberg eV + E_KohnSham -34.2793783132 -466.394868957 + E_Harris -34.2793784383 -466.394870659 + E_Fermi -0.170207307677 -2.31578922564 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107915753125 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101007570795 + + Density error is 4.4343963723e-05 + + Energy Rydberg eV + E_KohnSham -34.2793609811 -466.394633142 + E_Harris -34.2793609918 -466.394633287 + E_Fermi -0.170011673299 -2.31312748338 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107914646558 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101004435308 + + Density error is 1.82583140653e-05 + + Energy Rydberg eV + E_KohnSham -34.2793668459 -466.394712936 + E_Harris -34.2793668472 -466.394712954 + E_Fermi -0.170063252863 -2.31382925935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107911600409 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010100182138 + + Density error is 2.28597544675e-06 + + Energy Rydberg eV + E_KohnSham -34.2793653109 -466.394692052 + E_Harris -34.279365311 -466.394692052 + E_Fermi -0.170044447472 -2.31357339888 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107911133509 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101001629526 + + Density error is 3.79651363643e-07 + + Energy Rydberg eV + E_KohnSham -34.2793655437 -466.394695219 + E_Harris -34.2793655437 -466.394695219 + E_Fermi -0.170042168155 -2.31354238719 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107911181668 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101001669094 + + Density error is 1.47668413518e-07 + + Energy Rydberg eV + E_KohnSham -34.2793655734 -466.394695623 + E_Harris -34.2793655734 -466.394695623 + E_Fermi -0.170042043293 -2.31354068834 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107911173241 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101001663526 + + Density error is 9.56591656147e-09 + + Energy Rydberg eV + E_KohnSham -34.2793655752 -466.394695648 + E_Harris -34.2793655752 -466.394695648 + E_band -7.99100551819 -108.723207797 + E_one_elec -69.5511227859 -946.291572185 + E_Hartree +36.171681512 +492.140974805 + E_xc -8.23063350064 -111.983513758 + E_Ewald +7.45454146718 +101.424239931 + E_demet -4.55740267706e-85 -6.20066444885e-84 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195166076121 -2.65537069155 + E_Fermi -0.170041902701 -2.31353877549 + + charge density convergence is achieved + final etot is -466.394695648 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3226 2.00000 + 2 -13.4146 2.00000 + 3 -8.87422 2.00000 + 4 -6.75019 2.00000 + 5 1.43452 0.00000 + 6 4.64958 0.00000 + 7 11.0507 0.00000 + 8 11.2742 0.00000 + + EFERMI = -2.313538775493130 eV + OUT.ABACUS/ final etot is -466.3946956476259 eV + correction force for each atom along direction 1 is -2.54228e-05 + correction force for each atom along direction 2 is -0.000163629 + correction force for each atom along direction 3 is 2.66546e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.51551012 +1.1211344 +0.85854626 + H1 +0.64805842 -0.57716511 -0.67275137 + H2 -0.13254830 -0.54396929 -0.18579489 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3946956476259 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2833 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2732 1 7.3 1.e+02% + Potential init_pot 0.28537 2 0.14 3.9% + PW_Basis recip2real 0.30411 17 0.018 4.2% + PW_Basis gathers_scatterp 0.13673 17 0.0080 1.9% + Potential v_of_rho 1.0583 14 0.076 15.% + XC_Functional v_xc 0.30236 15 0.020 4.2% + H_Hartree_pw v_hartree 0.71027 14 0.051 9.8% + PW_Basis real2recip 0.70375 41 0.017 9.7% + PW_Basis gatherp_scatters 0.27394 41 0.0067 3.8% + ORB_control set_orb_tables 1.0958 1 1.1 15.% + ORB_gen_tables gen_tables 1.0958 1 1.1 15.% + ORB_table_phi init_Table 0.47652 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47120 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18572 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18415 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24814 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24618 66 0.0037 3.4% + LOOP_ions opt_ions 5.6466 1 5.6 78.% + ESolver_KS_LCAO Run 5.0816 1 5.1 70.% + HSolverLCAO solve 2.6240 12 0.22 36.% + HamiltLCAO updateHk 1.3565 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.3267 12 0.11 18.% + Gint_interface cal_gint 2.4460 25 0.098 34.% + Gint_Gamma distri_vl 2.6516 6 0.44 36.% + LCAO_Deepks cal_projected_DM 5.4857 14 0.39 75.% + LCAO_gen_fixedH add_v_delta 2.5057 6 0.42 34.% + LCAO_DESCRIPTOR add_v_delta 2.5058 6 0.42 34.% + ElecStateLCAO psiToRho 1.2498 12 0.10 17.% + Charge mix_rho 0.85188 11 0.077 12.% + LOOP_ions force_stress 0.56483 1 0.56 7.8% + Force_Stress_LCAO getForceStress 0.56480 1 0.56 7.8% + Force_LCAO_gamma ftable_gamma 0.34964 1 0.35 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.34173 1 0.34 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:52 2022 + Finish Time : Wed Sep 28 11:06:00 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e1e12942955ca79f7a8ccc7c4f0769c1128a2b01 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123894 ima = 3.69257e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123462113083 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112626916346 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113063034067 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113315737848 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113258432198 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113293846568 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113282904104 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113286069778 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113285379909 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011328529766 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113285285674 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113285278733 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/STRU new file mode 100644 index 0000000000000000000000000000000000000000..dd3126f95c7a80d0a855f664e8f76f3579d83e58 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.068265612983 20.827335353763 6.268632311155 0 0 0 +H +0.0 +2 +-9.695856878984 20.342792401972 5.206790068888 0 0 0 +-12.281069078922 19.472253509152 6.343143279289 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/conv new file mode 100644 index 0000000000000000000000000000000000000000..0d1c7caffb3b4fa026b239bb1a2d88fe911444f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/conv @@ -0,0 +1 @@ +209 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..80fc36539c003ebfaafa11e375f9dec8a6e5d116 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.744577532 0.01268925731 1.287984593 1.377838654 1.469585337 0.007853999256 0.02037077506 0.03888686381 +2.073637666e-18 0.001197667274 0.002455928771 0.01264810014 0.04410689114 7.515638969e-19 1.667509213e-06 5.161777628e-06 +0.001771211404 0.005685515486 + +H atom_index 1 n_descriptor 18 +1.265923494 0.03312054871 0.1142727995 0.1586568788 0.3274839471 0.02263418632 0.02937395271 0.03643214614 +-4.672356005e-18 4.250939438e-05 0.1059530305 0.1160657174 0.1363208345 8.010719619e-18 3.447193545e-06 0.01292039225 +0.02687011432 0.031549958 + +H atom_index 2 n_descriptor 18 +1.251170867 0.03363632937 0.1090539822 0.1516436178 0.3230450435 0.02199390947 0.02852730434 0.0368131347 +-2.198306231e-17 4.12543604e-05 0.1029573194 0.114843224 0.1302981196 -4.802915914e-19 4.192776192e-06 0.01292300302 +0.02634480931 0.03092431122 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..1250f17db81f84654625a90f96e5bf221a4c2504 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:52 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872898 SEC) : SETUP UNITCELL + DONE(0.097454 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115671 SEC) : INIT PLANEWAVE + DONE(0.16503 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446971 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651544e+02 0.000000e+00 2.176e-01 5.254e-01 + GE2 -4.663910e+02 -1.236607e+00 9.780e-02 4.749e-01 + GE3 -4.663949e+02 -3.820204e-03 6.256e-02 5.432e-01 + GE4 -4.663952e+02 -3.331602e-04 2.102e-03 4.068e-01 + GE5 -4.663943e+02 9.081050e-04 8.905e-04 4.116e-01 + GE6 -4.663949e+02 -5.894013e-04 2.095e-04 4.028e-01 + GE7 -4.663946e+02 2.358147e-04 4.434e-05 3.941e-01 + GE8 -4.663947e+02 -7.979374e-05 1.826e-05 3.859e-01 + GE9 -4.663947e+02 2.088390e-05 2.286e-06 3.877e-01 + GE10 -4.663947e+02 -3.167032e-06 3.797e-07 3.861e-01 + GE11 -4.663947e+02 -4.035416e-07 1.477e-07 3.844e-01 + GE12 -4.663947e+02 -2.477559e-08 9.566e-09 3.165e-01 +E_delta_band = -7.13338083e-02 Ry = -9.70546252e-01 eV +E_delta_NN= -1.95166076e-01 Ry = -2.65537069e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2833 11 0.66 1e+02 % + Run_lcao lcao_line 7.2732 1 7.3 1e+02 % + Potential init_pot 0.28537 2 0.14 3.9 % + PW_Basis recip2real 0.30411 17 0.018 4.2 % + PW_Basis gathers_scatterp 0.13673 17 0.008 1.9 % + Potential v_of_rho 1.0583 14 0.076 15 % + XC_Functional v_xc 0.30236 15 0.02 4.2 % + H_Hartree_pw v_hartree 0.71027 14 0.051 9.8 % + PW_Basis real2recip 0.70375 41 0.017 9.7 % + PW_Basis gatherp_scatters 0.27394 41 0.0067 3.8 % + ORB_control set_orb_tables 1.0958 1 1.1 15 % + ORB_gen_tables gen_tables 1.0958 1 1.1 15 % + ORB_table_phi init_Table 0.47652 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.4712 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.18572 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18415 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24814 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24618 66 0.0037 3.4 % + LOOP_ions opt_ions 5.6466 1 5.6 78 % + ESolver_KS_LCAO Run 5.0816 1 5.1 70 % + HSolverLCAO solve 2.624 12 0.22 36 % + HamiltLCAO updateHk 1.3565 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.3267 12 0.11 18 % + Gint_interface cal_gint 2.446 25 0.098 34 % + Gint_Gamma distri_vl 2.6516 6 0.44 36 % + LCAO_Deepks cal_projected_DM 5.4857 14 0.39 75 % + LCAO_gen_fixedH add_v_delta 2.5057 6 0.42 34 % + LCAO_DESCRIPTOR add_v_delta 2.5058 6 0.42 34 % + ElecStateLCAO psiToRho 1.2498 12 0.1 17 % + Charge mix_rho 0.85188 11 0.077 12 % + LOOP_ions force_stress 0.56483 1 0.56 7.8 % + Force_Stress_LCAO getForceStress 0.5648 1 0.56 7.8 % + Force_LCAO_gamma ftable_gamma 0.34964 1 0.35 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.34173 1 0.34 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:52 2022 + FINISH Time : Wed Sep 28 11:06:00 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/209/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ac475e987dda2d94636a047d1aeb1eb46f7210b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.537557 0.312455 0.437476 +H 0.601337 0.32143 0.428099 +H 0.522825 0.369845 0.466122 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0dce834b0afa6ce834399611e7463b7a3bea14ef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3972 2 + 2 -12.8096 2 + 3 -9.36793 2 + 4 -6.77042 2 + 5 1.28257 0 + 6 4.40927 0 + 7 11.0648 0 + 8 11.3421 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..5bd9dbfb5f346f313cb666b5c7acf01f9fed82c4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:56 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.0515928927 8.7487352888 12.2493345258 0 0 0 0 + tauc_H1 16.8374261147 9.00003338545 11.9867809227 0 0 0 0 + tauc_H2 14.6390912381 10.3556729861 13.0514053258 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0888334928078 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0892284042532 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107340909559 (SEC) + + DONE : INIT CHARGE Time : 0.15621891821 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437994 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00144 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000664 + + Density error is 0.213786418778 + + Energy Rydberg eV + E_KohnSham -34.1906350291 -465.187454635 + E_Harris -34.3806955557 -467.773360761 + E_Fermi -0.406702663507 -5.53347361547 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00136244298762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000878706918008 + + Density error is 0.097620950904 + + Energy Rydberg eV + E_KohnSham -34.2798140617 -466.40079762 + E_Harris -34.2866362084 -466.493617688 + E_Fermi -0.216401970424 -2.94429985619 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125885306293 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000843145979159 + + Density error is 0.062674790751 + + Energy Rydberg eV + E_KohnSham -34.2801208717 -466.404971983 + E_Harris -34.284540558 -466.465104901 + E_Fermi -0.205472214525 -2.79559289821 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107883818414 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000800355631358 + + Density error is 0.00194413431742 + + Energy Rydberg eV + E_KohnSham -34.2801023047 -466.404719367 + E_Harris -34.2801030666 -466.404729733 + E_Fermi -0.169694408817 -2.30881087865 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107776889355 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000801550740938 + + Density error is 0.0009174879881 + + Energy Rydberg eV + E_KohnSham -34.2800417658 -466.403895693 + E_Harris -34.28004322 -466.403915478 + E_Fermi -0.169098310002 -2.3007005382 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107585443305 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000800703563811 + + Density error is 0.00010392324354 + + Energy Rydberg eV + E_KohnSham -34.2800810075 -466.404429604 + E_Harris -34.2800810113 -466.404429655 + E_Fermi -0.169056463829 -2.30013119181 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107573841457 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000800730621849 + + Density error is 3.54913649298e-05 + + Energy Rydberg eV + E_KohnSham -34.2800695008 -466.404273048 + E_Harris -34.2800695073 -466.404273135 + E_Fermi -0.168960222532 -2.29882176178 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107571076621 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000800660257392 + + Density error is 1.78399736169e-05 + + Energy Rydberg eV + E_KohnSham -34.2800713327 -466.404297972 + E_Harris -34.2800713342 -466.404297992 + E_Fermi -0.169000415045 -2.29936860898 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107569518804 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000800671973176 + + Density error is 2.57921397066e-06 + + Energy Rydberg eV + E_KohnSham -34.2800698848 -466.404278271 + E_Harris -34.2800698848 -466.404278271 + E_Fermi -0.168984219622 -2.29914825894 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107569076524 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000800675022025 + + Density error is 2.03018181861e-07 + + Energy Rydberg eV + E_KohnSham -34.2800701624 -466.404282048 + E_Harris -34.2800701624 -466.404282048 + E_Fermi -0.168981689803 -2.29911383899 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107569071784 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00080067520474 + + Density error is 4.96942413588e-08 + + Energy Rydberg eV + E_KohnSham -34.2800702102 -466.404282698 + E_Harris -34.2800702102 -466.404282698 + E_band -7.98859529452 -108.690415021 + E_one_elec -69.3312338679 -943.299829973 + E_Hartree +36.0501186001 +490.487026537 + E_xc -8.21121335621 -111.719289138 + E_Ewald +7.33646937302 +99.8177866756 + E_demet -6.47470171446e-78 -8.8092836167e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19492092611 -2.65203525453 + E_Fermi -0.168981587947 -2.29911245316 + + charge density convergence is achieved + final etot is -466.404282698 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3972 2.00000 + 2 -12.8096 2.00000 + 3 -9.36793 2.00000 + 4 -6.77042 2.00000 + 5 1.28257 0.00000 + 6 4.40927 0.00000 + 7 11.0648 0.00000 + 8 11.3421 0.00000 + + EFERMI = -2.299112453163816 eV + OUT.ABACUS/ final etot is -466.4042826982308 eV + correction force for each atom along direction 1 is 0.000122101 + correction force for each atom along direction 2 is 6.10003e-05 + correction force for each atom along direction 3 is 1.49138e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.29916286 +0.25512940 +0.17701565 + H1 +0.72518359 -0.27485439 -0.27476933 + H2 -0.42602073 +0.019724983 +0.097753680 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4042826982308 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0121 11 0.55 1.0e+02% + Run_lcao lcao_line 6.0019 1 6.0 1.e+02% + Potential init_pot 0.28751 2 0.14 4.8% + PW_Basis recip2real 0.25946 16 0.016 4.3% + PW_Basis gathers_scatterp 0.11794 16 0.0074 2.0% + Charge atomic_rho 0.10042 1 0.10 1.7% + Potential v_of_rho 0.86557 13 0.067 14.% + XC_Functional v_xc 0.24963 14 0.018 4.2% + H_Hartree_pw v_hartree 0.58122 13 0.045 9.7% + PW_Basis real2recip 0.56376 38 0.015 9.4% + PW_Basis gatherp_scatters 0.22902 38 0.0060 3.8% + ORB_control set_orb_tables 1.1156 1 1.1 19.% + ORB_gen_tables gen_tables 1.1156 1 1.1 19.% + ORB_table_phi init_Table 0.48887 1 0.49 8.1% + ORB_table_phi cal_ST_Phi12_R 0.48386 126 0.0038 8.0% + ORB_table_beta init_Table_Beta 0.18951 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18806 56 0.0034 3.1% + ORB_table_alpha init_Table_Alpha 0.25665 1 0.26 4.3% + ORB_table_alpha S_PhiAlpha_R 0.25477 66 0.0039 4.2% + LOOP_ions opt_ions 4.3723 1 4.4 73.% + ESolver_KS_LCAO Run 3.8591 1 3.9 64.% + HSolverLCAO solve 1.8812 11 0.17 31.% + HamiltLCAO updateHk 1.0049 11 0.091 17.% + LCAO_Hamilt cal_Hgamma 0.97659 11 0.089 16.% + Gint_Gamma distri_vl_value 0.59771 11 0.054 9.9% + Gint_Gamma distri_vl 1.8675 6 0.31 31.% + LCAO_Deepks cal_projected_DM 4.0145 13 0.31 67.% + LCAO_gen_fixedH add_v_delta 1.7366 6 0.29 29.% + LCAO_DESCRIPTOR add_v_delta 1.7366 6 0.29 29.% + ElecStateLCAO psiToRho 0.85764 11 0.078 14.% + Charge mix_rho 0.65967 10 0.066 11.% + LOOP_ions force_stress 0.51311 1 0.51 8.5% + Force_Stress_LCAO getForceStress 0.51308 1 0.51 8.5% + Force_LCAO_gamma ftable_gamma 0.30204 1 0.30 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:56 2022 + Finish Time : Wed Sep 28 11:04:02 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..26286fc1e749c047cbe1399d97c4d24db8b9124c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012352 ima = 3.6834e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122730829663 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111613686329 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112196156254 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112453720387 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112397758723 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112427755347 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112425956783 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011242874841 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112427893366 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112427770475 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112427760284 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/STRU new file mode 100644 index 0000000000000000000000000000000000000000..2dfecf9a64265ceddf824fb826d49ab434118a16 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.948407107304 8.748735288791 12.249334525821 0 0 0 +H +0.0 +2 +-11.162573885278 9.000033385451 11.986780922731 0 0 0 +-13.360908761940 10.355672986130 13.051405325813 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/conv new file mode 100644 index 0000000000000000000000000000000000000000..283b6d0422c58d7cd731b47d1161589c8bbced5b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/conv @@ -0,0 +1 @@ +21 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c129a5b163288b76413695b045c25ccd597ca035 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753102344 0.01278485892 1.27250341 1.355273292 1.469700992 0.009262780317 0.01715437873 0.03913841123 +-4.139064702e-19 0.0009471288883 0.002801496644 0.01307913136 0.04668439976 -1.317483959e-19 2.642781303e-06 7.101621463e-06 +0.001596395035 0.006128303872 + +H atom_index 1 n_descriptor 18 +1.257477356 0.03449253629 0.1129615301 0.1530657291 0.3222746245 0.02333087692 0.02867913996 0.03763661931 +-4.401860934e-17 5.040225436e-05 0.1043270042 0.115872041 0.1313296136 -3.324544102e-18 2.974593835e-06 0.01331716493 +0.02711804152 0.03107767801 + +H atom_index 2 n_descriptor 18 +1.241494645 0.03503149918 0.1073215326 0.1456314046 0.316994055 0.02254863877 0.02774347125 0.03814030049 +4.074471621e-17 4.888319732e-05 0.1007323949 0.1148020762 0.1249127281 2.602550737e-18 3.874186203e-06 0.01345017832 +0.0265246992 0.03034411442 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..91d3d680f411d417b073bf25899d7ef599be6624 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:56 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0888586 SEC) : SETUP UNITCELL + DONE(0.0892448 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107364 SEC) : INIT PLANEWAVE + DONE(0.156344 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.43807 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651875e+02 0.000000e+00 2.138e-01 4.652e-01 + GE2 -4.664008e+02 -1.213343e+00 9.762e-02 3.888e-01 + GE3 -4.664050e+02 -4.174364e-03 6.267e-02 4.446e-01 + GE4 -4.664047e+02 2.526162e-04 1.944e-03 3.336e-01 + GE5 -4.664039e+02 8.236742e-04 9.175e-04 3.309e-01 + GE6 -4.664044e+02 -5.339111e-04 1.039e-04 3.274e-01 + GE7 -4.664043e+02 1.565566e-04 3.549e-05 3.175e-01 + GE8 -4.664043e+02 -2.492426e-05 1.784e-05 3.120e-01 + GE9 -4.664043e+02 1.970070e-05 2.579e-06 3.133e-01 + GE10 -4.664043e+02 -3.777318e-06 2.030e-07 3.120e-01 + GE11 -4.664043e+02 -6.497999e-07 4.969e-08 2.523e-01 +E_delta_band = -7.07099669e-02 Ry = -9.62058455e-01 eV +E_delta_NN= -1.94920926e-01 Ry = -2.65203525e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0121 11 0.55 1e+02 % + Run_lcao lcao_line 6.0019 1 6 1e+02 % + Potential init_pot 0.28751 2 0.14 4.8 % + PW_Basis recip2real 0.25946 16 0.016 4.3 % + PW_Basis gathers_scatterp 0.11794 16 0.0074 2 % + Charge atomic_rho 0.10042 1 0.1 1.7 % + Potential v_of_rho 0.86557 13 0.067 14 % + XC_Functional v_xc 0.24963 14 0.018 4.2 % + H_Hartree_pw v_hartree 0.58122 13 0.045 9.7 % + PW_Basis real2recip 0.56376 38 0.015 9.4 % + PW_Basis gatherp_scatters 0.22902 38 0.006 3.8 % + ORB_control set_orb_tables 1.1156 1 1.1 19 % + ORB_gen_tables gen_tables 1.1156 1 1.1 19 % + ORB_table_phi init_Table 0.48887 1 0.49 8.1 % + ORB_table_phi cal_ST_Phi12_R 0.48386 126 0.0038 8 % + ORB_table_beta init_Table_Beta 0.18951 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18806 56 0.0034 3.1 % + ORB_table_alpha init_Table_Alpha 0.25665 1 0.26 4.3 % + ORB_table_alpha S_PhiAlpha_R 0.25477 66 0.0039 4.2 % + LOOP_ions opt_ions 4.3723 1 4.4 73 % + ESolver_KS_LCAO Run 3.8591 1 3.9 64 % + HSolverLCAO solve 1.8812 11 0.17 31 % + HamiltLCAO updateHk 1.0049 11 0.091 17 % + LCAO_Hamilt cal_Hgamma 0.97659 11 0.089 16 % + Gint_Gamma distri_vl_value 0.59771 11 0.054 9.9 % + Gint_Gamma distri_vl 1.8675 6 0.31 31 % + LCAO_Deepks cal_projected_DM 4.0145 13 0.31 67 % + LCAO_gen_fixedH add_v_delta 1.7366 6 0.29 29 % + LCAO_DESCRIPTOR add_v_delta 1.7366 6 0.29 29 % + ElecStateLCAO psiToRho 0.85764 11 0.078 14 % + Charge mix_rho 0.65967 10 0.066 11 % + LOOP_ions force_stress 0.51311 1 0.51 8.5 % + Force_Stress_LCAO getForceStress 0.51308 1 0.51 8.5 % + Force_LCAO_gamma ftable_gamma 0.30204 1 0.3 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:56 2022 + FINISH Time : Wed Sep 28 11:04:02 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/21/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..040d536576ea56b199c13aaeaa3e373097aff944 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.601764 0.735361 0.228398 +H 0.639003 0.721321 0.176465 +H 0.613628 0.683505 0.265784 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..909cdeb3e7280a569346ceaa7d5da2734b02fec4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4115 2 + 2 -12.8998 2 + 3 -9.31442 2 + 4 -6.77311 2 + 5 1.323 0 + 6 4.46947 0 + 7 11.0576 0 + 8 11.329 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a47dd60e2445ec08288cfa5b4dc2093b4730a0f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:51 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.8493870688 20.5901112247 6.39513400326 0 0 0 0 + tauc_H1 17.8920775356 20.1969961496 4.94100828292 0 0 0 0 + tauc_H2 17.1815952958 19.1381322916 7.44196570794 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0878917347461 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0972948596373 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115361848202 (SEC) + + DONE : INIT CHARGE Time : 0.163630816281 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44503 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 0 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000828 + + Density error is 0.21432303306 + + Energy Rydberg eV + E_KohnSham -34.1909843254 -465.192207055 + E_Harris -34.3819834167 -467.790883008 + E_Fermi -0.408607004222 -5.55938350013 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00129869993954 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111541521449 + + Density error is 0.0976309991311 + + Energy Rydberg eV + E_KohnSham -34.2801781252 -466.405750957 + E_Harris -34.2869417902 -466.49777534 + E_Fermi -0.218137683327 -2.96791544177 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00122625571739 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107306128001 + + Density error is 0.06255984897 + + Energy Rydberg eV + E_KohnSham -34.2804493604 -466.409441302 + E_Harris -34.2848261959 -466.468991203 + E_Fermi -0.206495724265 -2.80951846264 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111911921861 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010244299128 + + Density error is 0.00195641846164 + + Energy Rydberg eV + E_KohnSham -34.280443238 -466.409358002 + E_Harris -34.2804442247 -466.409371427 + E_Fermi -0.1707563314 -2.32325907662 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00112148916482 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102698096337 + + Density error is 0.000889899341252 + + Energy Rydberg eV + E_KohnSham -34.2803801688 -466.408499902 + E_Harris -34.2803818356 -466.40852258 + E_Fermi -0.170003887672 -2.3130215545 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111974491111 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102585893651 + + Density error is 9.87265696827e-05 + + Energy Rydberg eV + E_KohnSham -34.2804231031 -466.409084052 + E_Harris -34.2804231054 -466.409084084 + E_Fermi -0.170050322156 -2.31365332806 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111956589563 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102592971323 + + Density error is 3.6924867544e-05 + + Energy Rydberg eV + E_KohnSham -34.2804098201 -466.408903328 + E_Harris -34.2804098276 -466.408903431 + E_Fermi -0.16994322487 -2.31219619473 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111953747105 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102585080784 + + Density error is 1.17206516883e-05 + + Energy Rydberg eV + E_KohnSham -34.2804118624 -466.408931115 + E_Harris -34.280411863 -466.408931123 + E_Fermi -0.16998678914 -2.31278891702 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111954463862 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102585327711 + + Density error is 2.15540029747e-06 + + Energy Rydberg eV + E_KohnSham -34.280410629 -466.408914334 + E_Harris -34.280410629 -466.408914335 + E_Fermi -0.169975998402 -2.3126421015 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111954254853 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102585573881 + + Density error is 1.0127849331e-07 + + Energy Rydberg eV + E_KohnSham -34.2804107934 -466.40891657 + E_Harris -34.2804107934 -466.40891657 + E_Fermi -0.169973607828 -2.31260957607 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.001119542889 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102585590774 + + Density error is 4.3559515822e-08 + + Energy Rydberg eV + E_KohnSham -34.2804108361 -466.408917152 + E_Harris -34.2804108361 -466.408917152 + E_band -7.99648479747 -108.797757216 + E_one_elec -69.4031996491 -944.278974659 + E_Hartree +36.0859927625 +490.975119556 + E_xc -8.2170262629 -111.798377791 + E_Ewald +7.3778910225 +100.381357129 + E_demet -3.3760792867e-80 -4.59339151988e-79 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195046287792 -2.65374088771 + E_Fermi -0.169973682023 -2.31261058555 + + charge density convergence is achieved + final etot is -466.408917152 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4115 2.00000 + 2 -12.8998 2.00000 + 3 -9.31442 2.00000 + 4 -6.77311 2.00000 + 5 1.32300 0.00000 + 6 4.46947 0.00000 + 7 11.0576 0.00000 + 8 11.3290 0.00000 + + EFERMI = -2.312610585553144 eV + OUT.ABACUS/ final etot is -466.4089171522909 eV + correction force for each atom along direction 1 is 1.04119e-05 + correction force for each atom along direction 2 is -0.000130404 + correction force for each atom along direction 3 is -8.97539e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.071963271 +0.27009138 -0.18710623 + H1 +0.13861096 +0.19144137 -0.46508917 + H2 -0.066647690 -0.46153275 +0.65219540 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4089171522909 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1489 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1391 1 6.1 1.e+02% + Potential init_pot 0.28711 2 0.14 4.7% + PW_Basis recip2real 0.26875 16 0.017 4.4% + PW_Basis gathers_scatterp 0.11634 16 0.0073 1.9% + Potential v_of_rho 0.87469 13 0.067 14.% + XC_Functional v_xc 0.23879 14 0.017 3.9% + H_Hartree_pw v_hartree 0.59860 13 0.046 9.7% + PW_Basis real2recip 0.55413 38 0.015 9.0% + PW_Basis gatherp_scatters 0.21351 38 0.0056 3.5% + ORB_control set_orb_tables 1.1131 1 1.1 18.% + ORB_gen_tables gen_tables 1.1131 1 1.1 18.% + ORB_table_phi init_Table 0.48682 1 0.49 7.9% + ORB_table_phi cal_ST_Phi12_R 0.48180 126 0.0038 7.8% + ORB_table_beta init_Table_Beta 0.19004 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18857 56 0.0034 3.1% + ORB_table_alpha init_Table_Alpha 0.25587 1 0.26 4.2% + ORB_table_alpha S_PhiAlpha_R 0.25398 66 0.0038 4.1% + LOOP_ions opt_ions 4.5033 1 4.5 73.% + ESolver_KS_LCAO Run 3.9715 1 4.0 65.% + HSolverLCAO solve 2.0034 11 0.18 33.% + HamiltLCAO updateHk 1.0614 11 0.096 17.% + LCAO_Hamilt cal_Hgamma 1.0234 11 0.093 17.% + Gint_interface cal_gint 1.8549 23 0.081 30.% + Gint_Gamma distri_vl 1.9225 6 0.32 31.% + LCAO_Deepks cal_projected_DM 4.3509 13 0.33 71.% + LCAO_gen_fixedH add_v_delta 1.7881 6 0.30 29.% + LCAO_DESCRIPTOR add_v_delta 1.7881 6 0.30 29.% + ElecStateLCAO psiToRho 0.92528 11 0.084 15.% + Charge mix_rho 0.65581 10 0.066 11.% + LOOP_ions force_stress 0.53156 1 0.53 8.6% + Force_Stress_LCAO getForceStress 0.53154 1 0.53 8.6% + Force_LCAO_gamma ftable_gamma 0.31907 1 0.32 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.31243 1 0.31 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:51 2022 + Finish Time : Wed Sep 28 11:02:57 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..dcac4e62e935501d2369db23130b34a6fcb3d97e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123575 ima = 3.69344e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122720424934 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111706901272 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112248488414 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112506130273 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112446311961 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112479533734 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112476920147 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112479510441 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112478985688 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011247888466 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112478883927 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/STRU new file mode 100644 index 0000000000000000000000000000000000000000..70b05099b74aa071a9c0de3a7d79de0db23ad1c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.150612931236 20.590111224663 6.395134003251 0 0 0 +H +0.0 +2 +-10.107922464387 20.196996149586 4.941008282942 0 0 0 +-10.818404704252 19.138132291625 7.441965707959 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/conv new file mode 100644 index 0000000000000000000000000000000000000000..baa196ca9b1441e276373e22720cb1a831b54a80 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/conv @@ -0,0 +1 @@ +210 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b5f3c2d6bc39e1106a15a26d3c40e24f8d2f238d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752190228 0.01278812451 1.276017248 1.359509005 1.469783706 0.009099834284 0.01755489181 0.03910796174 +-3.638853567e-18 0.0009918796788 0.0027801797 0.01300755534 0.04679365513 -5.111955891e-19 2.556850404e-06 6.92232816e-06 +0.001606289305 0.006102783217 + +H atom_index 1 n_descriptor 18 +1.249229298 0.03464854281 0.1094938393 0.1492241215 0.3197612242 0.0227674472 0.02820625955 0.03776341231 +-1.126737693e-17 4.964544448e-05 0.1026079135 0.1151122164 0.1280736721 3.37452229e-18 3.677907041e-06 0.01333077642 +0.02675976801 0.03071153585 + +H atom_index 2 n_descriptor 18 +1.258231977 0.03434413342 0.1126975623 0.1534612434 0.3226854708 0.02320328116 0.02873227377 0.03749438491 +1.532651887e-17 5.051414103e-05 0.1045504789 0.1157893111 0.1317237586 -6.287118763e-18 3.163416228e-06 0.01327958104 +0.02708916827 0.03111661718 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..dd96c8ad54c28ab12f4408105ff6e5ff3f7e2c12 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:51 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0879121 SEC) : SETUP UNITCELL + DONE(0.0973155 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115381 SEC) : INIT PLANEWAVE + DONE(0.163764 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445096 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651922e+02 0.000000e+00 2.143e-01 4.776e-01 + GE2 -4.664058e+02 -1.213544e+00 9.763e-02 3.990e-01 + GE3 -4.664094e+02 -3.690345e-03 6.256e-02 4.581e-01 + GE4 -4.664094e+02 8.329970e-05 1.956e-03 3.456e-01 + GE5 -4.664085e+02 8.581004e-04 8.899e-04 3.460e-01 + GE6 -4.664091e+02 -5.841503e-04 9.873e-05 3.339e-01 + GE7 -4.664089e+02 1.807242e-04 3.692e-05 3.246e-01 + GE8 -4.664089e+02 -2.778697e-05 1.172e-05 3.228e-01 + GE9 -4.664089e+02 1.678076e-05 2.155e-06 3.228e-01 + GE10 -4.664089e+02 -2.235906e-06 1.013e-07 3.200e-01 + GE11 -4.664089e+02 -5.819859e-07 4.356e-08 2.602e-01 +E_delta_band = -7.09775787e-02 Ry = -9.65699500e-01 eV +E_delta_NN= -1.95046288e-01 Ry = -2.65374089e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1489 11 0.56 1e+02 % + Run_lcao lcao_line 6.1391 1 6.1 1e+02 % + Potential init_pot 0.28711 2 0.14 4.7 % + PW_Basis recip2real 0.26875 16 0.017 4.4 % + PW_Basis gathers_scatterp 0.11634 16 0.0073 1.9 % + Potential v_of_rho 0.87469 13 0.067 14 % + XC_Functional v_xc 0.23879 14 0.017 3.9 % + H_Hartree_pw v_hartree 0.5986 13 0.046 9.7 % + PW_Basis real2recip 0.55413 38 0.015 9 % + PW_Basis gatherp_scatters 0.21351 38 0.0056 3.5 % + ORB_control set_orb_tables 1.1131 1 1.1 18 % + ORB_gen_tables gen_tables 1.1131 1 1.1 18 % + ORB_table_phi init_Table 0.48682 1 0.49 7.9 % + ORB_table_phi cal_ST_Phi12_R 0.4818 126 0.0038 7.8 % + ORB_table_beta init_Table_Beta 0.19004 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18857 56 0.0034 3.1 % + ORB_table_alpha init_Table_Alpha 0.25587 1 0.26 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.25398 66 0.0038 4.1 % + LOOP_ions opt_ions 4.5033 1 4.5 73 % + ESolver_KS_LCAO Run 3.9715 1 4 65 % + HSolverLCAO solve 2.0034 11 0.18 33 % + HamiltLCAO updateHk 1.0614 11 0.096 17 % + LCAO_Hamilt cal_Hgamma 1.0234 11 0.093 17 % + Gint_interface cal_gint 1.8549 23 0.081 30 % + Gint_Gamma distri_vl 1.9225 6 0.32 31 % + LCAO_Deepks cal_projected_DM 4.3509 13 0.33 71 % + LCAO_gen_fixedH add_v_delta 1.7881 6 0.3 29 % + LCAO_DESCRIPTOR add_v_delta 1.7881 6 0.3 29 % + ElecStateLCAO psiToRho 0.92528 11 0.084 15 % + Charge mix_rho 0.65581 10 0.066 11 % + LOOP_ions force_stress 0.53156 1 0.53 8.6 % + Force_Stress_LCAO getForceStress 0.53154 1 0.53 8.6 % + Force_LCAO_gamma ftable_gamma 0.31907 1 0.32 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.31243 1 0.31 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:51 2022 + FINISH Time : Wed Sep 28 11:02:57 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/210/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..1584e61418fad8657c517752ca1c449f0ce8beeb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.611354 0.715922 0.237498 +H 0.635778 0.735406 0.182947 +H 0.661318 0.706753 0.279105 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3530413fe1aca9e93504f33e05f2081e244e3dc9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4449 2 + 2 -13.3801 2 + 3 -8.9887 2 + 4 -6.77701 2 + 5 1.46803 0 + 6 4.74997 0 + 7 11.0275 0 + 8 11.2554 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c27bd2b2c411d81cdc43a3d59484af2d84e53ab8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:30 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.1179009911 20.0458067453 6.64993656903 0 0 0 0 + tauc_H1 17.8017754185 20.5913774094 5.12251343246 0 0 0 0 + tauc_H2 18.5168977903 19.789073451 7.81494291451 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870659382382 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0874647753778 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105495965585 (SEC) + + DONE : INIT CHARGE Time : 0.155094299895 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437081 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 0 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000799 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127 + + Density error is 0.218683045425 + + Energy Rydberg eV + E_KohnSham -34.1844226213 -465.102930489 + E_Harris -34.3843306626 -467.822818927 + E_Fermi -0.419296690454 -5.70482414272 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00091133925735 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113207075714 + + Density error is 0.0978739690079 + + Energy Rydberg eV + E_KohnSham -34.2770542807 -466.363248873 + E_Harris -34.2836698259 -466.453257983 + E_Fermi -0.224335254816 -3.05223772778 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000870609390824 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105400459643 + + Density error is 0.0626230101996 + + Energy Rydberg eV + E_KohnSham -34.2773845651 -466.367742622 + E_Harris -34.2816264597 -466.425456559 + E_Fermi -0.21100886144 -2.87092284407 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000817196496363 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092935053393 + + Density error is 0.00208730907643 + + Energy Rydberg eV + E_KohnSham -34.2774154771 -466.368163202 + E_Harris -34.2774184395 -466.368203507 + E_Fermi -0.175312172562 -2.38524447561 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000819269653225 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000928798254967 + + Density error is 0.000944272385378 + + Energy Rydberg eV + E_KohnSham -34.2773392091 -466.367125522 + E_Harris -34.2773409956 -466.367149829 + E_Fermi -0.174238124885 -2.37063130728 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818367978824 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000927451322724 + + Density error is 0.000164344688835 + + Energy Rydberg eV + E_KohnSham -34.2773859764 -466.367761824 + E_Harris -34.2773860475 -466.367762792 + E_Fermi -0.174417144179 -2.37306698972 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00081850523733 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092747845631 + + Density error is 4.95307701486e-05 + + Energy Rydberg eV + E_KohnSham -34.2773690782 -466.367531913 + E_Harris -34.2773690927 -466.367532109 + E_Fermi -0.174239998592 -2.37065680036 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818466217026 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000927455648392 + + Density error is 1.94677047753e-05 + + Energy Rydberg eV + E_KohnSham -34.2773741445 -466.367600843 + E_Harris -34.277374146 -466.367600863 + E_Fermi -0.174300911113 -2.37148555773 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00081846943164 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000927435319322 + + Density error is 2.41258303687e-06 + + Energy Rydberg eV + E_KohnSham -34.2773724226 -466.367577415 + E_Harris -34.2773724226 -466.367577415 + E_Fermi -0.174280558753 -2.37120864967 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818467964272 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000927434118893 + + Density error is 3.02213699196e-07 + + Energy Rydberg eV + E_KohnSham -34.2773726621 -466.367580674 + E_Harris -34.2773726621 -466.367580674 + E_Fermi -0.174278137791 -2.37117571078 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000818468370997 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000927434196449 + + Density error is 1.32501779189e-07 + + Energy Rydberg eV + E_KohnSham -34.2773727042 -466.367581246 + E_Harris -34.2773727042 -466.367581246 + E_Fermi -0.174278103649 -2.37117524626 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00081846849884 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000927434042749 + + Density error is 1.01034712144e-08 + + Energy Rydberg eV + E_KohnSham -34.2773727047 -466.367581254 + E_Harris -34.2773727047 -466.367581254 + E_band -8.02467833526 -109.181349977 + E_one_elec -69.7125542207 -948.487959535 + E_Hartree +36.243456618 +493.11752522 + E_xc -8.24260177275 -112.146350454 + E_Ewald +7.55782412944 +102.829472642 + E_demet -1.49333977045e-88 -2.03179299282e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195563083204 -2.66077225002 + E_Fermi -0.174277985107 -2.37117363342 + + charge density convergence is achieved + final etot is -466.367581254 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4449 2.00000 + 2 -13.3801 2.00000 + 3 -8.98870 2.00000 + 4 -6.77701 2.00000 + 5 1.46803 0.00000 + 6 4.74997 0.00000 + 7 11.0275 0.00000 + 8 11.2554 0.00000 + + EFERMI = -2.371173633418969 eV + OUT.ABACUS/ final etot is -466.3675812538234 eV + correction force for each atom along direction 1 is 4.42686e-05 + correction force for each atom along direction 2 is 0.000129666 + correction force for each atom along direction 3 is -5.66814e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.2386697 -0.79789139 +2.1887595 + H1 +1.1221847 +0.75560843 -2.0778945 + H2 +0.11648504 +0.042282966 -0.11086501 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3675812538234 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2234 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2136 1 7.2 1.e+02% + Potential init_pot 0.28418 2 0.14 3.9% + PW_Basis recip2real 0.31162 17 0.018 4.3% + PW_Basis gathers_scatterp 0.13325 17 0.0078 1.8% + Potential v_of_rho 1.0694 14 0.076 15.% + XC_Functional v_xc 0.29486 15 0.020 4.1% + H_Hartree_pw v_hartree 0.72873 14 0.052 10.% + PW_Basis real2recip 0.71178 41 0.017 9.9% + PW_Basis gatherp_scatters 0.26837 41 0.0065 3.7% + ORB_control set_orb_tables 1.0914 1 1.1 15.% + ORB_gen_tables gen_tables 1.0914 1 1.1 15.% + ORB_table_phi init_Table 0.47193 1 0.47 6.5% + ORB_table_phi cal_ST_Phi12_R 0.46676 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18350 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18194 56 0.0032 2.5% + ORB_table_alpha init_Table_Alpha 0.24888 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24694 66 0.0037 3.4% + LOOP_ions opt_ions 5.6076 1 5.6 78.% + ESolver_KS_LCAO Run 5.0524 1 5.1 70.% + HSolverLCAO solve 2.5637 12 0.21 35.% + HamiltLCAO updateHk 1.3343 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.3043 12 0.11 18.% + Gint_interface cal_gint 2.3655 25 0.095 33.% + Gint_Gamma distri_vl 2.6407 6 0.44 37.% + LCAO_Deepks cal_projected_DM 5.4415 14 0.39 75.% + LCAO_gen_fixedH add_v_delta 2.4962 6 0.42 35.% + LCAO_DESCRIPTOR add_v_delta 2.4963 6 0.42 35.% + ElecStateLCAO psiToRho 1.2122 12 0.10 17.% + Charge mix_rho 0.85507 11 0.078 12.% + LOOP_ions force_stress 0.55502 1 0.56 7.7% + Force_Stress_LCAO getForceStress 0.55499 1 0.55 7.7% + Force_LCAO_gamma ftable_gamma 0.33693 1 0.34 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.32895 1 0.33 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:30 2022 + Finish Time : Wed Sep 28 11:13:37 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c071ab30dc016605d913a9d70f9431df3e0e3f77 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124107 ima = 3.68513e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123338117466 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112347694163 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112798139757 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113081209702 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113015709048 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113052911936 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113044199638 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113047767771 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113047039608 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113046932855 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113046925192 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113046919348 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b52304feb980e67aec9d0b2045e90d62b7253483 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.882099008928 20.045806745264 6.649936569041 0 0 0 +H +0.0 +2 +-10.198224581549 20.591377409386 5.122513432480 0 0 0 +-9.483102209703 19.789073451017 7.814942914511 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/conv new file mode 100644 index 0000000000000000000000000000000000000000..4edcf319e8ba21bb850ee48dc4cf90072d6c3ba4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/conv @@ -0,0 +1 @@ +211 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4df32ef7fdfbffa9a784489b26ae024ef99f6b21 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746594528 0.01273401082 1.29014732 1.382621284 1.470177607 0.008238635842 0.01994379014 0.03895803193 +-2.369249207e-18 0.001208396328 0.002594257744 0.01281585541 0.04596794868 4.302197385e-20 1.919251175e-06 5.724900488e-06 +0.001712828231 0.005776794545 + +H atom_index 1 n_descriptor 18 +1.300606128 0.03222094814 0.1274352615 0.1757099588 0.3362408172 0.02434629827 0.03126247657 0.03616387347 +3.320307389e-17 4.988081809e-05 0.1081140776 0.1241818072 0.1508213126 5.014501384e-18 1.644473094e-06 0.01360982803 +0.0282038444 0.03280914229 + +H atom_index 2 n_descriptor 18 +1.238358503 0.03428645138 0.1046004327 0.1451704193 0.3180239013 0.02159851048 0.02770611293 0.03738884864 +-1.153753973e-17 4.422494053e-05 0.1002552277 0.1142562482 0.1247649856 -4.650948889e-18 4.939324017e-06 0.01315200005 +0.02608725661 0.03030459953 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..32b40cfb867d2a02522d48c6249a82bd039be983 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:30 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870879 SEC) : SETUP UNITCELL + DONE(0.0874811 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105514 SEC) : INIT PLANEWAVE + DONE(0.15522 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.43716 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651029e+02 0.000000e+00 2.187e-01 5.353e-01 + GE2 -4.663632e+02 -1.260318e+00 9.787e-02 4.717e-01 + GE3 -4.663677e+02 -4.493749e-03 6.262e-02 5.388e-01 + GE4 -4.663682e+02 -4.205799e-04 2.087e-03 4.011e-01 + GE5 -4.663671e+02 1.037680e-03 9.443e-04 4.029e-01 + GE6 -4.663678e+02 -6.363018e-04 1.643e-04 3.937e-01 + GE7 -4.663675e+02 2.299107e-04 4.953e-05 3.950e-01 + GE8 -4.663676e+02 -6.892952e-05 1.947e-05 3.812e-01 + GE9 -4.663676e+02 2.342777e-05 2.413e-06 3.847e-01 + GE10 -4.663676e+02 -3.259397e-06 3.022e-07 3.847e-01 + GE11 -4.663676e+02 -5.723243e-07 1.325e-07 3.851e-01 + GE12 -4.663676e+02 -7.345893e-09 1.010e-08 3.160e-01 +E_delta_band = -7.20656245e-02 Ry = -9.80503123e-01 eV +E_delta_NN= -1.95563083e-01 Ry = -2.66077225e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2234 11 0.66 1e+02 % + Run_lcao lcao_line 7.2136 1 7.2 1e+02 % + Potential init_pot 0.28418 2 0.14 3.9 % + PW_Basis recip2real 0.31162 17 0.018 4.3 % + PW_Basis gathers_scatterp 0.13325 17 0.0078 1.8 % + Potential v_of_rho 1.0694 14 0.076 15 % + XC_Functional v_xc 0.29486 15 0.02 4.1 % + H_Hartree_pw v_hartree 0.72873 14 0.052 10 % + PW_Basis real2recip 0.71178 41 0.017 9.9 % + PW_Basis gatherp_scatters 0.26837 41 0.0065 3.7 % + ORB_control set_orb_tables 1.0914 1 1.1 15 % + ORB_gen_tables gen_tables 1.0914 1 1.1 15 % + ORB_table_phi init_Table 0.47193 1 0.47 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.46676 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.1835 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18194 56 0.0032 2.5 % + ORB_table_alpha init_Table_Alpha 0.24888 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24694 66 0.0037 3.4 % + LOOP_ions opt_ions 5.6076 1 5.6 78 % + ESolver_KS_LCAO Run 5.0524 1 5.1 70 % + HSolverLCAO solve 2.5637 12 0.21 35 % + HamiltLCAO updateHk 1.3343 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.3043 12 0.11 18 % + Gint_interface cal_gint 2.3655 25 0.095 33 % + Gint_Gamma distri_vl 2.6407 6 0.44 37 % + LCAO_Deepks cal_projected_DM 5.4415 14 0.39 75 % + LCAO_gen_fixedH add_v_delta 2.4962 6 0.42 35 % + LCAO_DESCRIPTOR add_v_delta 2.4963 6 0.42 35 % + ElecStateLCAO psiToRho 1.2122 12 0.1 17 % + Charge mix_rho 0.85507 11 0.078 12 % + LOOP_ions force_stress 0.55502 1 0.56 7.7 % + Force_Stress_LCAO getForceStress 0.55499 1 0.55 7.7 % + Force_LCAO_gamma ftable_gamma 0.33693 1 0.34 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.32895 1 0.33 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:30 2022 + FINISH Time : Wed Sep 28 11:13:37 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/211/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9ee3b48a565aadd5eaea79b0a2e8f76a667daaa3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.614961 0.710026 0.249321 +H 0.630296 0.754548 0.199321 +H 0.672918 0.700874 0.27967 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bc20fcd58f0d17f94ec1c407e9dfe27a0c636594 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0031 2 + 2 -12.74 2 + 3 -9.11735 2 + 4 -6.68156 2 + 5 1.01105 0 + 6 3.97204 0 + 7 11.1455 0 + 8 11.3959 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4473a0afbe749ab0e8f54b4a39d5efc4ee13ce3b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:54 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.2189147097 19.8807243398 6.98098194359 0 0 0 0 + tauc_H1 17.6482884131 21.1273498695 5.58099524763 0 0 0 0 + tauc_H2 18.8416913452 19.6244616786 7.83075540214 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871085131878 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0874612882052 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105351404294 (SEC) + + DONE : INIT CHARGE Time : 0.153281535472 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.440094 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 0 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000565 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00156 + + Density error is 0.211728217551 + + Energy Rydberg eV + E_KohnSham -34.1898748887 -465.177112394 + E_Harris -34.374942251 -467.695083034 + E_Fermi -0.38780247539 -5.2763233638 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000747679589151 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128285307579 + + Density error is 0.098849901929 + + Energy Rydberg eV + E_KohnSham -34.2783247937 -466.380535089 + E_Harris -34.2854838371 -466.477938872 + E_Fermi -0.197944555464 -2.69317384238 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000721619454731 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118952959232 + + Density error is 0.0638472776294 + + Energy Rydberg eV + E_KohnSham -34.2787681279 -466.386566961 + E_Harris -34.2833410854 -466.448785239 + E_Fermi -0.191394087006 -2.60405014679 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000701590312819 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101931997914 + + Density error is 0.00197359511558 + + Energy Rydberg eV + E_KohnSham -34.278670179 -466.385234297 + E_Harris -34.2786725198 -466.385266145 + E_Fermi -0.156177965129 -2.12491022779 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000700815944252 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101977651212 + + Density error is 0.000939650727072 + + Energy Rydberg eV + E_KohnSham -34.278635455 -466.384761853 + E_Harris -34.2786357861 -466.384766358 + E_Fermi -0.156096815097 -2.12380612497 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000700739541522 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101713603654 + + Density error is 0.000181379447377 + + Energy Rydberg eV + E_KohnSham -34.2786497898 -466.384956888 + E_Harris -34.2786497965 -466.384956979 + E_Fermi -0.155669639773 -2.11799410652 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000700956109613 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101716705804 + + Density error is 2.78339762414e-05 + + Energy Rydberg eV + E_KohnSham -34.2786456819 -466.384900997 + E_Harris -34.2786456837 -466.384901022 + E_Fermi -0.15564355006 -2.11763913776 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000700899400974 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101715228746 + + Density error is 1.23324660026e-05 + + Energy Rydberg eV + E_KohnSham -34.2786481542 -466.384934634 + E_Harris -34.2786481548 -466.384934643 + E_Fermi -0.155658636049 -2.11784439318 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000700908135714 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101714106357 + + Density error is 2.85027207022e-06 + + Energy Rydberg eV + E_KohnSham -34.2786472315 -466.384922081 + E_Harris -34.2786472316 -466.384922081 + E_Fermi -0.15564771632 -2.11769582264 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000700909559504 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101713074021 + + Density error is 5.64974037742e-07 + + Energy Rydberg eV + E_KohnSham -34.2786474215 -466.384924666 + E_Harris -34.2786474215 -466.384924666 + E_Fermi -0.155645181745 -2.11766133798 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000700910014769 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101713066747 + + Density error is 2.03166162941e-07 + + Energy Rydberg eV + E_KohnSham -34.2786474331 -466.384924823 + E_Harris -34.2786474331 -466.384924823 + E_Fermi -0.155644913636 -2.11765769016 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000700910239077 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101713033758 + + Density error is 1.09349139238e-08 + + Energy Rydberg eV + E_KohnSham -34.2786474367 -466.384924873 + E_Harris -34.2786474367 -466.384924873 + E_band -7.87054083963 -107.084201761 + E_one_elec -68.6612715452 -934.184524939 + E_Hartree +35.7416295361 +486.289817495 + E_xc -8.16188458734 -111.048136806 + E_Ewald +6.92847321673 +94.2667141879 + E_demet -4.35673263359e-60 -5.92763884794e-59 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193717903758 -2.63566729573 + E_Fermi -0.155644717377 -2.11765501993 + + charge density convergence is achieved + final etot is -466.384924873 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0031 2.00000 + 2 -12.7400 2.00000 + 3 -9.11735 2.00000 + 4 -6.68156 2.00000 + 5 1.01105 0.00000 + 6 3.97204 0.00000 + 7 11.1455 0.00000 + 8 11.3959 0.00000 + + EFERMI = -2.117655019927858 eV + OUT.ABACUS/ final etot is -466.3849248728055 eV + correction force for each atom along direction 1 is 0.000183492 + correction force for each atom along direction 2 is 0.000104573 + correction force for each atom along direction 3 is 2.64497e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.49408792 +1.1434115 -1.2462873 + H1 -0.40055105 -1.1558496 +1.2949114 + H2 -0.093536874 +0.012438072 -0.048624123 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3849248728055 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3770 11 0.58 1.0e+02% + Run_lcao lcao_line 6.3669 1 6.4 1.e+02% + Potential init_pot 0.29700 2 0.15 4.7% + PW_Basis recip2real 0.28673 17 0.017 4.5% + PW_Basis gathers_scatterp 0.12472 17 0.0073 2.0% + Potential v_of_rho 0.95150 14 0.068 15.% + XC_Functional v_xc 0.25790 15 0.017 4.0% + H_Hartree_pw v_hartree 0.64955 14 0.046 10.% + PW_Basis real2recip 0.60332 41 0.015 9.5% + PW_Basis gatherp_scatters 0.23834 41 0.0058 3.7% + ORB_control set_orb_tables 1.1006 1 1.1 17.% + ORB_gen_tables gen_tables 1.1006 1 1.1 17.% + ORB_table_phi init_Table 0.48192 1 0.48 7.6% + ORB_table_phi cal_ST_Phi12_R 0.47698 126 0.0038 7.5% + ORB_table_beta init_Table_Beta 0.18520 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18367 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25431 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25240 66 0.0038 4.0% + LOOP_ions opt_ions 4.7501 1 4.8 74.% + ESolver_KS_LCAO Run 4.2143 1 4.2 66.% + HSolverLCAO solve 2.0835 12 0.17 33.% + HamiltLCAO updateHk 1.1044 12 0.092 17.% + LCAO_Hamilt cal_Hgamma 1.0631 12 0.089 17.% + Gint_interface cal_gint 1.9108 25 0.076 30.% + Gint_Gamma distri_vl 2.1935 6 0.37 34.% + LCAO_Deepks cal_projected_DM 4.5979 14 0.33 72.% + LCAO_gen_fixedH add_v_delta 2.0617 6 0.34 32.% + LCAO_DESCRIPTOR add_v_delta 2.0617 6 0.34 32.% + ElecStateLCAO psiToRho 0.95869 12 0.080 15.% + Charge mix_rho 0.71003 11 0.065 11.% + LOOP_ions force_stress 0.53561 1 0.54 8.4% + Force_Stress_LCAO getForceStress 0.53558 1 0.54 8.4% + Force_LCAO_gamma ftable_gamma 0.31366 1 0.31 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.30610 1 0.31 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:54 2022 + Finish Time : Wed Sep 28 11:05:01 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..db206e554f9cb0c99683294249d7c57f9fcc938d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123311 ima = 3.67701e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123562336018 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112127372531 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112900539139 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113102509852 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113086059381 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113096660006 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113092692508 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113094462474 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113093905737 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113093859255 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113093838914 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113093828334 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4a61e475b0ea12fe06e9e05397c6b7c5e6896f32 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.781085290278 19.880724339791 6.980981943605 0 0 0 +H +0.0 +2 +-10.351711586892 21.127349869551 5.580995247633 0 0 0 +-9.158308654816 19.624461678623 7.830755402138 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/conv new file mode 100644 index 0000000000000000000000000000000000000000..86b94ada3a63104c0946a2ee0121b588bfd2e9e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/conv @@ -0,0 +1 @@ +212 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7c1becc10e82bfbd719f6a813a12d9cbe68e08a3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75049444 0.01243860832 1.245044495 1.340623897 1.468136952 0.008512599099 0.01778090257 0.03910883786 +-2.090477335e-18 0.0008929032988 0.002432824593 0.01155576593 0.04197471513 -2.269363888e-20 1.687573618e-06 5.180556744e-06 +0.001603393739 0.0058748579 + +H atom_index 1 n_descriptor 18 +1.175944462 0.03673915598 0.08463039062 0.1188654158 0.2947774428 0.01862244908 0.02399990687 0.0404523491 +-3.15549013e-18 3.480197039e-05 0.08006855051 0.1012760053 0.1124541739 1.145885365e-17 6.592333004e-06 0.01490318592 +0.02270243968 0.02696014031 + +H atom_index 2 n_descriptor 18 +1.233785775 0.03491721486 0.1022171231 0.1427744272 0.3162047582 0.02129848832 0.02738518085 0.0381453514 +4.982910684e-18 3.962846977e-05 0.09495204432 0.1148554597 0.1222922803 4.194551757e-18 4.626705562e-06 0.01335948801 +0.02508046971 0.02998733838 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fb7eab6731b845c820f28848370f11090245e6eb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/e_base.npy 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0000000000000000000000000000000000000000..4ce2a602712d39c0a8d861881c7c771b66a488a5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..fe6b95b7b5b98e82ee40b05435a2556e2837f93b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..39fd97fb51ff672e1db3034f4c349854861dfd67 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:54 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871307 SEC) : SETUP UNITCELL + DONE(0.0874745 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105371 SEC) : INIT PLANEWAVE + DONE(0.153409 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.440173 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651771e+02 0.000000e+00 2.117e-01 4.690e-01 + GE2 -4.663805e+02 -1.203423e+00 9.885e-02 3.950e-01 + GE3 -4.663866e+02 -6.031872e-03 6.385e-02 4.490e-01 + GE4 -4.663852e+02 1.332664e-03 1.974e-03 3.400e-01 + GE5 -4.663848e+02 4.724445e-04 9.397e-04 3.360e-01 + GE6 -4.663850e+02 -1.950355e-04 1.814e-04 3.328e-01 + GE7 -4.663849e+02 5.589070e-05 2.783e-05 3.122e-01 + GE8 -4.663849e+02 -3.363658e-05 1.233e-05 3.098e-01 + GE9 -4.663849e+02 1.255308e-05 2.850e-06 3.114e-01 + GE10 -4.663849e+02 -2.584615e-06 5.650e-07 3.149e-01 + GE11 -4.663849e+02 -1.571796e-07 2.032e-07 3.215e-01 + GE12 -4.663849e+02 -5.004964e-08 1.093e-08 2.602e-01 +E_delta_band = -6.81238467e-02 Ry = -9.26872485e-01 eV +E_delta_NN= -1.93717904e-01 Ry = -2.63566730e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.377 11 0.58 1e+02 % + Run_lcao lcao_line 6.3669 1 6.4 1e+02 % + Potential init_pot 0.297 2 0.15 4.7 % + PW_Basis recip2real 0.28673 17 0.017 4.5 % + PW_Basis gathers_scatterp 0.12472 17 0.0073 2 % + Potential v_of_rho 0.9515 14 0.068 15 % + XC_Functional v_xc 0.2579 15 0.017 4 % + H_Hartree_pw v_hartree 0.64955 14 0.046 10 % + PW_Basis real2recip 0.60332 41 0.015 9.5 % + PW_Basis gatherp_scatters 0.23834 41 0.0058 3.7 % + ORB_control set_orb_tables 1.1006 1 1.1 17 % + ORB_gen_tables gen_tables 1.1006 1 1.1 17 % + ORB_table_phi init_Table 0.48192 1 0.48 7.6 % + ORB_table_phi cal_ST_Phi12_R 0.47698 126 0.0038 7.5 % + ORB_table_beta init_Table_Beta 0.1852 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18367 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.25431 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.2524 66 0.0038 4 % + LOOP_ions opt_ions 4.7501 1 4.8 74 % + ESolver_KS_LCAO Run 4.2143 1 4.2 66 % + HSolverLCAO solve 2.0835 12 0.17 33 % + HamiltLCAO updateHk 1.1044 12 0.092 17 % + LCAO_Hamilt cal_Hgamma 1.0631 12 0.089 17 % + Gint_interface cal_gint 1.9108 25 0.076 30 % + Gint_Gamma distri_vl 2.1935 6 0.37 34 % + LCAO_Deepks cal_projected_DM 4.5979 14 0.33 72 % + LCAO_gen_fixedH add_v_delta 2.0617 6 0.34 32 % + LCAO_DESCRIPTOR add_v_delta 2.0617 6 0.34 32 % + ElecStateLCAO psiToRho 0.95869 12 0.08 15 % + Charge mix_rho 0.71003 11 0.065 11 % + LOOP_ions force_stress 0.53561 1 0.54 8.4 % + Force_Stress_LCAO getForceStress 0.53558 1 0.54 8.4 % + Force_LCAO_gamma ftable_gamma 0.31366 1 0.31 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.3061 1 0.31 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:54 2022 + FINISH Time : Wed Sep 28 11:05:01 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/212/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..66dc08160494e2d2d88f6dfd4ed90e944f2c8fc6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.615944 0.702839 0.246909 +H 0.608374 0.76514 0.247999 +H 0.65708 0.690645 0.297283 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0b5209eafc667e802ddfbc69f4b1f7943c85e46c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4789 2 + 2 -13.1956 2 + 3 -9.14238 2 + 4 -6.78453 2 + 5 1.41617 0 + 6 4.69431 0 + 7 11.0295 0 + 8 11.2718 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..364f03662497758c5e9c00aeb8660314ba988788 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:01 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.2464308113 19.6794869972 6.91346254091 0 0 0 0 + tauc_H1 17.0344843613 21.4239278284 6.94396701835 0 0 0 0 + tauc_H2 18.3982467125 19.3380572338 8.32393006387 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0862820738084 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0908738920518 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.109068224154 (SEC) + + DONE : INIT CHARGE Time : 0.158676400683 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441305 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000518 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125 + + Density error is 0.216601006785 + + Energy Rydberg eV + E_KohnSham -34.1869627904 -465.137491264 + E_Harris -34.3827710719 -467.801599607 + E_Fermi -0.416550194796 -5.66745615224 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000795760317217 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132912962737 + + Density error is 0.097509219622 + + Energy Rydberg eV + E_KohnSham -34.2770979398 -466.363842886 + E_Harris -34.2837379028 -466.454184217 + E_Fermi -0.225034012346 -3.06174481171 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000767696872357 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125379895406 + + Density error is 0.0623191606888 + + Energy Rydberg eV + E_KohnSham -34.2772826435 -466.366355908 + E_Harris -34.2815391042 -466.424268027 + E_Fermi -0.211171023391 -2.87312917061 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000733048622485 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113695051541 + + Density error is 0.0020367413803 + + Energy Rydberg eV + E_KohnSham -34.2773174558 -466.366829554 + E_Harris -34.2773192748 -466.366854302 + E_Fermi -0.175452157715 -2.38714907132 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000734309547276 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011375456477 + + Density error is 0.000869971685399 + + Energy Rydberg eV + E_KohnSham -34.2772490618 -466.365899005 + E_Harris -34.2772508169 -466.365922884 + E_Fermi -0.174368541071 -2.37240571051 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000733471682319 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113607291138 + + Density error is 0.000123151081692 + + Energy Rydberg eV + E_KohnSham -34.2772951134 -466.36652557 + E_Harris -34.2772951402 -466.366525934 + E_Fermi -0.17456716858 -2.37510817642 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000733563178034 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113604697269 + + Density error is 5.01821120929e-05 + + Energy Rydberg eV + E_KohnSham -34.2772796661 -466.366315398 + E_Harris -34.2772796805 -466.366315595 + E_Fermi -0.174417675022 -2.37307421222 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000733488984922 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113598715864 + + Density error is 1.26853435878e-05 + + Energy Rydberg eV + E_KohnSham -34.2772835067 -466.366367652 + E_Harris -34.2772835073 -466.366367661 + E_Fermi -0.17447380015 -2.37383783375 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000733491094385 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113597244889 + + Density error is 1.51250746423e-06 + + Energy Rydberg eV + E_KohnSham -34.277281967 -466.366346704 + E_Harris -34.277281967 -466.366346704 + E_Fermi -0.174459816288 -2.37364757355 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000733494246392 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113597418914 + + Density error is 1.81923568071e-07 + + Energy Rydberg eV + E_KohnSham -34.2772821308 -466.366348933 + E_Harris -34.2772821308 -466.366348933 + E_Fermi -0.174458653895 -2.37363175839 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000733494605126 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011359745991 + + Density error is 7.41813669438e-08 + + Energy Rydberg eV + E_KohnSham -34.2772821587 -466.366349311 + E_Harris -34.2772821587 -466.366349311 + E_band -8.02625757186 -109.202836593 + E_one_elec -69.6591201643 -947.760951901 + E_Hartree +36.2128021518 +492.700449811 + E_xc -8.23783275788 -112.081464678 + E_Ewald +7.53045839809 +102.457142766 + E_demet -6.61223146094e-87 -8.99640243637e-86 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19553407795 -2.6603776133 + E_Fermi -0.174458674277 -2.37363203569 + + charge density convergence is achieved + final etot is -466.366349311 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4789 2.00000 + 2 -13.1956 2.00000 + 3 -9.14238 2.00000 + 4 -6.78453 2.00000 + 5 1.41617 0.00000 + 6 4.69431 0.00000 + 7 11.0295 0.00000 + 8 11.2718 0.00000 + + EFERMI = -2.373632035689249 eV + OUT.ABACUS/ final etot is -466.3663493114018 eV + correction force for each atom along direction 1 is 0.000121585 + correction force for each atom along direction 2 is 7.01570e-05 + correction force for each atom along direction 3 is 0.000162249 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.53421435 -2.6247188 +0.22825440 + H1 -0.36234764 +2.6352331 -0.0075781651 + H2 -0.17186670 -0.010514356 -0.22067624 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3663493114018 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8993 11 0.63 1.0e+02% + Run_lcao lcao_line 6.8897 1 6.9 1.e+02% + Potential init_pot 0.28421 2 0.14 4.1% + PW_Basis recip2real 0.27641 16 0.017 4.0% + PW_Basis gathers_scatterp 0.12950 16 0.0081 1.9% + Potential v_of_rho 0.97400 13 0.075 14.% + XC_Functional v_xc 0.28845 14 0.021 4.2% + H_Hartree_pw v_hartree 0.64518 13 0.050 9.4% + PW_Basis real2recip 0.65947 38 0.017 9.6% + PW_Basis gatherp_scatters 0.26983 38 0.0071 3.9% + ORB_control set_orb_tables 1.0966 1 1.1 16.% + ORB_gen_tables gen_tables 1.0966 1 1.1 16.% + ORB_table_phi init_Table 0.47763 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47241 126 0.0037 6.8% + ORB_table_beta init_Table_Beta 0.18543 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18390 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24860 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24660 66 0.0037 3.6% + LOOP_ions opt_ions 5.2743 1 5.3 76.% + ESolver_KS_LCAO Run 4.7174 1 4.7 68.% + HSolverLCAO solve 2.4197 11 0.22 35.% + HamiltLCAO updateHk 1.2605 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2331 11 0.11 18.% + Gint_interface cal_gint 1.8283 23 0.079 26.% + Gint_Gamma distri_vl_value 0.16759 11 0.015 2.4% + Gint_Gamma distri_vl 2.2870 6 0.38 33.% + LCAO_Deepks cal_projected_DM 5.0843 13 0.39 74.% + LCAO_gen_fixedH add_v_delta 2.1424 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1424 6 0.36 31.% + ElecStateLCAO psiToRho 1.1377 11 0.10 16.% + Charge mix_rho 0.77860 10 0.078 11.% + LOOP_ions force_stress 0.55665 1 0.56 8.1% + Force_Stress_LCAO getForceStress 0.55662 1 0.56 8.1% + Force_LCAO_gamma ftable_gamma 0.33869 1 0.34 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.29851 1 0.30 4.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:01 2022 + Finish Time : Wed Sep 28 11:09:08 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..69bdc937bc3c995071f68e67929d440ea40c405a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123857 ima = 3.66739e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122911419619 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001121049447 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112533617921 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112803633638 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112738701849 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112774562084 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112768464858 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112771835174 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112771351233 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011277128248 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112771278422 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ea3f2f457e9507168d3af9f53b6540946456eb46 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.753569188678 19.679486997172 6.913462540913 0 0 0 +H +0.0 +2 +-10.965515638725 21.423927828430 6.943967018367 0 0 0 +-9.601753287460 19.338057233812 8.323930063885 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/conv new file mode 100644 index 0000000000000000000000000000000000000000..bc085962faf8e1e3de5a66d945f1944ecf18b545 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/conv @@ -0,0 +1 @@ +213 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9bbbbb307cb1e39360d3425bb71267f156df266a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749334088 0.01275530599 1.283986615 1.377944332 1.47025271 0.008679865166 0.01896312011 0.03903973588 +2.013387077e-18 0.00113547387 0.002715282545 0.01286561112 0.04703957605 9.925671042e-20 2.225569896e-06 6.328191463e-06 +0.001645455961 0.00592287889 + +H atom_index 1 n_descriptor 18 +1.305180981 0.03245437842 0.129565253 0.1776279068 0.3368052364 0.0249159386 0.03145855519 0.03643584254 +-3.077519469e-18 5.388729418e-05 0.1080807951 0.1256222292 0.1523747166 2.226932288e-18 1.19842379e-06 0.01385127193 +0.02848668069 0.03294125559 + +H atom_index 2 n_descriptor 18 +1.229937478 0.03490665648 0.1019413793 0.1408432151 0.314125025 0.02145224129 0.02713386422 0.03801898123 +-1.624150351e-17 4.672858794e-05 0.09805071618 0.1140252262 0.1209622336 -6.076549739e-18 5.270362309e-06 0.0134362617 +0.0259036532 0.02984635655 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d976c5026d93c0a65fde916fe1bafc358a1ef3f8 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..3c73b51323cfd75a603bb0be24c3916a36599b05 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:01 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0863088 SEC) : SETUP UNITCELL + DONE(0.09089 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.109089 SEC) : INIT PLANEWAVE + DONE(0.158809 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.441372 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651375e+02 0.000000e+00 2.166e-01 5.321e-01 + GE2 -4.663638e+02 -1.226352e+00 9.751e-02 4.742e-01 + GE3 -4.663664e+02 -2.513023e-03 6.232e-02 5.451e-01 + GE4 -4.663668e+02 -4.736462e-04 2.037e-03 4.114e-01 + GE5 -4.663659e+02 9.305489e-04 8.700e-04 4.097e-01 + GE6 -4.663665e+02 -6.265644e-04 1.232e-04 3.947e-01 + GE7 -4.663663e+02 2.101720e-04 5.018e-05 4.051e-01 + GE8 -4.663664e+02 -5.225443e-05 1.269e-05 3.801e-01 + GE9 -4.663663e+02 2.094824e-05 1.513e-06 3.883e-01 + GE10 -4.663663e+02 -2.228648e-06 1.819e-07 3.924e-01 + GE11 -4.663663e+02 -3.787367e-07 7.418e-08 3.228e-01 +E_delta_band = -7.19442916e-02 Ry = -9.78852304e-01 eV +E_delta_NN= -1.95534078e-01 Ry = -2.66037761e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8993 11 0.63 1e+02 % + Run_lcao lcao_line 6.8897 1 6.9 1e+02 % + Potential init_pot 0.28421 2 0.14 4.1 % + PW_Basis recip2real 0.27641 16 0.017 4 % + PW_Basis gathers_scatterp 0.1295 16 0.0081 1.9 % + Potential v_of_rho 0.974 13 0.075 14 % + XC_Functional v_xc 0.28845 14 0.021 4.2 % + H_Hartree_pw v_hartree 0.64518 13 0.05 9.4 % + PW_Basis real2recip 0.65947 38 0.017 9.6 % + PW_Basis gatherp_scatters 0.26983 38 0.0071 3.9 % + ORB_control set_orb_tables 1.0966 1 1.1 16 % + ORB_gen_tables gen_tables 1.0966 1 1.1 16 % + ORB_table_phi init_Table 0.47763 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47241 126 0.0037 6.8 % + ORB_table_beta init_Table_Beta 0.18543 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.1839 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.2486 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.2466 66 0.0037 3.6 % + LOOP_ions opt_ions 5.2743 1 5.3 76 % + ESolver_KS_LCAO Run 4.7174 1 4.7 68 % + HSolverLCAO solve 2.4197 11 0.22 35 % + HamiltLCAO updateHk 1.2605 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.2331 11 0.11 18 % + Gint_interface cal_gint 1.8283 23 0.079 26 % + Gint_Gamma distri_vl_value 0.16759 11 0.015 2.4 % + Gint_Gamma distri_vl 2.287 6 0.38 33 % + LCAO_Deepks cal_projected_DM 5.0843 13 0.39 74 % + LCAO_gen_fixedH add_v_delta 2.1424 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1424 6 0.36 31 % + ElecStateLCAO psiToRho 1.1377 11 0.1 16 % + Charge mix_rho 0.7786 10 0.078 11 % + LOOP_ions force_stress 0.55665 1 0.56 8.1 % + Force_Stress_LCAO getForceStress 0.55662 1 0.56 8.1 % + Force_LCAO_gamma ftable_gamma 0.33869 1 0.34 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.29851 1 0.3 4.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:01 2022 + FINISH Time : Wed Sep 28 11:09:08 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/213/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..393fe84ae11d8fd1b351fcafbd0dfccd41ded10f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.61896 0.697101 0.252276 +H 0.562888 0.665315 0.272056 +H 0.662581 0.666368 0.292694 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d5d32b8d4aa4bb97ab1547a54e83ac28966c9b8a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1201 2 + 2 -12.5379 2 + 3 -9.36655 2 + 4 -6.71229 2 + 5 1.03745 0 + 6 3.9698 0 + 7 11.1312 0 + 8 11.4083 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..123f9198e1f517343f3889ec2a031acaa686c50e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:58 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.3308754253 19.5188366174 7.06372086679 0 0 0 0 + tauc_H1 15.7608628005 18.6288244308 7.61755962998 0 0 0 0 + tauc_H2 18.5522607211 18.6582941324 8.19542240069 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0968012522599 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.109214669195 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.12731072878 (SEC) + + DONE : INIT CHARGE Time : 0.170408146168 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.491873 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000884 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116 + + Density error is 0.211156596773 + + Energy Rydberg eV + E_KohnSham -34.1901749864 -465.181195431 + E_Harris -34.3744502969 -467.688389656 + E_Fermi -0.389341202699 -5.29725882289 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00112782056373 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113717396103 + + Density error is 0.0984700131846 + + Energy Rydberg eV + E_KohnSham -34.278669171 -466.385220583 + E_Harris -34.2858746403 -466.483256022 + E_Fermi -0.200648260819 -2.72995964093 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00107265100701 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106552045157 + + Density error is 0.0635735407814 + + Energy Rydberg eV + E_KohnSham -34.2791711408 -466.392050233 + E_Harris -34.2837882627 -466.454869399 + E_Fermi -0.194180990367 -2.64196791228 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00100055567356 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000939212556616 + + Density error is 0.00188869212221 + + Energy Rydberg eV + E_KohnSham -34.2790711037 -466.390689158 + E_Harris -34.2790714815 -466.390694298 + E_Fermi -0.158731600936 -2.1596542254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00100193278532 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000938914854614 + + Density error is 0.00101447208315 + + Energy Rydberg eV + E_KohnSham -34.2790287956 -466.390113527 + E_Harris -34.2790294898 -466.390122972 + E_Fermi -0.158766863083 -2.16013399152 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00100078958057 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000936920733301 + + Density error is 0.000140563334307 + + Energy Rydberg eV + E_KohnSham -34.279048513 -466.390381795 + E_Harris -34.2790485193 -466.390381882 + E_Fermi -0.158335887808 -2.15427027207 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0010009578718 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00093698549994 + + Density error is 3.03076657827e-05 + + Energy Rydberg eV + E_KohnSham -34.2790425237 -466.390300307 + E_Harris -34.2790425271 -466.390300352 + E_Fermi -0.158294330277 -2.15370485286 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00100089246256 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000936927422901 + + Density error is 1.20453858883e-05 + + Energy Rydberg eV + E_KohnSham -34.2790449135 -466.390332821 + E_Harris -34.2790449141 -466.390332829 + E_Fermi -0.158313598218 -2.15396700665 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00100089102873 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000936914001366 + + Density error is 1.75346941029e-06 + + Energy Rydberg eV + E_KohnSham -34.2790438883 -466.390318873 + E_Harris -34.2790438883 -466.390318873 + E_Fermi -0.158301361472 -2.15380051718 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0010008910814 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000936913561871 + + Density error is 1.98962805883e-07 + + Energy Rydberg eV + E_KohnSham -34.2790440473 -466.390321036 + E_Harris -34.2790440473 -466.390321036 + E_Fermi -0.158299792278 -2.1537791672 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00100089163533 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000936914079522 + + Density error is 3.09945621242e-08 + + Energy Rydberg eV + E_KohnSham -34.2790440739 -466.390321399 + E_Harris -34.2790440739 -466.390321399 + E_band -7.89916334828 -107.473630969 + E_one_elec -68.7435348871 -935.303775127 + E_Hartree +35.7714629694 +486.69572218 + E_xc -8.16646422764 -111.110446009 + E_Ewald +6.98490260901 +95.0344754577 + E_demet -2.09760594371e-62 -2.85393929931e-61 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193887647541 -2.63797677837 + E_Fermi -0.158299715126 -2.1537781175 + + charge density convergence is achieved + final etot is -466.390321399 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1201 2.00000 + 2 -12.5379 2.00000 + 3 -9.36655 2.00000 + 4 -6.71229 2.00000 + 5 1.03745 0.00000 + 6 3.96980 0.00000 + 7 11.1312 0.00000 + 8 11.4083 0.00000 + + EFERMI = -2.153778117496541 eV + OUT.ABACUS/ final etot is -466.3903213985411 eV + correction force for each atom along direction 1 is -6.32421e-05 + correction force for each atom along direction 2 is -0.000178722 + correction force for each atom along direction 3 is -6.76731e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.44809118 -1.1109628 +1.0113579 + H1 +0.55409278 +0.62965590 -0.50863976 + H2 -0.10600159 +0.48130694 -0.50271811 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3903213985411 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4677 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4587 1 6.5 1.e+02% + Potential init_pot 0.32360 2 0.16 5.0% + PW_Basis recip2real 0.32467 16 0.020 5.0% + PW_Basis gathers_scatterp 0.17667 16 0.011 2.7% + Potential v_of_rho 0.99193 13 0.076 15.% + XC_Functional v_xc 0.30317 14 0.022 4.7% + H_Hartree_pw v_hartree 0.64513 13 0.050 10.% + PW_Basis real2recip 0.71404 38 0.019 11.% + PW_Basis gatherp_scatters 0.29530 38 0.0078 4.6% + ORB_control set_orb_tables 1.0941 1 1.1 17.% + ORB_gen_tables gen_tables 1.0941 1 1.1 17.% + ORB_table_phi init_Table 0.47265 1 0.47 7.3% + ORB_table_phi cal_ST_Phi12_R 0.46744 126 0.0037 7.2% + ORB_table_beta init_Table_Beta 0.18319 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18167 56 0.0032 2.8% + ORB_table_alpha init_Table_Alpha 0.24891 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24687 66 0.0037 3.8% + LOOP_ions opt_ions 4.7961 1 4.8 74.% + ESolver_KS_LCAO Run 4.2936 1 4.3 66.% + HSolverLCAO solve 1.8375 11 0.17 28.% + HamiltLCAO updateHk 1.0101 11 0.092 16.% + LCAO_Hamilt cal_Hgamma 0.98267 11 0.089 15.% + Gint_interface cal_gint 1.3518 23 0.059 21.% + Gint_Gamma distri_vl 2.0774 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.6260 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9310 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9310 6 0.32 30.% + ElecStateLCAO psiToRho 0.80794 11 0.073 12.% + Charge mix_rho 0.90397 10 0.090 14.% + LOOP_ions force_stress 0.50228 1 0.50 7.8% + Force_Stress_LCAO getForceStress 0.50224 1 0.50 7.8% + Force_LCAO_gamma ftable_gamma 0.28587 1 0.29 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.25105 1 0.25 3.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:58 2022 + Finish Time : Wed Sep 28 11:11:05 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8942248e37a072fe6e30e7b4e31c7471dba00833 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123532 ima = 3.66118e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123157199762 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111607477359 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112412488482 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112637186555 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112611442657 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112626738571 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112622846616 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112624957015 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112624453663 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112624379694 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112624367234 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1815bf6662bde70fd47392f10fc1988fed9ed9a8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.669124574704 19.518836617402 7.063720866780 0 0 0 +H +0.0 +2 +-12.239137199503 18.628824430783 7.617559629962 0 0 0 +-9.447739278886 18.658294132384 8.195422400674 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/conv new file mode 100644 index 0000000000000000000000000000000000000000..b6d8edebf42376aad2925cb99c4d707799b2b594 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/conv @@ -0,0 +1 @@ +214 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ad833dba19e686c85db66a063f28d8e11b8f22f5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754099115 0.01257709455 1.249304893 1.332656862 1.468582857 0.009250344333 0.01645059827 0.03920847415 +-1.479457607e-18 0.0008114196973 0.002623550499 0.01232607459 0.04354890508 1.388481215e-18 2.224242168e-06 6.324627855e-06 +0.001569946545 0.00605491259 + +H atom_index 1 n_descriptor 18 +1.206985514 0.03622495135 0.09567581155 0.1307085033 0.3050356867 0.02071639138 0.02571744309 0.03957213154 +4.601364784e-17 4.090928208e-05 0.08931578075 0.1116821879 0.1138289803 1.975447908e-18 5.206537802e-06 0.01415471401 +0.02455482466 0.02857794735 + +H atom_index 2 n_descriptor 18 +1.21754123 0.03589023249 0.09902081112 0.1351620173 0.3089591365 0.02122916907 0.02634019051 0.03915331608 +3.883135133e-17 4.184000886e-05 0.09202966862 0.1142883369 0.1155883623 2.776760737e-18 4.754657782e-06 0.01388405865 +0.02498777837 0.02912842198 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..28de3b3cdbd1ac0c15fb9be06a691f31e05cbf54 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:58 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0968258 SEC) : SETUP UNITCELL + DONE(0.109231 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.127332 SEC) : INIT PLANEWAVE + DONE(0.17054 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.491947 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651812e+02 0.000000e+00 2.112e-01 4.930e-01 + GE2 -4.663852e+02 -1.204025e+00 9.847e-02 4.424e-01 + GE3 -4.663921e+02 -6.829650e-03 6.357e-02 5.141e-01 + GE4 -4.663907e+02 1.361075e-03 1.889e-03 3.714e-01 + GE5 -4.663901e+02 5.756310e-04 1.014e-03 3.708e-01 + GE6 -4.663904e+02 -2.682684e-04 1.406e-04 3.655e-01 + GE7 -4.663903e+02 8.148773e-05 3.031e-05 3.501e-01 + GE8 -4.663903e+02 -3.251377e-05 1.205e-05 3.469e-01 + GE9 -4.663903e+02 1.394809e-05 1.753e-06 3.498e-01 + GE10 -4.663903e+02 -2.163498e-06 1.990e-07 3.490e-01 + GE11 -4.663903e+02 -3.620731e-07 3.099e-08 2.775e-01 +E_delta_band = -6.84771099e-02 Ry = -9.31678878e-01 eV +E_delta_NN= -1.93887648e-01 Ry = -2.63797678e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4677 11 0.59 1e+02 % + Run_lcao lcao_line 6.4587 1 6.5 1e+02 % + Potential init_pot 0.3236 2 0.16 5 % + PW_Basis recip2real 0.32467 16 0.02 5 % + PW_Basis gathers_scatterp 0.17667 16 0.011 2.7 % + Potential v_of_rho 0.99193 13 0.076 15 % + XC_Functional v_xc 0.30317 14 0.022 4.7 % + H_Hartree_pw v_hartree 0.64513 13 0.05 10 % + PW_Basis real2recip 0.71404 38 0.019 11 % + PW_Basis gatherp_scatters 0.2953 38 0.0078 4.6 % + ORB_control set_orb_tables 1.0941 1 1.1 17 % + ORB_gen_tables gen_tables 1.0941 1 1.1 17 % + ORB_table_phi init_Table 0.47265 1 0.47 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.46744 126 0.0037 7.2 % + ORB_table_beta init_Table_Beta 0.18319 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18167 56 0.0032 2.8 % + ORB_table_alpha init_Table_Alpha 0.24891 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24687 66 0.0037 3.8 % + LOOP_ions opt_ions 4.7961 1 4.8 74 % + ESolver_KS_LCAO Run 4.2936 1 4.3 66 % + HSolverLCAO solve 1.8375 11 0.17 28 % + HamiltLCAO updateHk 1.0101 11 0.092 16 % + LCAO_Hamilt cal_Hgamma 0.98267 11 0.089 15 % + Gint_interface cal_gint 1.3518 23 0.059 21 % + Gint_Gamma distri_vl 2.0774 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.626 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.931 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.931 6 0.32 30 % + ElecStateLCAO psiToRho 0.80794 11 0.073 12 % + Charge mix_rho 0.90397 10 0.09 14 % + LOOP_ions force_stress 0.50228 1 0.5 7.8 % + Force_Stress_LCAO getForceStress 0.50224 1 0.5 7.8 % + Force_LCAO_gamma ftable_gamma 0.28587 1 0.29 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.25105 1 0.25 3.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:58 2022 + FINISH Time : Wed Sep 28 11:11:05 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/214/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..2539576ae0636b7fe60d9758d965f7ccef6b3023 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.610565 0.680485 0.264338 +H 0.621323 0.68838 0.202006 +H 0.664293 0.696869 0.293165 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..7f6e2ef29400f9bda06ff8098b17223a4095fde2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6165 2 + 2 -13.4277 2 + 3 -9.09375 2 + 4 -6.81731 2 + 5 1.59856 0 + 6 4.92979 0 + 7 10.9897 0 + 8 11.2267 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f4014e6a49c4c6ccaef13824dfde214243ffb2b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:31 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.0958216831 19.053593758 7.40146345607 0 0 0 0 + tauc_H1 17.3970545418 19.2746428526 5.65617832899 0 0 0 0 + tauc_H2 18.6002055537 19.5123308658 8.2086266866 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0862353551751 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0866360628406 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104796846973 (SEC) + + DONE : INIT CHARGE Time : 0.153756097672 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.434848 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 144 9 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000633 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00162 + + Density error is 0.219922152591 + + Energy Rydberg eV + E_KohnSham -34.1830523138 -465.084286499 + E_Harris -34.3857748599 -467.842468239 + E_Fermi -0.428102603132 -5.82463473123 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000858667698831 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138644250158 + + Density error is 0.0973996501149 + + Energy Rydberg eV + E_KohnSham -34.2762589564 -466.352427931 + E_Harris -34.2828353943 -466.441904959 + E_Fermi -0.232492445911 -3.16322200634 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000828509609973 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127795066469 + + Density error is 0.0621155177233 + + Energy Rydberg eV + E_KohnSham -34.2765835175 -466.35684381 + E_Harris -34.2807662531 -466.413752848 + E_Fermi -0.217321185887 -2.95680642418 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000792840472802 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011028281133 + + Density error is 0.00210670791307 + + Energy Rydberg eV + E_KohnSham -34.2766471049 -466.357708962 + E_Harris -34.2766500101 -466.357748489 + E_Fermi -0.18145363379 -2.46880334234 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000795624224522 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110172132496 + + Density error is 0.000963591884611 + + Energy Rydberg eV + E_KohnSham -34.2765587037 -466.356506202 + E_Harris -34.2765619226 -466.356549998 + E_Fermi -0.180025393391 -2.44937113481 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000794548629635 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110022835068 + + Density error is 0.00011374440496 + + Energy Rydberg eV + E_KohnSham -34.2766181188 -466.357314586 + E_Harris -34.276618147 -466.357314969 + E_Fermi -0.180438023528 -2.45498525584 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000794661366315 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109993879021 + + Density error is 5.67384268837e-05 + + Energy Rydberg eV + E_KohnSham -34.2765983782 -466.357046001 + E_Harris -34.2765983951 -466.357046231 + E_Fermi -0.18026798618 -2.45267177903 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000794593825251 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109999751921 + + Density error is 1.12229954914e-05 + + Energy Rydberg eV + E_KohnSham -34.2766019341 -466.357094382 + E_Harris -34.2766019346 -466.357094389 + E_Fermi -0.180336904767 -2.45360946451 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000794596778561 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109998487635 + + Density error is 1.79976052443e-06 + + Energy Rydberg eV + E_KohnSham -34.276600456 -466.357074271 + E_Harris -34.276600456 -466.357074271 + E_Fermi -0.180325426797 -2.45345329872 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000794599312235 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001099979373 + + Density error is 1.78281442737e-07 + + Energy Rydberg eV + E_KohnSham -34.2766005968 -466.357076187 + E_Harris -34.2766005968 -466.357076187 + E_Fermi -0.180323337174 -2.45342486795 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000794599303427 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109997988767 + + Density error is 3.55600420245e-08 + + Energy Rydberg eV + E_KohnSham -34.276600636 -466.35707672 + E_Harris -34.276600636 -466.35707672 + E_band -8.07827767916 -109.910606463 + E_one_elec -70.0103359786 -952.539488203 + E_Hartree +36.3801966236 +494.977968441 + E_xc -8.26480750283 -112.448474912 + E_Ewald +7.74120559453 +105.324505475 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196155683074 -2.66883498489 + E_Fermi -0.180323499314 -2.45342707396 + + charge density convergence is achieved + final etot is -466.35707672 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6165 2.00000 + 2 -13.4277 2.00000 + 3 -9.09375 2.00000 + 4 -6.81731 2.00000 + 5 1.59856 0.00000 + 6 4.92979 0.00000 + 7 10.9897 0.00000 + 8 11.2267 0.00000 + + EFERMI = -2.453427073963323 eV + OUT.ABACUS/ final etot is -466.3570767195614 eV + correction force for each atom along direction 1 is 8.70908e-06 + correction force for each atom along direction 2 is -7.41626e-05 + correction force for each atom along direction 3 is 6.32027e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -2.1836880 -0.78969311 +0.59995424 + H1 +0.28458033 +0.20817714 -1.6107242 + H2 +1.8991077 +0.58151597 +1.0107700 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3570767195614 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0434 11 0.55 1.0e+02% + Run_lcao lcao_line 6.0341 1 6.0 1.e+02% + Potential init_pot 0.28444 2 0.14 4.7% + PW_Basis recip2real 0.27002 16 0.017 4.5% + PW_Basis gathers_scatterp 0.11728 16 0.0073 1.9% + Potential v_of_rho 0.86592 13 0.067 14.% + XC_Functional v_xc 0.22825 14 0.016 3.8% + H_Hartree_pw v_hartree 0.59724 13 0.046 9.9% + PW_Basis real2recip 0.56018 38 0.015 9.3% + PW_Basis gatherp_scatters 0.21866 38 0.0058 3.6% + ORB_control set_orb_tables 1.1143 1 1.1 18.% + ORB_gen_tables gen_tables 1.1143 1 1.1 18.% + ORB_table_phi init_Table 0.48661 1 0.49 8.1% + ORB_table_phi cal_ST_Phi12_R 0.48166 126 0.0038 8.0% + ORB_table_beta init_Table_Beta 0.18934 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18785 56 0.0034 3.1% + ORB_table_alpha init_Table_Alpha 0.25842 1 0.26 4.3% + ORB_table_alpha S_PhiAlpha_R 0.25652 66 0.0039 4.2% + LOOP_ions opt_ions 4.4068 1 4.4 73.% + ESolver_KS_LCAO Run 3.8746 1 3.9 64.% + HSolverLCAO solve 1.9073 11 0.17 32.% + HamiltLCAO updateHk 1.0181 11 0.093 17.% + LCAO_Hamilt cal_Hgamma 0.98428 11 0.089 16.% + Gint_interface cal_gint 1.6166 23 0.070 27.% + Gint_Gamma distri_vl 1.8832 6 0.31 31.% + LCAO_Deepks cal_projected_DM 4.2363 13 0.33 70.% + LCAO_gen_fixedH add_v_delta 1.7528 6 0.29 29.% + LCAO_DESCRIPTOR add_v_delta 1.7528 6 0.29 29.% + ElecStateLCAO psiToRho 0.87423 11 0.079 14.% + Charge mix_rho 0.65919 10 0.066 11.% + LOOP_ions force_stress 0.53203 1 0.53 8.8% + Force_Stress_LCAO getForceStress 0.53200 1 0.53 8.8% + Force_LCAO_gamma ftable_gamma 0.30745 1 0.31 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.27764 1 0.28 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:31 2022 + Finish Time : Wed Sep 28 11:07:37 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..9461053776cb1a6e02a3ae6ffd40d3a43d2240a4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/OUT.ABACUS/warning.log @@ -0,0 +1,73 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123954 ima = 3.66301e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 3 + 3 1 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123051248254 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112168762518 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112549930698 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112858063237 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112774314007 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112820816372 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112815360503 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112818613583 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112818171487 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112818086335 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112818090285 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a614f2214fc0c4c73a840cabf67d7c77798dfb95 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.904178316878 19.053593758073 7.401463456052 0 0 0 +H +0.0 +2 +-10.602945458186 19.274642852566 5.656178328988 0 0 0 +-9.399794446273 19.512330865777 8.208626686603 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/conv new file mode 100644 index 0000000000000000000000000000000000000000..85f701e5d62ebd3312df64c3351903dcdbfc51e7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/conv @@ -0,0 +1 @@ +215 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..6f393b433dbfd021967703308aa460dd87155524 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748058519 0.01284701212 1.303781841 1.387203884 1.471003679 0.008587079964 0.01973357848 0.03900156974 +1.485061233e-18 0.001255745025 0.002750959638 0.01335224893 0.0481673625 -2.13738148e-19 2.29601216e-06 6.440801448e-06 +0.001682934716 0.005872980974 + +H atom_index 1 n_descriptor 18 +1.282344203 0.03294527863 0.1208203738 0.1656937761 0.3305167061 0.02388682424 0.03017649353 0.03637240689 +-4.929811917e-18 5.339315773e-05 0.1086512125 0.1199232953 0.1425060568 -2.082747519e-18 2.452942312e-06 0.01328510631 +0.02809078872 0.0321629714 + +H atom_index 2 n_descriptor 18 +1.295791488 0.03253111493 0.1260752337 0.1726548688 0.3342012029 0.02448878886 0.03093732445 0.03624786885 +1.979717038e-17 5.468400181e-05 0.1086128743 0.1237952764 0.1483831356 -2.632102073e-18 1.731411531e-06 0.0135669462 +0.0285075581 0.0326485197 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..30aa43fbe253c23380c8dc6e00ed67193171dfd8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:31 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0862568 SEC) : SETUP UNITCELL + DONE(0.0866536 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104816 SEC) : INIT PLANEWAVE + DONE(0.153889 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.434921 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650843e+02 0.000000e+00 2.199e-01 4.652e-01 + GE2 -4.663524e+02 -1.268141e+00 9.740e-02 3.947e-01 + GE3 -4.663568e+02 -4.415880e-03 6.212e-02 4.487e-01 + GE4 -4.663577e+02 -8.651515e-04 2.107e-03 3.378e-01 + GE5 -4.663565e+02 1.202760e-03 9.636e-04 3.391e-01 + GE6 -4.663573e+02 -8.083842e-04 1.137e-04 3.164e-01 + GE7 -4.663570e+02 2.685852e-04 5.674e-05 3.189e-01 + GE8 -4.663571e+02 -4.838097e-05 1.122e-05 3.124e-01 + GE9 -4.663571e+02 2.011062e-05 1.800e-06 3.141e-01 + GE10 -4.663571e+02 -1.915683e-06 1.783e-07 3.100e-01 + GE11 -4.663571e+02 -5.326644e-07 3.556e-08 2.555e-01 +E_delta_band = -7.32963104e-02 Ry = -9.97247464e-01 eV +E_delta_NN= -1.96155683e-01 Ry = -2.66883498e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0434 11 0.55 1e+02 % + Run_lcao lcao_line 6.0341 1 6 1e+02 % + Potential init_pot 0.28444 2 0.14 4.7 % + PW_Basis recip2real 0.27002 16 0.017 4.5 % + PW_Basis gathers_scatterp 0.11728 16 0.0073 1.9 % + Potential v_of_rho 0.86592 13 0.067 14 % + XC_Functional v_xc 0.22825 14 0.016 3.8 % + H_Hartree_pw v_hartree 0.59724 13 0.046 9.9 % + PW_Basis real2recip 0.56018 38 0.015 9.3 % + PW_Basis gatherp_scatters 0.21866 38 0.0058 3.6 % + ORB_control set_orb_tables 1.1143 1 1.1 18 % + ORB_gen_tables gen_tables 1.1143 1 1.1 18 % + ORB_table_phi init_Table 0.48661 1 0.49 8.1 % + ORB_table_phi cal_ST_Phi12_R 0.48166 126 0.0038 8 % + ORB_table_beta init_Table_Beta 0.18934 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18785 56 0.0034 3.1 % + ORB_table_alpha init_Table_Alpha 0.25842 1 0.26 4.3 % + ORB_table_alpha S_PhiAlpha_R 0.25652 66 0.0039 4.2 % + LOOP_ions opt_ions 4.4068 1 4.4 73 % + ESolver_KS_LCAO Run 3.8746 1 3.9 64 % + HSolverLCAO solve 1.9073 11 0.17 32 % + HamiltLCAO updateHk 1.0181 11 0.093 17 % + LCAO_Hamilt cal_Hgamma 0.98428 11 0.089 16 % + Gint_interface cal_gint 1.6166 23 0.07 27 % + Gint_Gamma distri_vl 1.8832 6 0.31 31 % + LCAO_Deepks cal_projected_DM 4.2363 13 0.33 70 % + LCAO_gen_fixedH add_v_delta 1.7528 6 0.29 29 % + LCAO_DESCRIPTOR add_v_delta 1.7528 6 0.29 29 % + ElecStateLCAO psiToRho 0.87423 11 0.079 14 % + Charge mix_rho 0.65919 10 0.066 11 % + LOOP_ions force_stress 0.53203 1 0.53 8.8 % + Force_Stress_LCAO getForceStress 0.532 1 0.53 8.8 % + Force_LCAO_gamma ftable_gamma 0.30745 1 0.31 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.27764 1 0.28 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:31 2022 + FINISH Time : Wed Sep 28 11:07:37 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/215/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..345443122fb5b39648975942547794b3aa8a2b2d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.603639 0.66836 0.257719 +H 0.624664 0.711213 0.210677 +H 0.60434 0.714931 0.309322 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2b26c14de6148018bc9926a0e3aa8c0250863d21 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0203 2 + 2 -12.2283 2 + 3 -9.5211 2 + 4 -6.69389 2 + 5 0.838323 0 + 6 3.69919 0 + 7 11.1633 0 + 8 11.4458 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0b77744f6925195f9329195ee3e075c428339ef3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:57 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.901880993 18.7140703408 7.21611946492 0 0 0 0 + tauc_H1 17.4905918788 19.9139743011 5.89895328669 0 0 0 0 + tauc_H2 16.9215207658 20.0180781952 8.66100659029 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.10036804429 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100726000167 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118751717205 (SEC) + + DONE : INIT CHARGE Time : 0.161912884551 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445108 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 144 9 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000997 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000779 + + Density error is 0.207957392971 + + Energy Rydberg eV + E_KohnSham -34.1873488467 -465.142743829 + E_Harris -34.365613341 -467.568156702 + E_Fermi -0.379338564275 -5.16116594528 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00128594632832 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113800107964 + + Density error is 0.0984713550623 + + Energy Rydberg eV + E_KohnSham -34.2732277016 -466.311185594 + E_Harris -34.2806605404 -466.412314553 + E_Fermi -0.194094382146 -2.64078954697 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00122729395533 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109380620222 + + Density error is 0.0636738284442 + + Energy Rydberg eV + E_KohnSham -34.2737111765 -466.317763607 + E_Harris -34.2784226988 -466.381867156 + E_Fermi -0.189331417406 -2.57598608713 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116168120383 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106206559737 + + Density error is 0.00185456251974 + + Energy Rydberg eV + E_KohnSham -34.2735624667 -466.315740306 + E_Harris -34.2735624467 -466.315740034 + E_Fermi -0.154029840538 -2.09568349335 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116280809591 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106152011314 + + Density error is 0.000918591152881 + + Energy Rydberg eV + E_KohnSham -34.2735520517 -466.315598603 + E_Harris -34.2735527676 -466.315608344 + E_Fermi -0.154503052638 -2.10212187427 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116213389834 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106164844094 + + Density error is 0.000147346136586 + + Energy Rydberg eV + E_KohnSham -34.2735493496 -466.315561839 + E_Harris -34.2735493528 -466.315561882 + E_Fermi -0.153798557273 -2.09253672309 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116219904293 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106176134811 + + Density error is 2.3020844302e-05 + + Energy Rydberg eV + E_KohnSham -34.2735530794 -466.315612585 + E_Harris -34.2735530796 -466.315612588 + E_Fermi -0.153841440393 -2.09312017787 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116215600478 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106169970792 + + Density error is 4.74840631939e-06 + + Energy Rydberg eV + E_KohnSham -34.2735531233 -466.315613183 + E_Harris -34.2735531234 -466.315613184 + E_Fermi -0.153831797933 -2.09298898548 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116215358628 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106170055467 + + Density error is 2.05167152603e-06 + + Energy Rydberg eV + E_KohnSham -34.2735528522 -466.315609494 + E_Harris -34.2735528522 -466.315609494 + E_Fermi -0.153827982347 -2.09293707176 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116214903571 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106170097591 + + Density error is 2.96487093595e-07 + + Energy Rydberg eV + E_KohnSham -34.273552904 -466.315610199 + E_Harris -34.273552904 -466.315610199 + E_Fermi -0.153826740332 -2.09292017328 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116214966128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106170157145 + + Density error is 1.29261306847e-07 + + Energy Rydberg eV + E_KohnSham -34.2735528998 -466.315610142 + E_Harris -34.2735528998 -466.315610142 + E_Fermi -0.153826404775 -2.09291560779 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116214971749 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106170143238 + + Density error is 1.16507064323e-08 + + Energy Rydberg eV + E_KohnSham -34.2735529107 -466.315610289 + E_Harris -34.2735529107 -466.315610289 + E_band -7.85900604707 -106.927262857 + E_one_elec -68.406424441 -930.717152204 + E_Hartree +35.6055761739 +484.438716538 + E_xc -8.14007321711 -110.75137789 + E_Ewald +6.79340690758 +92.4290427756 + E_demet -4.54650562938e-53 -6.18583825486e-52 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193358573927 -2.63077836256 + E_Fermi -0.153826520033 -2.09291717596 + + charge density convergence is achieved + final etot is -466.315610289 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0203 2.00000 + 2 -12.2283 2.00000 + 3 -9.52110 2.00000 + 4 -6.69389 2.00000 + 5 0.838323 0.00000 + 6 3.69919 0.00000 + 7 11.1633 0.00000 + 8 11.4458 0.00000 + + EFERMI = -2.092917175955547 eV + OUT.ABACUS/ final etot is -466.3156102894745 eV + correction force for each atom along direction 1 is -0.000121013 + correction force for each atom along direction 2 is 0.000167886 + correction force for each atom along direction 3 is 4.00888e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.38812634 +2.5196574 +1.1296101 + H1 -0.18840970 -0.78590403 -0.032158734 + H2 -0.19971664 -1.7337534 -1.0974513 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3156102894745 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7702 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7604 1 6.8 1.e+02% + Potential init_pot 0.28341 2 0.14 4.2% + PW_Basis recip2real 0.30050 17 0.018 4.4% + PW_Basis gathers_scatterp 0.12935 17 0.0076 1.9% + Potential v_of_rho 1.0751 14 0.077 16.% + XC_Functional v_xc 0.30291 15 0.020 4.5% + H_Hartree_pw v_hartree 0.72364 14 0.052 11.% + PW_Basis real2recip 0.76239 41 0.019 11.% + PW_Basis gatherp_scatters 0.29859 41 0.0073 4.4% + ORB_control set_orb_tables 1.1005 1 1.1 16.% + ORB_gen_tables gen_tables 1.1005 1 1.1 16.% + ORB_table_phi init_Table 0.47974 1 0.48 7.1% + ORB_table_phi cal_ST_Phi12_R 0.47439 126 0.0038 7.0% + ORB_table_beta init_Table_Beta 0.18353 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18197 56 0.0032 2.7% + ORB_table_alpha init_Table_Alpha 0.24785 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.24589 66 0.0037 3.6% + LOOP_ions opt_ions 5.1374 1 5.1 76.% + ESolver_KS_LCAO Run 4.6350 1 4.6 68.% + HSolverLCAO solve 1.9590 12 0.16 29.% + HamiltLCAO updateHk 1.0635 12 0.089 16.% + LCAO_Hamilt cal_Hgamma 1.0336 12 0.086 15.% + Gint_interface cal_gint 1.6475 25 0.066 24.% + Gint_Gamma distri_vl 2.4177 6 0.40 36.% + LCAO_Deepks cal_projected_DM 4.9909 14 0.36 74.% + LCAO_gen_fixedH add_v_delta 2.2726 6 0.38 34.% + LCAO_DESCRIPTOR add_v_delta 2.2727 6 0.38 34.% + ElecStateLCAO psiToRho 0.87695 12 0.073 13.% + Charge mix_rho 0.98957 11 0.090 15.% + LOOP_ions force_stress 0.50227 1 0.50 7.4% + Force_Stress_LCAO getForceStress 0.50224 1 0.50 7.4% + Force_LCAO_gamma ftable_gamma 0.28361 1 0.28 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.26917 1 0.27 4.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:57 2022 + Finish Time : Wed Sep 28 11:13:04 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..add60ac2ce2b5104f2b1219d243dd31a51a849ca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/OUT.ABACUS/warning.log @@ -0,0 +1,77 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123683 ima = 3.65291e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 3 + 3 1 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122985647989 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111439092927 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112347189808 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112533051002 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011254264452 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112536928635 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112537435487 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112537942373 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112537792832 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112537789329 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112537769172 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112537775741 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a3d142367b6651418461abecfc72661486ee0f93 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.098119007033 18.714070340790 7.216119464898 0 0 0 +H +0.0 +2 +-10.509408121206 19.913974301121 5.898953286694 0 0 0 +-11.078479234221 20.018078195173 8.661006590272 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/conv new file mode 100644 index 0000000000000000000000000000000000000000..a19d094c1d492b17f15fa22832cca44ea050c66f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/conv @@ -0,0 +1 @@ +216 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e2834c09cba75d3db385efb8257bedbaa20dc5ec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.757163305 0.01246910194 1.233238823 1.315776001 1.468322996 0.009842311441 0.01526713155 0.03935428951 +-1.883659376e-19 0.0006724980863 0.002621535562 0.01243129835 0.04217376546 1.21425727e-19 2.228882982e-06 6.514729864e-06 +0.001546933652 0.005992139463 + +H atom_index 1 n_descriptor 18 +1.217758196 0.03618971913 0.1010746919 0.1352791836 0.3086170182 0.02173283564 0.02633270401 0.03946709979 +3.689633478e-17 3.927370348e-05 0.09163059126 0.1146221658 0.1155009534 -2.316647058e-18 3.721801098e-06 0.01397186328 +0.02505708098 0.02911955117 + +H atom_index 2 n_descriptor 18 +1.163632177 0.03770222371 0.08459336576 0.1136031938 0.2871436998 0.01905876309 0.02314129041 0.0415989351 +3.474072428e-17 3.493403776e-05 0.07828627871 0.09637735406 0.1112631311 -4.396382254e-18 5.583982793e-06 0.01567394386 +0.02275761561 0.02614432174 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..1626e8bed198b2c0884cfc551f578d1bb9477f40 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/e_base.npy new file mode 100644 index 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TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:57 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.10039 SEC) : SETUP UNITCELL + DONE(0.100741 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118771 SEC) : INIT PLANEWAVE + DONE(0.162044 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445174 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651427e+02 0.000000e+00 2.080e-01 4.886e-01 + GE2 -4.663112e+02 -1.168442e+00 9.847e-02 4.432e-01 + GE3 -4.663178e+02 -6.578013e-03 6.367e-02 5.113e-01 + GE4 -4.663157e+02 2.023301e-03 1.855e-03 3.719e-01 + GE5 -4.663156e+02 1.417031e-04 9.186e-04 3.700e-01 + GE6 -4.663156e+02 3.676399e-05 1.473e-04 3.685e-01 + GE7 -4.663156e+02 -5.074583e-05 2.302e-05 3.486e-01 + GE8 -4.663156e+02 -5.980625e-07 4.748e-06 3.510e-01 + GE9 -4.663156e+02 3.688758e-06 2.052e-06 3.487e-01 + GE10 -4.663156e+02 -7.048442e-07 2.965e-07 3.476e-01 + GE11 -4.663156e+02 5.685947e-08 1.293e-07 3.489e-01 + GE12 -4.663156e+02 -1.474088e-07 1.165e-08 2.739e-01 +E_delta_band = -6.73202399e-02 Ry = -9.15938854e-01 eV +E_delta_NN= -1.93358574e-01 Ry = -2.63077836e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7702 11 0.62 1e+02 % + Run_lcao lcao_line 6.7604 1 6.8 1e+02 % + Potential init_pot 0.28341 2 0.14 4.2 % + PW_Basis recip2real 0.3005 17 0.018 4.4 % + PW_Basis gathers_scatterp 0.12935 17 0.0076 1.9 % + Potential v_of_rho 1.0751 14 0.077 16 % + XC_Functional v_xc 0.30291 15 0.02 4.5 % + H_Hartree_pw v_hartree 0.72364 14 0.052 11 % + PW_Basis real2recip 0.76239 41 0.019 11 % + PW_Basis gatherp_scatters 0.29859 41 0.0073 4.4 % + ORB_control set_orb_tables 1.1005 1 1.1 16 % + ORB_gen_tables gen_tables 1.1005 1 1.1 16 % + ORB_table_phi init_Table 0.47974 1 0.48 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.47439 126 0.0038 7 % + ORB_table_beta init_Table_Beta 0.18353 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18197 56 0.0032 2.7 % + ORB_table_alpha init_Table_Alpha 0.24785 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.24589 66 0.0037 3.6 % + LOOP_ions opt_ions 5.1374 1 5.1 76 % + ESolver_KS_LCAO Run 4.635 1 4.6 68 % + HSolverLCAO solve 1.959 12 0.16 29 % + HamiltLCAO updateHk 1.0635 12 0.089 16 % + LCAO_Hamilt cal_Hgamma 1.0336 12 0.086 15 % + Gint_interface cal_gint 1.6475 25 0.066 24 % + Gint_Gamma distri_vl 2.4177 6 0.4 36 % + LCAO_Deepks cal_projected_DM 4.9909 14 0.36 74 % + LCAO_gen_fixedH add_v_delta 2.2726 6 0.38 34 % + LCAO_DESCRIPTOR add_v_delta 2.2727 6 0.38 34 % + ElecStateLCAO psiToRho 0.87695 12 0.073 13 % + Charge mix_rho 0.98957 11 0.09 15 % + LOOP_ions force_stress 0.50227 1 0.5 7.4 % + Force_Stress_LCAO getForceStress 0.50224 1 0.5 7.4 % + Force_LCAO_gamma ftable_gamma 0.28361 1 0.28 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.26917 1 0.27 4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:57 2022 + FINISH Time : Wed Sep 28 11:13:04 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/216/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fd3aca134c69f7f9565b182b9f58a8f7bf0217e9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.59869 0.667754 0.226939 +H 0.628377 0.706318 0.181224 +H 0.565116 0.703144 0.269471 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8429e1e8aa30dae68f2a1258a3c2cca457d2c892 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1074 2 + 2 -13.3424 2 + 3 -8.74164 2 + 4 -6.69772 2 + 5 1.26176 0 + 6 4.41731 0 + 7 11.0991 0 + 8 11.3144 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c03bb6f0eb2ea81a5e1c687a82d121657fd6d462 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:44 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.7633114093 18.6971121806 6.35428769439 0 0 0 0 + tauc_H1 17.5945467661 19.7768914725 5.07428221506 0 0 0 0 + tauc_H2 15.8232578221 19.6880277667 7.54517978572 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0864557629294 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0987640473419 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117071307719 (SEC) + + DONE : INIT CHARGE Time : 0.167341736144 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448258 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 0 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00101 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118 + + Density error is 0.215788523877 + + Energy Rydberg eV + E_KohnSham -34.1884383286 -465.15756699 + E_Harris -34.3814433854 -467.783535506 + E_Fermi -0.400926242981 -5.45488138228 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00118719342285 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130571826873 + + Density error is 0.0983726537113 + + Energy Rydberg eV + E_KohnSham -34.2780200222 -466.37638846 + E_Harris -34.2847114605 -466.467430148 + E_Fermi -0.209276187946 -2.84734861178 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00113557931419 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123920464666 + + Density error is 0.0631072100709 + + Energy Rydberg eV + E_KohnSham -34.2782899982 -466.380061672 + E_Harris -34.2825779486 -466.43840223 + E_Fermi -0.19829906309 -2.69799716608 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105725913568 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011341495733 + + Density error is 0.00214194118547 + + Energy Rydberg eV + E_KohnSham -34.2782765533 -466.379878745 + E_Harris -34.2782811866 -466.379941784 + E_Fermi -0.163233319696 -2.22090325132 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105546001165 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113324784357 + + Density error is 0.000851463811321 + + Energy Rydberg eV + E_KohnSham -34.2782285329 -466.379225393 + E_Harris -34.2782291103 -466.37923325 + E_Fermi -0.162451791895 -2.21027002008 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105445780794 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001131922234 + + Density error is 0.000212858899153 + + Energy Rydberg eV + E_KohnSham -34.278258472 -466.379632736 + E_Harris -34.278258566 -466.379634015 + E_Fermi -0.162389985575 -2.20942910195 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105469271291 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113211480129 + + Density error is 3.85215393036e-05 + + Energy Rydberg eV + E_KohnSham -34.278246256 -466.379466528 + E_Harris -34.2782462636 -466.379466632 + E_Fermi -0.162246662203 -2.20747908744 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105460559481 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113205767011 + + Density error is 1.72373472573e-05 + + Energy Rydberg eV + E_KohnSham -34.2782516263 -466.379539595 + E_Harris -34.2782516275 -466.379539612 + E_Fermi -0.162286652367 -2.20802318153 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105459779274 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113204632998 + + Density error is 2.30352021734e-06 + + Energy Rydberg eV + E_KohnSham -34.2782502114 -466.379520345 + E_Harris -34.2782502114 -466.379520345 + E_Fermi -0.162269244382 -2.20778633374 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105459836541 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113204173976 + + Density error is 5.15125350192e-07 + + Energy Rydberg eV + E_KohnSham -34.2782504482 -466.379523567 + E_Harris -34.2782504482 -466.379523567 + E_Fermi -0.162267133368 -2.20775761193 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105459892748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113204246253 + + Density error is 1.73700169085e-07 + + Energy Rydberg eV + E_KohnSham -34.2782504701 -466.379523864 + E_Harris -34.2782504701 -466.379523864 + E_Fermi -0.162266890201 -2.20775430347 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105459902344 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113204254493 + + Density error is 9.81715259779e-09 + + Energy Rydberg eV + E_KohnSham -34.2782504735 -466.37952391 + E_Harris -34.2782504735 -466.37952391 + E_band -7.92155428579 -107.778275303 + E_one_elec -69.1717164769 -941.129484527 + E_Hartree +35.9980633374 +489.778778354 + E_xc -8.2023745287 -111.59903072 + E_Ewald +7.22242103041 +98.2660793685 + E_demet -2.81931568053e-73 -3.83587577159e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194392341481 -2.6448434917 + E_Fermi -0.162266719851 -2.20775198574 + + charge density convergence is achieved + final etot is -466.37952391 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1074 2.00000 + 2 -13.3424 2.00000 + 3 -8.74164 2.00000 + 4 -6.69772 2.00000 + 5 1.26176 0.00000 + 6 4.41731 0.00000 + 7 11.0991 0.00000 + 8 11.3144 0.00000 + + EFERMI = -2.207751985738069 eV + OUT.ABACUS/ final etot is -466.3795239103209 eV + correction force for each atom along direction 1 is 6.81754e-05 + correction force for each atom along direction 2 is 0.000138182 + correction force for each atom along direction 3 is -1.57668e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.79935876 -0.74244177 -1.0195274 + H1 -0.57382824 -0.079726134 +0.80444921 + H2 -0.22553052 +0.82216790 +0.21507820 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3795239103209 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1151 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1054 1 7.1 1.e+02% + Potential init_pot 0.28455 2 0.14 4.0% + PW_Basis recip2real 0.30628 17 0.018 4.3% + PW_Basis gathers_scatterp 0.12929 17 0.0076 1.8% + Potential v_of_rho 1.0691 14 0.076 15.% + XC_Functional v_xc 0.29999 15 0.020 4.2% + H_Hartree_pw v_hartree 0.72403 14 0.052 10.% + PW_Basis real2recip 0.69467 41 0.017 9.8% + PW_Basis gatherp_scatters 0.26092 41 0.0064 3.7% + ORB_control set_orb_tables 1.0960 1 1.1 15.% + ORB_gen_tables gen_tables 1.0960 1 1.1 15.% + ORB_table_phi init_Table 0.47220 1 0.47 6.6% + ORB_table_phi cal_ST_Phi12_R 0.46702 126 0.0037 6.6% + ORB_table_beta init_Table_Beta 0.18722 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18561 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.25011 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24811 66 0.0038 3.5% + LOOP_ions opt_ions 5.4826 1 5.5 77.% + ESolver_KS_LCAO Run 4.9191 1 4.9 69.% + HSolverLCAO solve 2.4454 12 0.20 34.% + HamiltLCAO updateHk 1.2858 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2490 12 0.10 18.% + Gint_interface cal_gint 2.2542 25 0.090 32.% + Gint_Gamma distri_vl 2.5693 6 0.43 36.% + LCAO_Deepks cal_projected_DM 5.3255 14 0.38 75.% + LCAO_gen_fixedH add_v_delta 2.4242 6 0.40 34.% + LCAO_DESCRIPTOR add_v_delta 2.4243 6 0.40 34.% + ElecStateLCAO psiToRho 1.1425 12 0.095 16.% + Charge mix_rho 0.84961 11 0.077 12.% + LOOP_ions force_stress 0.56323 1 0.56 7.9% + Force_Stress_LCAO getForceStress 0.56320 1 0.56 7.9% + Force_LCAO_gamma ftable_gamma 0.34341 1 0.34 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.33542 1 0.34 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:44 2022 + Finish Time : Wed Sep 28 11:03:51 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0871ff22b1de18911715966fab952c0e274982e5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123649 ima = 3.69621e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123843007597 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112954361263 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113465665808 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011367525948 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113638354089 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113662645667 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113652689116 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113655569355 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113654872827 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113654802366 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011365478476 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113654776008 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/STRU new file mode 100644 index 0000000000000000000000000000000000000000..cd7e7908c59b43116c1cc1c4f5f670a1685f3af6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.236688590694 18.697112180622 6.354287694389 0 0 0 +H +0.0 +2 +-10.405453233950 19.776891472528 5.074282215086 0 0 0 +-12.176742177913 19.688027766704 7.545179785725 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/conv new file mode 100644 index 0000000000000000000000000000000000000000..85501083f8e8cd5737ab78ff3ca10e1683ef246e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/conv @@ -0,0 +1 @@ +217 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7630a294709fcfce663cb10e08e3f87d9793e541 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742709802 0.01252231961 1.272368094 1.370127811 1.468538412 0.007466443829 0.0206471254 0.03883308897 +-3.776718348e-19 0.001122599091 0.002271863234 0.01213185303 0.04121330827 -5.175140831e-19 1.329852127e-06 4.366997574e-06 +0.0018156705 0.005522578053 + +H atom_index 1 n_descriptor 18 +1.209453859 0.03495272077 0.09553716129 0.1341159035 0.3106726487 0.01996774842 0.02623331125 0.03821886562 +2.421476311e-17 3.245058662e-05 0.09097673109 0.1138440922 0.1148862787 6.231418827e-18 5.481526899e-06 0.01342136123 +0.02435191718 0.02900618999 + +H atom_index 2 n_descriptor 18 +1.255492646 0.03332303621 0.1106297766 0.1545741506 0.3256088229 0.02195248423 0.02888971045 0.03661217674 +-2.049625582e-17 3.589863216e-05 0.1029711161 0.1151442386 0.1326573914 1.886148013e-18 3.748083616e-06 0.01278761982 +0.02612009393 0.03115835692 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..1e0bc2221b43e8ffaa90c1aa5c6bcdf48c939b6b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:44 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0864819 SEC) : SETUP UNITCELL + DONE(0.0987828 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.117092 SEC) : INIT PLANEWAVE + DONE(0.167476 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448314 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651576e+02 0.000000e+00 2.158e-01 5.223e-01 + GE2 -4.663764e+02 -1.218821e+00 9.837e-02 4.646e-01 + GE3 -4.663801e+02 -3.673212e-03 6.311e-02 5.280e-01 + GE4 -4.663799e+02 1.829268e-04 2.142e-03 3.960e-01 + GE5 -4.663792e+02 6.533519e-04 8.515e-04 3.949e-01 + GE6 -4.663796e+02 -4.073434e-04 2.129e-04 3.856e-01 + GE7 -4.663795e+02 1.662081e-04 3.852e-05 3.764e-01 + GE8 -4.663795e+02 -7.306665e-05 1.724e-05 3.695e-01 + GE9 -4.663795e+02 1.924985e-05 2.304e-06 3.713e-01 + GE10 -4.663795e+02 -3.222076e-06 5.151e-07 3.720e-01 + GE11 -4.663795e+02 -2.971370e-07 1.737e-07 3.711e-01 + GE12 -4.663795e+02 -4.610117e-08 9.817e-09 3.049e-01 +E_delta_band = -6.97485058e-02 Ry = -9.48977106e-01 eV +E_delta_NN= -1.94392341e-01 Ry = -2.64484349e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1151 11 0.65 1e+02 % + Run_lcao lcao_line 7.1054 1 7.1 1e+02 % + Potential init_pot 0.28455 2 0.14 4 % + PW_Basis recip2real 0.30628 17 0.018 4.3 % + PW_Basis gathers_scatterp 0.12929 17 0.0076 1.8 % + Potential v_of_rho 1.0691 14 0.076 15 % + XC_Functional v_xc 0.29999 15 0.02 4.2 % + H_Hartree_pw v_hartree 0.72403 14 0.052 10 % + PW_Basis real2recip 0.69467 41 0.017 9.8 % + PW_Basis gatherp_scatters 0.26092 41 0.0064 3.7 % + ORB_control set_orb_tables 1.096 1 1.1 15 % + ORB_gen_tables gen_tables 1.096 1 1.1 15 % + ORB_table_phi init_Table 0.4722 1 0.47 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.46702 126 0.0037 6.6 % + ORB_table_beta init_Table_Beta 0.18722 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18561 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.25011 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24811 66 0.0038 3.5 % + LOOP_ions opt_ions 5.4826 1 5.5 77 % + ESolver_KS_LCAO Run 4.9191 1 4.9 69 % + HSolverLCAO solve 2.4454 12 0.2 34 % + HamiltLCAO updateHk 1.2858 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.249 12 0.1 18 % + Gint_interface cal_gint 2.2542 25 0.09 32 % + Gint_Gamma distri_vl 2.5693 6 0.43 36 % + LCAO_Deepks cal_projected_DM 5.3255 14 0.38 75 % + LCAO_gen_fixedH add_v_delta 2.4242 6 0.4 34 % + LCAO_DESCRIPTOR add_v_delta 2.4243 6 0.4 34 % + ElecStateLCAO psiToRho 1.1425 12 0.095 16 % + Charge mix_rho 0.84961 11 0.077 12 % + LOOP_ions force_stress 0.56323 1 0.56 7.9 % + Force_Stress_LCAO getForceStress 0.5632 1 0.56 7.9 % + Force_LCAO_gamma ftable_gamma 0.34341 1 0.34 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.33542 1 0.34 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:44 2022 + FINISH Time : Wed Sep 28 11:03:51 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/217/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d0ee019c872d91cfb202d4bf6db5d01f4ff68859 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.599274 0.662564 0.197315 +H 0.634826 0.711201 0.178249 +H 0.540868 0.690386 0.204819 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..241858ebaea6e92a6d6c35b7b99bf0c0e2d9c6e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5684 2 + 2 -13.1394 2 + 3 -9.25466 2 + 4 -6.80564 2 + 5 1.46952 0 + 6 4.74853 0 + 7 11.0147 0 + 8 11.2718 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..5826d15e95b3cf0adbf9321878949675045ecd3d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:04 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.7796812034 18.5517883386 5.52482653972 0 0 0 0 + tauc_H1 17.7751223297 19.913630094 4.99098530699 0 0 0 0 + tauc_H2 15.1443070344 19.3308081756 5.73493148606 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0728506980913 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.085426384853 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.101179998402 (SEC) + + DONE : INIT CHARGE Time : 0.142661125845 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388707 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0007 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00168 + + Density error is 0.217179171245 + + Energy Rydberg eV + E_KohnSham -34.1866178367 -465.132797927 + E_Harris -34.3836931993 -467.814145794 + E_Fermi -0.420108072421 -5.71586356072 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000901770475362 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00141855906688 + + Density error is 0.0973758078749 + + Energy Rydberg eV + E_KohnSham -34.2776012827 -466.370691217 + E_Harris -34.2842616864 -466.461310658 + E_Fermi -0.227778557779 -3.09908626801 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000858440873103 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130196017059 + + Density error is 0.0622007269435 + + Energy Rydberg eV + E_KohnSham -34.2778696219 -466.374342159 + E_Harris -34.2821458893 -466.432523761 + E_Fermi -0.213809832458 -2.90903200985 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000801965640434 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110066461118 + + Density error is 0.00202922184891 + + Energy Rydberg eV + E_KohnSham -34.2779092654 -466.374881537 + E_Harris -34.2779110404 -466.374905687 + E_Fermi -0.177904619667 -2.420516528 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000804361693854 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109798959012 + + Density error is 0.000927244632119 + + Energy Rydberg eV + E_KohnSham -34.2778314612 -466.373822955 + E_Harris -34.2778341814 -466.373859967 + E_Fermi -0.176752443922 -2.40484037276 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000803223850307 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010962425585 + + Density error is 9.80391016528e-05 + + Energy Rydberg eV + E_KohnSham -34.2778849742 -466.374551038 + E_Harris -34.2778849857 -466.374551194 + E_Fermi -0.177017073573 -2.40844084388 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000803231197329 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109586869566 + + Density error is 5.33329419235e-05 + + Energy Rydberg eV + E_KohnSham -34.2778678842 -466.374318516 + E_Harris -34.2778678992 -466.374318721 + E_Fermi -0.176877911469 -2.40654744631 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000803184854082 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109591905269 + + Density error is 9.4458535822e-06 + + Energy Rydberg eV + E_KohnSham -34.2778706564 -466.374356235 + E_Harris -34.2778706568 -466.374356239 + E_Fermi -0.176938595746 -2.40737309826 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000803190312673 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109590773172 + + Density error is 1.75999693829e-06 + + Energy Rydberg eV + E_KohnSham -34.2778692521 -466.374337128 + E_Harris -34.2778692521 -466.374337128 + E_Fermi -0.176930158668 -2.40725830593 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00080319162983 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109590395063 + + Density error is 1.03976036714e-07 + + Energy Rydberg eV + E_KohnSham -34.2778693723 -466.374338763 + E_Harris -34.2778693723 -466.374338763 + E_Fermi -0.176928129341 -2.40723069552 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000803191583594 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109590409225 + + Density error is 4.57511925995e-08 + + Energy Rydberg eV + E_KohnSham -34.2778694095 -466.37433927 + E_Harris -34.2778694095 -466.37433927 + E_band -8.05075600443 -109.536154868 + E_one_elec -69.7735679057 -949.318093307 + E_Hartree +36.2630306697 +493.383843857 + E_xc -8.24580346282 -112.189911682 + E_Ewald +7.60179595099 +103.427739967 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195748849292 -2.66329972731 + E_Fermi -0.176928207621 -2.40723176057 + + charge density convergence is achieved + final etot is -466.37433927 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5684 2.00000 + 2 -13.1394 2.00000 + 3 -9.25466 2.00000 + 4 -6.80564 2.00000 + 5 1.46952 0.00000 + 6 4.74853 0.00000 + 7 11.0147 0.00000 + 8 11.2718 0.00000 + + EFERMI = -2.407231760572798 eV + OUT.ABACUS/ final etot is -466.3743392696074 eV + correction force for each atom along direction 1 is 1.93321e-05 + correction force for each atom along direction 2 is 0.000164258 + correction force for each atom along direction 3 is -0.000170465 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.87471322 -1.6420031 +0.56112956 + H1 +1.4853019 +1.6102665 -0.70018596 + H2 -0.61058863 +0.031736513 +0.13905640 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3743392696074 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4529 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4454 1 6.4 1.e+02% + Potential init_pot 0.24337 2 0.12 3.8% + PW_Basis recip2real 0.26885 16 0.017 4.2% + PW_Basis gathers_scatterp 0.10969 16 0.0069 1.7% + Potential v_of_rho 0.91592 13 0.070 14.% + XC_Functional v_xc 0.26189 14 0.019 4.1% + H_Hartree_pw v_hartree 0.61615 13 0.047 9.5% + PW_Basis real2recip 0.59944 38 0.016 9.3% + PW_Basis gatherp_scatters 0.22347 38 0.0059 3.5% + ORB_control set_orb_tables 0.89952 1 0.90 14.% + ORB_gen_tables gen_tables 0.89952 1 0.90 14.% + ORB_table_phi init_Table 0.37888 1 0.38 5.9% + ORB_table_phi cal_ST_Phi12_R 0.37462 126 0.0030 5.8% + ORB_table_beta init_Table_Beta 0.15384 1 0.15 2.4% + ORB_table_beta VNL_PhiBeta_R 0.15256 56 0.0027 2.4% + ORB_table_alpha init_Table_Alpha 0.20901 1 0.21 3.2% + ORB_table_alpha S_PhiAlpha_R 0.20732 66 0.0031 3.2% + LOOP_ions opt_ions 5.0877 1 5.1 79.% + ESolver_KS_LCAO Run 4.5452 1 4.5 70.% + HSolverLCAO solve 2.3749 11 0.22 37.% + HamiltLCAO updateHk 1.2353 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2017 11 0.11 19.% + Gint_interface cal_gint 2.2534 23 0.098 35.% + Gint_Gamma distri_vl 2.1931 6 0.37 34.% + LCAO_Deepks cal_projected_DM 4.9410 13 0.38 77.% + LCAO_gen_fixedH add_v_delta 2.0633 6 0.34 32.% + LCAO_DESCRIPTOR add_v_delta 2.0633 6 0.34 32.% + ElecStateLCAO psiToRho 1.1232 11 0.10 17.% + Charge mix_rho 0.76379 10 0.076 12.% + LOOP_ions force_stress 0.54242 1 0.54 8.4% + Force_Stress_LCAO getForceStress 0.54238 1 0.54 8.4% + Force_LCAO_gamma ftable_gamma 0.34560 1 0.35 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.33814 1 0.34 5.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:04 2022 + Finish Time : Wed Sep 28 11:03:11 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0cb5bfe273855f4966b3a056abe149558c85567a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123984 ima = 3.66918e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122727458287 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111792309328 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112234077409 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112525657834 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112449235141 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112491178147 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112487404649 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112490564363 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112490169764 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112490082907 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112490083748 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/STRU new file mode 100644 index 0000000000000000000000000000000000000000..92199927bcb51bba80243837208630acb38a7368 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.220318796566 18.551788338603 5.524826539709 0 0 0 +H +0.0 +2 +-10.224877670361 19.913630093933 4.990985306998 0 0 0 +-12.855692965638 19.330808175612 5.734931486040 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/conv new file mode 100644 index 0000000000000000000000000000000000000000..8ca474f427bd9879ee9b09e3441f1c8b12d3b1c9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/conv @@ -0,0 +1 @@ +218 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c38804afae21f37dea16425b358a37e1a375e49f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750923708 0.01284189414 1.290128232 1.376066474 1.470584921 0.009002527708 0.01843691502 0.03907303888 +-2.583451781e-19 0.001116872359 0.002835792059 0.01329055895 0.04831970327 2.00597574e-19 2.598712373e-06 6.992931423e-06 +0.001623232875 0.00603528697 + +H atom_index 1 n_descriptor 18 +1.297238844 0.03291335372 0.1272714042 0.1730774951 0.3341472495 0.02495636235 0.03097913058 0.03660582216 +-2.509074356e-18 5.653271523e-05 0.1085351322 0.1240281345 0.1485755066 7.730938637e-18 1.305485218e-06 0.01369147169 +0.02860854225 0.0326792538 + +H atom_index 2 n_descriptor 18 +1.254495555 0.03428513791 0.1110848944 0.1517138036 0.3214982274 0.02293397688 0.02852249669 0.03739006702 +-1.858420816e-17 5.233956196e-05 0.105081879 0.1152075111 0.1303988277 8.387528237e-18 3.688134266e-06 0.01326287502 +0.02718886873 0.03097728228 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..49d18cf1737b6b996306a164817be418ed4c5db2 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:04 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0728674 SEC) : SETUP UNITCELL + DONE(0.0854386 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.101193 SEC) : INIT PLANEWAVE + DONE(0.142764 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.388752 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651328e+02 0.000000e+00 2.172e-01 4.923e-01 + GE2 -4.663707e+02 -1.237893e+00 9.738e-02 4.621e-01 + GE3 -4.663743e+02 -3.650943e-03 6.220e-02 5.274e-01 + GE4 -4.663749e+02 -5.393772e-04 2.029e-03 4.020e-01 + GE5 -4.663738e+02 1.058581e-03 9.272e-04 4.003e-01 + GE6 -4.663746e+02 -7.280822e-04 9.804e-05 3.755e-01 + GE7 -4.663743e+02 2.325217e-04 5.333e-05 3.848e-01 + GE8 -4.663744e+02 -3.771859e-05 9.446e-06 3.767e-01 + GE9 -4.663743e+02 1.910708e-05 1.760e-06 3.788e-01 + GE10 -4.663743e+02 -1.635749e-06 1.040e-07 3.822e-01 + GE11 -4.663743e+02 -5.063158e-07 4.575e-08 3.093e-01 +E_delta_band = -7.24241875e-02 Ry = -9.85381623e-01 eV +E_delta_NN= -1.95748849e-01 Ry = -2.66329973e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4529 11 0.59 1e+02 % + Run_lcao lcao_line 6.4454 1 6.4 1e+02 % + Potential init_pot 0.24337 2 0.12 3.8 % + PW_Basis recip2real 0.26885 16 0.017 4.2 % + PW_Basis gathers_scatterp 0.10969 16 0.0069 1.7 % + Potential v_of_rho 0.91592 13 0.07 14 % + XC_Functional v_xc 0.26189 14 0.019 4.1 % + H_Hartree_pw v_hartree 0.61615 13 0.047 9.5 % + PW_Basis real2recip 0.59944 38 0.016 9.3 % + PW_Basis gatherp_scatters 0.22347 38 0.0059 3.5 % + ORB_control set_orb_tables 0.89952 1 0.9 14 % + ORB_gen_tables gen_tables 0.89952 1 0.9 14 % + ORB_table_phi init_Table 0.37888 1 0.38 5.9 % + ORB_table_phi cal_ST_Phi12_R 0.37462 126 0.003 5.8 % + ORB_table_beta init_Table_Beta 0.15384 1 0.15 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.15256 56 0.0027 2.4 % + ORB_table_alpha init_Table_Alpha 0.20901 1 0.21 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.20732 66 0.0031 3.2 % + LOOP_ions opt_ions 5.0877 1 5.1 79 % + ESolver_KS_LCAO Run 4.5452 1 4.5 70 % + HSolverLCAO solve 2.3749 11 0.22 37 % + HamiltLCAO updateHk 1.2353 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.2017 11 0.11 19 % + Gint_interface cal_gint 2.2534 23 0.098 35 % + Gint_Gamma distri_vl 2.1931 6 0.37 34 % + LCAO_Deepks cal_projected_DM 4.941 13 0.38 77 % + LCAO_gen_fixedH add_v_delta 2.0633 6 0.34 32 % + LCAO_DESCRIPTOR add_v_delta 2.0633 6 0.34 32 % + ElecStateLCAO psiToRho 1.1232 11 0.1 17 % + Charge mix_rho 0.76379 10 0.076 12 % + LOOP_ions force_stress 0.54242 1 0.54 8.4 % + Force_Stress_LCAO getForceStress 0.54238 1 0.54 8.4 % + Force_LCAO_gamma ftable_gamma 0.3456 1 0.35 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.33814 1 0.34 5.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:04 2022 + FINISH Time : Wed Sep 28 11:03:11 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/218/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..6db2228d2dcbe00c5301d02be257409d3b2c49c4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.599431 0.652697 0.175375 +H 0.631152 0.713095 0.17341 +H 0.534919 0.664157 0.177883 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..65dec70a2774ec050a526294442af13a48baeeb9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9922 2 + 2 -13.0089 2 + 3 -8.89847 2 + 4 -6.67359 2 + 5 1.0819 0 + 6 4.11913 0 + 7 11.1377 0 + 8 11.3686 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..90572685385e517e662fe9c09214255bb785c36c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:54 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.7840606023 18.275505365 4.91051286353 0 0 0 0 + tauc_H1 17.6722571369 19.9666617102 4.85549189529 0 0 0 0 + tauc_H2 14.9777325456 18.5963921439 4.98071343479 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0867116356008 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100442386256 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118695702191 (SEC) + + DONE : INIT CHARGE Time : 0.167358815427 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450291 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000545 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00185 + + Density error is 0.213164439497 + + Energy Rydberg eV + E_KohnSham -34.1898520137 -465.176801163 + E_Harris -34.3773250526 -467.727502713 + E_Fermi -0.390704500866 -5.31580744603 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000782112033821 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00144359627684 + + Density error is 0.0987461746077 + + Energy Rydberg eV + E_KohnSham -34.2782649422 -466.379720768 + E_Harris -34.2852227521 -466.474386627 + E_Fermi -0.200579988263 -2.72903074515 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000754359675053 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132537636764 + + Density error is 0.0636395636169 + + Energy Rydberg eV + E_KohnSham -34.2786015278 -466.384300249 + E_Harris -34.2830616826 -466.444983768 + E_Fermi -0.192396866353 -2.61769365974 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000726253353626 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109861057574 + + Density error is 0.00207430797904 + + Energy Rydberg eV + E_KohnSham -34.2785355449 -466.383402506 + E_Harris -34.2785396259 -466.383458031 + E_Fermi -0.157316940448 -2.14040678201 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000727195864304 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109579186586 + + Density error is 0.000879430768061 + + Energy Rydberg eV + E_KohnSham -34.278501864 -466.382944254 + E_Harris -34.2785020719 -466.382947082 + E_Fermi -0.15697591737 -2.13576692501 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000726895826591 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109273945329 + + Density error is 0.000198861410623 + + Energy Rydberg eV + E_KohnSham -34.2785183937 -466.383169152 + E_Harris -34.2785183923 -466.383169133 + E_Fermi -0.156661996523 -2.13149581277 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000727054789434 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109251918825 + + Density error is 2.87687797077e-05 + + Energy Rydberg eV + E_KohnSham -34.2785132895 -466.383099706 + E_Harris -34.2785132916 -466.383099734 + E_Fermi -0.156597871816 -2.13062335138 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000727040327698 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109249689102 + + Density error is 1.39797411431e-05 + + Energy Rydberg eV + E_KohnSham -34.2785162036 -466.383139354 + E_Harris -34.2785162045 -466.383139367 + E_Fermi -0.156617064173 -2.13088447678 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000727046855607 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109247659137 + + Density error is 2.56465503401e-06 + + Energy Rydberg eV + E_KohnSham -34.2785151841 -466.383125484 + E_Harris -34.2785151841 -466.383125484 + E_Fermi -0.156604150558 -2.13070877804 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000727042243149 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109246475175 + + Density error is 6.07152760328e-07 + + Energy Rydberg eV + E_KohnSham -34.2785154484 -466.383129079 + E_Harris -34.2785154484 -466.383129079 + E_Fermi -0.156602284003 -2.13068338225 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000727043053006 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109246451591 + + Density error is 1.99074061513e-07 + + Energy Rydberg eV + E_KohnSham -34.2785154401 -466.383128967 + E_Harris -34.2785154401 -466.383128967 + E_Fermi -0.156601971203 -2.13067912639 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000727043231048 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109246404841 + + Density error is 1.04437590284e-08 + + Energy Rydberg eV + E_KohnSham -34.2785154448 -466.38312903 + E_Harris -34.2785154448 -466.38312903 + E_band -7.87510654063 -107.14632131 + E_one_elec -68.7946526748 -935.999268309 + E_Hartree +35.81342842 +487.266691427 + E_xc -8.17308257608 -111.200493259 + E_Ewald +7.00115668 +95.2556234388 + E_demet -3.30887516876e-63 -4.50195562658e-62 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193843940218 -2.63738210974 + E_Fermi -0.156601774036 -2.13067644379 + + charge density convergence is achieved + final etot is -466.38312903 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9922 2.00000 + 2 -13.0089 2.00000 + 3 -8.89847 2.00000 + 4 -6.67359 2.00000 + 5 1.08190 0.00000 + 6 4.11913 0.00000 + 7 11.1377 0.00000 + 8 11.3686 0.00000 + + EFERMI = -2.130676443793804 eV + OUT.ABACUS/ final etot is -466.3831290304323 eV + correction force for each atom along direction 1 is -1.03995e-05 + correction force for each atom along direction 2 is 0.000145761 + correction force for each atom along direction 3 is -5.05968e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.1252110 +1.0014996 -0.059533913 + H1 -1.0365479 -1.3312425 +0.058294651 + H2 -0.088663037 +0.32974291 +0.0012392615 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3831290304323 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7083 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6992 1 6.7 1.e+02% + Potential init_pot 0.29082 2 0.15 4.3% + PW_Basis recip2real 0.28987 17 0.017 4.3% + PW_Basis gathers_scatterp 0.12451 17 0.0073 1.9% + Potential v_of_rho 0.94148 14 0.067 14.% + XC_Functional v_xc 0.25847 15 0.017 3.9% + H_Hartree_pw v_hartree 0.64225 14 0.046 9.6% + PW_Basis real2recip 0.59699 41 0.015 8.9% + PW_Basis gatherp_scatters 0.22976 41 0.0056 3.4% + ORB_control set_orb_tables 1.1055 1 1.1 16.% + ORB_gen_tables gen_tables 1.1055 1 1.1 16.% + ORB_table_phi init_Table 0.47986 1 0.48 7.2% + ORB_table_phi cal_ST_Phi12_R 0.47500 126 0.0038 7.1% + ORB_table_beta init_Table_Beta 0.18865 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18717 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25582 1 0.26 3.8% + ORB_table_alpha S_PhiAlpha_R 0.25398 66 0.0038 3.8% + LOOP_ions opt_ions 5.0648 1 5.1 76.% + ESolver_KS_LCAO Run 4.5024 1 4.5 67.% + HSolverLCAO solve 2.3662 12 0.20 35.% + HamiltLCAO updateHk 1.2274 12 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1900 12 0.099 18.% + Gint_interface cal_gint 2.2428 25 0.090 33.% + Gint_Gamma distri_vl 2.3364 6 0.39 35.% + LCAO_Deepks cal_projected_DM 4.9019 14 0.35 73.% + LCAO_gen_fixedH add_v_delta 2.2040 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2040 6 0.37 33.% + ElecStateLCAO psiToRho 1.1242 12 0.094 17.% + Charge mix_rho 0.72007 11 0.065 11.% + LOOP_ions force_stress 0.56218 1 0.56 8.4% + Force_Stress_LCAO getForceStress 0.56215 1 0.56 8.4% + Force_LCAO_gamma ftable_gamma 0.35274 1 0.35 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.34603 1 0.35 5.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:54 2022 + Finish Time : Wed Sep 28 11:12:01 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..bb296889352e55eb72237c055a8e94cfa7aef85a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123791 ima = 3.69506e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123761708513 + charge after normalized = 8.00000000000004 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112556823398 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113221340928 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113411627539 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113392814338 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113404811907 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113400185315 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113402074535 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113401373891 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113401373995 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113401351288 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011340134089 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d603aa4ac6bc106b431fb7d20fc2d1bc94e4d080 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.215939397657 18.275505364992 4.910512863512 0 0 0 +H +0.0 +2 +-10.327742863111 19.966661710225 4.855491895301 0 0 0 +-13.022267454450 18.596392143931 4.980713434764 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/conv new file mode 100644 index 0000000000000000000000000000000000000000..15a03d075fdf8e32acb1b468661e57a7ede223ba --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/conv @@ -0,0 +1 @@ +219 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0f21bc62070cd64ed8a26b7102f4c1c96a6680b6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746453062 0.01242100721 1.252848203 1.352896297 1.468017941 0.007879806137 0.0192138004 0.03896345528 +4.01586714e-19 0.000994202379 0.002311701836 0.01151692571 0.04107248669 9.047416475e-20 1.404861183e-06 4.54609376e-06 +0.001698370552 0.005692026998 + +H atom_index 1 n_descriptor 18 +1.180996947 0.03623029714 0.08598958011 0.121729483 0.2987333136 0.01863535756 0.0244446044 0.0398456315 +-1.196802222e-17 3.201863545e-05 0.08172821844 0.1038598217 0.1128821393 8.12899089e-18 6.351487751e-06 0.0144755072 +0.02285371728 0.02737190621 + +H atom_index 2 n_descriptor 18 +1.240596131 0.0342580265 0.1042980311 0.1467514762 0.3199233354 0.02129861634 0.02791230716 0.03749281443 +-4.823828069e-18 3.666380803e-05 0.09734470523 0.1148342007 0.1257972355 -6.359668827e-19 4.450805173e-06 0.0130589251 +0.02526317493 0.0303993931 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0255b2366c0446e11544a35153c3b367e8b67ffa Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:54 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0867326 SEC) : SETUP UNITCELL + DONE(0.100461 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118713 SEC) : INIT PLANEWAVE + DONE(0.167491 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450346 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651768e+02 0.000000e+00 2.132e-01 4.926e-01 + GE2 -4.663797e+02 -1.202920e+00 9.875e-02 4.141e-01 + GE3 -4.663843e+02 -4.579482e-03 6.364e-02 4.720e-01 + GE4 -4.663834e+02 8.977438e-04 2.074e-03 3.643e-01 + GE5 -4.663829e+02 4.582517e-04 8.794e-04 3.617e-01 + GE6 -4.663832e+02 -2.248983e-04 1.989e-04 3.578e-01 + GE7 -4.663831e+02 6.944656e-05 2.877e-05 3.422e-01 + GE8 -4.663831e+02 -3.964888e-05 1.398e-05 3.383e-01 + GE9 -4.663831e+02 1.387079e-05 2.565e-06 3.354e-01 + GE10 -4.663831e+02 -3.595476e-06 6.072e-07 3.398e-01 + GE11 -4.663831e+02 1.122763e-07 1.991e-07 3.413e-01 + GE12 -4.663831e+02 -6.360202e-08 1.044e-08 2.815e-01 +E_delta_band = -6.84786463e-02 Ry = -9.31699781e-01 eV +E_delta_NN= -1.93843940e-01 Ry = -2.63738211e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7083 11 0.61 1e+02 % + Run_lcao lcao_line 6.6992 1 6.7 1e+02 % + Potential init_pot 0.29082 2 0.15 4.3 % + PW_Basis recip2real 0.28987 17 0.017 4.3 % + PW_Basis gathers_scatterp 0.12451 17 0.0073 1.9 % + Potential v_of_rho 0.94148 14 0.067 14 % + XC_Functional v_xc 0.25847 15 0.017 3.9 % + H_Hartree_pw v_hartree 0.64225 14 0.046 9.6 % + PW_Basis real2recip 0.59699 41 0.015 8.9 % + PW_Basis gatherp_scatters 0.22976 41 0.0056 3.4 % + ORB_control set_orb_tables 1.1055 1 1.1 16 % + ORB_gen_tables gen_tables 1.1055 1 1.1 16 % + ORB_table_phi init_Table 0.47986 1 0.48 7.2 % + ORB_table_phi cal_ST_Phi12_R 0.475 126 0.0038 7.1 % + ORB_table_beta init_Table_Beta 0.18865 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18717 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25582 1 0.26 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.25398 66 0.0038 3.8 % + LOOP_ions opt_ions 5.0648 1 5.1 76 % + ESolver_KS_LCAO Run 4.5024 1 4.5 67 % + HSolverLCAO solve 2.3662 12 0.2 35 % + HamiltLCAO updateHk 1.2274 12 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.19 12 0.099 18 % + Gint_interface cal_gint 2.2428 25 0.09 33 % + Gint_Gamma distri_vl 2.3364 6 0.39 35 % + LCAO_Deepks cal_projected_DM 4.9019 14 0.35 73 % + LCAO_gen_fixedH add_v_delta 2.204 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.204 6 0.37 33 % + ElecStateLCAO psiToRho 1.1242 12 0.094 17 % + Charge mix_rho 0.72007 11 0.065 11 % + LOOP_ions force_stress 0.56218 1 0.56 8.4 % + Force_Stress_LCAO getForceStress 0.56215 1 0.56 8.4 % + Force_LCAO_gamma ftable_gamma 0.35274 1 0.35 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.34603 1 0.35 5.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:54 2022 + FINISH Time : Wed Sep 28 11:12:01 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/219/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..258f9094a85ce4fbc38a6f3688d73ef06c21ad0c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.53212 0.315345 0.442149 +H 0.596639 0.324792 0.429209 +H 0.499571 0.361075 0.407906 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6debf23a4ae8a68cdb1d7ebd48d91cde1785c712 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1407 2 + 2 -13.0588 2 + 3 -8.99084 2 + 4 -6.71024 2 + 5 1.22023 0 + 6 4.28301 0 + 7 11.1047 0 + 8 11.3464 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..45f86ba66163be69c6ae7c4f5a76616e4f488c56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:03 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.8993604595 8.82965540838 12.3801669405 0 0 0 0 + tauc_H1 16.7058917136 9.09417058706 12.0178416093 0 0 0 0 + tauc_H2 13.9879872763 10.1101109413 11.4213564344 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.113607594795 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.114161248689 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.13605734452 (SEC) + + DONE : INIT CHARGE Time : 0.179173256015 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.459587 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000911 + + Density error is 0.214440521638 + + Energy Rydberg eV + E_KohnSham -34.1910963847 -465.193731699 + E_Harris -34.381432681 -467.783389864 + E_Fermi -0.398418136768 -5.42075684659 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127553806836 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967777237267 + + Density error is 0.0984434919989 + + Energy Rydberg eV + E_KohnSham -34.2807934594 -466.414123009 + E_Harris -34.2876394396 -466.507267348 + E_Fermi -0.207237897415 -2.81961624638 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120025861944 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914099066976 + + Density error is 0.0633251915469 + + Energy Rydberg eV + E_KohnSham -34.2811625257 -466.419144413 + E_Harris -34.2855740376 -466.479166112 + E_Fermi -0.197811729742 -2.69136665573 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107690848235 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000824139694158 + + Density error is 0.002023029158 + + Energy Rydberg eV + E_KohnSham -34.2811217723 -466.418589935 + E_Harris -34.2811243427 -466.418624908 + E_Fermi -0.162481816491 -2.21067852566 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107644147121 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000822445778625 + + Density error is 0.000926928186032 + + Energy Rydberg eV + E_KohnSham -34.2810704826 -466.417892103 + E_Harris -34.28107109 -466.417900367 + E_Fermi -0.161982704287 -2.20388775576 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107482376874 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821284261456 + + Density error is 0.000182740973833 + + Energy Rydberg eV + E_KohnSham -34.2810981956 -466.418269158 + E_Harris -34.2810982277 -466.418269595 + E_Fermi -0.161801127701 -2.20141727956 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107494902506 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821377742729 + + Density error is 3.54052585508e-05 + + Energy Rydberg eV + E_KohnSham -34.2810883036 -466.418134571 + E_Harris -34.2810883096 -466.418134651 + E_Fermi -0.161697579695 -2.20000843666 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107489134918 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821328905711 + + Density error is 1.62251586897e-05 + + Energy Rydberg eV + E_KohnSham -34.2810923957 -466.418190246 + E_Harris -34.2810923968 -466.418190262 + E_Fermi -0.161731663407 -2.20047216935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107487865582 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821317851278 + + Density error is 1.94916151911e-06 + + Energy Rydberg eV + E_KohnSham -34.2810910577 -466.418172042 + E_Harris -34.2810910578 -466.418172042 + E_Fermi -0.161715095854 -2.20024675623 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107487681749 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00082131754382 + + Density error is 3.43062383712e-07 + + Energy Rydberg eV + E_KohnSham -34.2810912986 -466.41817532 + E_Harris -34.2810912986 -466.41817532 + E_Fermi -0.161713274812 -2.20022197969 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107487707458 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821318037551 + + Density error is 1.10270108246e-07 + + Energy Rydberg eV + E_KohnSham -34.2810913206 -466.418175619 + E_Harris -34.2810913206 -466.418175619 + E_Fermi -0.161713144559 -2.2002202075 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107487696138 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821318061493 + + Density error is 1.02447435417e-08 + + Energy Rydberg eV + E_KohnSham -34.2810913241 -466.418175666 + E_Harris -34.2810913241 -466.418175666 + E_band -7.92323511508 -107.801144159 + E_one_elec -69.0653024234 -939.681647052 + E_Hartree +35.9378383702 +488.959375638 + E_xc -8.19302290887 -111.471795405 + E_Ewald +7.16421287206 +97.4741167449 + E_demet -2.7079047339e-71 -3.68429340222e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194339570521 -2.64412550596 + E_Fermi -0.161713044227 -2.20021884242 + + charge density convergence is achieved + final etot is -466.418175666 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1407 2.00000 + 2 -13.0588 2.00000 + 3 -8.99084 2.00000 + 4 -6.71024 2.00000 + 5 1.22023 0.00000 + 6 4.28301 0.00000 + 7 11.1047 0.00000 + 8 11.3464 0.00000 + + EFERMI = -2.200218842417870 eV + OUT.ABACUS/ final etot is -466.4181756662560 eV + correction force for each atom along direction 1 is 1.26785e-05 + correction force for each atom along direction 2 is 3.61821e-05 + correction force for each atom along direction 3 is -3.40198e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.39195815 -0.13427117 +0.076062539 + H1 -0.53390565 +0.059610389 -0.0041531194 + H2 +0.14194751 +0.074660777 -0.071909419 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4181756662560 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5852 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5762 1 7.6 1.e+02% + Potential init_pot 0.28196 2 0.14 3.7% + PW_Basis recip2real 0.26782 17 0.016 3.5% + PW_Basis gathers_scatterp 0.12177 17 0.0072 1.6% + Potential v_of_rho 0.87115 14 0.062 11.% + XC_Functional v_xc 0.23168 15 0.015 3.1% + H_Hartree_pw v_hartree 0.59917 14 0.043 7.9% + PW_Basis real2recip 0.69603 41 0.017 9.2% + PW_Basis gatherp_scatters 0.28323 41 0.0069 3.7% + ORB_control set_orb_tables 1.0987 1 1.1 14.% + ORB_gen_tables gen_tables 1.0986 1 1.1 14.% + ORB_table_phi init_Table 0.47397 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46874 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18525 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18368 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.25056 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24860 66 0.0038 3.3% + LOOP_ions opt_ions 5.9410 1 5.9 78.% + ESolver_KS_LCAO Run 5.3669 1 5.4 71.% + HSolverLCAO solve 3.0176 12 0.25 40.% + HamiltLCAO updateHk 1.5212 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4915 12 0.12 20.% + Gint_interface cal_gint 0.16314 25 0.0065 2.2% + Gint_Gamma distri_vl_value 0.99936 12 0.083 13.% + Gint_Gamma distri_vl 2.7864 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.4906 14 0.39 72.% + LCAO_gen_fixedH add_v_delta 2.6578 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6580 6 0.44 35.% + ElecStateLCAO psiToRho 1.4616 12 0.12 19.% + Charge mix_rho 0.87525 11 0.080 12.% + LOOP_ions force_stress 0.57402 1 0.57 7.6% + Force_Stress_LCAO getForceStress 0.57400 1 0.57 7.6% + Force_LCAO_gamma ftable_gamma 0.37867 1 0.38 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:03 2022 + Finish Time : Wed Sep 28 11:08:10 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..43044591e41b629391b399fede98e021680d24f1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012372 ima = 3.66596e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123519089188 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112301307544 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112916604415 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113138500915 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113101902945 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113123671187 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011311657365 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113119268896 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113118562392 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113118496154 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113118481703 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113118476584 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/STRU new file mode 100644 index 0000000000000000000000000000000000000000..aef7701ce54296a3b68e9cb1ddbbcd0e753974fb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.100639540481 8.829655408397 12.380166940504 0 0 0 +H +0.0 +2 +-11.294108286352 9.094170587077 12.017841609323 0 0 0 +-14.012012723694 10.110110941283 11.421356434440 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/conv new file mode 100644 index 0000000000000000000000000000000000000000..76824d2c1ec8e7dc2c003642ff0dac76c81a6ce4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/conv @@ -0,0 +1 @@ +22 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..82784b984ded83401bce0e666ba19fa0ef5b2dad --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747437288 0.01257378862 1.265501507 1.357513834 1.468652249 0.008111988859 0.01898990132 0.03897649365 +-4.53501417e-18 0.001037366478 0.002440370926 0.01199037636 0.04300408365 2.362130903e-19 1.685121345e-06 5.160405868e-06 +0.001685973823 0.005829690547 + +H atom_index 1 n_descriptor 18 +1.221582394 0.03502381488 0.09841981662 0.1378480672 0.3126528137 0.02064978822 0.0267374808 0.03824304083 +4.502590081e-17 3.874864813e-05 0.09329127053 0.1141995837 0.1181397606 -2.675079116e-18 5.425732776e-06 0.01345163188 +0.02484492901 0.02945498856 + +H atom_index 2 n_descriptor 18 +1.237753463 0.03446508604 0.1036705645 0.1449639494 0.3181372608 0.02138362447 0.02767969821 0.03764779914 +-8.698570709e-18 4.012455044e-05 0.09756579052 0.1146389439 0.1243383093 8.776393575e-18 4.723149507e-06 0.01317468062 +0.02547711813 0.03023724945 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5698f3175dda9c03a129467f65ac5fdefcb7473d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:03 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.113647 SEC) : SETUP UNITCELL + DONE(0.11418 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.136083 SEC) : INIT PLANEWAVE + DONE(0.179326 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.459654 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651937e+02 0.000000e+00 2.144e-01 5.447e-01 + GE2 -4.664141e+02 -1.220391e+00 9.844e-02 4.997e-01 + GE3 -4.664191e+02 -5.021404e-03 6.333e-02 5.633e-01 + GE4 -4.664186e+02 5.544785e-04 2.023e-03 4.277e-01 + GE5 -4.664179e+02 6.978313e-04 9.269e-04 4.271e-01 + GE6 -4.664183e+02 -3.770544e-04 1.827e-04 4.226e-01 + GE7 -4.664181e+02 1.345872e-04 3.541e-05 4.152e-01 + GE8 -4.664182e+02 -5.567540e-05 1.623e-05 4.113e-01 + GE9 -4.664182e+02 1.820378e-05 1.949e-06 4.107e-01 + GE10 -4.664182e+02 -3.277392e-06 3.431e-07 4.119e-01 + GE11 -4.664182e+02 -2.989726e-07 1.103e-07 4.122e-01 + GE12 -4.664182e+02 -4.771602e-08 1.024e-08 3.558e-01 +E_delta_band = -6.95223364e-02 Ry = -9.45899914e-01 eV +E_delta_NN= -1.94339571e-01 Ry = -2.64412551e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5852 11 0.69 1e+02 % + Run_lcao lcao_line 7.5762 1 7.6 1e+02 % + Potential init_pot 0.28196 2 0.14 3.7 % + PW_Basis recip2real 0.26782 17 0.016 3.5 % + PW_Basis gathers_scatterp 0.12177 17 0.0072 1.6 % + Potential v_of_rho 0.87115 14 0.062 11 % + XC_Functional v_xc 0.23168 15 0.015 3.1 % + H_Hartree_pw v_hartree 0.59917 14 0.043 7.9 % + PW_Basis real2recip 0.69603 41 0.017 9.2 % + PW_Basis gatherp_scatters 0.28323 41 0.0069 3.7 % + ORB_control set_orb_tables 1.0987 1 1.1 14 % + ORB_gen_tables gen_tables 1.0986 1 1.1 14 % + ORB_table_phi init_Table 0.47397 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.46874 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18525 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18368 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.25056 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.2486 66 0.0038 3.3 % + LOOP_ions opt_ions 5.941 1 5.9 78 % + ESolver_KS_LCAO Run 5.3669 1 5.4 71 % + HSolverLCAO solve 3.0176 12 0.25 40 % + HamiltLCAO updateHk 1.5212 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4915 12 0.12 20 % + Gint_interface cal_gint 0.16314 25 0.0065 2.2 % + Gint_Gamma distri_vl_value 0.99936 12 0.083 13 % + Gint_Gamma distri_vl 2.7864 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.4906 14 0.39 72 % + LCAO_gen_fixedH add_v_delta 2.6578 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.658 6 0.44 35 % + ElecStateLCAO psiToRho 1.4616 12 0.12 19 % + Charge mix_rho 0.87525 11 0.08 12 % + LOOP_ions force_stress 0.57402 1 0.57 7.6 % + Force_Stress_LCAO getForceStress 0.574 1 0.57 7.6 % + Force_LCAO_gamma ftable_gamma 0.37867 1 0.38 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:03 2022 + FINISH Time : Wed Sep 28 11:08:10 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/22/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..27ac728d4117d7220049ff9756433e3741a4c01d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.602121 0.651359 0.15085 +H 0.627134 0.709678 0.14461 +H 0.544238 0.662714 0.173213 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9f38af4e0b1a41fc0df267286c4c928faf732f71 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6731 2 + 2 -13.3076 2 + 3 -9.21665 2 + 4 -6.82895 2 + 5 1.58637 0 + 6 4.92761 0 + 7 10.985 0 + 8 11.2351 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d1cd4b7c2303c4a3162802afe245cef649a6cf4c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:50 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.8593933995 18.2380644757 4.22379968086 0 0 0 0 + tauc_H1 17.5597642406 19.8709887386 4.04909256045 0 0 0 0 + tauc_H2 15.2386506001 18.5559980673 4.84997142177 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0866296456037 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0976863339392 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116015496939 (SEC) + + DONE : INIT CHARGE Time : 0.165554985977 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446442 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000546 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00185 + + Density error is 0.218748983687 + + Energy Rydberg eV + E_KohnSham -34.1845683697 -465.104913498 + E_Harris -34.3848200557 -467.829477463 + E_Fermi -0.427859405405 -5.82132585639 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000834917500713 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00153798718761 + + Density error is 0.0970807900296 + + Energy Rydberg eV + E_KohnSham -34.2759681434 -466.348471217 + E_Harris -34.2825709784 -466.438307395 + E_Fermi -0.23445393944 -3.18990949493 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000803325729992 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00140524786028 + + Density error is 0.0617837007304 + + Energy Rydberg eV + E_KohnSham -34.2761878332 -466.351460249 + E_Harris -34.280370793 -466.408372338 + E_Fermi -0.218502706424 -2.97288183578 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000765553194636 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118597283871 + + Density error is 0.00209118713268 + + Energy Rydberg eV + E_KohnSham -34.2762625271 -466.352476513 + E_Harris -34.2762656788 -466.352519393 + E_Fermi -0.182638682441 -2.4849267564 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000769692599185 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118317555764 + + Density error is 0.000942612659749 + + Energy Rydberg eV + E_KohnSham -34.2761770509 -466.351313549 + E_Harris -34.2761807918 -466.351364446 + E_Fermi -0.181099661263 -2.46398729904 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000768315584126 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118175157525 + + Density error is 0.000112805008649 + + Energy Rydberg eV + E_KohnSham -34.2762399926 -466.352169915 + E_Harris -34.2762400229 -466.352170327 + E_Fermi -0.181607783672 -2.4709006591 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00076823007323 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118128151117 + + Density error is 5.08548993029e-05 + + Energy Rydberg eV + E_KohnSham -34.2762189992 -466.351884285 + E_Harris -34.2762190125 -466.351884466 + E_Fermi -0.18145322408 -2.46879776797 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000768196079521 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118135568459 + + Density error is 1.52949730708e-05 + + Energy Rydberg eV + E_KohnSham -34.2762221572 -466.351927252 + E_Harris -34.2762221582 -466.351927265 + E_Fermi -0.181516132849 -2.46965368566 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000768213256408 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118132729885 + + Density error is 2.18330537332e-06 + + Energy Rydberg eV + E_KohnSham -34.2762206708 -466.351907028 + E_Harris -34.2762206708 -466.351907028 + E_Fermi -0.181499883234 -2.46943259831 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000768215433426 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118132320117 + + Density error is 3.18721668574e-07 + + Energy Rydberg eV + E_KohnSham -34.276220869 -466.351909725 + E_Harris -34.276220869 -466.351909725 + E_Fermi -0.181498056325 -2.46940774195 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000768215966928 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118132303372 + + Density error is 1.19453298655e-07 + + Energy Rydberg eV + E_KohnSham -34.2762209019 -466.351910173 + E_Harris -34.2762209019 -466.351910173 + E_Fermi -0.181497899226 -2.4694056045 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00076821601521 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118132271929 + + Density error is 9.89705968096e-09 + + Energy Rydberg eV + E_KohnSham -34.2762209037 -466.351910197 + E_Harris -34.2762209037 -466.351910197 + E_band -8.08870977656 -110.05254243 + E_one_elec -70.0294068017 -952.798960064 + E_Hartree +36.3850262416 +495.043678765 + E_xc -8.26558462871 -112.459048252 + E_Ewald +7.7565486923 +105.53325903 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196227101845 -2.66980668711 + E_Fermi -0.181497764327 -2.46940376911 + + charge density convergence is achieved + final etot is -466.351910197 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6731 2.00000 + 2 -13.3076 2.00000 + 3 -9.21665 2.00000 + 4 -6.82895 2.00000 + 5 1.58637 0.00000 + 6 4.92761 0.00000 + 7 10.9850 0.00000 + 8 11.2351 0.00000 + + EFERMI = -2.469403769113087 eV + OUT.ABACUS/ final etot is -466.3519101971395 eV + correction force for each atom along direction 1 is -6.23019e-05 + correction force for each atom along direction 2 is 7.76413e-05 + correction force for each atom along direction 3 is -0.000103866 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.3589071 -1.7117117 -0.60997066 + H1 +0.83003156 +1.4789719 -0.22861071 + H2 -2.1889387 +0.23273988 +0.83858137 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3519101971395 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6092 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5998 1 7.6 1.e+02% + Potential init_pot 0.28630 2 0.14 3.8% + PW_Basis recip2real 0.30347 17 0.018 4.0% + PW_Basis gathers_scatterp 0.12790 17 0.0075 1.7% + Potential v_of_rho 1.0664 14 0.076 14.% + XC_Functional v_xc 0.30321 15 0.020 4.0% + H_Hartree_pw v_hartree 0.71833 14 0.051 9.4% + PW_Basis real2recip 0.70890 41 0.017 9.3% + PW_Basis gatherp_scatters 0.27406 41 0.0067 3.6% + ORB_control set_orb_tables 1.0906 1 1.1 14.% + ORB_gen_tables gen_tables 1.0906 1 1.1 14.% + ORB_table_phi init_Table 0.47219 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46706 126 0.0037 6.1% + ORB_table_beta init_Table_Beta 0.18303 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18150 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24844 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24647 66 0.0037 3.2% + LOOP_ions opt_ions 5.9850 1 6.0 79.% + ESolver_KS_LCAO Run 5.3714 1 5.4 71.% + HSolverLCAO solve 2.8855 12 0.24 38.% + HamiltLCAO updateHk 1.4668 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4367 12 0.12 19.% + Gint_interface cal_gint 2.7445 25 0.11 36.% + Gint_Gamma distri_vl 2.7996 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.8167 14 0.42 76.% + LCAO_gen_fixedH add_v_delta 2.6549 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6549 6 0.44 35.% + ElecStateLCAO psiToRho 1.4006 12 0.12 18.% + Charge mix_rho 0.85360 11 0.078 11.% + LOOP_ions force_stress 0.61333 1 0.61 8.1% + Force_Stress_LCAO getForceStress 0.61329 1 0.61 8.1% + Force_LCAO_gamma ftable_gamma 0.39024 1 0.39 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.38225 1 0.38 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:50 2022 + Finish Time : Wed Sep 28 11:12:58 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ee04bcdbaad531c24d0fc4ac9a480ae066bf1928 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124214 ima = 3.70487e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122672773184 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011193125046 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112280701211 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011258621994 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112497708623 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112547840102 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112543274178 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112546381522 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112545771945 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011254568546 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112545675935 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112545670352 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9437374513202d8926fb3af377f2bb17f4ee19b2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.140606600482 18.238064475643 4.223799680856 0 0 0 +H +0.0 +2 +-10.440235759388 19.870988738572 4.049092560458 0 0 0 +-12.761349399872 18.555998067318 4.849971421744 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/conv new file mode 100644 index 0000000000000000000000000000000000000000..ef025bf69a432c2497ac4d2558d332c6b6067bd6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/conv @@ -0,0 +1 @@ +220 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a20aa3cf615e84522f14cf1e4f68dc72fd07071a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750093033 0.0128845116 1.302547683 1.384672609 1.471151566 0.008951733918 0.01902756884 0.0390509753 +-1.594869513e-18 0.001206616412 0.002867172383 0.01355648585 0.04925449345 -3.831664584e-19 2.633161183e-06 7.040613373e-06 +0.001639543939 0.005984740453 + +H atom_index 1 n_descriptor 18 +1.283729777 0.03318764106 0.1219068361 0.1660549542 0.3303089706 0.02428407553 0.03021377849 0.03659063094 +-3.295880006e-18 5.672258833e-05 0.1089161163 0.1206710527 0.1427846385 1.629956711e-18 2.114346583e-06 0.01340159383 +0.02838254004 0.03220381855 + +H atom_index 2 n_descriptor 18 +1.298669797 0.03273838588 0.1278265717 0.1738470913 0.3344399466 0.0249773503 0.03106127335 0.03646115564 +1.519287833e-17 5.81962904e-05 0.108721816 0.1251387484 0.1493540857 -8.702428746e-18 1.336392827e-06 0.01373158833 +0.02883981131 0.03274122917 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..737b69d08f0e0ed4f5fd811245abd0fdb6d6a5a9 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:50 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0866526 SEC) : SETUP UNITCELL + DONE(0.0977073 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116038 SEC) : INIT PLANEWAVE + DONE(0.165685 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446507 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651049e+02 0.000000e+00 2.187e-01 5.519e-01 + GE2 -4.663485e+02 -1.243558e+00 9.708e-02 5.046e-01 + GE3 -4.663515e+02 -2.989033e-03 6.178e-02 5.684e-01 + GE4 -4.663525e+02 -1.016264e-03 2.091e-03 4.337e-01 + GE5 -4.663513e+02 1.162964e-03 9.426e-04 4.270e-01 + GE6 -4.663522e+02 -8.563656e-04 1.128e-04 4.173e-01 + GE7 -4.663519e+02 2.856301e-04 5.085e-05 4.212e-01 + GE8 -4.663519e+02 -4.296756e-05 1.529e-05 4.085e-01 + GE9 -4.663519e+02 2.022406e-05 2.183e-06 4.126e-01 + GE10 -4.663519e+02 -2.696440e-06 3.187e-07 4.091e-01 + GE11 -4.663519e+02 -4.482070e-07 1.195e-07 4.116e-01 + GE12 -4.663519e+02 -2.426602e-08 9.897e-09 3.433e-01 +E_delta_band = -7.34226947e-02 Ry = -9.98967011e-01 eV +E_delta_NN= -1.96227102e-01 Ry = -2.66980669e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6092 11 0.69 1e+02 % + Run_lcao lcao_line 7.5998 1 7.6 1e+02 % + Potential init_pot 0.2863 2 0.14 3.8 % + PW_Basis recip2real 0.30347 17 0.018 4 % + PW_Basis gathers_scatterp 0.1279 17 0.0075 1.7 % + Potential v_of_rho 1.0664 14 0.076 14 % + XC_Functional v_xc 0.30321 15 0.02 4 % + H_Hartree_pw v_hartree 0.71833 14 0.051 9.4 % + PW_Basis real2recip 0.7089 41 0.017 9.3 % + PW_Basis gatherp_scatters 0.27406 41 0.0067 3.6 % + ORB_control set_orb_tables 1.0906 1 1.1 14 % + ORB_gen_tables gen_tables 1.0906 1 1.1 14 % + ORB_table_phi init_Table 0.47219 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.46706 126 0.0037 6.1 % + ORB_table_beta init_Table_Beta 0.18303 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.1815 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24844 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24647 66 0.0037 3.2 % + LOOP_ions opt_ions 5.985 1 6 79 % + ESolver_KS_LCAO Run 5.3714 1 5.4 71 % + HSolverLCAO solve 2.8855 12 0.24 38 % + HamiltLCAO updateHk 1.4668 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.4367 12 0.12 19 % + Gint_interface cal_gint 2.7445 25 0.11 36 % + Gint_Gamma distri_vl 2.7996 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.8167 14 0.42 76 % + LCAO_gen_fixedH add_v_delta 2.6549 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6549 6 0.44 35 % + ElecStateLCAO psiToRho 1.4006 12 0.12 18 % + Charge mix_rho 0.8536 11 0.078 11 % + LOOP_ions force_stress 0.61333 1 0.61 8.1 % + Force_Stress_LCAO getForceStress 0.61329 1 0.61 8.1 % + Force_LCAO_gamma ftable_gamma 0.39024 1 0.39 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.38225 1 0.38 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:50 2022 + FINISH Time : Wed Sep 28 11:12:58 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/220/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ed52b94ac72f955e3fc628478ed017f1ddfe1528 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.600909 0.6691 0.139462 +H 0.629102 0.727185 0.125568 +H 0.536504 0.67975 0.143232 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..60e7792c7663ba7b7618110eff105d618de06620 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1959 2 + 2 -13.1416 2 + 3 -8.97362 2 + 4 -6.72258 2 + 5 1.27973 0 + 6 4.38327 0 + 7 11.0896 0 + 8 11.3283 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ac79204305ab464c0394c2ad2479eeea9bf0ce7f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:42 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.8254551491 18.7348036754 3.90493559558 0 0 0 0 + tauc_H1 17.6148491173 20.3611913806 3.51589961533 0 0 0 0 + tauc_H2 15.0221002135 19.0329928883 4.01050549419 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0734699534045 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0876310693105 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103888658688 (SEC) + + DONE : INIT CHARGE Time : 0.144940713769 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.390687 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000534 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00187 + + Density error is 0.214953829725 + + Energy Rydberg eV + E_KohnSham -34.1915226003 -465.19953066 + E_Harris -34.3827366422 -467.801131167 + E_Fermi -0.40217170228 -5.47182672537 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000797695381126 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00146559933794 + + Density error is 0.0981472369128 + + Energy Rydberg eV + E_KohnSham -34.2808683546 -466.41514201 + E_Harris -34.2876115087 -466.506887329 + E_Fermi -0.210995316732 -2.87073855887 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00076970570094 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134210576476 + + Density error is 0.063009657337 + + Energy Rydberg eV + E_KohnSham -34.2811591289 -466.419098198 + E_Harris -34.2855069085 -466.478252773 + E_Fermi -0.200251099832 -2.72455598849 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000740693845231 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111581822451 + + Density error is 0.00203765176573 + + Energy Rydberg eV + E_KohnSham -34.2811403694 -466.418842962 + E_Harris -34.2811429964 -466.418878704 + E_Fermi -0.164915528578 -2.24379087734 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000742168867024 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111274256256 + + Density error is 0.000881684223313 + + Energy Rydberg eV + E_KohnSham -34.2810877351 -466.418126835 + E_Harris -34.2810886229 -466.418138914 + E_Fermi -0.164254628156 -2.23479886579 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741647635087 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111015087937 + + Density error is 0.000184338556109 + + Energy Rydberg eV + E_KohnSham -34.2811187548 -466.418548879 + E_Harris -34.2811187961 -466.418549442 + E_Fermi -0.164173693975 -2.23369769977 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741854782982 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110987573348 + + Density error is 3.64826413332e-05 + + Energy Rydberg eV + E_KohnSham -34.2811073707 -466.418393991 + E_Harris -34.2811073772 -466.41839408 + E_Fermi -0.164048456126 -2.23199375142 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741806611374 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110987659051 + + Density error is 1.84369812851e-05 + + Energy Rydberg eV + E_KohnSham -34.2811117623 -466.418453742 + E_Harris -34.2811117639 -466.418453763 + E_Fermi -0.164086882989 -2.23251657571 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00074181804663 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110984449618 + + Density error is 2.53540101316e-06 + + Energy Rydberg eV + E_KohnSham -34.281110299 -466.418433833 + E_Harris -34.281110299 -466.418433833 + E_Fermi -0.164068916754 -2.23227213255 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741816375364 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110983492707 + + Density error is 5.06372626472e-07 + + Energy Rydberg eV + E_KohnSham -34.2811105939 -466.418437845 + E_Harris -34.2811105939 -466.418437845 + E_Fermi -0.164066495514 -2.23223918988 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741817199886 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011098349561 + + Density error is 1.75069832486e-07 + + Energy Rydberg eV + E_KohnSham -34.2811106148 -466.41843813 + E_Harris -34.2811106148 -466.41843813 + E_Fermi -0.164066269702 -2.23223611756 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741817419491 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110983456853 + + Density error is 1.03502312216e-08 + + Energy Rydberg eV + E_KohnSham -34.2811106186 -466.418438181 + E_Harris -34.2811106186 -466.418438181 + E_band -7.94280634668 -108.067424425 + E_one_elec -69.1997548808 -941.510966583 + E_Hartree +36.0021127313 +489.833873183 + E_xc -8.20337847457 -111.612690105 + E_Ewald +7.24445365468 +98.5658486006 + E_demet -5.15166853576e-75 -7.00920462936e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194571041213 -2.64727482629 + E_Fermi -0.16406609983 -2.23223380632 + + charge density convergence is achieved + final etot is -466.418438181 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1959 2.00000 + 2 -13.1416 2.00000 + 3 -8.97362 2.00000 + 4 -6.72258 2.00000 + 5 1.27973 0.00000 + 6 4.38327 0.00000 + 7 11.0896 0.00000 + 8 11.3283 0.00000 + + EFERMI = -2.232233806322888 eV + OUT.ABACUS/ final etot is -466.4184381812799 eV + correction force for each atom along direction 1 is -1.45602e-05 + correction force for each atom along direction 2 is 0.000179734 + correction force for each atom along direction 3 is 0.000123283 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.51183850 -0.11918674 -0.015375771 + H1 -0.27098087 -0.11310269 +0.042751864 + H2 -0.24085763 +0.23228943 -0.027376092 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4184381812799 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0544 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0469 1 7.0 1.e+02% + Potential init_pot 0.24558 2 0.12 3.5% + PW_Basis recip2real 0.28315 17 0.017 4.0% + PW_Basis gathers_scatterp 0.11359 17 0.0067 1.6% + Potential v_of_rho 1.0034 14 0.072 14.% + XC_Functional v_xc 0.29903 15 0.020 4.2% + H_Hartree_pw v_hartree 0.66304 14 0.047 9.4% + PW_Basis real2recip 0.64768 41 0.016 9.2% + PW_Basis gatherp_scatters 0.24127 41 0.0059 3.4% + ORB_control set_orb_tables 0.89345 1 0.89 13.% + ORB_gen_tables gen_tables 0.89345 1 0.89 13.% + ORB_table_phi init_Table 0.37252 1 0.37 5.3% + ORB_table_phi cal_ST_Phi12_R 0.36824 126 0.0029 5.2% + ORB_table_beta init_Table_Beta 0.15396 1 0.15 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15261 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20963 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20800 66 0.0032 2.9% + LOOP_ions opt_ions 5.6919 1 5.7 81.% + ESolver_KS_LCAO Run 5.1224 1 5.1 73.% + HSolverLCAO solve 2.7549 12 0.23 39.% + HamiltLCAO updateHk 1.4052 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3699 12 0.11 19.% + Gint_interface cal_gint 2.6458 25 0.11 38.% + Gint_Gamma distri_vl 2.6617 6 0.44 38.% + LCAO_Deepks cal_projected_DM 5.5371 14 0.40 78.% + LCAO_gen_fixedH add_v_delta 2.5333 6 0.42 36.% + LCAO_DESCRIPTOR add_v_delta 2.5333 6 0.42 36.% + ElecStateLCAO psiToRho 1.3321 12 0.11 19.% + Charge mix_rho 0.82335 11 0.075 12.% + LOOP_ions force_stress 0.56938 1 0.57 8.1% + Force_Stress_LCAO getForceStress 0.56936 1 0.57 8.1% + Force_LCAO_gamma ftable_gamma 0.37051 1 0.37 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.36329 1 0.36 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:42 2022 + Finish Time : Wed Sep 28 11:02:49 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c737a6d983a9e4299c8cf21ac200507efb89d86f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123537 ima = 3.67203e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123419765482 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112409036677 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112953973383 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001131779222 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113137120737 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113161517045 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113153912777 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011315676707 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113155923838 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113155855193 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113155836586 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113155827922 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7f4631f04f4207d822b6643c7e26cd9dd946d6a3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.174544850901 18.734803675434 3.904935595597 0 0 0 +H +0.0 +2 +-10.385150882718 20.361191380611 3.515899615302 0 0 0 +-12.977899786463 19.032992888317 4.010505494200 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/conv new file mode 100644 index 0000000000000000000000000000000000000000..e4cc2a7d2b3bc9abdfe80752ca3e20565868a7b7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/conv @@ -0,0 +1 @@ +221 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f6a38e06c1f3ef692d057e3d9acf864dd98ecff2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746887201 0.01261586307 1.271443662 1.36279838 1.468927148 0.008072530941 0.01927091314 0.03895991622 +-6.812161924e-20 0.001077511295 0.002458969803 0.01216436937 0.0434839025 9.529120657e-21 1.712288971e-06 5.229625828e-06 +0.0017025679 0.005816383324 + +H atom_index 1 n_descriptor 18 +1.230672503 0.03464696302 0.1014970389 0.1418659265 0.3158236073 0.02108087687 0.02727577158 0.03781889329 +2.193674247e-17 3.995154318e-05 0.09623647256 0.1143502986 0.1216965205 -7.638983891e-18 5.099148252e-06 0.01325863513 +0.02531212622 0.02991459773 + +H atom_index 2 n_descriptor 18 +1.245253428 0.034137395 0.1063534125 0.14843134 0.3206320946 0.02173892429 0.0281239778 0.03731584852 +1.297840297e-17 4.120922147e-05 0.1000328289 0.1147844535 0.1273941488 8.659112668e-18 4.419761539e-06 0.01306982889 +0.02586949102 0.03059877139 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..6215dd4231832604a0b9b8efad22949278d6ea66 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:42 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0734853 SEC) : SETUP UNITCELL + DONE(0.0876418 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103902 SEC) : INIT PLANEWAVE + DONE(0.145039 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.390732 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651995e+02 0.000000e+00 2.150e-01 5.106e-01 + GE2 -4.664151e+02 -1.215611e+00 9.815e-02 4.777e-01 + GE3 -4.664191e+02 -3.956187e-03 6.301e-02 5.394e-01 + GE4 -4.664188e+02 2.552358e-04 2.038e-03 4.155e-01 + GE5 -4.664181e+02 7.161264e-04 8.817e-04 4.156e-01 + GE6 -4.664185e+02 -4.220441e-04 1.843e-04 4.101e-01 + GE7 -4.664184e+02 1.548883e-04 3.648e-05 3.988e-01 + GE8 -4.664185e+02 -5.975096e-05 1.844e-05 3.928e-01 + GE9 -4.664184e+02 1.990936e-05 2.535e-06 3.917e-01 + GE10 -4.664184e+02 -4.012149e-06 5.064e-07 3.949e-01 + GE11 -4.664184e+02 -2.853843e-07 1.751e-07 3.941e-01 + GE12 -4.664184e+02 -5.114418e-08 1.035e-08 3.264e-01 +E_delta_band = -7.00273921e-02 Ry = -9.52771548e-01 eV +E_delta_NN= -1.94571041e-01 Ry = -2.64727483e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0544 11 0.64 1e+02 % + Run_lcao lcao_line 7.0469 1 7 1e+02 % + Potential init_pot 0.24558 2 0.12 3.5 % + PW_Basis recip2real 0.28315 17 0.017 4 % + PW_Basis gathers_scatterp 0.11359 17 0.0067 1.6 % + Potential v_of_rho 1.0034 14 0.072 14 % + XC_Functional v_xc 0.29903 15 0.02 4.2 % + H_Hartree_pw v_hartree 0.66304 14 0.047 9.4 % + PW_Basis real2recip 0.64768 41 0.016 9.2 % + PW_Basis gatherp_scatters 0.24127 41 0.0059 3.4 % + ORB_control set_orb_tables 0.89345 1 0.89 13 % + ORB_gen_tables gen_tables 0.89345 1 0.89 13 % + ORB_table_phi init_Table 0.37252 1 0.37 5.3 % + ORB_table_phi cal_ST_Phi12_R 0.36824 126 0.0029 5.2 % + ORB_table_beta init_Table_Beta 0.15396 1 0.15 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15261 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20963 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.208 66 0.0032 2.9 % + LOOP_ions opt_ions 5.6919 1 5.7 81 % + ESolver_KS_LCAO Run 5.1224 1 5.1 73 % + HSolverLCAO solve 2.7549 12 0.23 39 % + HamiltLCAO updateHk 1.4052 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3699 12 0.11 19 % + Gint_interface cal_gint 2.6458 25 0.11 38 % + Gint_Gamma distri_vl 2.6617 6 0.44 38 % + LCAO_Deepks cal_projected_DM 5.5371 14 0.4 78 % + LCAO_gen_fixedH add_v_delta 2.5333 6 0.42 36 % + LCAO_DESCRIPTOR add_v_delta 2.5333 6 0.42 36 % + ElecStateLCAO psiToRho 1.3321 12 0.11 19 % + Charge mix_rho 0.82335 11 0.075 12 % + LOOP_ions force_stress 0.56938 1 0.57 8.1 % + Force_Stress_LCAO getForceStress 0.56936 1 0.57 8.1 % + Force_LCAO_gamma ftable_gamma 0.37051 1 0.37 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.36329 1 0.36 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:42 2022 + FINISH Time : Wed Sep 28 11:02:49 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/221/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b7ab0944d325a5b09349ad1b5c23316f559bbf3e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.597963 0.685871 0.133127 +H 0.631146 0.743098 0.129962 +H 0.535568 0.704798 0.117772 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..06f09c4ddddf4b759f7749219a91f285a026e7d3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1398 2 + 2 -12.7967 2 + 3 -9.18769 2 + 4 -6.71366 2 + 5 1.1381 0 + 6 4.13559 0 + 7 11.116 0 + 8 11.3766 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..430e791db443c0950d31de3185cec30df17f4955 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:06 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.7429548056 19.2043751321 3.72754344821 0 0 0 0 + tauc_H1 17.6720880399 20.8067546733 3.63892512198 0 0 0 0 + tauc_H2 14.9959092971 19.7343552568 3.29762922227 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0855977780133 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100603347467 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118647912695 (SEC) + + DONE : INIT CHARGE Time : 0.167104266072 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446648 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000569 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0017 + + Density error is 0.212341078107 + + Energy Rydberg eV + E_KohnSham -34.1923998877 -465.211466767 + E_Harris -34.3786925739 -467.746108795 + E_Fermi -0.39399278334 -5.3605468243 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000805212745329 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00137907552662 + + Density error is 0.0983042137773 + + Energy Rydberg eV + E_KohnSham -34.2806295797 -466.411893311 + E_Harris -34.2875930578 -466.506636292 + E_Fermi -0.204807272637 -2.7865458997 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000772751492975 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127109303834 + + Density error is 0.0633212569306 + + Energy Rydberg eV + E_KohnSham -34.2809872966 -466.4167603 + E_Harris -34.2854807053 -466.477896261 + E_Fermi -0.196316475334 -2.67102267582 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000740087502258 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106612981265 + + Density error is 0.00194700047602 + + Energy Rydberg eV + E_KohnSham -34.2809239285 -466.415898132 + E_Harris -34.280925182 -466.415915186 + E_Fermi -0.160910542218 -2.18930024243 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741303940389 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106418898339 + + Density error is 0.000903001232957 + + Energy Rydberg eV + E_KohnSham -34.2808815935 -466.415322134 + E_Harris -34.2808822111 -466.415330538 + E_Fermi -0.160650838726 -2.18576679516 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000740856313361 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106140317315 + + Density error is 0.000156384204373 + + Energy Rydberg eV + E_KohnSham -34.2809031182 -466.415614994 + E_Harris -34.2809031239 -466.415615071 + E_Fermi -0.160361933533 -2.18183603835 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741003936446 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010612722075 + + Density error is 3.00802183925e-05 + + Energy Rydberg eV + E_KohnSham -34.2808964461 -466.415524215 + E_Harris -34.2808964497 -466.415524264 + E_Fermi -0.16029242967 -2.18089038977 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000740959908 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106124102255 + + Density error is 1.43578962203e-05 + + Energy Rydberg eV + E_KohnSham -34.2808992957 -466.415562986 + E_Harris -34.2808992967 -466.415562999 + E_Fermi -0.160316934051 -2.18122378898 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000740969308319 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106121969201 + + Density error is 2.14162602577e-06 + + Energy Rydberg eV + E_KohnSham -34.2808981307 -466.415547135 + E_Harris -34.2808981307 -466.415547135 + E_Fermi -0.160303243714 -2.18103752239 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000740968754253 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106121335602 + + Density error is 4.2580166471e-07 + + Energy Rydberg eV + E_KohnSham -34.2808983609 -466.415550268 + E_Harris -34.280898361 -466.415550268 + E_Fermi -0.160301286632 -2.18101089493 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000740969430757 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106121359456 + + Density error is 1.36846047983e-07 + + Energy Rydberg eV + E_KohnSham -34.2808983802 -466.415550529 + E_Harris -34.2808983802 -466.415550529 + E_Fermi -0.160301094278 -2.18100827781 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000740969614635 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106121337746 + + Density error is 1.10299871958e-08 + + Energy Rydberg eV + E_KohnSham -34.2808983846 -466.41555059 + E_Harris -34.2808983846 -466.41555059 + E_band -7.91401184709 -107.67565516 + E_one_elec -68.9181281109 -937.679237802 + E_Hartree +35.8608118702 +487.911376341 + E_xc -8.18082314214 -111.305809063 + E_Ewald +7.0823279294 +96.3600149444 + E_demet -2.74697156026e-67 -3.73744654635e-66 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194154799486 -2.64161156705 + E_Fermi -0.160300969163 -2.18100657554 + + charge density convergence is achieved + final etot is -466.41555059 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1398 2.00000 + 2 -12.7967 2.00000 + 3 -9.18769 2.00000 + 4 -6.71366 2.00000 + 5 1.13810 0.00000 + 6 4.13559 0.00000 + 7 11.1160 0.00000 + 8 11.3766 0.00000 + + EFERMI = -2.181006575541145 eV + OUT.ABACUS/ final etot is -466.4155505899812 eV + correction force for each atom along direction 1 is -3.66351e-05 + correction force for each atom along direction 2 is 0.000163700 + correction force for each atom along direction 3 is -4.83119e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.63862409 +0.55676258 -0.21906013 + H1 -0.012749591 -0.24146503 +0.038553607 + H2 +0.65137368 -0.31529755 +0.18050653 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4155505899812 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8335 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8243 1 6.8 1.e+02% + Potential init_pot 0.28724 2 0.14 4.2% + PW_Basis recip2real 0.28412 17 0.017 4.2% + PW_Basis gathers_scatterp 0.12071 17 0.0071 1.8% + Potential v_of_rho 0.93842 14 0.067 14.% + XC_Functional v_xc 0.26158 15 0.017 3.8% + H_Hartree_pw v_hartree 0.63768 14 0.046 9.3% + PW_Basis real2recip 0.60527 41 0.015 8.9% + PW_Basis gatherp_scatters 0.23602 41 0.0058 3.5% + ORB_control set_orb_tables 1.1043 1 1.1 16.% + ORB_gen_tables gen_tables 1.1043 1 1.1 16.% + ORB_table_phi init_Table 0.48352 1 0.48 7.1% + ORB_table_phi cal_ST_Phi12_R 0.47856 126 0.0038 7.0% + ORB_table_beta init_Table_Beta 0.18739 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18591 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25595 1 0.26 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25401 66 0.0038 3.7% + LOOP_ions opt_ions 5.1964 1 5.2 76.% + ESolver_KS_LCAO Run 4.6124 1 4.6 67.% + HSolverLCAO solve 2.4749 12 0.21 36.% + HamiltLCAO updateHk 1.2811 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2399 12 0.10 18.% + Gint_interface cal_gint 2.3645 25 0.095 35.% + Gint_Gamma distri_vl 2.4024 6 0.40 35.% + LCAO_Deepks cal_projected_DM 5.0315 14 0.36 74.% + LCAO_gen_fixedH add_v_delta 2.2703 6 0.38 33.% + LCAO_DESCRIPTOR add_v_delta 2.2702 6 0.38 33.% + ElecStateLCAO psiToRho 1.1781 12 0.098 17.% + Charge mix_rho 0.71659 11 0.065 10.% + LOOP_ions force_stress 0.58386 1 0.58 8.5% + Force_Stress_LCAO getForceStress 0.58383 1 0.58 8.5% + Force_LCAO_gamma ftable_gamma 0.36692 1 0.37 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.36030 1 0.36 5.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:06 2022 + Finish Time : Wed Sep 28 11:09:12 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..361c86309153a9d689e604d8d8df8293e7593b1b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123529 ima = 3.65375e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123209036403 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111961661996 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112638433496 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112853486271 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112825556821 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112841680481 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112837098859 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112839384943 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112838710644 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112838647142 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112838628799 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112838622215 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/STRU new file mode 100644 index 0000000000000000000000000000000000000000..6e9f365ba90e4d14c79b1932b9f3e3f81c41333e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.257045194451 19.204375132164 3.727543448197 0 0 0 +H +0.0 +2 +-10.327911960151 20.806754673274 3.638925121987 0 0 0 +-13.004090702879 19.734355256804 3.297629222291 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/conv new file mode 100644 index 0000000000000000000000000000000000000000..42aad09bce7e103e756e2e35cb60ee6d1a22f204 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/conv @@ -0,0 +1 @@ +222 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..63692b4b4bc252b318cc426046e100657e47ce60 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750991018 0.01258411255 1.25730516 1.345727176 1.468669176 0.008681566307 0.01766402201 0.03910181487 +-2.94474152e-18 0.0009288065275 0.002548331806 0.01206925802 0.04362443556 1.557407002e-19 1.977719078e-06 5.776452502e-06 +0.001609353153 0.005984189612 + +H atom_index 1 n_descriptor 18 +1.230659888 0.03510479835 0.1018299622 0.1411368191 0.3145083752 0.02139377529 0.02716611501 0.03829781874 +1.223917527e-17 4.230693954e-05 0.09536653302 0.1145977536 0.1209333368 3.614018608e-18 4.796187757e-06 0.01346840199 +0.02531678547 0.02982677312 + +H atom_index 2 n_descriptor 18 +1.213940591 0.03566208009 0.09646054414 0.1339069213 0.3085646585 0.02060580223 0.02618439926 0.03894117433 +6.759660215e-18 4.081904236e-05 0.09099060669 0.1140285836 0.1146155301 -2.980973552e-18 5.540160312e-06 0.01382394443 +0.02464825045 0.02898678731 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..6af23a0268d727380642fbccaf85ed8ae2871428 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:06 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.085619 SEC) : SETUP UNITCELL + DONE(0.100622 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118667 SEC) : INIT PLANEWAVE + DONE(0.16722 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446706 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652115e+02 0.000000e+00 2.123e-01 4.997e-01 + GE2 -4.664119e+02 -1.200427e+00 9.830e-02 4.210e-01 + GE3 -4.664168e+02 -4.866989e-03 6.332e-02 4.845e-01 + GE4 -4.664159e+02 8.621676e-04 1.947e-03 3.731e-01 + GE5 -4.664153e+02 5.759978e-04 9.030e-04 3.737e-01 + GE6 -4.664156e+02 -2.928595e-04 1.564e-04 3.642e-01 + GE7 -4.664155e+02 9.077930e-05 3.008e-05 3.502e-01 + GE8 -4.664156e+02 -3.877171e-05 1.436e-05 3.473e-01 + GE9 -4.664155e+02 1.585110e-05 2.142e-06 3.479e-01 + GE10 -4.664156e+02 -3.132626e-06 4.258e-07 3.467e-01 + GE11 -4.664156e+02 -2.616952e-07 1.368e-07 3.495e-01 + GE12 -4.664156e+02 -6.051250e-08 1.103e-08 2.931e-01 +E_delta_band = -6.90678682e-02 Ry = -9.39716556e-01 eV +E_delta_NN= -1.94154799e-01 Ry = -2.64161157e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8335 11 0.62 1e+02 % + Run_lcao lcao_line 6.8243 1 6.8 1e+02 % + Potential init_pot 0.28724 2 0.14 4.2 % + PW_Basis recip2real 0.28412 17 0.017 4.2 % + PW_Basis gathers_scatterp 0.12071 17 0.0071 1.8 % + Potential v_of_rho 0.93842 14 0.067 14 % + XC_Functional v_xc 0.26158 15 0.017 3.8 % + H_Hartree_pw v_hartree 0.63768 14 0.046 9.3 % + PW_Basis real2recip 0.60527 41 0.015 8.9 % + PW_Basis gatherp_scatters 0.23602 41 0.0058 3.5 % + ORB_control set_orb_tables 1.1043 1 1.1 16 % + ORB_gen_tables gen_tables 1.1043 1 1.1 16 % + ORB_table_phi init_Table 0.48352 1 0.48 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.47856 126 0.0038 7 % + ORB_table_beta init_Table_Beta 0.18739 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18591 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.25595 1 0.26 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25401 66 0.0038 3.7 % + LOOP_ions opt_ions 5.1964 1 5.2 76 % + ESolver_KS_LCAO Run 4.6124 1 4.6 67 % + HSolverLCAO solve 2.4749 12 0.21 36 % + HamiltLCAO updateHk 1.2811 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.2399 12 0.1 18 % + Gint_interface cal_gint 2.3645 25 0.095 35 % + Gint_Gamma distri_vl 2.4024 6 0.4 35 % + LCAO_Deepks cal_projected_DM 5.0315 14 0.36 74 % + LCAO_gen_fixedH add_v_delta 2.2703 6 0.38 33 % + LCAO_DESCRIPTOR add_v_delta 2.2702 6 0.38 33 % + ElecStateLCAO psiToRho 1.1781 12 0.098 17 % + Charge mix_rho 0.71659 11 0.065 10 % + LOOP_ions force_stress 0.58386 1 0.58 8.5 % + Force_Stress_LCAO getForceStress 0.58383 1 0.58 8.5 % + Force_LCAO_gamma ftable_gamma 0.36692 1 0.37 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.3603 1 0.36 5.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:06 2022 + FINISH Time : Wed Sep 28 11:09:12 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/222/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..8145732da0e070f3c12b384e6a2efaafede0092d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.581089 0.682683 0.131593 +H 0.640045 0.705705 0.146964 +H 0.554263 0.726296 0.0930222 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..693db7e5d3a6837f11723c1a682b04f22a12b150 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3955 2 + 2 -13.278 2 + 3 -9.03102 2 + 4 -6.76779 2 + 5 1.43473 0 + 6 4.64756 0 + 7 11.0422 0 + 8 11.2813 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..dcec7bad40172b1e8e12d3f9f3c9b91e92bcbea5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.2705025804 19.1151323981 3.68460790519 0 0 0 0 + tauc_H1 17.9212699938 19.7597519202 4.114992777 0 0 0 0 + tauc_H2 15.519370648 20.3362791999 2.60462126137 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0859771142838 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0940885986504 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.112280919212 (SEC) + + DONE : INIT CHARGE Time : 0.160624285936 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.43874 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000901 + + Density error is 0.217112765883 + + Energy Rydberg eV + E_KohnSham -34.1888043684 -465.162547218 + E_Harris -34.3850304254 -467.832339689 + E_Fermi -0.413969188362 -5.63233975816 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121437816431 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102877117 + + Density error is 0.0977867366639 + + Energy Rydberg eV + E_KohnSham -34.2796972456 -466.399208255 + E_Harris -34.2863253529 -466.489388281 + E_Fermi -0.221278548726 -3.01064910784 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113947331045 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000975299907613 + + Density error is 0.0625297720993 + + Energy Rydberg eV + E_KohnSham -34.2799909177 -466.403203869 + E_Harris -34.2842511344 -466.46116709 + E_Fermi -0.208300726984 -2.83407678452 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010215736487 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000891843612744 + + Density error is 0.00205133628424 + + Energy Rydberg eV + E_KohnSham -34.2800137618 -466.403514679 + E_Harris -34.2800158607 -466.403543236 + E_Fermi -0.172713417731 -2.3498866022 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001021791935 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000891670043842 + + Density error is 0.000910662628523 + + Energy Rydberg eV + E_KohnSham -34.2799431978 -466.402554606 + E_Harris -34.2799449468 -466.402578403 + E_Fermi -0.171688667412 -2.33594415883 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102041663365 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000890593993759 + + Density error is 0.000162348276873 + + Energy Rydberg eV + E_KohnSham -34.2799890705 -466.403178737 + E_Harris -34.2799891308 -466.403179557 + E_Fermi -0.171858744599 -2.33825817768 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010204619356 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000890688611727 + + Density error is 4.42833622782e-05 + + Energy Rydberg eV + E_KohnSham -34.2799723294 -466.402950963 + E_Harris -34.2799723402 -466.402951109 + E_Fermi -0.171694757691 -2.33602702133 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102043335358 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000890638476693 + + Density error is 1.62689035201e-05 + + Energy Rydberg eV + E_KohnSham -34.2799769552 -466.4030139 + E_Harris -34.2799769563 -466.403013914 + E_Fermi -0.171746105616 -2.33672564569 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102041779683 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000890626412898 + + Density error is 1.63270768937e-06 + + Energy Rydberg eV + E_KohnSham -34.2799754638 -466.402993608 + E_Harris -34.2799754638 -466.402993608 + E_Fermi -0.171728582915 -2.33648723711 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102041603615 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000890627383802 + + Density error is 1.37595446107e-07 + + Energy Rydberg eV + E_KohnSham -34.2799756825 -466.402996583 + E_Harris -34.2799756825 -466.402996583 + E_Fermi -0.171726970668 -2.33646530137 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010204164219 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000890627850346 + + Density error is 3.37403401619e-08 + + Energy Rydberg eV + E_KohnSham -34.2799757109 -466.40299697 + E_Harris -34.2799757109 -466.40299697 + E_band -8.00728247776 -108.944667193 + E_one_elec -69.5862953542 -946.770119528 + E_Hartree +36.1824095014 +492.286936588 + E_xc -8.23257959665 -112.009991753 + E_Ewald +7.48022354571 +101.773662535 + E_demet -4.35868230945e-86 -5.93029151803e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195314502174 -2.6573901316 + E_Fermi -0.171727017813 -2.33646594281 + + charge density convergence is achieved + final etot is -466.40299697 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3955 2.00000 + 2 -13.2780 2.00000 + 3 -9.03102 2.00000 + 4 -6.76779 2.00000 + 5 1.43473 0.00000 + 6 4.64756 0.00000 + 7 11.0422 0.00000 + 8 11.2813 0.00000 + + EFERMI = -2.336465942807525 eV + OUT.ABACUS/ final etot is -466.4029969695217 eV + correction force for each atom along direction 1 is 1.93878e-05 + correction force for each atom along direction 2 is 6.77351e-05 + correction force for each atom along direction 3 is 5.22244e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.065977678 -1.2192071 +0.74803299 + H1 +0.40237055 +0.25080771 +0.048167859 + H2 -0.46834823 +0.96839943 -0.79620085 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4029969695217 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4784 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4691 1 6.5 1.e+02% + Potential init_pot 0.28322 2 0.14 4.4% + PW_Basis recip2real 0.26541 16 0.017 4.1% + PW_Basis gathers_scatterp 0.11340 16 0.0071 1.8% + Potential v_of_rho 0.87898 13 0.068 14.% + XC_Functional v_xc 0.25574 14 0.018 3.9% + H_Hartree_pw v_hartree 0.58704 13 0.045 9.1% + PW_Basis real2recip 0.55205 38 0.015 8.5% + PW_Basis gatherp_scatters 0.21281 38 0.0056 3.3% + ORB_control set_orb_tables 1.1068 1 1.1 17.% + ORB_gen_tables gen_tables 1.1068 1 1.1 17.% + ORB_table_phi init_Table 0.48670 1 0.49 7.5% + ORB_table_phi cal_ST_Phi12_R 0.48176 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18684 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18540 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25290 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25107 66 0.0038 3.9% + LOOP_ions opt_ions 4.8466 1 4.8 75.% + ESolver_KS_LCAO Run 4.2718 1 4.3 66.% + HSolverLCAO solve 2.3010 11 0.21 36.% + HamiltLCAO updateHk 1.1966 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1579 11 0.11 18.% + Gint_interface cal_gint 2.1983 23 0.096 34.% + Gint_Gamma distri_vl 2.0553 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.6827 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9229 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9229 6 0.32 30.% + ElecStateLCAO psiToRho 1.0897 11 0.099 17.% + Charge mix_rho 0.65494 10 0.065 10.% + LOOP_ions force_stress 0.57463 1 0.57 8.9% + Force_Stress_LCAO getForceStress 0.57460 1 0.57 8.9% + Force_LCAO_gamma ftable_gamma 0.36288 1 0.36 5.6% + Force_LCAO_gamma cal_fvl_dphi 0.35620 1 0.36 5.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:17 2022 + Finish Time : Wed Sep 28 11:04:24 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..82e29b737d7f91477f355adb7f403d15d5bf97fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124012 ima = 3.67376e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123169116401 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112249279617 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112707541665 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112972945334 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112910464142 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112947169802 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112939006977 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112942118745 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112941484192 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112941415051 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112941410752 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9ecb9cf32cffffcf355b1f04a2988197fb3250c6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.729497419605 19.115132398113 3.684607905186 0 0 0 +H +0.0 +2 +-10.078730006206 19.759751920195 4.114992777021 0 0 0 +-12.480629351967 20.336279199912 2.604621261380 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/conv new file mode 100644 index 0000000000000000000000000000000000000000..fbeeaf54cd144a3d7a5421601b6b11d170f0edf7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/conv @@ -0,0 +1 @@ +223 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e7f935b3cf5592732ffa768e7810d7561242190c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747364239 0.01274276653 1.28673666 1.374777581 1.469875182 0.008295424084 0.01947109093 0.03896976636 +-2.400569935e-19 0.001161591223 0.002596988685 0.01272464603 0.0457323906 8.890670876e-20 1.982351389e-06 5.819522736e-06 +0.001697125207 0.005861150044 + +H atom_index 1 n_descriptor 18 +1.251269404 0.03395254084 0.1088932993 0.150899501 0.3219145544 0.02222067839 0.02843140753 0.03709715365 +-5.407454029e-18 4.567993007e-05 0.1030284787 0.1148839604 0.1296707394 -4.266209258e-18 4.214551349e-06 0.01307729055 +0.02651367174 0.03086984171 + +H atom_index 2 n_descriptor 18 +1.274098774 0.03317145083 0.1170951428 0.1618803471 0.3288398889 0.02324915221 0.02974655362 0.03653293946 +-6.087555373e-18 4.777909536e-05 0.1071329649 0.1173247108 0.1390847799 -8.326010324e-18 2.957316824e-06 0.01311200439 +0.027316934 0.03183281699 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c9e4e16fa4a0d8d8d983f2412be71ef455ca70d9 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0860004 SEC) : SETUP UNITCELL + DONE(0.0941109 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.112299 SEC) : INIT PLANEWAVE + DONE(0.160745 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438805 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651625e+02 0.000000e+00 2.171e-01 5.015e-01 + GE2 -4.663992e+02 -1.236661e+00 9.779e-02 4.270e-01 + GE3 -4.664032e+02 -3.995614e-03 6.253e-02 4.806e-01 + GE4 -4.664035e+02 -3.108106e-04 2.051e-03 3.756e-01 + GE5 -4.664026e+02 9.600733e-04 9.107e-04 3.740e-01 + GE6 -4.664032e+02 -6.241307e-04 1.623e-04 3.597e-01 + GE7 -4.664030e+02 2.277740e-04 4.428e-05 3.556e-01 + GE8 -4.664030e+02 -6.293687e-05 1.627e-05 3.500e-01 + GE9 -4.664030e+02 2.029204e-05 1.633e-06 3.500e-01 + GE10 -4.664030e+02 -2.975311e-06 1.376e-07 3.475e-01 + GE11 -4.664030e+02 -3.867097e-07 3.374e-08 2.888e-01 +E_delta_band = -7.15806951e-02 Ry = -9.73905320e-01 eV +E_delta_NN= -1.95314502e-01 Ry = -2.65739013e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4784 11 0.59 1e+02 % + Run_lcao lcao_line 6.4691 1 6.5 1e+02 % + Potential init_pot 0.28322 2 0.14 4.4 % + PW_Basis recip2real 0.26541 16 0.017 4.1 % + PW_Basis gathers_scatterp 0.1134 16 0.0071 1.8 % + Potential v_of_rho 0.87898 13 0.068 14 % + XC_Functional v_xc 0.25574 14 0.018 3.9 % + H_Hartree_pw v_hartree 0.58704 13 0.045 9.1 % + PW_Basis real2recip 0.55205 38 0.015 8.5 % + PW_Basis gatherp_scatters 0.21281 38 0.0056 3.3 % + ORB_control set_orb_tables 1.1068 1 1.1 17 % + ORB_gen_tables gen_tables 1.1068 1 1.1 17 % + ORB_table_phi init_Table 0.4867 1 0.49 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.48176 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18684 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.1854 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.2529 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25107 66 0.0038 3.9 % + LOOP_ions opt_ions 4.8466 1 4.8 75 % + ESolver_KS_LCAO Run 4.2718 1 4.3 66 % + HSolverLCAO solve 2.301 11 0.21 36 % + HamiltLCAO updateHk 1.1966 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1579 11 0.11 18 % + Gint_interface cal_gint 2.1983 23 0.096 34 % + Gint_Gamma distri_vl 2.0553 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.6827 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9229 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9229 6 0.32 30 % + ElecStateLCAO psiToRho 1.0897 11 0.099 17 % + Charge mix_rho 0.65494 10 0.065 10 % + LOOP_ions force_stress 0.57463 1 0.57 8.9 % + Force_Stress_LCAO getForceStress 0.5746 1 0.57 8.9 % + Force_LCAO_gamma ftable_gamma 0.36288 1 0.36 5.6 % + Force_LCAO_gamma cal_fvl_dphi 0.3562 1 0.36 5.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:17 2022 + FINISH Time : Wed Sep 28 11:04:24 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/223/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..0aae3d4e2330f61a95b30ece6b223d66fd08e19a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.571092 0.681322 0.13153 +H 0.626797 0.658528 0.163506 +H 0.588027 0.744809 0.126249 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..cdcc0d6fe06d6f88b0738844050ed86beb1f577f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1474 2 + 2 -12.5607 2 + 3 -9.36532 2 + 4 -6.71736 2 + 5 1.04288 0 + 6 4.01927 0 + 7 11.1248 0 + 8 11.3987 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e900d33b1d26d0ce65dbd33fb0520c717405eb10 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:02 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.9905624741 19.0770129546 3.68282610738 0 0 0 0 + tauc_H1 17.550323623 18.4387797487 4.57816064905 0 0 0 0 + tauc_H2 16.464744227 20.8546557088 3.53496731324 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.096843110312 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.108302327539 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.128535545262 (SEC) + + DONE : INIT CHARGE Time : 0.183248424801 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.469697 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00162 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000735 + + Density error is 0.21062143769 + + Energy Rydberg eV + E_KohnSham -34.1910720661 -465.193400827 + E_Harris -34.374357398 -467.687125702 + E_Fermi -0.391016107892 -5.32004707712 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00145743378737 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000929409021168 + + Density error is 0.0981740105831 + + Energy Rydberg eV + E_KohnSham -34.2782387024 -466.379363757 + E_Harris -34.2853129483 -466.475613811 + E_Fermi -0.203119514258 -2.76358276891 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00133869852682 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000892473547064 + + Density error is 0.0632414717927 + + Energy Rydberg eV + E_KohnSham -34.2785758506 -466.383950894 + E_Harris -34.2831332276 -466.445957189 + E_Fermi -0.195437939841 -2.65906958722 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111135004253 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000854507130556 + + Density error is 0.0018947578971 + + Energy Rydberg eV + E_KohnSham -34.2784894382 -466.382775193 + E_Harris -34.2784895274 -466.382776406 + E_Fermi -0.159956765135 -2.17632343949 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011102553907 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000855090763506 + + Density error is 0.000865277523711 + + Energy Rydberg eV + E_KohnSham -34.2784577451 -466.382343986 + E_Harris -34.2784580795 -466.382348535 + E_Fermi -0.159931829259 -2.17598416949 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110722940502 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000854795000752 + + Density error is 0.000123369391574 + + Energy Rydberg eV + E_KohnSham -34.2784721191 -466.382539554 + E_Harris -34.2784721157 -466.382539508 + E_Fermi -0.159542770408 -2.17069075225 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110709212907 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000854957275802 + + Density error is 2.39704500666e-05 + + Energy Rydberg eV + E_KohnSham -34.278469189 -466.382499688 + E_Harris -34.2784691908 -466.382499712 + E_Fermi -0.159489772592 -2.16996967997 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110704504182 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000854902848157 + + Density error is 1.08413327849e-05 + + Energy Rydberg eV + E_KohnSham -34.2784706507 -466.382519576 + E_Harris -34.2784706513 -466.382519583 + E_Fermi -0.15950475411 -2.17017351399 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110702746006 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000854908273101 + + Density error is 1.6047484734e-06 + + Energy Rydberg eV + E_KohnSham -34.2784697639 -466.38250751 + E_Harris -34.2784697639 -466.38250751 + E_Fermi -0.159494524297 -2.17003433024 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110702311829 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000854909435656 + + Density error is 3.22799226353e-07 + + Energy Rydberg eV + E_KohnSham -34.2784699513 -466.38251006 + E_Harris -34.2784699513 -466.38251006 + E_Fermi -0.159493286973 -2.17001749558 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110702326236 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000854909844961 + + Density error is 8.98789379931e-08 + + Energy Rydberg eV + E_KohnSham -34.2784699649 -466.382510244 + E_Harris -34.2784699649 -466.382510244 + E_band -7.90710464876 -107.581677905 + E_one_elec -68.7952857059 -936.007881138 + E_Hartree +35.7960406166 +487.030118225 + E_xc -8.17051414765 -111.165547998 + E_Ewald +7.01658673507 +95.4655601082 + E_demet -3.22061074904e-63 -4.38186572269e-62 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193994084305 -2.63942492483 + E_Fermi -0.159493129976 -2.17001535953 + + charge density convergence is achieved + final etot is -466.382510244 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1474 2.00000 + 2 -12.5607 2.00000 + 3 -9.36532 2.00000 + 4 -6.71736 2.00000 + 5 1.04288 0.00000 + 6 4.01927 0.00000 + 7 11.1248 0.00000 + 8 11.3987 0.00000 + + EFERMI = -2.170015359534188 eV + OUT.ABACUS/ final etot is -466.3825102441756 eV + correction force for each atom along direction 1 is 2.40350e-05 + correction force for each atom along direction 2 is -2.58628e-06 + correction force for each atom along direction 3 is 0.000138382 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.5480924 -0.29757187 +0.82343913 + H1 -1.2476725 +0.11257953 -0.63457821 + H2 -0.30041987 +0.18499233 -0.18886092 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3825102441756 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6579 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6471 1 6.6 1.e+02% + Potential init_pot 0.29116 2 0.15 4.4% + PW_Basis recip2real 0.26914 16 0.017 4.0% + PW_Basis gathers_scatterp 0.11531 16 0.0072 1.7% + Charge atomic_rho 0.10060 1 0.10 1.5% + Potential v_of_rho 0.88463 13 0.068 13.% + XC_Functional v_xc 0.25390 14 0.018 3.8% + H_Hartree_pw v_hartree 0.59316 13 0.046 8.9% + PW_Basis real2recip 0.55657 38 0.015 8.4% + PW_Basis gatherp_scatters 0.21548 38 0.0057 3.2% + ORB_control set_orb_tables 1.1650 1 1.2 17.% + ORB_gen_tables gen_tables 1.1650 1 1.2 17.% + ORB_table_phi init_Table 0.50601 1 0.51 7.6% + ORB_table_phi cal_ST_Phi12_R 0.50076 126 0.0040 7.5% + ORB_table_beta init_Table_Beta 0.19548 1 0.20 2.9% + ORB_table_beta VNL_PhiBeta_R 0.19389 56 0.0035 2.9% + ORB_table_alpha init_Table_Alpha 0.26288 1 0.26 3.9% + ORB_table_alpha S_PhiAlpha_R 0.26094 66 0.0040 3.9% + LOOP_ions opt_ions 4.9264 1 4.9 74.% + ESolver_KS_LCAO Run 4.3425 1 4.3 65.% + HSolverLCAO solve 2.3448 11 0.21 35.% + HamiltLCAO updateHk 1.2071 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1726 11 0.11 18.% + Gint_interface cal_gint 2.2286 23 0.097 33.% + Gint_Gamma distri_vl 2.0890 6 0.35 31.% + LCAO_Deepks cal_projected_DM 4.7475 13 0.37 71.% + LCAO_gen_fixedH add_v_delta 1.9561 6 0.33 29.% + LCAO_DESCRIPTOR add_v_delta 1.9561 6 0.33 29.% + ElecStateLCAO psiToRho 1.1077 11 0.10 17.% + Charge mix_rho 0.66507 10 0.067 10.% + LOOP_ions force_stress 0.58372 1 0.58 8.8% + Force_Stress_LCAO getForceStress 0.58370 1 0.58 8.8% + Force_LCAO_gamma ftable_gamma 0.36827 1 0.37 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.36147 1 0.36 5.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:02 2022 + Finish Time : Wed Sep 28 11:05:08 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..9f2c853e5e05a3af4e92e00d067fb093be3c9f3e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012348 ima = 3.66404e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122955918126 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111651257618 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112389051369 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112596274895 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011257840884 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112587788775 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001125857699 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112587494411 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112586954403 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112586909028 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112586893205 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/STRU new file mode 100644 index 0000000000000000000000000000000000000000..003ae2c08bc2dffb6981c18ec9665cd47607da38 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.009437525950 19.077012954600 3.682826107367 0 0 0 +H +0.0 +2 +-10.449676377005 18.438779748728 4.578160649035 0 0 0 +-11.535255772991 20.854655708838 3.534967313214 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/conv new file mode 100644 index 0000000000000000000000000000000000000000..9197d19b2f7bc9fce0a7fb5b124b2c952fa22df8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/conv @@ -0,0 +1 @@ +224 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..676965747d7914cf9fca797b85017d6931dbc94d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754042257 0.01258413747 1.249346616 1.336630539 1.468713996 0.009263881876 0.01653186942 0.03920912559 +6.460807992e-20 0.0008222628255 0.002641330455 0.01235612206 0.04386199867 2.873201886e-19 2.242390306e-06 6.384688339e-06 +0.001568597325 0.006048934127 + +H atom_index 1 n_descriptor 18 +1.190836217 0.0367021896 0.09073212804 0.1241319318 0.2988259062 0.01993872316 0.02476749203 0.04021295572 +1.763555022e-17 3.983645127e-05 0.08536071668 0.1059064061 0.1129856663 2.187404906e-19 5.859202386e-06 0.01463430305 +0.02391008911 0.02771315704 + +H atom_index 2 n_descriptor 18 +1.239880363 0.03514285481 0.1064181676 0.1450031747 0.3168661979 0.02232008107 0.02765667562 0.03831122734 +-3.469016659e-17 4.417551568e-05 0.09787889212 0.1151648954 0.1241804642 -6.305441398e-18 3.711936537e-06 0.0134581389 +0.02590390752 0.03024145758 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..b1e477d3150d8604e14005abd4d9234dfc10a394 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..b78348607cd00a2c30ac676337bd6e438aed9844 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:02 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0968674 SEC) : SETUP UNITCELL + DONE(0.10832 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.128556 SEC) : INIT PLANEWAVE + DONE(0.183377 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.469761 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651934e+02 0.000000e+00 2.106e-01 5.438e-01 + GE2 -4.663794e+02 -1.185963e+00 9.817e-02 4.379e-01 + GE3 -4.663840e+02 -4.587137e-03 6.324e-02 4.921e-01 + GE4 -4.663828e+02 1.175701e-03 1.895e-03 3.776e-01 + GE5 -4.663823e+02 4.312071e-04 8.653e-04 3.724e-01 + GE6 -4.663825e+02 -1.955684e-04 1.234e-04 3.675e-01 + GE7 -4.663825e+02 3.986615e-05 2.397e-05 3.521e-01 + GE8 -4.663825e+02 -1.988755e-05 1.084e-05 3.506e-01 + GE9 -4.663825e+02 1.206596e-05 1.605e-06 3.489e-01 + GE10 -4.663825e+02 -2.550118e-06 3.228e-07 3.468e-01 + GE11 -4.663825e+02 -1.844279e-07 8.988e-08 2.894e-01 +E_delta_band = -6.86966213e-02 Ry = -9.34665483e-01 eV +E_delta_NN= -1.93994084e-01 Ry = -2.63942492e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6579 11 0.61 1e+02 % + Run_lcao lcao_line 6.6471 1 6.6 1e+02 % + Potential init_pot 0.29116 2 0.15 4.4 % + PW_Basis recip2real 0.26914 16 0.017 4 % + PW_Basis gathers_scatterp 0.11531 16 0.0072 1.7 % + Charge atomic_rho 0.1006 1 0.1 1.5 % + Potential v_of_rho 0.88463 13 0.068 13 % + XC_Functional v_xc 0.2539 14 0.018 3.8 % + H_Hartree_pw v_hartree 0.59316 13 0.046 8.9 % + PW_Basis real2recip 0.55657 38 0.015 8.4 % + PW_Basis gatherp_scatters 0.21548 38 0.0057 3.2 % + ORB_control set_orb_tables 1.165 1 1.2 17 % + ORB_gen_tables gen_tables 1.165 1 1.2 17 % + ORB_table_phi init_Table 0.50601 1 0.51 7.6 % + ORB_table_phi cal_ST_Phi12_R 0.50076 126 0.004 7.5 % + ORB_table_beta init_Table_Beta 0.19548 1 0.2 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.19389 56 0.0035 2.9 % + ORB_table_alpha init_Table_Alpha 0.26288 1 0.26 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.26094 66 0.004 3.9 % + LOOP_ions opt_ions 4.9264 1 4.9 74 % + ESolver_KS_LCAO Run 4.3425 1 4.3 65 % + HSolverLCAO solve 2.3448 11 0.21 35 % + HamiltLCAO updateHk 1.2071 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1726 11 0.11 18 % + Gint_interface cal_gint 2.2286 23 0.097 33 % + Gint_Gamma distri_vl 2.089 6 0.35 31 % + LCAO_Deepks cal_projected_DM 4.7475 13 0.37 71 % + LCAO_gen_fixedH add_v_delta 1.9561 6 0.33 29 % + LCAO_DESCRIPTOR add_v_delta 1.9561 6 0.33 29 % + ElecStateLCAO psiToRho 1.1077 11 0.1 17 % + Charge mix_rho 0.66507 10 0.067 10 % + LOOP_ions force_stress 0.58372 1 0.58 8.8 % + Force_Stress_LCAO getForceStress 0.5837 1 0.58 8.8 % + Force_LCAO_gamma ftable_gamma 0.36827 1 0.37 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.36147 1 0.36 5.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:02 2022 + FINISH Time : Wed Sep 28 11:05:08 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/224/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..07b7dedcc1bc2490f900b444c3e256fbf6694ee1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.582853 0.679502 0.136389 +H 0.587085 0.617621 0.15108 +H 0.64373 0.706955 0.138112 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..62fdc5efa6ef92c7965173bf07d0f41789882aea --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2304 2 + 2 -13.3262 2 + 3 -8.85378 2 + 4 -6.7266 2 + 5 1.31972 0 + 6 4.52527 0 + 7 11.0745 0 + 8 11.2947 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4baa2f67909dbec76782ddea9e1e2925f964c9f0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:42 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.3198830976 19.0260540468 3.818902259 0 0 0 0 + tauc_H1 16.4383680587 17.2933939424 4.23023043191 0 0 0 0 + tauc_H2 18.0244321943 19.7947387925 3.86712468747 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874605665787 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0960976002979 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.114646068373 (SEC) + + DONE : INIT CHARGE Time : 0.165448514971 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446543 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000709 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00157 + + Density error is 0.21609189597 + + Energy Rydberg eV + E_KohnSham -34.1881718901 -465.153941909 + E_Harris -34.3822591136 -467.794634058 + E_Fermi -0.407024440202 -5.53785161201 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000890726378766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012904869788 + + Density error is 0.0981506384559 + + Energy Rydberg eV + E_KohnSham -34.2779047787 -466.374820492 + E_Harris -34.2845498102 -466.465230783 + E_Fermi -0.214992059397 -2.92511703255 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000849127334799 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119098312574 + + Density error is 0.0628640912907 + + Energy Rydberg eV + E_KohnSham -34.2781064061 -466.377563774 + E_Harris -34.2823733814 -466.43561895 + E_Fermi -0.202826025354 -2.75958964751 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000783317993863 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102088993128 + + Density error is 0.00209363406183 + + Energy Rydberg eV + E_KohnSham -34.2781123128 -466.377644138 + E_Harris -34.2781153586 -466.377685578 + E_Fermi -0.167539178945 -2.2794874719 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000781668305859 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101882488133 + + Density error is 0.000856764544911 + + Energy Rydberg eV + E_KohnSham -34.2780574403 -466.376897559 + E_Harris -34.2780582436 -466.376908489 + E_Fermi -0.166677415402 -2.26776257738 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00078080528883 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101704336938 + + Density error is 0.000192757998793 + + Energy Rydberg eV + E_KohnSham -34.2780915669 -466.377361875 + E_Harris -34.2780916378 -466.37736284 + E_Fermi -0.166695284087 -2.26800569332 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000780894662838 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101690124924 + + Density error is 4.29756033329e-05 + + Energy Rydberg eV + E_KohnSham -34.2780785726 -466.377185079 + E_Harris -34.2780785829 -466.37718522 + E_Fermi -0.166534816949 -2.2658224259 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000780841196559 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101689508079 + + Density error is 1.76657595993e-05 + + Energy Rydberg eV + E_KohnSham -34.2780837442 -466.377255443 + E_Harris -34.2780837456 -466.377255461 + E_Fermi -0.166582516941 -2.26647141758 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000780831596006 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101686501733 + + Density error is 1.40058355515e-06 + + Energy Rydberg eV + E_KohnSham -34.2780821705 -466.377234031 + E_Harris -34.2780821705 -466.377234031 + E_Fermi -0.16656284955 -2.26620382899 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000780833602379 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101686348716 + + Density error is 2.44830190614e-07 + + Energy Rydberg eV + E_KohnSham -34.2780824393 -466.377237688 + E_Harris -34.2780824393 -466.377237688 + E_Fermi -0.16656192798 -2.2661912904 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000780834047625 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101686343596 + + Density error is 8.27997123654e-08 + + Energy Rydberg eV + E_KohnSham -34.2780824588 -466.377237954 + E_Harris -34.2780824588 -466.377237954 + E_band -7.95798857852 -108.273989287 + E_one_elec -69.3488731482 -943.539824695 + E_Hartree +36.077062443 +490.853616326 + E_xc -8.21546935922 -111.77719503 + E_Ewald +7.33346002475 +99.7768423918 + E_demet -4.29954003675e-78 -5.8498243279e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194811630919 -2.65054821717 + E_Fermi -0.166561891272 -2.26619079095 + + charge density convergence is achieved + final etot is -466.377237954 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2304 2.00000 + 2 -13.3262 2.00000 + 3 -8.85378 2.00000 + 4 -6.72660 2.00000 + 5 1.31972 0.00000 + 6 4.52527 0.00000 + 7 11.0745 0.00000 + 8 11.2947 0.00000 + + EFERMI = -2.266190790949938 eV + OUT.ABACUS/ final etot is -466.3772379540901 eV + correction force for each atom along direction 1 is 0.000155499 + correction force for each atom along direction 2 is -3.67283e-05 + correction force for each atom along direction 3 is -3.77174e-07 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.15140410 +2.1806370 -0.47982448 + H1 +0.47441595 -1.5203233 +0.41051541 + H2 -0.62582005 -0.66031375 +0.069309073 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3772379540901 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2623 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2531 1 7.3 1.e+02% + Potential init_pot 0.28411 2 0.14 3.9% + PW_Basis recip2real 0.28385 16 0.018 3.9% + PW_Basis gathers_scatterp 0.12116 16 0.0076 1.7% + Potential v_of_rho 0.98527 13 0.076 14.% + XC_Functional v_xc 0.29884 14 0.021 4.1% + H_Hartree_pw v_hartree 0.64697 13 0.050 8.9% + PW_Basis real2recip 0.64486 38 0.017 8.9% + PW_Basis gatherp_scatters 0.24361 38 0.0064 3.4% + ORB_control set_orb_tables 1.0875 1 1.1 15.% + ORB_gen_tables gen_tables 1.0875 1 1.1 15.% + ORB_table_phi init_Table 0.46974 1 0.47 6.5% + ORB_table_phi cal_ST_Phi12_R 0.46473 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18465 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18313 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24762 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24573 66 0.0037 3.4% + LOOP_ions opt_ions 5.6398 1 5.6 78.% + ESolver_KS_LCAO Run 5.0359 1 5.0 69.% + HSolverLCAO solve 2.7696 11 0.25 38.% + HamiltLCAO updateHk 1.4191 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3917 11 0.13 19.% + Gint_interface cal_gint 2.6452 23 0.12 36.% + Gint_Gamma distri_vl 2.4134 6 0.40 33.% + LCAO_Deepks cal_projected_DM 5.4613 13 0.42 75.% + LCAO_gen_fixedH add_v_delta 2.2691 6 0.38 31.% + LCAO_DESCRIPTOR add_v_delta 2.2691 6 0.38 31.% + ElecStateLCAO psiToRho 1.3349 11 0.12 18.% + Charge mix_rho 0.78143 10 0.078 11.% + LOOP_ions force_stress 0.60370 1 0.60 8.3% + Force_Stress_LCAO getForceStress 0.60367 1 0.60 8.3% + Force_LCAO_gamma ftable_gamma 0.38712 1 0.39 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.37922 1 0.38 5.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:42 2022 + Finish Time : Wed Sep 28 11:12:50 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..45e27f0665a40f92e6c24ff4a24fa074e87eda24 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123859 ima = 3.68309e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012354332866 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112691239825 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011316245539 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113392340263 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113347219673 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113374237722 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113365034807 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113368244171 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113367498731 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113367447441 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113367440893 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/STRU new file mode 100644 index 0000000000000000000000000000000000000000..73ad566848256792d740b01f4c7298376cd1306b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.680116902340 19.026054046802 3.818902259012 0 0 0 +H +0.0 +2 +-11.561631941336 17.293393942438 4.230230431897 0 0 0 +-9.975567805769 19.794738792490 3.867124687479 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/conv new file mode 100644 index 0000000000000000000000000000000000000000..e91d70ace6a183947d3f75c06176b48e1b9e54f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/conv @@ -0,0 +1 @@ +225 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8c18530a45328b0ccecd52f73e524f5e2b1426e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.7446175 0.01259643428 1.276468723 1.374452413 1.469136608 0.007806785206 0.020233618 0.03889508513 +8.514317385e-19 0.001147001678 0.002401954629 0.012282728 0.04313396536 9.623280098e-20 1.538672354e-06 4.902282608e-06 +0.001760338214 0.005643941277 + +H atom_index 1 n_descriptor 18 +1.279361147 0.03268214249 0.1189293874 0.165473551 0.3316172214 0.02310268005 0.03015952268 0.03623667476 +-1.329618734e-17 4.182766882e-05 0.1071146266 0.1179467356 0.1420424551 5.101540672e-19 2.737545508e-06 0.01302596133 +0.02710660718 0.03207773937 + +H atom_index 2 n_descriptor 18 +1.210906399 0.03506341557 0.0956323987 0.1340083795 0.3100423747 0.02011828661 0.02621585689 0.03830271304 +1.555937031e-17 3.62157065e-05 0.09161423255 0.1137496723 0.1148706775 -2.305413359e-18 5.792814008e-06 0.01351682411 +0.02456876918 0.02901349232 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..38e015025a07875047d603c2e26980f5c8d93aeb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:42 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874867 SEC) : SETUP UNITCELL + DONE(0.0961199 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.114669 SEC) : INIT PLANEWAVE + DONE(0.165576 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446613 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651539e+02 0.000000e+00 2.161e-01 5.649e-01 + GE2 -4.663748e+02 -1.220879e+00 9.815e-02 5.059e-01 + GE3 -4.663776e+02 -2.743282e-03 6.286e-02 5.725e-01 + GE4 -4.663776e+02 -8.036437e-05 2.094e-03 4.388e-01 + GE5 -4.663769e+02 7.465785e-04 8.568e-04 4.380e-01 + GE6 -4.663774e+02 -4.643159e-04 1.928e-04 4.301e-01 + GE7 -4.663772e+02 1.767963e-04 4.298e-05 4.154e-01 + GE8 -4.663773e+02 -7.036374e-05 1.767e-05 4.216e-01 + GE9 -4.663772e+02 2.141204e-05 1.401e-06 4.197e-01 + GE10 -4.663772e+02 -3.657246e-06 2.448e-07 4.177e-01 + GE11 -4.663772e+02 -2.659805e-07 8.280e-08 3.487e-01 +E_delta_band = -7.05492118e-02 Ry = -9.59871270e-01 eV +E_delta_NN= -1.94811631e-01 Ry = -2.65054822e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2623 11 0.66 1e+02 % + Run_lcao lcao_line 7.2531 1 7.3 1e+02 % + Potential init_pot 0.28411 2 0.14 3.9 % + PW_Basis recip2real 0.28385 16 0.018 3.9 % + PW_Basis gathers_scatterp 0.12116 16 0.0076 1.7 % + Potential v_of_rho 0.98527 13 0.076 14 % + XC_Functional v_xc 0.29884 14 0.021 4.1 % + H_Hartree_pw v_hartree 0.64697 13 0.05 8.9 % + PW_Basis real2recip 0.64486 38 0.017 8.9 % + PW_Basis gatherp_scatters 0.24361 38 0.0064 3.4 % + ORB_control set_orb_tables 1.0875 1 1.1 15 % + ORB_gen_tables gen_tables 1.0875 1 1.1 15 % + ORB_table_phi init_Table 0.46974 1 0.47 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.46473 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18465 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18313 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24762 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24573 66 0.0037 3.4 % + LOOP_ions opt_ions 5.6398 1 5.6 78 % + ESolver_KS_LCAO Run 5.0359 1 5 69 % + HSolverLCAO solve 2.7696 11 0.25 38 % + HamiltLCAO updateHk 1.4191 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3917 11 0.13 19 % + Gint_interface cal_gint 2.6452 23 0.12 36 % + Gint_Gamma distri_vl 2.4134 6 0.4 33 % + LCAO_Deepks cal_projected_DM 5.4613 13 0.42 75 % + LCAO_gen_fixedH add_v_delta 2.2691 6 0.38 31 % + LCAO_DESCRIPTOR add_v_delta 2.2691 6 0.38 31 % + ElecStateLCAO psiToRho 1.3349 11 0.12 18 % + Charge mix_rho 0.78143 10 0.078 11 % + LOOP_ions force_stress 0.6037 1 0.6 8.3 % + Force_Stress_LCAO getForceStress 0.60367 1 0.6 8.3 % + Force_LCAO_gamma ftable_gamma 0.38712 1 0.39 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.37922 1 0.38 5.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:42 2022 + FINISH Time : Wed Sep 28 11:12:50 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/225/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9fe81342dec02857e1ab72de618507ac7c065f3d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.607074 0.677715 0.150668 +H 0.561257 0.657545 0.195 +H 0.637124 0.621746 0.143063 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3f7fdefd0f96ccde81fd9e011ed2bc8c559ee231 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4436 2 + 2 -12.7371 2 + 3 -9.44384 2 + 4 -6.77905 2 + 5 1.2496 0 + 6 4.42884 0 + 7 11.0595 0 + 8 11.3383 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..2b24f15f314c32b380560325686c265b4ee02126 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:03 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.9980831238 18.9760266982 4.21871051346 0 0 0 0 + tauc_H1 15.7151890211 18.4112702838 5.45999395358 0 0 0 0 + tauc_H2 17.8394806525 17.4088972815 4.00576426661 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0727108865931 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0730472802297 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0887517859019 (SEC) + + DONE : INIT CHARGE Time : 0.130905308849 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.373897 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00148 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108 + + Density error is 0.213789420614 + + Energy Rydberg eV + E_KohnSham -34.1880789337 -465.152677172 + E_Harris -34.3783127483 -467.740941003 + E_Fermi -0.407545612099 -5.54494251944 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013650021178 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124489118988 + + Density error is 0.0976123634119 + + Energy Rydberg eV + E_KohnSham -34.2772657684 -466.366126311 + E_Harris -34.2841154363 -466.459320823 + E_Fermi -0.218086793274 -2.96722304708 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125707384372 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117563123623 + + Density error is 0.0626185626183 + + Energy Rydberg eV + E_KohnSham -34.2775623573 -466.37016161 + E_Harris -34.2820023109 -466.430570278 + E_Fermi -0.207055562004 -2.81713544585 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107099073352 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107200137465 + + Density error is 0.00193407703012 + + Energy Rydberg eV + E_KohnSham -34.2775425503 -466.369892121 + E_Harris -34.2775432352 -466.36990144 + E_Fermi -0.17111282806 -2.32810946251 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107093290323 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107426726199 + + Density error is 0.000895083259724 + + Energy Rydberg eV + E_KohnSham -34.2774842673 -466.369099141 + E_Harris -34.2774856985 -466.369118613 + E_Fermi -0.170581104275 -2.32087498927 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106876459107 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107260197162 + + Density error is 9.20384276278e-05 + + Energy Rydberg eV + E_KohnSham -34.2775216162 -466.369607299 + E_Harris -34.2775216221 -466.369607379 + E_Fermi -0.170504961109 -2.31983900835 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106854867596 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107239252548 + + Density error is 3.98797829975e-05 + + Energy Rydberg eV + E_KohnSham -34.277510552 -466.369456762 + E_Harris -34.277510561 -466.369456885 + E_Fermi -0.170400271372 -2.3184146314 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106856317643 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107236003497 + + Density error is 1.08108576741e-05 + + Energy Rydberg eV + E_KohnSham -34.2775125347 -466.369483738 + E_Harris -34.2775125351 -466.369483744 + E_Fermi -0.170444575035 -2.31901741366 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010685525794 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107236711415 + + Density error is 2.13131121524e-06 + + Energy Rydberg eV + E_KohnSham -34.2775112728 -466.36946657 + E_Harris -34.2775112729 -466.36946657 + E_Fermi -0.170435112655 -2.31888867138 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106854752816 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107236656032 + + Density error is 1.6487713628e-07 + + Energy Rydberg eV + E_KohnSham -34.2775114145 -466.369468498 + E_Harris -34.2775114145 -466.369468498 + E_Fermi -0.170432920371 -2.31885884382 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106854780236 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010723669724 + + Density error is 6.36017216887e-08 + + Energy Rydberg eV + E_KohnSham -34.2775114556 -466.369469056 + E_Harris -34.2775114556 -466.369469056 + E_band -7.99717910626 -108.807203772 + E_one_elec -69.3549022632 -943.621855013 + E_Hartree +36.0586161341 +490.602641418 + E_xc -8.2126635221 -111.739019657 + E_Ewald +7.35560130281 +100.078089934 + E_demet -2.32107271046e-77 -3.15798143345e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194999687339 -2.65310685603 + E_Fermi -0.170432885774 -2.31885837311 + + charge density convergence is achieved + final etot is -466.369469056 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4436 2.00000 + 2 -12.7371 2.00000 + 3 -9.44384 2.00000 + 4 -6.77905 2.00000 + 5 1.24960 0.00000 + 6 4.42884 0.00000 + 7 11.0595 0.00000 + 8 11.3383 0.00000 + + EFERMI = -2.318858373107072 eV + OUT.ABACUS/ final etot is -466.3694690563541 eV + correction force for each atom along direction 1 is 4.84448e-05 + correction force for each atom along direction 2 is -4.51405e-05 + correction force for each atom along direction 3 is -3.82335e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.3092388 +0.60573032 +0.89934055 + H1 +0.17241663 +0.64609241 -0.34329474 + H2 +1.1368221 -1.2518227 -0.55604581 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3694690563541 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6761 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6691 1 6.7 1.e+02% + Potential init_pot 0.24104 2 0.12 3.6% + PW_Basis recip2real 0.25997 16 0.016 3.9% + PW_Basis gathers_scatterp 0.10730 16 0.0067 1.6% + Potential v_of_rho 0.91394 13 0.070 14.% + XC_Functional v_xc 0.27155 14 0.019 4.1% + H_Hartree_pw v_hartree 0.60478 13 0.047 9.1% + PW_Basis real2recip 0.60027 38 0.016 9.0% + PW_Basis gatherp_scatters 0.22162 38 0.0058 3.3% + ORB_control set_orb_tables 0.89885 1 0.90 13.% + ORB_gen_tables gen_tables 0.89884 1 0.90 13.% + ORB_table_phi init_Table 0.37644 1 0.38 5.6% + ORB_table_phi cal_ST_Phi12_R 0.37219 126 0.0030 5.6% + ORB_table_beta init_Table_Beta 0.15554 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15426 56 0.0028 2.3% + ORB_table_alpha init_Table_Alpha 0.20864 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20699 66 0.0031 3.1% + LOOP_ions opt_ions 5.3260 1 5.3 80.% + ESolver_KS_LCAO Run 4.7707 1 4.8 71.% + HSolverLCAO solve 2.6006 11 0.24 39.% + HamiltLCAO updateHk 1.3300 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.2985 11 0.12 19.% + Gint_interface cal_gint 2.4916 23 0.11 37.% + Gint_Gamma distri_vl 2.2914 6 0.38 34.% + LCAO_Deepks cal_projected_DM 5.1711 13 0.40 77.% + LCAO_gen_fixedH add_v_delta 2.1617 6 0.36 32.% + LCAO_DESCRIPTOR add_v_delta 2.1619 6 0.36 32.% + ElecStateLCAO psiToRho 1.2525 11 0.11 19.% + Charge mix_rho 0.76262 10 0.076 11.% + LOOP_ions force_stress 0.55515 1 0.56 8.3% + Force_Stress_LCAO getForceStress 0.55513 1 0.56 8.3% + Force_LCAO_gamma ftable_gamma 0.35894 1 0.36 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.35156 1 0.35 5.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:03 2022 + Finish Time : Wed Sep 28 11:02:10 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..5f492fcb140f809fa4e76f86026d87cf61f66622 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124 ima = 3.70465e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122597784101 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111442950297 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112035759682 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112297355837 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011224326846 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112272148095 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112269810434 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112272543806 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112272063519 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112271959083 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112271952477 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c6df33a21eb05f439e98110ce538f52972792994 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.001916876160 18.976026698206 4.218710513476 0 0 0 +H +0.0 +2 +-12.284810978912 18.411270283846 5.459993953588 0 0 0 +-10.160519347483 17.408897281468 4.005764266595 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/conv new file mode 100644 index 0000000000000000000000000000000000000000..7a028c27b57190e57fdebbe456d2a6b0617afdcf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/conv @@ -0,0 +1 @@ +226 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e20c0ebb991f48eb4b977c472857336a08947c3b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754325954 0.01279027119 1.269385496 1.356931708 1.469884095 0.009543445039 0.01678969957 0.03917870174 +5.129065499e-19 0.0009112701151 0.002872281131 0.01332562579 0.04718212363 4.077131885e-19 2.819021532e-06 7.490216663e-06 +0.001584113199 0.006134386438 + +H atom_index 1 n_descriptor 18 +1.219063907 0.03592822898 0.1006662835 0.1356872047 0.3087721794 0.02170196488 0.02641167418 0.03911689843 +-7.41265054e-17 4.74099442e-05 0.09560026269 0.1138352434 0.1162185096 4.273339522e-18 4.735541701e-06 0.01391424167 +0.02584912191 0.02923673518 + +H atom_index 2 n_descriptor 18 +1.282519189 0.03384294133 0.1233791802 0.1654041312 0.3297703255 0.0248545755 0.03012561772 0.03721811621 +7.244487272e-17 5.335934839e-05 0.1077782807 0.1202375976 0.1418208972 1.704752926e-18 1.340293818e-06 0.01348291572 +0.02818300825 0.03212766417 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fb943bec064f2d2312482870d3f095c460e16739 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..27c18cf49e7883a106a4921bda6489ef5b4ab28d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:03 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0727254 SEC) : SETUP UNITCELL + DONE(0.0730576 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0887652 SEC) : INIT PLANEWAVE + DONE(0.131011 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.37394 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651527e+02 0.000000e+00 2.138e-01 5.133e-01 + GE2 -4.663661e+02 -1.213449e+00 9.761e-02 4.810e-01 + GE3 -4.663702e+02 -4.035299e-03 6.262e-02 5.448e-01 + GE4 -4.663699e+02 2.694891e-04 1.934e-03 4.197e-01 + GE5 -4.663691e+02 7.929799e-04 8.951e-04 4.172e-01 + GE6 -4.663696e+02 -5.081576e-04 9.204e-05 4.098e-01 + GE7 -4.663695e+02 1.505364e-04 3.988e-05 3.998e-01 + GE8 -4.663695e+02 -2.697548e-05 1.081e-05 3.972e-01 + GE9 -4.663695e+02 1.716784e-05 2.131e-06 4.006e-01 + GE10 -4.663695e+02 -1.928046e-06 1.649e-07 3.982e-01 + GE11 -4.663695e+02 -5.584645e-07 6.360e-08 3.334e-01 +E_delta_band = -7.08365802e-02 Ry = -9.63781117e-01 eV +E_delta_NN= -1.94999687e-01 Ry = -2.65310686e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6761 11 0.61 1e+02 % + Run_lcao lcao_line 6.6691 1 6.7 1e+02 % + Potential init_pot 0.24104 2 0.12 3.6 % + PW_Basis recip2real 0.25997 16 0.016 3.9 % + PW_Basis gathers_scatterp 0.1073 16 0.0067 1.6 % + Potential v_of_rho 0.91394 13 0.07 14 % + XC_Functional v_xc 0.27155 14 0.019 4.1 % + H_Hartree_pw v_hartree 0.60478 13 0.047 9.1 % + PW_Basis real2recip 0.60027 38 0.016 9 % + PW_Basis gatherp_scatters 0.22162 38 0.0058 3.3 % + ORB_control set_orb_tables 0.89885 1 0.9 13 % + ORB_gen_tables gen_tables 0.89884 1 0.9 13 % + ORB_table_phi init_Table 0.37644 1 0.38 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.37219 126 0.003 5.6 % + ORB_table_beta init_Table_Beta 0.15554 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15426 56 0.0028 2.3 % + ORB_table_alpha init_Table_Alpha 0.20864 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20699 66 0.0031 3.1 % + LOOP_ions opt_ions 5.326 1 5.3 80 % + ESolver_KS_LCAO Run 4.7707 1 4.8 71 % + HSolverLCAO solve 2.6006 11 0.24 39 % + HamiltLCAO updateHk 1.33 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.2985 11 0.12 19 % + Gint_interface cal_gint 2.4916 23 0.11 37 % + Gint_Gamma distri_vl 2.2914 6 0.38 34 % + LCAO_Deepks cal_projected_DM 5.1711 13 0.4 77 % + LCAO_gen_fixedH add_v_delta 2.1617 6 0.36 32 % + LCAO_DESCRIPTOR add_v_delta 2.1619 6 0.36 32 % + ElecStateLCAO psiToRho 1.2525 11 0.11 19 % + Charge mix_rho 0.76262 10 0.076 11 % + LOOP_ions force_stress 0.55515 1 0.56 8.3 % + Force_Stress_LCAO getForceStress 0.55513 1 0.56 8.3 % + Force_LCAO_gamma ftable_gamma 0.35894 1 0.36 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.35156 1 0.35 5.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:03 2022 + FINISH Time : Wed Sep 28 11:02:10 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/226/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ce96e287cb26223e9e4aef8d01419eba421f096f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.613501 0.682556 0.163911 +H 0.596257 0.718924 0.218218 +H 0.555166 0.652135 0.141021 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..7b74084efce7e351f8748efa8e4f6653717bfe3c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.7423 2 + 2 -12.7227 2 + 3 -8.91323 2 + 4 -6.61868 2 + 5 0.833031 0 + 6 3.69378 0 + 7 11.1993 0 + 8 11.4314 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e9a6faa9c80b2f529e84e001dcdd9864e7818bf6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:45 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.1780292489 19.1115668596 4.58949685415 0 0 0 0 + tauc_H1 16.6951925726 20.1298805201 6.11009880843 0 0 0 0 + tauc_H2 15.5446517577 18.2597824205 3.9485894386 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0873458851951 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0975914421518 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115866699337 (SEC) + + DONE : INIT CHARGE Time : 0.165463831414 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447272 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000834 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131 + + Density error is 0.210561664308 + + Energy Rydberg eV + E_KohnSham -34.1866818701 -465.133669147 + E_Harris -34.3688497668 -467.612190534 + E_Fermi -0.375288794692 -5.10606600337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108641294904 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111326304637 + + Density error is 0.0996729136931 + + Energy Rydberg eV + E_KohnSham -34.2743119515 -466.32593757 + E_Harris -34.2817687916 -466.427393084 + E_Fermi -0.186039369403 -2.5311954762 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103914867519 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104144136842 + + Density error is 0.0645666064619 + + Energy Rydberg eV + E_KohnSham -34.2748075336 -466.332680311 + E_Harris -34.2794807902 -466.396263228 + E_Fermi -0.182024565189 -2.47657126254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000973830123622 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909105331342 + + Density error is 0.00208857332762 + + Energy Rydberg eV + E_KohnSham -34.2746656202 -466.330749479 + E_Harris -34.2746716613 -466.330831672 + E_Fermi -0.147302047863 -2.004147178 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000971591822421 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908318713964 + + Density error is 0.000953063687237 + + Energy Rydberg eV + E_KohnSham -34.2746493453 -466.330528048 + E_Harris -34.2746495183 -466.330530402 + E_Fermi -0.147397680108 -2.00544832145 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000970686654385 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906170935193 + + Density error is 0.000213288252061 + + Energy Rydberg eV + E_KohnSham -34.2746519851 -466.330563965 + E_Harris -34.2746519935 -466.330564078 + E_Fermi -0.146787853441 -1.99715120399 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00097083777753 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906345450518 + + Density error is 2.59024150042e-05 + + Energy Rydberg eV + E_KohnSham -34.2746529499 -466.330577091 + E_Harris -34.2746529507 -466.330577103 + E_Fermi -0.146837598985 -1.99782802684 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000970770105285 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906293971597 + + Density error is 8.26319444469e-06 + + Energy Rydberg eV + E_KohnSham -34.2746541835 -466.330593876 + E_Harris -34.2746541838 -466.33059388 + E_Fermi -0.146837423576 -1.99782564027 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000970766855126 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00090628451889 + + Density error is 1.15181160192e-06 + + Energy Rydberg eV + E_KohnSham -34.2746535689 -466.330585514 + E_Harris -34.2746535689 -466.330585514 + E_Fermi -0.146828336654 -1.99770200636 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000970767986642 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906284003416 + + Density error is 4.21563729743e-07 + + Energy Rydberg eV + E_KohnSham -34.2746537077 -466.330587401 + E_Harris -34.2746537077 -466.330587401 + E_Fermi -0.14682825081 -1.99770083839 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000970768428418 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906283831548 + + Density error is 8.89210891097e-08 + + Energy Rydberg eV + E_KohnSham -34.2746537022 -466.330587326 + E_Harris -34.2746537022 -466.330587327 + E_band -7.79039585378 -105.993773287 + E_one_elec -68.2296515478 -928.312033605 + E_Hartree +35.5450837887 +483.615675414 + E_xc -8.13032987643 -110.618812939 + E_Ewald +6.66670260475 +90.7051422961 + E_demet -1.13368666022e-49 -1.54245983256e-48 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.1929078136 -2.62464545369 + E_Fermi -0.146827966078 -1.99769696441 + + charge density convergence is achieved + final etot is -466.330587326 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.7423 2.00000 + 2 -12.7227 2.00000 + 3 -8.91323 2.00000 + 4 -6.61868 2.00000 + 5 0.833031 0.00000 + 6 3.69378 0.00000 + 7 11.1993 0.00000 + 8 11.4314 0.00000 + + EFERMI = -1.997696964405478 eV + OUT.ABACUS/ final etot is -466.3305873264875 eV + correction force for each atom along direction 1 is -0.000128783 + correction force for each atom along direction 2 is -6.11682e-05 + correction force for each atom along direction 3 is 4.44018e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.8513022 -0.42593454 +0.0044851582 + H1 +0.026625022 -0.72600759 -0.98828462 + H2 +1.8246772 +1.1519421 +0.98379947 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3305873264875 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0655 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0557 1 7.1 1.e+02% + Potential init_pot 0.28469 2 0.14 4.0% + PW_Basis recip2real 0.28781 16 0.018 4.1% + PW_Basis gathers_scatterp 0.12144 16 0.0076 1.7% + Potential v_of_rho 1.0007 13 0.077 14.% + XC_Functional v_xc 0.29188 14 0.021 4.1% + H_Hartree_pw v_hartree 0.66783 13 0.051 9.5% + PW_Basis real2recip 0.65012 38 0.017 9.2% + PW_Basis gatherp_scatters 0.24467 38 0.0064 3.5% + ORB_control set_orb_tables 1.0991 1 1.1 16.% + ORB_gen_tables gen_tables 1.0991 1 1.1 16.% + ORB_table_phi init_Table 0.47626 1 0.48 6.7% + ORB_table_phi cal_ST_Phi12_R 0.47105 126 0.0037 6.7% + ORB_table_beta init_Table_Beta 0.18658 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18503 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.25023 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24827 66 0.0038 3.5% + LOOP_ions opt_ions 5.4318 1 5.4 77.% + ESolver_KS_LCAO Run 4.8324 1 4.8 68.% + HSolverLCAO solve 2.5434 11 0.23 36.% + HamiltLCAO updateHk 1.3304 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2956 11 0.12 18.% + Gint_interface cal_gint 2.4003 23 0.10 34.% + Gint_Gamma distri_vl 2.3156 6 0.39 33.% + LCAO_Deepks cal_projected_DM 5.2508 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1711 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1711 6 0.36 31.% + ElecStateLCAO psiToRho 1.1965 11 0.11 17.% + Charge mix_rho 0.78020 10 0.078 11.% + LOOP_ions force_stress 0.59916 1 0.60 8.5% + Force_Stress_LCAO getForceStress 0.59912 1 0.60 8.5% + Force_LCAO_gamma ftable_gamma 0.37839 1 0.38 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.37040 1 0.37 5.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:45 2022 + Finish Time : Wed Sep 28 11:08:52 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2e5e3dbea09d5bae42303a1154e8ec230d714dc0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123492 ima = 3.6908e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124160025909 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011258490263 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113467502672 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113628580587 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113632652119 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113633321522 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113631986659 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113633163048 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113632786961 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113632785293 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113632764837 + charge after normalized = 8.00000000000003 + charge before normalized = 8.00000000000003 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/STRU new file mode 100644 index 0000000000000000000000000000000000000000..985527c716757dc80d78389e03a8258524f6c6d4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.821970751053 19.111566859649 4.589496854140 0 0 0 +H +0.0 +2 +-11.304807427364 20.129880520139 6.110098808448 0 0 0 +-12.455348242304 18.259782420526 3.948589438625 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/conv new file mode 100644 index 0000000000000000000000000000000000000000..a119d8f65d8a99b14f3872cc102f5769890a4d62 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/conv @@ -0,0 +1 @@ +227 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..642cfb0e68a6029743f199af5c6f839a3ff0f2cf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748156099 0.01217282058 1.229707934 1.330546201 1.467063085 0.00796614004 0.01846104084 0.03906326038 +1.124974456e-18 0.0008548851438 0.002184925497 0.01076851799 0.03851120296 -1.215915175e-19 1.19413102e-06 3.972495777e-06 +0.001636563091 0.005619307207 + +H atom_index 1 n_descriptor 18 +1.196963513 0.03589093125 0.08994157624 0.1280198155 0.3047880698 0.01919146204 0.02536332858 0.03941421648 +6.688302736e-18 3.068431474e-05 0.08386280442 0.1092656342 0.1139199385 -3.227722915e-18 5.620470152e-06 0.01403840511 +0.02305998135 0.02819149757 + +H atom_index 2 n_descriptor 18 +1.151641343 0.03715070719 0.07741096568 0.1106839778 0.2869571368 0.01717505475 0.0227355554 0.04125720133 +1.351366569e-17 2.746840848e-05 0.0726985488 0.09388751939 0.1112935879 1.17253414e-17 6.345027234e-06 0.0155497088 +0.02115646055 0.02568498768 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..793da53d683b5e95f9434cdfeb1ba60860bf0ab8 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..3836a6d8c9ec8f13c31477e47adc5bd48a872561 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..52986fcaadc078e7763975dcf252422f22aa32aa Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..be01285e7bfee2852e24556ede36a9f6f1c8b502 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:45 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0873692 SEC) : SETUP UNITCELL + DONE(0.0976178 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115889 SEC) : INIT PLANEWAVE + DONE(0.165589 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447327 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651337e+02 0.000000e+00 2.106e-01 5.614e-01 + GE2 -4.663259e+02 -1.192268e+00 9.967e-02 4.872e-01 + GE3 -4.663327e+02 -6.742740e-03 6.457e-02 5.524e-01 + GE4 -4.663307e+02 1.930831e-03 2.089e-03 4.185e-01 + GE5 -4.663305e+02 2.214313e-04 9.531e-04 4.190e-01 + GE6 -4.663306e+02 -3.591651e-05 2.133e-04 4.132e-01 + GE7 -4.663306e+02 -1.312668e-05 2.590e-05 3.938e-01 + GE8 -4.663306e+02 -1.678433e-05 8.263e-06 3.965e-01 + GE9 -4.663306e+02 8.362154e-06 1.152e-06 3.958e-01 + GE10 -4.663306e+02 -1.887888e-06 4.216e-07 3.978e-01 + GE11 -4.663306e+02 7.490914e-08 8.892e-08 3.344e-01 +E_delta_band = -6.64491422e-02 Ry = -9.04086961e-01 eV +E_delta_NN= -1.92907814e-01 Ry = -2.62464545e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0655 11 0.64 1e+02 % + Run_lcao lcao_line 7.0557 1 7.1 1e+02 % + Potential init_pot 0.28469 2 0.14 4 % + PW_Basis recip2real 0.28781 16 0.018 4.1 % + PW_Basis gathers_scatterp 0.12144 16 0.0076 1.7 % + Potential v_of_rho 1.0007 13 0.077 14 % + XC_Functional v_xc 0.29188 14 0.021 4.1 % + H_Hartree_pw v_hartree 0.66783 13 0.051 9.5 % + PW_Basis real2recip 0.65012 38 0.017 9.2 % + PW_Basis gatherp_scatters 0.24467 38 0.0064 3.5 % + ORB_control set_orb_tables 1.0991 1 1.1 16 % + ORB_gen_tables gen_tables 1.0991 1 1.1 16 % + ORB_table_phi init_Table 0.47626 1 0.48 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.47105 126 0.0037 6.7 % + ORB_table_beta init_Table_Beta 0.18658 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18503 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.25023 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24827 66 0.0038 3.5 % + LOOP_ions opt_ions 5.4318 1 5.4 77 % + ESolver_KS_LCAO Run 4.8324 1 4.8 68 % + HSolverLCAO solve 2.5434 11 0.23 36 % + HamiltLCAO updateHk 1.3304 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2956 11 0.12 18 % + Gint_interface cal_gint 2.4003 23 0.1 34 % + Gint_Gamma distri_vl 2.3156 6 0.39 33 % + LCAO_Deepks cal_projected_DM 5.2508 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.1711 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1711 6 0.36 31 % + ElecStateLCAO psiToRho 1.1965 11 0.11 17 % + Charge mix_rho 0.7802 10 0.078 11 % + LOOP_ions force_stress 0.59916 1 0.6 8.5 % + Force_Stress_LCAO getForceStress 0.59912 1 0.6 8.5 % + Force_LCAO_gamma ftable_gamma 0.37839 1 0.38 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.3704 1 0.37 5.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:45 2022 + FINISH Time : Wed Sep 28 11:08:52 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/227/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..33abe4e8f3e955b5fdb6317c809ecb8567b35a9d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.61027 0.692807 0.180646 +H 0.638254 0.750407 0.188955 +H 0.556353 0.708426 0.158467 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..baddc859e6c37a5de3359533067f2118e3c35479 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.9115 2 + 2 -13.3681 2 + 3 -9.32164 2 + 4 -6.87573 2 + 5 1.65267 0 + 6 5.1845 0 + 7 10.9342 0 + 8 11.1737 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0f184622b3e95d2b20e16a2a31bba8f7d5e8046c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:11 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.0875724768 19.3985844197 5.05809152332 0 0 0 0 + tauc_H1 17.871113647 21.0113984742 5.2907481538 0 0 0 0 + tauc_H2 15.5778731756 19.8359251101 4.43706226788 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0876492818583 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0962613365457 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115252872515 (SEC) + + DONE : INIT CHARGE Time : 0.165637603758 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446696 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000647 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00193 + + Density error is 0.221151377924 + + Energy Rydberg eV + E_KohnSham -34.1722438997 -464.937230481 + E_Harris -34.3787917437 -467.747458069 + E_Fermi -0.441591547255 -6.0081612313 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000926392111766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00162351234234 + + Density error is 0.0967707369131 + + Energy Rydberg eV + E_KohnSham -34.2652687097 -466.202897953 + E_Harris -34.2719516462 -466.293823969 + E_Fermi -0.246654890422 -3.3559119493 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883684498283 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00147790054328 + + Density error is 0.0613217844307 + + Energy Rydberg eV + E_KohnSham -34.2654582467 -466.205476736 + E_Harris -34.2695989161 -466.261813434 + E_Fermi -0.228358915657 -3.10698244204 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000828608554264 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124622116193 + + Density error is 0.00221753401445 + + Energy Rydberg eV + E_KohnSham -34.2655768024 -466.207089769 + E_Harris -34.265582274 -466.207164215 + E_Fermi -0.192216311318 -2.61523708247 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000833432974641 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124432947319 + + Density error is 0.000961986246677 + + Energy Rydberg eV + E_KohnSham -34.2654885471 -466.205888994 + E_Harris -34.2654920093 -466.2059361 + E_Fermi -0.190544228055 -2.59248722256 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000832239452343 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124272632619 + + Density error is 0.000230918918535 + + Energy Rydberg eV + E_KohnSham -34.2655510013 -466.206738727 + E_Harris -34.2655512678 -466.206742353 + E_Fermi -0.191134730841 -2.60052142513 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00083231159715 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012421579056 + + Density error is 4.62223263346e-05 + + Energy Rydberg eV + E_KohnSham -34.2655265485 -466.206406031 + E_Harris -34.2655265568 -466.206406142 + E_Fermi -0.190859981262 -2.59678326534 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000832295105365 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012422156653 + + Density error is 1.71582619866e-05 + + Energy Rydberg eV + E_KohnSham -34.2655327948 -466.206491015 + E_Harris -34.2655327954 -466.206491024 + E_Fermi -0.1909108774 -2.59747574282 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000832282629391 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124214778114 + + Density error is 2.43490464824e-06 + + Energy Rydberg eV + E_KohnSham -34.2655316885 -466.206475964 + E_Harris -34.2655316886 -466.206475964 + E_Fermi -0.190892842738 -2.59723036865 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000832283570338 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124214554211 + + Density error is 7.09885873328e-07 + + Energy Rydberg eV + E_KohnSham -34.2655317475 -466.206476766 + E_Harris -34.2655317475 -466.206476766 + E_Fermi -0.190891308529 -2.59720949467 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000832284363486 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012421448491 + + Density error is 2.07649102265e-07 + + Energy Rydberg eV + E_KohnSham -34.2655317723 -466.206477103 + E_Harris -34.2655317723 -466.206477103 + E_Fermi -0.190890871436 -2.59720354771 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000832284502611 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124214438715 + + Density error is 1.02906429577e-08 + + Energy Rydberg eV + E_KohnSham -34.265531778 -466.206477181 + E_Harris -34.265531778 -466.206477181 + E_band -8.15495473826 -110.953851372 + E_one_elec -70.4050650852 -957.910053219 + E_Hartree +36.5587593035 +497.407438337 + E_xc -8.29441040031 -112.851242995 + E_Ewald +7.99724626444 +108.808117506 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.197049069389 -2.68099012929 + E_Fermi -0.190890641098 -2.5972004138 + + charge density convergence is achieved + final etot is -466.206477181 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.9115 2.00000 + 2 -13.3681 2.00000 + 3 -9.32164 2.00000 + 4 -6.87573 2.00000 + 5 1.65267 0.00000 + 6 5.18450 0.00000 + 7 10.9342 0.00000 + 8 11.1737 0.00000 + + EFERMI = -2.597200413803507 eV + OUT.ABACUS/ final etot is -466.2064771812406 eV + correction force for each atom along direction 1 is -7.68812e-05 + correction force for each atom along direction 2 is 0.000188188 + correction force for each atom along direction 3 is -0.000115007 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +4.2390425 -1.7710513 +1.7664352 + H1 +0.74325869 +0.73840698 +0.26124683 + H2 -4.9823012 +1.0326443 -2.0276820 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2064771812406 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6019 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5920 1 7.6 1.e+02% + Potential init_pot 0.28552 2 0.14 3.8% + PW_Basis recip2real 0.30286 17 0.018 4.0% + PW_Basis gathers_scatterp 0.12599 17 0.0074 1.7% + Potential v_of_rho 1.0793 14 0.077 14.% + XC_Functional v_xc 0.31601 15 0.021 4.2% + H_Hartree_pw v_hartree 0.71801 14 0.051 9.4% + PW_Basis real2recip 0.69911 41 0.017 9.2% + PW_Basis gatherp_scatters 0.26744 41 0.0065 3.5% + ORB_control set_orb_tables 1.0933 1 1.1 14.% + ORB_gen_tables gen_tables 1.0933 1 1.1 14.% + ORB_table_phi init_Table 0.47428 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46910 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18394 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18237 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24826 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24630 66 0.0037 3.2% + LOOP_ions opt_ions 5.9736 1 6.0 79.% + ESolver_KS_LCAO Run 5.3666 1 5.4 71.% + HSolverLCAO solve 2.8787 12 0.24 38.% + HamiltLCAO updateHk 1.4670 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4303 12 0.12 19.% + Gint_interface cal_gint 2.7243 25 0.11 36.% + Gint_Gamma distri_vl 2.8000 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.8024 14 0.41 76.% + LCAO_gen_fixedH add_v_delta 2.6557 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6557 6 0.44 35.% + ElecStateLCAO psiToRho 1.3935 12 0.12 18.% + Charge mix_rho 0.85107 11 0.077 11.% + LOOP_ions force_stress 0.60681 1 0.61 8.0% + Force_Stress_LCAO getForceStress 0.60676 1 0.61 8.0% + Force_LCAO_gamma ftable_gamma 0.38309 1 0.38 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.37500 1 0.37 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:11 2022 + Finish Time : Wed Sep 28 11:02:18 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0f02386ed76d276768519daad7bb4078f184a5b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124203 ima = 3.68186e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122638018333 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111966584958 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011224215959 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112586479588 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112496012843 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112548314486 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112535948277 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011253839384 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112538141631 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112538056199 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112538032624 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112538022159 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5ebc50a52505fac810c4f96e918ad9d3d5b7f59d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.912427523212 19.398584419675 5.058091523342 0 0 0 +H +0.0 +2 +-10.128886352988 21.011398474189 5.290748153785 0 0 0 +-12.422126824342 19.835925110136 4.437062267889 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/conv new file mode 100644 index 0000000000000000000000000000000000000000..0e6989d35b0b38406c47c1a119e5c90848f74c2a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/conv @@ -0,0 +1 @@ +228 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..648709cc1395fed23e8f48dc5d97a9d17de2a5e3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751934122 0.0128722591 1.308585999 1.401426019 1.472374079 0.009495495681 0.01910870313 0.03914848249 +6.638610383e-20 0.001250300666 0.003073533266 0.01413207066 0.05184817113 -4.254931859e-19 3.039266298e-06 7.720663446e-06 +0.001586416624 0.005919689897 + +H atom_index 1 n_descriptor 18 +1.266520214 0.03394173848 0.1163605202 0.1572665381 0.3245353494 0.02386485537 0.02919383797 0.03707221302 +1.112762341e-17 6.03361671e-05 0.1093327248 0.1173697613 0.1354459597 -3.4683e-18 2.860589908e-06 0.0133499393 +0.02841278658 0.03153950926 + +H atom_index 2 n_descriptor 18 +1.358435799 0.03190385245 0.1557480132 0.2084780815 0.3476493963 0.02816567237 0.03425400555 0.03814550371 +-2.08067028e-17 6.903970232e-05 0.1042534861 0.1488835321 0.1778617513 1.752884459e-17 1.226924259e-07 0.01733289992 +0.03078922161 0.03424279412 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3c06673ece8147745fb34c704000302bc18a15df Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:11 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087674 SEC) : SETUP UNITCELL + DONE(0.0962799 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115272 SEC) : INIT PLANEWAVE + DONE(0.165772 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446765 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.649372e+02 0.000000e+00 2.212e-01 5.556e-01 + GE2 -4.662029e+02 -1.265667e+00 9.677e-02 4.977e-01 + GE3 -4.662055e+02 -2.578782e-03 6.132e-02 5.691e-01 + GE4 -4.662071e+02 -1.613033e-03 2.218e-03 4.324e-01 + GE5 -4.662059e+02 1.200775e-03 9.620e-04 4.338e-01 + GE6 -4.662067e+02 -8.497325e-04 2.309e-04 4.260e-01 + GE7 -4.662064e+02 3.326963e-04 4.622e-05 4.212e-01 + GE8 -4.662065e+02 -8.498466e-05 1.716e-05 4.045e-01 + GE9 -4.662065e+02 1.505155e-05 2.435e-06 4.075e-01 + GE10 -4.662065e+02 -8.020623e-07 7.099e-07 4.086e-01 + GE11 -4.662065e+02 -3.371408e-07 2.076e-07 4.068e-01 + GE12 -4.662065e+02 -7.839773e-08 1.029e-08 3.401e-01 +E_delta_band = -7.49872089e-02 Ry = -1.02025332e+00 eV +E_delta_NN= -1.97049069e-01 Ry = -2.68099013e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6019 11 0.69 1e+02 % + Run_lcao lcao_line 7.592 1 7.6 1e+02 % + Potential init_pot 0.28552 2 0.14 3.8 % + PW_Basis recip2real 0.30286 17 0.018 4 % + PW_Basis gathers_scatterp 0.12599 17 0.0074 1.7 % + Potential v_of_rho 1.0793 14 0.077 14 % + XC_Functional v_xc 0.31601 15 0.021 4.2 % + H_Hartree_pw v_hartree 0.71801 14 0.051 9.4 % + PW_Basis real2recip 0.69911 41 0.017 9.2 % + PW_Basis gatherp_scatters 0.26744 41 0.0065 3.5 % + ORB_control set_orb_tables 1.0933 1 1.1 14 % + ORB_gen_tables gen_tables 1.0933 1 1.1 14 % + ORB_table_phi init_Table 0.47428 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.4691 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18394 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18237 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24826 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.2463 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9736 1 6 79 % + ESolver_KS_LCAO Run 5.3666 1 5.4 71 % + HSolverLCAO solve 2.8787 12 0.24 38 % + HamiltLCAO updateHk 1.467 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.4303 12 0.12 19 % + Gint_interface cal_gint 2.7243 25 0.11 36 % + Gint_Gamma distri_vl 2.8 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.8024 14 0.41 76 % + LCAO_gen_fixedH add_v_delta 2.6557 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6557 6 0.44 35 % + ElecStateLCAO psiToRho 1.3935 12 0.12 18 % + Charge mix_rho 0.85107 11 0.077 11 % + LOOP_ions force_stress 0.60681 1 0.61 8 % + Force_Stress_LCAO getForceStress 0.60676 1 0.61 8 % + Force_LCAO_gamma ftable_gamma 0.38309 1 0.38 5 % + Force_LCAO_gamma cal_fvl_dphi 0.375 1 0.37 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:11 2022 + FINISH Time : Wed Sep 28 11:02:18 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/228/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..55b0ea85e9e00475535c970e67c6434269906b94 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.614188 0.699274 0.177874 +H 0.64305 0.759081 0.180659 +H 0.547907 0.712693 0.186952 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..61077e9cfe9f1143ae3880afbc64ac8c0966258f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9903 2 + 2 -12.7731 2 + 3 -9.08483 2 + 4 -6.67862 2 + 5 1.02759 0 + 6 3.97238 0 + 7 11.1471 0 + 8 11.3964 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..5bbd22212ef5bd65a21c14562e88d2cdaf7c5a47 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/running_scf.log @@ -0,0 +1,802 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:43 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.197271899 19.5796755597 4.98047888176 0 0 0 0 + tauc_H1 18.0054107479 21.2542585007 5.05845715947 0 0 0 0 + tauc_H2 15.3414070796 19.9553995571 5.23464929825 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.102376287421 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.102736227562 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.120688571294 (SEC) + + DONE : INIT CHARGE Time : 0.163538511893 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446218 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000496 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00172 + + Density error is 0.21155822822 + + Energy Rydberg eV + E_KohnSham -34.1912418027 -465.195710212 + E_Harris -34.3756152769 -467.704240022 + E_Fermi -0.386672278417 -5.26094624512 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000740577108753 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00135881265393 + + Density error is 0.098823563099 + + Energy Rydberg eV + E_KohnSham -34.2790197743 -466.389990784 + E_Harris -34.2861227391 -466.48663158 + E_Fermi -0.197953693786 -2.69329817564 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000713981325776 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125387467073 + + Density error is 0.0637430342593 + + Energy Rydberg eV + E_KohnSham -34.2794087861 -466.395283562 + E_Harris -34.2839604436 -466.457212039 + E_Fermi -0.191000106938 -2.59868977296 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000692408246226 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104651342844 + + Density error is 0.00198475008152 + + Energy Rydberg eV + E_KohnSham -34.2793169881 -466.394034586 + E_Harris -34.2793196705 -466.394071082 + E_Fermi -0.155824093219 -2.12009555346 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000692676047365 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104428992398 + + Density error is 0.000912050591952 + + Energy Rydberg eV + E_KohnSham -34.2792861885 -466.393615536 + E_Harris -34.2792863771 -466.393618103 + E_Fermi -0.155720368681 -2.11868430873 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000692516628667 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104122787032 + + Density error is 0.000183105652848 + + Energy Rydberg eV + E_KohnSham -34.2792986147 -466.393784603 + E_Harris -34.2792986069 -466.393784497 + E_Fermi -0.155315270706 -2.11317266801 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00069266810561 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104107611311 + + Density error is 2.59356707787e-05 + + Energy Rydberg eV + E_KohnSham -34.2792955808 -466.393743326 + E_Harris -34.2792955828 -466.393743352 + E_Fermi -0.15527133405 -2.11257487914 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000692628446908 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010410372432 + + Density error is 1.19867670929e-05 + + Energy Rydberg eV + E_KohnSham -34.2792978715 -466.393774492 + E_Harris -34.2792978722 -466.393774501 + E_Fermi -0.15528590124 -2.11277307593 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000692636187094 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104101897032 + + Density error is 1.80568056748e-06 + + Energy Rydberg eV + E_KohnSham -34.2792969291 -466.39376167 + E_Harris -34.2792969291 -466.39376167 + E_Fermi -0.155274497561 -2.11261792091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000692636198981 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104101330191 + + Density error is 4.16992969598e-07 + + Energy Rydberg eV + E_KohnSham -34.2792971321 -466.393764431 + E_Harris -34.2792971321 -466.393764431 + E_Fermi -0.15527306368 -2.11259841197 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000692636841714 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104101340847 + + Density error is 1.22966837657e-07 + + Energy Rydberg eV + E_KohnSham -34.2792971418 -466.393764564 + E_Harris -34.2792971418 -466.393764564 + E_Fermi -0.155272851521 -2.11259552539 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000692637027417 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010410131797 + + Density error is 1.12743981064e-08 + + Energy Rydberg eV + E_KohnSham -34.2792971469 -466.393764633 + E_Harris -34.2792971469 -466.393764633 + E_band -7.86830857096 -107.053830187 + E_one_elec -68.6625145649 -934.20143709 + E_Hartree +35.7434712231 +486.314874934 + E_xc -8.16204252763 -111.050285694 + E_Ewald +6.92739172749 +94.2519997719 + E_demet -1.64902089129e-60 -2.24360802426e-59 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193693712118 -2.63533815158 + E_Fermi -0.15527274169 -2.11259403107 + + charge density convergence is achieved + final etot is -466.393764633 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9903 2.00000 + 2 -12.7731 2.00000 + 3 -9.08483 2.00000 + 4 -6.67862 2.00000 + 5 1.02759 0.00000 + 6 3.97238 0.00000 + 7 11.1471 0.00000 + 8 11.3964 0.00000 + + EFERMI = -2.112594031067322 eV + OUT.ABACUS/ final etot is -466.3937646325480 eV + correction force for each atom along direction 1 is -2.96842e-05 + correction force for each atom along direction 2 is 0.000139250 + correction force for each atom along direction 3 is 0.000168765 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.2856911 +0.61066645 +0.21965666 + H1 -0.22013961 -0.35042517 -0.014232606 + H2 +1.5058307 -0.26024127 -0.20542405 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3937646325480 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4646 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4554 1 7.5 1.e+02% + Potential init_pot 0.28309 2 0.14 3.8% + PW_Basis recip2real 0.28530 17 0.017 3.8% + PW_Basis gathers_scatterp 0.12913 17 0.0076 1.7% + Potential v_of_rho 1.0401 14 0.074 14.% + XC_Functional v_xc 0.31351 15 0.021 4.2% + H_Hartree_pw v_hartree 0.68065 14 0.049 9.1% + PW_Basis real2recip 0.73779 41 0.018 9.9% + PW_Basis gatherp_scatters 0.28508 41 0.0070 3.8% + ORB_control read_orb_first 0.12616 1 0.13 1.7% + LCAO_Orbitals Read_Orbitals 0.12616 1 0.13 1.7% + ORB_control set_orb_tables 1.0944 1 1.1 15.% + ORB_gen_tables gen_tables 1.0944 1 1.1 15.% + ORB_table_phi init_Table 0.47466 1 0.47 6.4% + ORB_table_phi cal_ST_Phi12_R 0.46948 126 0.0037 6.3% + ORB_table_beta init_Table_Beta 0.18300 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18143 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24955 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24757 66 0.0038 3.3% + LOOP_ions opt_ions 5.7814 1 5.8 77.% + ESolver_KS_LCAO Run 5.2517 1 5.3 70.% + HSolverLCAO solve 2.6110 12 0.22 35.% + HamiltLCAO updateHk 1.3583 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.3287 12 0.11 18.% + Gint_interface cal_gint 2.3783 25 0.095 32.% + Gint_Gamma distri_vl 2.7381 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.6271 14 0.40 75.% + LCAO_gen_fixedH add_v_delta 2.5900 6 0.43 35.% + LCAO_DESCRIPTOR add_v_delta 2.5901 6 0.43 35.% + ElecStateLCAO psiToRho 1.2298 12 0.10 16.% + Charge mix_rho 0.99237 11 0.090 13.% + LOOP_ions force_stress 0.52957 1 0.53 7.1% + Force_Stress_LCAO getForceStress 0.52954 1 0.53 7.1% + Force_LCAO_gamma ftable_gamma 0.31566 1 0.32 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.30757 1 0.31 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:43 2022 + Finish Time : Wed Sep 28 11:10:50 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..53117f5fdd6a7819cda62130cdb3d18c1446ac21 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123695 ima = 3.67612e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123510650162 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112157566243 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112902475292 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113094109589 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113080534481 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113089071497 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113085701647 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113087519473 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113086935766 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113086895098 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011308687595 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113086870198 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/STRU new file mode 100644 index 0000000000000000000000000000000000000000..89ff79a3c0a9a2bb76e57aab73e5026682c4d110 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.802728100973 19.579675559699 4.980478881768 0 0 0 +H +0.0 +2 +-9.994589252067 21.254258500751 5.058457159457 0 0 0 +-12.658592920421 19.955399557061 5.234649298265 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/conv new file mode 100644 index 0000000000000000000000000000000000000000..637a321ebc4e92a40d515419dfb4a2490cd7865a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/conv @@ -0,0 +1 @@ +229 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e762cb2060c06b4a66da8f24758d23ba423ffa56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749906774 0.01243778572 1.246717541 1.340495403 1.468065885 0.008397465407 0.01795572721 0.03908657556 +-2.3376856e-19 0.0009054255191 0.002408397908 0.01153321939 0.04174752945 2.752932257e-21 1.644280479e-06 5.061077241e-06 +0.001617248608 0.005861612711 + +H atom_index 1 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/log.scf @@ -0,0 +1,104 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:43 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.102398 SEC) : SETUP UNITCELL + DONE(0.102751 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.120709 SEC) : INIT PLANEWAVE + DONE(0.163673 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446282 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651957e+02 0.000000e+00 2.116e-01 5.335e-01 + GE2 -4.663900e+02 -1.194281e+00 9.882e-02 4.947e-01 + GE3 -4.663953e+02 -5.292778e-03 6.374e-02 5.654e-01 + GE4 -4.663940e+02 1.248977e-03 1.985e-03 4.226e-01 + GE5 -4.663936e+02 4.190500e-04 9.121e-04 4.224e-01 + GE6 -4.663938e+02 -1.690671e-04 1.831e-04 4.167e-01 + GE7 -4.663937e+02 4.127712e-05 2.594e-05 4.020e-01 + GE8 -4.663938e+02 -3.116591e-05 1.199e-05 4.008e-01 + GE9 -4.663938e+02 1.282186e-05 1.806e-06 4.017e-01 + GE10 -4.663938e+02 -2.761284e-06 4.170e-07 4.003e-01 + GE11 -4.663938e+02 -1.325783e-07 1.230e-07 4.008e-01 + GE12 -4.663938e+02 -6.885878e-08 1.127e-08 3.285e-01 +E_delta_band = -6.80907071e-02 Ry = -9.26421598e-01 eV +E_delta_NN= -1.93693712e-01 Ry = -2.63533815e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4646 11 0.68 1e+02 % + Run_lcao lcao_line 7.4554 1 7.5 1e+02 % + Potential init_pot 0.28309 2 0.14 3.8 % + PW_Basis recip2real 0.2853 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.12913 17 0.0076 1.7 % + Potential v_of_rho 1.0401 14 0.074 14 % + XC_Functional v_xc 0.31351 15 0.021 4.2 % + H_Hartree_pw v_hartree 0.68065 14 0.049 9.1 % + PW_Basis real2recip 0.73779 41 0.018 9.9 % + PW_Basis gatherp_scatters 0.28508 41 0.007 3.8 % + ORB_control read_orb_first 0.12616 1 0.13 1.7 % + LCAO_Orbitals Read_Orbitals 0.12616 1 0.13 1.7 % + ORB_control set_orb_tables 1.0944 1 1.1 15 % + ORB_gen_tables gen_tables 1.0944 1 1.1 15 % + ORB_table_phi init_Table 0.47466 1 0.47 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.46948 126 0.0037 6.3 % + ORB_table_beta init_Table_Beta 0.183 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18143 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24955 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24757 66 0.0038 3.3 % + LOOP_ions opt_ions 5.7814 1 5.8 77 % + ESolver_KS_LCAO Run 5.2517 1 5.3 70 % + HSolverLCAO solve 2.611 12 0.22 35 % + HamiltLCAO updateHk 1.3583 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.3287 12 0.11 18 % + Gint_interface cal_gint 2.3783 25 0.095 32 % + Gint_Gamma distri_vl 2.7381 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.6271 14 0.4 75 % + LCAO_gen_fixedH add_v_delta 2.59 6 0.43 35 % + LCAO_DESCRIPTOR add_v_delta 2.5901 6 0.43 35 % + ElecStateLCAO psiToRho 1.2298 12 0.1 16 % + Charge mix_rho 0.99237 11 0.09 13 % + LOOP_ions force_stress 0.52957 1 0.53 7.1 % + Force_Stress_LCAO getForceStress 0.52954 1 0.53 7.1 % + Force_LCAO_gamma ftable_gamma 0.31566 1 0.32 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.30757 1 0.31 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:43 2022 + FINISH Time : Wed Sep 28 11:10:50 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/229/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4a1097cadc471447073466204741a219c87db5dc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.517813 0.33308 0.442663 +H 0.566159 0.333478 0.400039 +H 0.47616 0.297789 0.408964 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bc7b6d1f5975e187c1f26f69641954c5c664a783 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6265 2 + 2 -12.9105 2 + 3 -9.4546 2 + 4 -6.81834 2 + 5 1.4279 0 + 6 4.69468 0 + 7 11.0156 0 + 8 11.2987 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4138cff96f726629be60a68aa71657f039d3d818 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:09 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.4987722697 9.3262393381 12.3945753363 0 0 0 0 + tauc_H1 15.8524621561 9.33737295206 11.2010803564 0 0 0 0 + tauc_H2 13.3324813245 8.33808175341 11.450981219 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0982192582163 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.111921910012 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.130014935831 (SEC) + + DONE : INIT CHARGE Time : 0.174303075641 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.45379 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124 + + Density error is 0.216629351332 + + Energy Rydberg eV + E_KohnSham -34.185455842 -465.116988179 + E_Harris -34.3816042627 -467.785724353 + E_Fermi -0.419572729044 -5.70857984041 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00140084507814 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125770512913 + + Density error is 0.0973174787803 + + Energy Rydberg eV + E_KohnSham -34.2768956605 -466.361090735 + E_Harris -34.2836551508 -466.453058318 + E_Fermi -0.227192336032 -3.09111031197 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00132248694399 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117201837126 + + Density error is 0.0622536899686 + + Energy Rydberg eV + E_KohnSham -34.2772375735 -466.3657427 + E_Harris -34.2815997549 -466.425093222 + E_Fermi -0.214265172278 -2.91522722593 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120398928995 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010333840464 + + Density error is 0.00201070845379 + + Energy Rydberg eV + E_KohnSham -34.2772592854 -466.366038104 + E_Harris -34.277261044 -466.366062032 + E_Fermi -0.178141942224 -2.42374546703 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120725626555 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103492812404 + + Density error is 0.000977776759207 + + Energy Rydberg eV + E_KohnSham -34.27718075 -466.364969576 + E_Harris -34.2771836177 -466.365008593 + E_Fermi -0.177220421763 -2.41120753794 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120515761771 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103286371326 + + Density error is 0.000110749678521 + + Energy Rydberg eV + E_KohnSham -34.2772334287 -466.365686306 + E_Harris -34.2772334512 -466.365686613 + E_Fermi -0.177380354669 -2.41338353676 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120492900977 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103250402442 + + Density error is 4.38382280547e-05 + + Energy Rydberg eV + E_KohnSham -34.2772168823 -466.365461181 + E_Harris -34.277216893 -466.365461327 + E_Fermi -0.177259315862 -2.4117367193 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120488240127 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103249792008 + + Density error is 2.36219606794e-05 + + Energy Rydberg eV + E_KohnSham -34.2772193959 -466.365495381 + E_Harris -34.2772193983 -466.365495413 + E_Fermi -0.177318699631 -2.41254467694 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012048715953 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103247576667 + + Density error is 2.0341546273e-06 + + Energy Rydberg eV + E_KohnSham -34.2772176517 -466.365471649 + E_Harris -34.2772176517 -466.36547165 + E_Fermi -0.17729287122 -2.41219326337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120487159963 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103247543142 + + Density error is 2.26541082683e-07 + + Energy Rydberg eV + E_KohnSham -34.2772179929 -466.365476291 + E_Harris -34.2772179929 -466.365476291 + E_Fermi -0.177290947771 -2.4121670935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120487228544 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103247613156 + + Density error is 5.22817509374e-08 + + Energy Rydberg eV + E_KohnSham -34.2772180271 -466.365476757 + E_Harris -34.2772180271 -466.365476757 + E_band -8.05690577352 -109.619826769 + E_one_elec -69.7400240785 -948.861706125 + E_Hartree +36.2405990559 +493.078646094 + E_xc -8.24189479516 -112.136731531 + E_Ewald +7.58746028026 +103.23269316 + E_demet -1.45902283219e-88 -1.98510240299e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195683699 -2.66241331211 + E_Fermi -0.177290937118 -2.41216694856 + + charge density convergence is achieved + final etot is -466.365476757 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6265 2.00000 + 2 -12.9105 2.00000 + 3 -9.45460 2.00000 + 4 -6.81834 2.00000 + 5 1.42790 0.00000 + 6 4.69468 0.00000 + 7 11.0156 0.00000 + 8 11.2987 0.00000 + + EFERMI = -2.412166948558789 eV + OUT.ABACUS/ final etot is -466.3654767566817 eV + correction force for each atom along direction 1 is -3.93340e-05 + correction force for each atom along direction 2 is 1.65997e-05 + correction force for each atom along direction 3 is -6.29401e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.10648882 +0.46749992 +0.83957057 + H1 +1.2600417 +0.32560705 -0.47273630 + H2 -1.3665306 -0.79310697 -0.36683426 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3654767566817 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6653 11 0.70 1.0e+02% + Run_lcao lcao_line 7.6559 1 7.7 1.e+02% + Potential init_pot 0.28091 2 0.14 3.7% + PW_Basis recip2real 0.25662 16 0.016 3.3% + PW_Basis gathers_scatterp 0.11874 16 0.0074 1.5% + Potential v_of_rho 1.0574 13 0.081 14.% + XC_Functional v_xc 0.38473 14 0.027 5.0% + H_Hartree_pw v_hartree 0.63496 13 0.049 8.3% + PW_Basis real2recip 0.71122 38 0.019 9.3% + PW_Basis gatherp_scatters 0.32646 38 0.0086 4.3% + ORB_control set_orb_tables 1.0967 1 1.1 14.% + ORB_gen_tables gen_tables 1.0967 1 1.1 14.% + ORB_table_phi init_Table 0.47431 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46919 126 0.0037 6.1% + ORB_table_beta init_Table_Beta 0.18274 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18126 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.25049 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24852 66 0.0038 3.2% + LOOP_ions opt_ions 6.0283 1 6.0 79.% + ESolver_KS_LCAO Run 5.4460 1 5.4 71.% + HSolverLCAO solve 2.9630 11 0.27 39.% + HamiltLCAO updateHk 1.4931 11 0.14 19.% + LCAO_Hamilt cal_Hgamma 1.4657 11 0.13 19.% + Gint_interface cal_gint 0.21012 23 0.0091 2.7% + Gint_Gamma distri_vl_value 0.96135 11 0.087 13.% + Gint_Gamma distri_vl 2.6181 6 0.44 34.% + LCAO_Deepks cal_projected_DM 5.5881 13 0.43 73.% + LCAO_gen_fixedH add_v_delta 2.4878 6 0.41 32.% + LCAO_DESCRIPTOR add_v_delta 2.4879 6 0.41 32.% + ElecStateLCAO psiToRho 1.4250 11 0.13 19.% + Charge mix_rho 0.85746 10 0.086 11.% + LOOP_ions force_stress 0.58214 1 0.58 7.6% + Force_Stress_LCAO getForceStress 0.58211 1 0.58 7.6% + Force_LCAO_gamma ftable_gamma 0.36788 1 0.37 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:09 2022 + Finish Time : Wed Sep 28 11:06:17 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..bc95a8e2cc2146695874a2d4d375dc9b2e0ec92b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124287 ima = 3.67501e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122491646338 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001113488461 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111864376247 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001121679294 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112090010504 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112132082862 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112129496276 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112132834227 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112131847612 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112131759008 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112131747906 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/STRU new file mode 100644 index 0000000000000000000000000000000000000000..bb1c611bf4406abbc9bd8b765293d566162d5359 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.501227730270 9.326239338085 12.394575336298 0 0 0 +H +0.0 +2 +-12.147537843938 9.337372952077 11.201080356418 0 0 0 +-14.667518675466 8.338081753424 11.450981219061 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/conv new file mode 100644 index 0000000000000000000000000000000000000000..45f3109f6cb40d2bef132687b8c3a292288244c8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/conv @@ -0,0 +1 @@ +23 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..2655ebf841513d6dbed4436836969cbf041fc1f9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753938014 0.01291426396 1.288116114 1.367541466 1.470664045 0.009605749656 0.01721089272 0.03914436398 +-2.030199686e-19 0.001001676723 0.00299375534 0.01390266572 0.04920758761 -1.032109646e-18 3.169409796e-06 8.028322517e-06 +0.001596510277 0.006171721296 + +H atom_index 1 n_descriptor 18 +1.271684811 0.03417706031 0.1195943293 0.1598681481 0.3261245978 0.02446635942 0.02949130682 0.03737852517 +3.063683383e-18 5.623585526e-05 0.1082926001 0.1184267444 0.1372682437 -9.079838619e-19 1.907052737e-06 0.01341322702 +0.02829552626 0.03171332502 + +H atom_index 2 n_descriptor 18 +1.278211547 0.03396847476 0.1221042412 0.1631269916 0.3281033554 0.02479163213 0.02986892173 0.03724644663 +1.223243147e-17 5.686126125e-05 0.1086554538 0.1199491825 0.1400422096 -3.2242148e-18 1.563739188e-06 0.01346683248 +0.0285132121 0.03197831531 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..db9d59b4f002bafe5d47c38bcc2b3e954241f3e1 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:09 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0982423 SEC) : SETUP UNITCELL + DONE(0.111941 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.130038 SEC) : INIT PLANEWAVE + DONE(0.174449 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.453856 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651170e+02 0.000000e+00 2.166e-01 5.811e-01 + GE2 -4.663611e+02 -1.244103e+00 9.732e-02 5.479e-01 + GE3 -4.663657e+02 -4.651965e-03 6.225e-02 6.221e-01 + GE4 -4.663660e+02 -2.954048e-04 2.011e-03 4.791e-01 + GE5 -4.663650e+02 1.068529e-03 9.778e-04 4.776e-01 + GE6 -4.663657e+02 -7.167305e-04 1.107e-04 4.711e-01 + GE7 -4.663655e+02 2.251248e-04 4.384e-05 4.659e-01 + GE8 -4.663655e+02 -3.419966e-05 2.362e-05 4.546e-01 + GE9 -4.663655e+02 2.373149e-05 2.034e-06 4.532e-01 + GE10 -4.663655e+02 -4.641693e-06 2.265e-07 4.533e-01 + GE11 -4.663655e+02 -4.655036e-07 5.228e-08 3.707e-01 +E_delta_band = -7.23252095e-02 Ry = -9.84034958e-01 eV +E_delta_NN= -1.95683699e-01 Ry = -2.66241331e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6653 11 0.7 1e+02 % + Run_lcao lcao_line 7.6559 1 7.7 1e+02 % + Potential init_pot 0.28091 2 0.14 3.7 % + PW_Basis recip2real 0.25662 16 0.016 3.3 % + PW_Basis gathers_scatterp 0.11874 16 0.0074 1.5 % + Potential v_of_rho 1.0574 13 0.081 14 % + XC_Functional v_xc 0.38473 14 0.027 5 % + H_Hartree_pw v_hartree 0.63496 13 0.049 8.3 % + PW_Basis real2recip 0.71122 38 0.019 9.3 % + PW_Basis gatherp_scatters 0.32646 38 0.0086 4.3 % + ORB_control set_orb_tables 1.0967 1 1.1 14 % + ORB_gen_tables gen_tables 1.0967 1 1.1 14 % + ORB_table_phi init_Table 0.47431 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.46919 126 0.0037 6.1 % + ORB_table_beta init_Table_Beta 0.18274 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18126 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.25049 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24852 66 0.0038 3.2 % + LOOP_ions opt_ions 6.0283 1 6 79 % + ESolver_KS_LCAO Run 5.446 1 5.4 71 % + HSolverLCAO solve 2.963 11 0.27 39 % + HamiltLCAO updateHk 1.4931 11 0.14 19 % + LCAO_Hamilt cal_Hgamma 1.4657 11 0.13 19 % + Gint_interface cal_gint 0.21012 23 0.0091 2.7 % + Gint_Gamma distri_vl_value 0.96135 11 0.087 13 % + Gint_Gamma distri_vl 2.6181 6 0.44 34 % + LCAO_Deepks cal_projected_DM 5.5881 13 0.43 73 % + LCAO_gen_fixedH add_v_delta 2.4878 6 0.41 32 % + LCAO_DESCRIPTOR add_v_delta 2.4879 6 0.41 32 % + ElecStateLCAO psiToRho 1.425 11 0.13 19 % + Charge mix_rho 0.85746 10 0.086 11 % + LOOP_ions force_stress 0.58214 1 0.58 7.6 % + Force_Stress_LCAO getForceStress 0.58211 1 0.58 7.6 % + Force_LCAO_gamma ftable_gamma 0.36788 1 0.37 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:09 2022 + FINISH Time : Wed Sep 28 11:06:17 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/23/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e935ac37b69a14c9220da644695b0d31817ec128 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.621818 0.720501 0.16458 +H 0.648287 0.778395 0.186137 +H 0.561388 0.725528 0.180339 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..29a891d50ff36bc4b706df1d26152bfb56b59530 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4273 2 + 2 -13.0851 2 + 3 -9.17336 2 + 4 -6.7717 2 + 5 1.31983 0 + 6 4.59685 0 + 7 11.0454 0 + 8 11.2873 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..cf7b819ee9d95089c0d86c53c111d720de3bc0a5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:07 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.4109015725 20.1740394684 4.60824020685 0 0 0 0 + tauc_H1 18.15203555 21.7950463327 5.21184864274 0 0 0 0 + tauc_H2 15.7188640888 20.3147821939 5.04948434635 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0883401355007 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0969821739241 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115239984542 (SEC) + + DONE : INIT CHARGE Time : 0.165221450516 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447594 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000633 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00197 + + Density error is 0.216183747019 + + Energy Rydberg eV + E_KohnSham -34.1852785989 -465.114576662 + E_Harris -34.3803603064 -467.76879946 + E_Fermi -0.413359708878 -5.62404736436 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000950342948586 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0015653047 + + Density error is 0.0977525427936 + + Energy Rydberg eV + E_KohnSham -34.2758976573 -466.347512204 + E_Harris -34.282628309 -466.439087419 + E_Fermi -0.221381395455 -3.01204840938 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000911385359932 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00142739133924 + + Density error is 0.0625698463874 + + Energy Rydberg eV + E_KohnSham -34.2761721608 -466.351247015 + E_Harris -34.2805053162 -466.41020262 + E_Fermi -0.209017257493 -2.84382568223 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000864565668193 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118541484845 + + Density error is 0.00202071455833 + + Energy Rydberg eV + E_KohnSham -34.2761807515 -466.351363899 + E_Harris -34.2761828163 -466.351391991 + E_Fermi -0.173206219468 -2.3565915138 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000868326741058 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118344014067 + + Density error is 0.000883818151973 + + Energy Rydberg eV + E_KohnSham -34.2761182778 -466.3505139 + E_Harris -34.2761195807 -466.350531626 + E_Fermi -0.172388014542 -2.34545926468 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000867265416714 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118082831036 + + Density error is 0.000166579588112 + + Energy Rydberg eV + E_KohnSham -34.2761577558 -466.351051026 + E_Harris -34.2761578286 -466.351052016 + E_Fermi -0.172443166041 -2.34620963932 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000867390773627 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118057716281 + + Density error is 4.21236156983e-05 + + Energy Rydberg eV + E_KohnSham -34.2761428205 -466.35084782 + E_Harris -34.2761428291 -466.350847938 + E_Fermi -0.172304307448 -2.34432037124 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000867340842879 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118058153749 + + Density error is 2.1071669517e-05 + + Energy Rydberg eV + E_KohnSham -34.2761476185 -466.350913101 + E_Harris -34.2761476205 -466.350913128 + E_Fermi -0.172348972266 -2.34492806727 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000867351096742 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118053982902 + + Density error is 2.81054753879e-06 + + Energy Rydberg eV + E_KohnSham -34.2761459602 -466.350890539 + E_Harris -34.2761459603 -466.35089054 + E_Fermi -0.172327916275 -2.34464158581 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000867351008333 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118052997771 + + Density error is 1.64530381521e-07 + + Energy Rydberg eV + E_KohnSham -34.2761462568 -466.350894573 + E_Harris -34.2761462568 -466.350894573 + E_Fermi -0.172324812061 -2.34459935081 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000867351524913 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118053047288 + + Density error is 7.91397950978e-08 + + Energy Rydberg eV + E_KohnSham -34.2761463098 -466.350895296 + E_Harris -34.2761463098 -466.350895296 + E_band -8.00509574451 -108.914915161 + E_one_elec -69.5086302123 -945.713431062 + E_Hartree +36.1405530332 +491.717450122 + E_xc -8.22633793313 -111.925069564 + E_Ewald +7.44216952021 +101.255910957 + E_demet -1.9693023895e-81 -2.67937335822e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195295228951 -2.65712790595 + E_Fermi -0.1723248323 -2.34459962617 + + charge density convergence is achieved + final etot is -466.350895296 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4273 2.00000 + 2 -13.0851 2.00000 + 3 -9.17336 2.00000 + 4 -6.77170 2.00000 + 5 1.31983 0.00000 + 6 4.59685 0.00000 + 7 11.0454 0.00000 + 8 11.2873 0.00000 + + EFERMI = -2.344599626170012 eV + OUT.ABACUS/ final etot is -466.3508952955582 eV + correction force for each atom along direction 1 is -3.54302e-05 + correction force for each atom along direction 2 is 1.43881e-05 + correction force for each atom along direction 3 is -2.57017e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +3.0111796 +0.71470422 -0.32998349 + H1 -0.28028329 -0.84209005 -0.33587733 + H2 -2.7308963 +0.12738583 +0.66586082 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3508952955582 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2228 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2130 1 7.2 1.e+02% + Potential init_pot 0.28655 2 0.14 4.0% + PW_Basis recip2real 0.28341 16 0.018 3.9% + PW_Basis gathers_scatterp 0.12233 16 0.0076 1.7% + Potential v_of_rho 1.0029 13 0.077 14.% + XC_Functional v_xc 0.30032 14 0.021 4.2% + H_Hartree_pw v_hartree 0.65960 13 0.051 9.1% + PW_Basis real2recip 0.65422 38 0.017 9.1% + PW_Basis gatherp_scatters 0.24934 38 0.0066 3.5% + ORB_control set_orb_tables 1.0946 1 1.1 15.% + ORB_gen_tables gen_tables 1.0946 1 1.1 15.% + ORB_table_phi init_Table 0.47675 1 0.48 6.6% + ORB_table_phi cal_ST_Phi12_R 0.47163 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18491 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18335 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24697 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24503 66 0.0037 3.4% + LOOP_ions opt_ions 5.5931 1 5.6 77.% + ESolver_KS_LCAO Run 4.9926 1 5.0 69.% + HSolverLCAO solve 2.7044 11 0.25 37.% + HamiltLCAO updateHk 1.3843 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.3567 11 0.12 19.% + Gint_interface cal_gint 2.5687 23 0.11 36.% + Gint_Gamma distri_vl 2.4010 6 0.40 33.% + LCAO_Deepks cal_projected_DM 5.4233 13 0.42 75.% + LCAO_gen_fixedH add_v_delta 2.2546 6 0.38 31.% + LCAO_DESCRIPTOR add_v_delta 2.2547 6 0.38 31.% + ElecStateLCAO psiToRho 1.3036 11 0.12 18.% + Charge mix_rho 0.78484 10 0.078 11.% + LOOP_ions force_stress 0.60033 1 0.60 8.3% + Force_Stress_LCAO getForceStress 0.60029 1 0.60 8.3% + Force_LCAO_gamma ftable_gamma 0.38068 1 0.38 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.37269 1 0.37 5.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:07 2022 + Finish Time : Wed Sep 28 11:07:14 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..374cbc505d89c93c1d018c6d9f5c8c561a1b02d9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123979 ima = 3.70464e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012306746717 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112075226143 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112582315461 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112847840774 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112793163623 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112825786477 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112817412404 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112820627711 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112819709748 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112819581303 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112819576932 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/STRU new file mode 100644 index 0000000000000000000000000000000000000000..f43cea03ff6fcf6aea4b77366b4f41bbd78adb9a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.589098427459 20.174039468442 4.608240206831 0 0 0 +H +0.0 +2 +-9.847964450018 21.795046332680 5.211848642736 0 0 0 +-12.281135911165 20.314782193871 5.049484346377 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/conv new file mode 100644 index 0000000000000000000000000000000000000000..2c58efe3705b7d7c812bad887ad600d26a7301fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/conv @@ -0,0 +1 @@ +230 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..eb8eb098ca2acd85c60d9763ee84c2c1aac6beca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750154189 0.01269679803 1.273996152 1.37481985 1.470019021 0.008780469682 0.01860435251 0.03907717708 +-3.506455835e-19 0.001079572811 0.002707572101 0.01265476666 0.04661472818 5.000070174e-19 2.193164973e-06 6.300550622e-06 +0.00162139584 0.005924881049 + +H atom_index 1 n_descriptor 18 +1.207699418 0.03573646725 0.0948034655 0.1312859601 0.306145586 0.02041641021 0.02582203793 0.03899859429 +4.928037687e-18 4.40665849e-05 0.09151599142 0.1125268914 0.1134038921 1.003835846e-17 6.192978728e-06 0.01395976928 +0.02488392147 0.02870751783 + +H atom_index 2 n_descriptor 18 +1.308397085 0.03246944086 0.1308314607 0.1793421558 0.3376734727 0.0250944112 0.03163290272 0.0365467171 +-3.302996473e-18 5.354446617e-05 0.1078554159 0.1261680188 0.1537336243 3.608389815e-18 1.003079392e-06 0.01397012954 +0.02845996486 0.03303692915 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..8a309652148c6c1482ff7b88ce6fec28651ca75a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:07 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0883616 SEC) : SETUP UNITCELL + DONE(0.097002 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115261 SEC) : INIT PLANEWAVE + DONE(0.165356 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447661 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651146e+02 0.000000e+00 2.162e-01 5.538e-01 + GE2 -4.663475e+02 -1.232936e+00 9.775e-02 5.007e-01 + GE3 -4.663512e+02 -3.734811e-03 6.257e-02 5.703e-01 + GE4 -4.663514e+02 -1.168835e-04 2.021e-03 4.358e-01 + GE5 -4.663505e+02 8.499989e-04 8.838e-04 4.365e-01 + GE6 -4.663511e+02 -5.371264e-04 1.666e-04 4.306e-01 + GE7 -4.663508e+02 2.032059e-04 4.212e-05 4.204e-01 + GE8 -4.663509e+02 -6.528057e-05 2.107e-05 4.107e-01 + GE9 -4.663509e+02 2.256190e-05 2.811e-06 4.125e-01 + GE10 -4.663509e+02 -4.034201e-06 1.645e-07 4.127e-01 + GE11 -4.663509e+02 -7.222857e-07 7.914e-08 3.464e-01 +E_delta_band = -7.13945111e-02 Ry = -9.71372157e-01 eV +E_delta_NN= -1.95295229e-01 Ry = -2.65712791e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2228 11 0.66 1e+02 % + Run_lcao lcao_line 7.213 1 7.2 1e+02 % + Potential init_pot 0.28655 2 0.14 4 % + PW_Basis recip2real 0.28341 16 0.018 3.9 % + PW_Basis gathers_scatterp 0.12233 16 0.0076 1.7 % + Potential v_of_rho 1.0029 13 0.077 14 % + XC_Functional v_xc 0.30032 14 0.021 4.2 % + H_Hartree_pw v_hartree 0.6596 13 0.051 9.1 % + PW_Basis real2recip 0.65422 38 0.017 9.1 % + PW_Basis gatherp_scatters 0.24934 38 0.0066 3.5 % + ORB_control set_orb_tables 1.0946 1 1.1 15 % + ORB_gen_tables gen_tables 1.0946 1 1.1 15 % + ORB_table_phi init_Table 0.47675 1 0.48 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.47163 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.18491 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18335 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24697 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24503 66 0.0037 3.4 % + LOOP_ions opt_ions 5.5931 1 5.6 77 % + ESolver_KS_LCAO Run 4.9926 1 5 69 % + HSolverLCAO solve 2.7044 11 0.25 37 % + HamiltLCAO updateHk 1.3843 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.3567 11 0.12 19 % + Gint_interface cal_gint 2.5687 23 0.11 36 % + Gint_Gamma distri_vl 2.401 6 0.4 33 % + LCAO_Deepks cal_projected_DM 5.4233 13 0.42 75 % + LCAO_gen_fixedH add_v_delta 2.2546 6 0.38 31 % + LCAO_DESCRIPTOR add_v_delta 2.2547 6 0.38 31 % + ElecStateLCAO psiToRho 1.3036 11 0.12 18 % + Charge mix_rho 0.78484 10 0.078 11 % + LOOP_ions force_stress 0.60033 1 0.6 8.3 % + Force_Stress_LCAO getForceStress 0.60029 1 0.6 8.3 % + Force_LCAO_gamma ftable_gamma 0.38068 1 0.38 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.37269 1 0.37 5.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:07 2022 + FINISH Time : Wed Sep 28 11:07:14 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/230/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..2840f73918c55c27ccf2a817ad8edab082bf40aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.619465 0.743278 0.152602 +H 0.656436 0.794893 0.16726 +H 0.575186 0.740766 0.203922 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..566f2121187923e9a9a04ee870f0b25efdddc2f5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1452 2 + 2 -12.8633 2 + 3 -9.13536 2 + 4 -6.71261 2 + 5 1.1378 0 + 6 4.18641 0 + 7 11.112 0 + 8 11.3641 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a5a09c137f0d82d6b2c297eb7abc8b3703f189e3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:46 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.3450117702 20.8117933835 4.27284505992 0 0 0 0 + tauc_H1 18.3802199461 22.2569970593 4.68329156522 0 0 0 0 + tauc_H2 16.1052097513 20.7414572247 5.70980503024 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0877558877677 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0881716372623 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106409485027 (SEC) + + DONE : INIT CHARGE Time : 0.156612102942 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44783 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000561 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121 + + Density error is 0.213059152608 + + Energy Rydberg eV + E_KohnSham -34.1906829713 -465.188106922 + E_Harris -34.3785367872 -467.743989209 + E_Fermi -0.395475503286 -5.3807202641 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000898462321359 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122019767434 + + Density error is 0.0984204934524 + + Energy Rydberg eV + E_KohnSham -34.2795693524 -466.397468179 + E_Harris -34.2865182006 -466.492012109 + E_Fermi -0.205774690382 -2.79970829338 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00086796279947 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114917156005 + + Density error is 0.0633327488285 + + Energy Rydberg eV + E_KohnSham -34.2799322769 -466.402406019 + E_Harris -34.2844098043 -466.463325905 + E_Fermi -0.197100235957 -2.68168628615 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000839723353592 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010304822162 + + Density error is 0.00196786666638 + + Energy Rydberg eV + E_KohnSham -34.2798729134 -466.401598338 + E_Harris -34.2798742357 -466.401616328 + E_Fermi -0.161667932509 -2.19960506601 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00084015037564 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102937056497 + + Density error is 0.000905289285984 + + Energy Rydberg eV + E_KohnSham -34.279828289 -466.400991192 + E_Harris -34.2798287807 -466.400997882 + E_Fermi -0.161351572272 -2.19530076416 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000839718231965 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102770273185 + + Density error is 0.000161029548048 + + Energy Rydberg eV + E_KohnSham -34.2798513495 -466.401304946 + E_Harris -34.2798513669 -466.401305183 + E_Fermi -0.161080146926 -2.19160783287 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000839937565188 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102778248138 + + Density error is 3.34475340798e-05 + + Energy Rydberg eV + E_KohnSham -34.2798436737 -466.401200511 + E_Harris -34.2798436784 -466.401200576 + E_Fermi -0.161010169673 -2.1906557435 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000839857225748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102771507807 + + Density error is 1.40330339028e-05 + + Energy Rydberg eV + E_KohnSham -34.2798469801 -466.401245498 + E_Harris -34.279846981 -466.401245509 + E_Fermi -0.161036358699 -2.19101206348 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000839862682733 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102770209825 + + Density error is 1.69152995387e-06 + + Energy Rydberg eV + E_KohnSham -34.2798457712 -466.40122905 + E_Harris -34.2798457712 -466.40122905 + E_Fermi -0.161021629599 -2.19081166379 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000839865793526 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102770287441 + + Density error is 3.29862379882e-07 + + Energy Rydberg eV + E_KohnSham -34.2798459764 -466.401231842 + E_Harris -34.2798459764 -466.401231842 + E_Fermi -0.161020424072 -2.19079526176 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000839866382953 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102770331303 + + Density error is 8.88401241424e-08 + + Energy Rydberg eV + E_KohnSham -34.2798459994 -466.401232155 + E_Harris -34.2798459994 -466.401232155 + E_band -7.91674350915 -107.712821329 + E_one_elec -68.9564145519 -938.200151556 + E_Hartree +35.8807777036 +488.18302544 + E_xc -8.18413667104 -111.350891937 + E_Ewald +7.10493330454 +96.6675768518 + E_demet -1.17162221872e-67 -1.59407380779e-66 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194231973051 -2.64266156727 + E_Fermi -0.161020293689 -2.1907934878 + + charge density convergence is achieved + final etot is -466.401232155 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1452 2.00000 + 2 -12.8633 2.00000 + 3 -9.13536 2.00000 + 4 -6.71261 2.00000 + 5 1.13780 0.00000 + 6 4.18641 0.00000 + 7 11.1120 0.00000 + 8 11.3641 0.00000 + + EFERMI = -2.190793487801786 eV + OUT.ABACUS/ final etot is -466.4012321546032 eV + correction force for each atom along direction 1 is -7.81952e-05 + correction force for each atom along direction 2 is -4.90189e-06 + correction force for each atom along direction 3 is 0.000145295 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.1774723 -0.46432939 +0.90554202 + H1 +0.34014280 +0.44207504 +0.095336390 + H2 +0.83732948 +0.022254352 -1.0008784 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4012321546032 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2880 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2779 1 7.3 1.e+02% + Potential init_pot 0.29448 2 0.15 4.0% + PW_Basis recip2real 0.29597 16 0.018 4.1% + PW_Basis gathers_scatterp 0.13216 16 0.0083 1.8% + Charge atomic_rho 0.11083 1 0.11 1.5% + Potential v_of_rho 1.0002 13 0.077 14.% + XC_Functional v_xc 0.29394 14 0.021 4.0% + H_Hartree_pw v_hartree 0.66333 13 0.051 9.1% + PW_Basis real2recip 0.64964 38 0.017 8.9% + PW_Basis gatherp_scatters 0.24851 38 0.0065 3.4% + ORB_control set_orb_tables 1.0957 1 1.1 15.% + ORB_gen_tables gen_tables 1.0956 1 1.1 15.% + ORB_table_phi init_Table 0.47539 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47021 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18587 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18429 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24813 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24618 66 0.0037 3.4% + LOOP_ions opt_ions 5.6557 1 5.7 78.% + ESolver_KS_LCAO Run 5.0581 1 5.1 69.% + HSolverLCAO solve 2.7631 11 0.25 38.% + HamiltLCAO updateHk 1.4113 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.3833 11 0.13 19.% + Gint_interface cal_gint 2.6307 23 0.11 36.% + Gint_Gamma distri_vl 2.4319 6 0.41 33.% + LCAO_Deepks cal_projected_DM 5.4821 13 0.42 75.% + LCAO_gen_fixedH add_v_delta 2.2883 6 0.38 31.% + LCAO_DESCRIPTOR add_v_delta 2.2883 6 0.38 31.% + ElecStateLCAO psiToRho 1.3358 11 0.12 18.% + Charge mix_rho 0.78311 10 0.078 11.% + LOOP_ions force_stress 0.59743 1 0.60 8.2% + Force_Stress_LCAO getForceStress 0.59740 1 0.60 8.2% + Force_LCAO_gamma ftable_gamma 0.37942 1 0.38 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.37154 1 0.37 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:46 2022 + Finish Time : Wed Sep 28 11:13:54 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e45d433f07ffc46d152a50254ab9fa39a8d26cd5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123702 ima = 3.71317e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123302432062 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011203831192 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112707561436 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112927107752 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112897286175 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112915066654 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112909477889 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112911932082 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011291132025 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112911253295 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011291123989 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c31aa6fc70ee8596a289f8765329b7707092f0a7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.654988229741 20.811793383455 4.272845059917 0 0 0 +H +0.0 +2 +-9.619780053925 22.256997059309 4.683291565204 0 0 0 +-11.894790248727 20.741457224732 5.709805030241 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/conv new file mode 100644 index 0000000000000000000000000000000000000000..a04353254d33ee99164c494856cd2dec8e3ac6a8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/conv @@ -0,0 +1 @@ +231 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4b933096473cc2d33b7f44ef66944ec19b43b552 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750178945 0.01256124914 1.256889185 1.351207224 1.468698461 0.008556259576 0.01803240805 0.03907637586 +-1.553255491e-18 0.0009575852947 0.002524581596 0.01197219085 0.04356052684 -6.14611561e-20 1.876744115e-06 5.599481977e-06 +0.001619672835 0.005928134807 + +H atom_index 1 n_descriptor 18 +1.253451739 0.03421928489 0.1092562178 0.1516726103 0.3224207542 0.02233677679 0.02852108412 0.03743381035 +-5.27310436e-17 4.368294559e-05 0.1010943486 0.1153988725 0.1300829796 1.790524064e-18 3.766729892e-06 0.01315452436 +0.02611871098 0.03090960753 + +H atom_index 2 n_descriptor 18 +1.194474293 0.03618001451 0.09027227308 0.1260418806 0.3017056127 0.01958994317 0.02506939885 0.03963216419 +1.169928139e-17 3.84884252e-05 0.08587262513 0.1077160971 0.1132359481 -1.334130739e-18 6.331386371e-06 0.01431045165 +0.02378008067 0.02798300872 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f5347b08edf73fb6c86901e16670e35941bca45e Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..8d669eb88e83cef9d9f094e9a515c02280f56099 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..b6e10a082906d88b7eaaee11ab5e645eabfeb3a2 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..5560131b96eeebceb7897e0630c9b0831f2ae825 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..a32e4405f888df9834a81a76a651bb88991c091a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:46 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0877774 SEC) : SETUP UNITCELL + DONE(0.0881916 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106429 SEC) : INIT PLANEWAVE + DONE(0.156743 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447897 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651881e+02 0.000000e+00 2.131e-01 5.626e-01 + GE2 -4.663975e+02 -1.209361e+00 9.842e-02 5.062e-01 + GE3 -4.664024e+02 -4.937840e-03 6.333e-02 5.770e-01 + GE4 -4.664016e+02 8.076817e-04 1.968e-03 4.390e-01 + GE5 -4.664010e+02 6.071454e-04 9.053e-04 4.408e-01 + GE6 -4.664013e+02 -3.137537e-04 1.610e-04 4.335e-01 + GE7 -4.664012e+02 1.044347e-04 3.345e-05 4.256e-01 + GE8 -4.664012e+02 -4.498616e-05 1.403e-05 4.199e-01 + GE9 -4.664012e+02 1.644805e-05 1.692e-06 4.185e-01 + GE10 -4.664012e+02 -2.792366e-06 3.299e-07 4.203e-01 + GE11 -4.664012e+02 -3.126796e-07 8.884e-08 3.520e-01 +E_delta_band = -6.92261885e-02 Ry = -9.41870614e-01 eV +E_delta_NN= -1.94231973e-01 Ry = -2.64266157e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.288 11 0.66 1e+02 % + Run_lcao lcao_line 7.2779 1 7.3 1e+02 % + Potential init_pot 0.29448 2 0.15 4 % + PW_Basis recip2real 0.29597 16 0.018 4.1 % + PW_Basis gathers_scatterp 0.13216 16 0.0083 1.8 % + Charge atomic_rho 0.11083 1 0.11 1.5 % + Potential v_of_rho 1.0002 13 0.077 14 % + XC_Functional v_xc 0.29394 14 0.021 4 % + H_Hartree_pw v_hartree 0.66333 13 0.051 9.1 % + PW_Basis real2recip 0.64964 38 0.017 8.9 % + PW_Basis gatherp_scatters 0.24851 38 0.0065 3.4 % + ORB_control set_orb_tables 1.0957 1 1.1 15 % + ORB_gen_tables gen_tables 1.0956 1 1.1 15 % + ORB_table_phi init_Table 0.47539 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.47021 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.18587 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18429 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24813 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24618 66 0.0037 3.4 % + LOOP_ions opt_ions 5.6557 1 5.7 78 % + ESolver_KS_LCAO Run 5.0581 1 5.1 69 % + HSolverLCAO solve 2.7631 11 0.25 38 % + HamiltLCAO updateHk 1.4113 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.3833 11 0.13 19 % + Gint_interface cal_gint 2.6307 23 0.11 36 % + Gint_Gamma distri_vl 2.4319 6 0.41 33 % + LCAO_Deepks cal_projected_DM 5.4821 13 0.42 75 % + LCAO_gen_fixedH add_v_delta 2.2883 6 0.38 31 % + LCAO_DESCRIPTOR add_v_delta 2.2883 6 0.38 31 % + ElecStateLCAO psiToRho 1.3358 11 0.12 18 % + Charge mix_rho 0.78311 10 0.078 11 % + LOOP_ions force_stress 0.59743 1 0.6 8.2 % + Force_Stress_LCAO getForceStress 0.5974 1 0.6 8.2 % + Force_LCAO_gamma ftable_gamma 0.37942 1 0.38 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.37154 1 0.37 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:46 2022 + FINISH Time : Wed Sep 28 11:13:54 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/231/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fe309637b2a6c07ea88f307621660f0039ed8708 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.605458 0.749901 0.147791 +H 0.662546 0.78713 0.143243 +H 0.60521 0.724004 0.207703 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..225ceb365ca22106cf5bfe3ea11d997e47bc7aa0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0401 2 + 2 -12.9634 2 + 3 -8.97222 2 + 4 -6.68601 2 + 5 1.09428 0 + 6 4.14223 0 + 7 11.1291 0 + 8 11.3659 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..8f6ec3800deed34abfa59cc7528a8c73dbc3ee75 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:06 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.9528247863 20.9972242436 4.13813590197 0 0 0 0 + tauc_H1 18.5513002871 22.0396482878 4.01079043277 0 0 0 0 + tauc_H2 16.9458917246 20.2721143718 5.81567159258 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871223380366 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0874852926397 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105522012971 (SEC) + + DONE : INIT CHARGE Time : 0.148867703795 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.429355 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000936 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000687 + + Density error is 0.213373576021 + + Energy Rydberg eV + E_KohnSham -34.1892981166 -465.169265006 + E_Harris -34.3776755819 -467.732271909 + E_Fermi -0.392656216493 -5.34236189942 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121832909135 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904167479946 + + Density error is 0.0988182234462 + + Energy Rydberg eV + E_KohnSham -34.27852433 -466.383249919 + E_Harris -34.2855103395 -466.478299454 + E_Fermi -0.201960488974 -2.74781342092 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011611510908 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000871545923898 + + Density error is 0.0636759591204 + + Energy Rydberg eV + E_KohnSham -34.2789056549 -466.388438111 + E_Harris -34.2833883609 -466.449428455 + E_Fermi -0.193951625351 -2.63884724113 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107727168898 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000836264866576 + + Density error is 0.00202610435313 + + Energy Rydberg eV + E_KohnSham -34.2788371933 -466.387506643 + E_Harris -34.2788400467 -466.387545466 + E_Fermi -0.158725000421 -2.15956442077 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107721842733 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000836665081161 + + Density error is 0.000919389881142 + + Energy Rydberg eV + E_KohnSham -34.2787957333 -466.38694255 + E_Harris -34.2787962596 -466.386949712 + E_Fermi -0.158410287045 -2.15528252562 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107604164818 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000836237008794 + + Density error is 0.000188465548956 + + Energy Rydberg eV + E_KohnSham -34.2788160095 -466.387218423 + E_Harris -34.2788160442 -466.387218895 + E_Fermi -0.158088238309 -2.15090082779 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107629884527 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000836489111427 + + Density error is 3.3839455531e-05 + + Energy Rydberg eV + E_KohnSham -34.2788088377 -466.387120845 + E_Harris -34.278808842 -466.387120905 + E_Fermi -0.158037021229 -2.15020398366 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107623105122 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000836438199103 + + Density error is 1.42235484834e-05 + + Energy Rydberg eV + E_KohnSham -34.2788125072 -466.387170772 + E_Harris -34.278812508 -466.387170783 + E_Fermi -0.158060611644 -2.15052494773 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107622408579 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000836439794819 + + Density error is 1.88359629794e-06 + + Energy Rydberg eV + E_KohnSham -34.2788113419 -466.387154917 + E_Harris -34.2788113419 -466.387154917 + E_Fermi -0.158045915804 -2.15032500057 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107622075284 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000836437974723 + + Density error is 5.39771254143e-07 + + Energy Rydberg eV + E_KohnSham -34.2788115459 -466.387157693 + E_Harris -34.2788115459 -466.387157693 + E_Fermi -0.158044542565 -2.15030631668 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107622154335 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000836438751917 + + Density error is 1.80613565175e-07 + + Energy Rydberg eV + E_KohnSham -34.2788115585 -466.387157865 + E_Harris -34.2788115585 -466.387157865 + E_Fermi -0.158044288321 -2.15030285751 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107622170121 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000836438984384 + + Density error is 1.08192170539e-08 + + Energy Rydberg eV + E_KohnSham -34.2788115623 -466.387157916 + E_Harris -34.2788115623 -466.387157916 + E_band -7.88813418495 -107.323571504 + E_one_elec -68.8438167095 -936.668179317 + E_Hartree +35.8337671979 +487.543414697 + E_xc -8.17652671521 -111.247353176 + E_Ewald +7.03301721734 +95.6891082879 + E_demet -2.03185264958e-64 -2.76447735307e-63 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193975958772 -2.63917831431 + E_Fermi -0.158044111115 -2.15030044651 + + charge density convergence is achieved + final etot is -466.387157916 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0401 2.00000 + 2 -12.9634 2.00000 + 3 -8.97222 2.00000 + 4 -6.68601 2.00000 + 5 1.09428 0.00000 + 6 4.14223 0.00000 + 7 11.1291 0.00000 + 8 11.3659 0.00000 + + EFERMI = -2.150300446506716 eV + OUT.ABACUS/ final etot is -466.3871579157570 eV + correction force for each atom along direction 1 is 0.000112045 + correction force for each atom along direction 2 is 1.29122e-05 + correction force for each atom along direction 3 is 9.27925e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.1643205 +1.0239405 -0.70993746 + H1 -1.3415522 -0.95566208 +0.29515050 + H2 +0.17723172 -0.068278409 +0.41478696 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3871579157570 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2081 11 0.66 1.0e+02% + Run_lcao lcao_line 7.1982 1 7.2 1.e+02% + Potential init_pot 0.28243 2 0.14 3.9% + PW_Basis recip2real 0.28493 17 0.017 4.0% + PW_Basis gathers_scatterp 0.12930 17 0.0076 1.8% + Potential v_of_rho 1.0504 14 0.075 15.% + XC_Functional v_xc 0.31916 15 0.021 4.4% + H_Hartree_pw v_hartree 0.68389 14 0.049 9.5% + PW_Basis real2recip 0.73731 41 0.018 10.% + PW_Basis gatherp_scatters 0.28151 41 0.0069 3.9% + ORB_control set_orb_tables 1.0967 1 1.1 15.% + ORB_gen_tables gen_tables 1.0967 1 1.1 15.% + ORB_table_phi init_Table 0.47534 1 0.48 6.6% + ORB_table_phi cal_ST_Phi12_R 0.47005 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18566 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18410 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.24841 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24637 66 0.0037 3.4% + LOOP_ions opt_ions 5.5949 1 5.6 78.% + ESolver_KS_LCAO Run 5.0692 1 5.1 70.% + HSolverLCAO solve 2.4258 12 0.20 34.% + HamiltLCAO updateHk 1.2814 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2519 12 0.10 17.% + Gint_interface cal_gint 2.1909 25 0.088 30.% + Gint_Gamma distri_vl 2.6444 6 0.44 37.% + LCAO_Deepks cal_projected_DM 5.4433 14 0.39 76.% + LCAO_gen_fixedH add_v_delta 2.4954 6 0.42 35.% + LCAO_DESCRIPTOR add_v_delta 2.4954 6 0.42 35.% + ElecStateLCAO psiToRho 1.1269 12 0.094 16.% + Charge mix_rho 0.99137 11 0.090 14.% + LOOP_ions force_stress 0.52551 1 0.53 7.3% + Force_Stress_LCAO getForceStress 0.52548 1 0.53 7.3% + Force_LCAO_gamma ftable_gamma 0.30977 1 0.31 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.30153 1 0.30 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:06 2022 + Finish Time : Wed Sep 28 11:05:13 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6699140bba142e50057fa54bea10c6e9f67b7b64 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123444 ima = 3.69808e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012371641093 + charge after normalized = 8.00000000000004 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112450813809 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113135391464 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113343862407 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113319318976 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011333529343 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113328832789 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113331183337 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113330595826 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113330548177 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113330529065 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113330519663 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/STRU new file mode 100644 index 0000000000000000000000000000000000000000..cc88bc498690201d139b7c90308170f44927c895 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.047175213643 20.997224243619 4.138135901947 0 0 0 +H +0.0 +2 +-9.448699712913 22.039648287808 4.010790432774 0 0 0 +-11.054108275430 20.272114371761 5.815671592602 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/conv new file mode 100644 index 0000000000000000000000000000000000000000..3aa59264f17875a22c971ecc38d1dcf32c26dba4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/conv @@ -0,0 +1 @@ +232 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..cdbeaf3f3773adb03ddc841803518615c35632e4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747677801 0.01245950942 1.253337598 1.352940825 1.468259056 0.008094788175 0.0188460841 0.03900660151 +2.811151699e-18 0.0009854828954 0.002378306102 0.01160620528 0.04190417552 1.803708685e-19 1.531993008e-06 4.85299555e-06 +0.001667773725 0.005766599678 + +H atom_index 1 n_descriptor 18 +1.181171759 0.03633140613 0.08600589218 0.1214306586 0.2980676171 0.01871598874 0.02439721167 0.03994470165 +2.975191546e-19 3.374039013e-05 0.08186361025 0.1036166083 0.1127922345 1.177670707e-18 6.515886642e-06 0.01455673795 +0.02293918084 0.02733693578 + +H atom_index 2 n_descriptor 18 +1.248556607 0.03410408715 0.1069893557 0.1500282431 0.3219441264 0.02176156407 0.02832433356 0.03734360283 +-1.143674309e-17 3.92246057e-05 0.0994251078 0.1150922763 0.1286512668 -6.223571342e-18 4.129152055e-06 0.01304961588 +0.02564643276 0.03073455549 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e990c889e47163a622209dff4cd233f27a8523a4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:06 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871548 SEC) : SETUP UNITCELL + DONE(0.0875007 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105542 SEC) : INIT PLANEWAVE + DONE(0.149017 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.429419 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651693e+02 0.000000e+00 2.134e-01 5.152e-01 + GE2 -4.663832e+02 -1.213985e+00 9.882e-02 4.778e-01 + GE3 -4.663884e+02 -5.188192e-03 6.368e-02 5.518e-01 + GE4 -4.663875e+02 9.314675e-04 2.026e-03 4.072e-01 + GE5 -4.663869e+02 5.640928e-04 9.194e-04 4.067e-01 + GE6 -4.663872e+02 -2.758730e-04 1.885e-04 4.032e-01 + GE7 -4.663871e+02 9.757830e-05 3.384e-05 3.891e-01 + GE8 -4.663872e+02 -4.992640e-05 1.422e-05 3.829e-01 + GE9 -4.663872e+02 1.585438e-05 1.884e-06 3.863e-01 + GE10 -4.663872e+02 -2.775746e-06 5.398e-07 3.862e-01 + GE11 -4.663872e+02 -1.716081e-07 1.806e-07 3.852e-01 + GE12 -4.663872e+02 -5.124627e-08 1.082e-08 3.139e-01 +E_delta_band = -6.87234059e-02 Ry = -9.35029906e-01 eV +E_delta_NN= -1.93975959e-01 Ry = -2.63917831e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2081 11 0.66 1e+02 % + Run_lcao lcao_line 7.1982 1 7.2 1e+02 % + Potential init_pot 0.28243 2 0.14 3.9 % + PW_Basis recip2real 0.28493 17 0.017 4 % + PW_Basis gathers_scatterp 0.1293 17 0.0076 1.8 % + Potential v_of_rho 1.0504 14 0.075 15 % + XC_Functional v_xc 0.31916 15 0.021 4.4 % + H_Hartree_pw v_hartree 0.68389 14 0.049 9.5 % + PW_Basis real2recip 0.73731 41 0.018 10 % + PW_Basis gatherp_scatters 0.28151 41 0.0069 3.9 % + ORB_control set_orb_tables 1.0967 1 1.1 15 % + ORB_gen_tables gen_tables 1.0967 1 1.1 15 % + ORB_table_phi init_Table 0.47534 1 0.48 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.47005 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.18566 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.1841 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.24841 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24637 66 0.0037 3.4 % + LOOP_ions opt_ions 5.5949 1 5.6 78 % + ESolver_KS_LCAO Run 5.0692 1 5.1 70 % + HSolverLCAO solve 2.4258 12 0.2 34 % + HamiltLCAO updateHk 1.2814 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.2519 12 0.1 17 % + Gint_interface cal_gint 2.1909 25 0.088 30 % + Gint_Gamma distri_vl 2.6444 6 0.44 37 % + LCAO_Deepks cal_projected_DM 5.4433 14 0.39 76 % + LCAO_gen_fixedH add_v_delta 2.4954 6 0.42 35 % + LCAO_DESCRIPTOR add_v_delta 2.4954 6 0.42 35 % + ElecStateLCAO psiToRho 1.1269 12 0.094 16 % + Charge mix_rho 0.99137 11 0.09 14 % + LOOP_ions force_stress 0.52551 1 0.53 7.3 % + Force_Stress_LCAO getForceStress 0.52548 1 0.53 7.3 % + Force_LCAO_gamma ftable_gamma 0.30977 1 0.31 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.30153 1 0.3 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:06 2022 + FINISH Time : Wed Sep 28 11:05:13 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/232/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..62616c0b737ad065f7b0a021365ff141da768055 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.602545 0.760618 0.156746 +H 0.658862 0.786439 0.137884 +H 0.615125 0.735857 0.215808 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b705ef8fdc90473f47ebc22272b8db0856d0ce2d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3664 2 + 2 -13.124 2 + 3 -9.12065 2 + 4 -6.76187 2 + 5 1.37386 0 + 6 4.53942 0 + 7 11.0558 0 + 8 11.3061 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..6bf1448cbbd9c87d7f10ae8e4535c77a6560eca6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:06 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.8712473325 21.297301266 4.38889121141 0 0 0 0 + tauc_H1 18.4481444826 22.0203057211 3.86075628075 0 0 0 0 + tauc_H2 17.2235035449 20.6039843657 6.04261097399 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0877296866284 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0968697274533 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115066255117 (SEC) + + DONE : INIT CHARGE Time : 0.163463280381 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44469 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000935 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00062 + + Density error is 0.216074555141 + + Energy Rydberg eV + E_KohnSham -34.1897766372 -465.175775613 + E_Harris -34.3841470535 -467.820320798 + E_Fermi -0.410858735581 -5.59001987697 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127135689887 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000823225657587 + + Density error is 0.0979012171259 + + Energy Rydberg eV + E_KohnSham -34.2806326305 -466.41193482 + E_Harris -34.2873449131 -466.503260109 + E_Fermi -0.218017330964 -2.96627796387 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121434080421 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000793946477097 + + Density error is 0.0627879091271 + + Energy Rydberg eV + E_KohnSham -34.2809648552 -466.416454968 + E_Harris -34.285299432 -466.475429911 + E_Fermi -0.206305182923 -2.80692601468 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113280309219 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000763349414498 + + Density error is 0.00200817714187 + + Energy Rydberg eV + E_KohnSham -34.2809654749 -466.4164634 + E_Harris -34.2809668206 -466.416481709 + E_Fermi -0.170652955568 -2.32185257627 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113423896291 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000764962941052 + + Density error is 0.00094480942333 + + Energy Rydberg eV + E_KohnSham -34.2808960139 -466.415518335 + E_Harris -34.2808978377 -466.415543149 + E_Fermi -0.169819064735 -2.31050690942 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113284408326 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000764230090895 + + Density error is 0.000139341089157 + + Energy Rydberg eV + E_KohnSham -34.2809399554 -466.41611619 + E_Harris -34.2809398284 -466.416114462 + E_Fermi -0.169885842486 -2.31141546734 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113300491527 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000764446021583 + + Density error is 4.1024010528e-05 + + Energy Rydberg eV + E_KohnSham -34.2809246784 -466.415908335 + E_Harris -34.2809246879 -466.415908464 + E_Fermi -0.169751674893 -2.30959002359 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113291626123 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000764374746623 + + Density error is 1.6645858557e-05 + + Energy Rydberg eV + E_KohnSham -34.2809285664 -466.415961234 + E_Harris -34.2809285676 -466.41596125 + E_Fermi -0.169800415553 -2.31025317429 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113290988719 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000764379939606 + + Density error is 1.93208644889e-06 + + Energy Rydberg eV + E_KohnSham -34.2809270784 -466.415940988 + E_Harris -34.2809270784 -466.415940989 + E_Fermi -0.169782852727 -2.31001421978 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113291149642 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000764382256013 + + Density error is 2.55585960013e-07 + + Energy Rydberg eV + E_KohnSham -34.2809273116 -466.415944162 + E_Harris -34.2809273116 -466.415944162 + E_Fermi -0.16978100077 -2.30998902262 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113291212736 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000764382626453 + + Density error is 8.55884118537e-08 + + Energy Rydberg eV + E_KohnSham -34.2809273414 -466.415944567 + E_Harris -34.2809273414 -466.415944567 + E_band -7.99266642468 -108.745805589 + E_one_elec -69.4562138313 -945.000269612 + E_Hartree +36.1177969134 +491.407837229 + E_xc -8.22215636071 -111.868176353 + E_Ewald +7.40363331874 +100.731599037 + E_demet -2.86738320847e-82 -3.90127499847e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195100855234 -2.65448331586 + E_Fermi -0.169780941537 -2.30998821671 + + charge density convergence is achieved + final etot is -466.415944567 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3664 2.00000 + 2 -13.1240 2.00000 + 3 -9.12065 2.00000 + 4 -6.76187 2.00000 + 5 1.37386 0.00000 + 6 4.53942 0.00000 + 7 11.0558 0.00000 + 8 11.3061 0.00000 + + EFERMI = -2.309988216708283 eV + OUT.ABACUS/ final etot is -466.4159445670693 eV + correction force for each atom along direction 1 is 3.05507e-05 + correction force for each atom along direction 2 is -9.63098e-05 + correction force for each atom along direction 3 is 1.53868e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.76832224 -0.17512676 -0.12006354 + H1 +0.71057254 +0.34041076 -0.26271114 + H2 +0.057749698 -0.16528400 +0.38277468 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4159445670693 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5229 11 0.59 1.0e+02% + Run_lcao lcao_line 6.5124 1 6.5 1.e+02% + Potential init_pot 0.28363 2 0.14 4.3% + PW_Basis recip2real 0.26363 16 0.016 4.0% + PW_Basis gathers_scatterp 0.11188 16 0.0070 1.7% + Potential v_of_rho 0.87377 13 0.067 13.% + XC_Functional v_xc 0.25042 14 0.018 3.8% + H_Hartree_pw v_hartree 0.58767 13 0.045 9.0% + PW_Basis real2recip 0.55195 38 0.015 8.5% + PW_Basis gatherp_scatters 0.21183 38 0.0056 3.2% + ORB_control set_orb_tables 1.1112 1 1.1 17.% + ORB_gen_tables gen_tables 1.1112 1 1.1 17.% + ORB_table_phi init_Table 0.48274 1 0.48 7.4% + ORB_table_phi cal_ST_Phi12_R 0.47783 126 0.0038 7.3% + ORB_table_beta init_Table_Beta 0.18800 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18651 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25688 1 0.26 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25491 66 0.0039 3.9% + LOOP_ions opt_ions 4.8801 1 4.9 75.% + ESolver_KS_LCAO Run 4.3114 1 4.3 66.% + HSolverLCAO solve 2.3538 11 0.21 36.% + HamiltLCAO updateHk 1.2217 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.1835 11 0.11 18.% + Gint_interface cal_gint 2.2473 23 0.098 34.% + Gint_Gamma distri_vl 2.0659 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.7080 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9331 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9331 6 0.32 30.% + ElecStateLCAO psiToRho 1.1186 11 0.10 17.% + Charge mix_rho 0.64881 10 0.065 9.9% + LOOP_ions force_stress 0.56854 1 0.57 8.7% + Force_Stress_LCAO getForceStress 0.56851 1 0.57 8.7% + Force_LCAO_gamma ftable_gamma 0.35456 1 0.35 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.34789 1 0.35 5.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:06 2022 + Finish Time : Wed Sep 28 11:08:13 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4b86c919596a378cdaa4275aca5fd98a68a2084f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123705 ima = 3.7285e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123110475204 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112019861315 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011254731172 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112811495421 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112751098253 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112786043406 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112779518819 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112782569297 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112781886961 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112781807506 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112781796803 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/STRU new file mode 100644 index 0000000000000000000000000000000000000000..f4aed32a35f91976b65dcc9e74fa7e18592c7964 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.128752667488 21.297301266066 4.388891211438 0 0 0 +H +0.0 +2 +-9.551855517384 22.020305721105 3.860756280770 0 0 0 +-10.776496455102 20.603984365737 6.042610974008 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/conv new file mode 100644 index 0000000000000000000000000000000000000000..244d6afea3dbc1cf472222229a2ca531c44f1d97 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/conv @@ -0,0 +1 @@ +233 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5f05934dc956c4183005c0660908bed6a9f7e4be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749028165 0.01273913467 1.280356112 1.367358771 1.469664281 0.008524091831 0.0187529957 0.03901401487 +1.933516836e-18 0.001093120433 0.002638934942 0.01265575306 0.04583497659 -9.578916929e-20 2.123047729e-06 6.084803499e-06 +0.001658172355 0.005957914223 + +H atom_index 1 n_descriptor 18 +1.261183039 0.0338263813 0.1124633861 0.155282883 0.324550833 0.02281723716 0.02896508432 0.03703115307 +1.187223811e-18 4.77904263e-05 0.1047865298 0.1157121056 0.1333729896 -1.112780935e-17 3.527088723e-06 0.01312511364 +0.026870773 0.03127288 + +H atom_index 2 n_descriptor 18 +1.250022221 0.0342097985 0.1085254729 0.1500155715 0.3210296888 0.02230085338 0.02831758545 0.03734948776 +3.869990749e-17 4.674603208e-05 0.1023426028 0.1149353198 0.1288394756 6.966000285e-18 4.149236964e-06 0.01316618877 +0.02646609934 0.03078148066 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f9416aaa040fab76d047fe17f254a7fd0d8ef2f3 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:06 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0877517 SEC) : SETUP UNITCELL + DONE(0.0968876 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115093 SEC) : INIT PLANEWAVE + DONE(0.163591 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444753 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651758e+02 0.000000e+00 2.161e-01 5.041e-01 + GE2 -4.664119e+02 -1.236159e+00 9.790e-02 4.282e-01 + GE3 -4.664165e+02 -4.520148e-03 6.279e-02 4.824e-01 + GE4 -4.664165e+02 -8.431724e-06 2.008e-03 3.782e-01 + GE5 -4.664155e+02 9.450650e-04 9.448e-04 3.719e-01 + GE6 -4.664161e+02 -5.978554e-04 1.393e-04 3.675e-01 + GE7 -4.664159e+02 2.078549e-04 4.102e-05 3.633e-01 + GE8 -4.664160e+02 -5.289933e-05 1.665e-05 3.518e-01 + GE9 -4.664159e+02 2.024588e-05 1.932e-06 3.490e-01 + GE10 -4.664159e+02 -3.173562e-06 2.556e-07 3.545e-01 + GE11 -4.664159e+02 -4.050888e-07 8.559e-08 2.985e-01 +E_delta_band = -7.11134737e-02 Ry = -9.67548447e-01 eV +E_delta_NN= -1.95100855e-01 Ry = -2.65448332e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5229 11 0.59 1e+02 % + Run_lcao lcao_line 6.5124 1 6.5 1e+02 % + Potential init_pot 0.28363 2 0.14 4.3 % + PW_Basis recip2real 0.26363 16 0.016 4 % + PW_Basis gathers_scatterp 0.11188 16 0.007 1.7 % + Potential v_of_rho 0.87377 13 0.067 13 % + XC_Functional v_xc 0.25042 14 0.018 3.8 % + H_Hartree_pw v_hartree 0.58767 13 0.045 9 % + PW_Basis real2recip 0.55195 38 0.015 8.5 % + PW_Basis gatherp_scatters 0.21183 38 0.0056 3.2 % + ORB_control set_orb_tables 1.1112 1 1.1 17 % + ORB_gen_tables gen_tables 1.1112 1 1.1 17 % + ORB_table_phi init_Table 0.48274 1 0.48 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.47783 126 0.0038 7.3 % + ORB_table_beta init_Table_Beta 0.188 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18651 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.25688 1 0.26 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25491 66 0.0039 3.9 % + LOOP_ions opt_ions 4.8801 1 4.9 75 % + ESolver_KS_LCAO Run 4.3114 1 4.3 66 % + HSolverLCAO solve 2.3538 11 0.21 36 % + HamiltLCAO updateHk 1.2217 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.1835 11 0.11 18 % + Gint_interface cal_gint 2.2473 23 0.098 34 % + Gint_Gamma distri_vl 2.0659 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.708 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9331 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9331 6 0.32 30 % + ElecStateLCAO psiToRho 1.1186 11 0.1 17 % + Charge mix_rho 0.64881 10 0.065 9.9 % + LOOP_ions force_stress 0.56854 1 0.57 8.7 % + Force_Stress_LCAO getForceStress 0.56851 1 0.57 8.7 % + Force_LCAO_gamma ftable_gamma 0.35456 1 0.35 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.34789 1 0.35 5.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:06 2022 + FINISH Time : Wed Sep 28 11:08:13 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/233/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a0f1efc64bf5356b2271f9c53b4fab79aaeaa7f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.606777 0.767318 0.161769 +H 0.643022 0.808005 0.127064 +H 0.630333 0.769658 0.223758 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..60744d4b944fce606b2f884f4f61abbe7e45cec3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2497 2 + 2 -13.1514 2 + 3 -9.00689 2 + 4 -6.73448 2 + 5 1.30515 0 + 6 4.44289 0 + 7 11.0781 0 + 8 11.3179 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7ab7b8f2da92b9d7d006f794772bcb963ca32402 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:53 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.989755526 21.484895627 4.52952692283 0 0 0 0 + tauc_H1 18.0046099487 22.6241360693 3.55778010134 0 0 0 0 + tauc_H2 17.6493108107 21.5504196309 6.26521599812 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0872899475578 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0954331321871 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.113616864401 (SEC) + + DONE : INIT CHARGE Time : 0.162189224216 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441132 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 0 81 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000815 + + Density error is 0.215545987186 + + Energy Rydberg eV + E_KohnSham -34.1901849788 -465.181331386 + E_Harris -34.3829690749 -467.804293576 + E_Fermi -0.405373048876 -5.51538328034 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00119507302682 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101140496675 + + Density error is 0.0981591162337 + + Energy Rydberg eV + E_KohnSham -34.2803283592 -466.407794996 + E_Harris -34.2870645695 -466.499445839 + E_Fermi -0.213327810651 -2.90247376672 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113186212919 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000970154792908 + + Density error is 0.0629563702991 + + Energy Rydberg eV + E_KohnSham -34.2806378112 -466.412005307 + E_Harris -34.284984186 -466.47114077 + E_Fermi -0.202338520943 -2.75295680972 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0010386566802 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000919743401492 + + Density error is 0.00202744395696 + + Energy Rydberg eV + E_KohnSham -34.2806239741 -466.411817043 + E_Harris -34.2806261633 -466.411846828 + E_Fermi -0.166887874354 -2.27062601832 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103958126011 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920832575675 + + Density error is 0.000902519643882 + + Energy Rydberg eV + E_KohnSham -34.2805651654 -466.41101691 + E_Harris -34.2805663022 -466.411032376 + E_Fermi -0.166174346258 -2.26091797053 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103827211548 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000919989811184 + + Density error is 0.000176655648481 + + Energy Rydberg eV + E_KohnSham -34.2806004764 -466.411497341 + E_Harris -34.280600377 -466.411495988 + E_Fermi -0.166136232838 -2.26039941085 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0010384395394 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920264943626 + + Density error is 3.89237537171e-05 + + Energy Rydberg eV + E_KohnSham -34.2805872904 -466.411317936 + E_Harris -34.2805872982 -466.411318042 + E_Fermi -0.166004441672 -2.25860630005 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103839237104 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920186831844 + + Density error is 1.62949081143e-05 + + Energy Rydberg eV + E_KohnSham -34.2805919108 -466.4113808 + E_Harris -34.2805919119 -466.411380814 + E_Fermi -0.16604585523 -2.25916976041 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103838265554 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092018577631 + + Density error is 1.62980270061e-06 + + Energy Rydberg eV + E_KohnSham -34.2805905272 -466.411361975 + E_Harris -34.2805905272 -466.411361975 + E_Fermi -0.166028142626 -2.25892876807 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103838081622 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920187905491 + + Density error is 2.47434418761e-07 + + Energy Rydberg eV + E_KohnSham -34.2805907436 -466.411364919 + E_Harris -34.2805907436 -466.411364919 + E_Fermi -0.166026809575 -2.25891063099 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103838130737 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092018818429 + + Density error is 9.91404892112e-08 + + Energy Rydberg eV + E_KohnSham -34.280590769 -466.411365265 + E_Harris -34.280590769 -466.411365265 + E_band -7.95879205607 -108.28492116 + E_one_elec -69.2865770278 -942.692242494 + E_Hartree +36.0418096193 +490.373977053 + E_xc -8.20986325873 -111.70092012 + E_Ewald +7.29839920516 +99.2998154688 + E_demet -3.54386510505e-77 -4.82167583721e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194755322105 -2.64978209645 + E_Fermi -0.166026791595 -2.25891038634 + + charge density convergence is achieved + final etot is -466.411365265 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2497 2.00000 + 2 -13.1514 2.00000 + 3 -9.00689 2.00000 + 4 -6.73448 2.00000 + 5 1.30515 0.00000 + 6 4.44289 0.00000 + 7 11.0781 0.00000 + 8 11.3179 0.00000 + + EFERMI = -2.258910386344536 eV + OUT.ABACUS/ final etot is -466.4113652649336 eV + correction force for each atom along direction 1 is 0.000193535 + correction force for each atom along direction 2 is -4.62319e-05 + correction force for each atom along direction 3 is 8.79440e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.53394489 -0.69879973 +0.82728022 + H1 +0.59300950 +0.61529849 -0.37428416 + H2 -0.059064605 +0.083501238 -0.45299606 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4113652649336 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5203 11 0.59 1.0e+02% + Run_lcao lcao_line 6.5102 1 6.5 1.e+02% + Potential init_pot 0.28465 2 0.14 4.4% + PW_Basis recip2real 0.26999 16 0.017 4.1% + PW_Basis gathers_scatterp 0.11760 16 0.0074 1.8% + Potential v_of_rho 0.88313 13 0.068 14.% + XC_Functional v_xc 0.25232 14 0.018 3.9% + H_Hartree_pw v_hartree 0.59286 13 0.046 9.1% + PW_Basis real2recip 0.56078 38 0.015 8.6% + PW_Basis gatherp_scatters 0.21819 38 0.0057 3.3% + ORB_control set_orb_tables 1.1143 1 1.1 17.% + ORB_gen_tables gen_tables 1.1143 1 1.1 17.% + ORB_table_phi init_Table 0.48567 1 0.49 7.4% + ORB_table_phi cal_ST_Phi12_R 0.48069 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18948 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18796 56 0.0034 2.9% + ORB_table_alpha init_Table_Alpha 0.25560 1 0.26 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25372 66 0.0038 3.9% + LOOP_ions opt_ions 4.8782 1 4.9 75.% + ESolver_KS_LCAO Run 4.3126 1 4.3 66.% + HSolverLCAO solve 2.3283 11 0.21 36.% + HamiltLCAO updateHk 1.2096 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.1747 11 0.11 18.% + Gint_interface cal_gint 2.2196 23 0.097 34.% + Gint_Gamma distri_vl 2.0729 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.7113 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9412 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9412 6 0.32 30.% + ElecStateLCAO psiToRho 1.1052 11 0.10 17.% + Charge mix_rho 0.65947 10 0.066 10.% + LOOP_ions force_stress 0.56539 1 0.57 8.7% + Force_Stress_LCAO getForceStress 0.56536 1 0.57 8.7% + Force_LCAO_gamma ftable_gamma 0.35245 1 0.35 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.34575 1 0.35 5.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:53 2022 + Finish Time : Wed Sep 28 11:12:59 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..fc0215717b7e3bf93e6b6f105224383efeb85aee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012372 ima = 3.69595e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123362629822 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112307737592 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112853341315 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113095244262 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113048463146 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113076777578 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113068406795 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113071254992 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113070624802 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113070559732 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113070553516 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ba52f654ddf97e9a08f1d9fdf021404e138028aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.010244474003 21.484895626994 4.529526922811 0 0 0 +H +0.0 +2 +-9.995390051292 22.624136069249 3.557780101352 0 0 0 +-10.350689189312 21.550419630833 6.265215998127 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/conv new file mode 100644 index 0000000000000000000000000000000000000000..4157f4c14c275634e5bdba29d1bf40e36415d087 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/conv @@ -0,0 +1 @@ +234 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..577ac16a5b0352ceb5465f1498350c7ce1b40f10 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747374917 0.01264538286 1.27368466 1.365758745 1.469170727 0.00818718039 0.01920177321 0.03897332361 +8.086822593e-19 0.001089282911 0.002507488111 0.01228332337 0.04418065509 3.378421711e-19 1.802094283e-06 5.439119567e-06 +0.001690664267 0.005841946692 + +H atom_index 1 n_descriptor 18 +1.263166762 0.03356108377 0.1127020623 0.1566947749 0.3259611874 0.02261889282 0.02913908432 0.0368336399 +-3.756674912e-17 4.412104941e-05 0.1044536276 0.1157749865 0.134536804 -9.12358802e-18 3.515719211e-06 0.01302831996 +0.0266257292 0.03137791684 + +H atom_index 2 n_descriptor 18 +1.224193303 0.03491413952 0.09948627934 0.1388757211 0.3133188785 0.02085402412 0.02687614703 0.03809279929 +-3.180532437e-17 4.068127507e-05 0.09483018725 0.1141209667 0.1191171051 -4.637790325e-18 5.434083083e-06 0.0134081132 +0.02516155847 0.02958938859 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..540dc607882ecb5f8b0bf75559b1d46888a84672 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:53 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0873138 SEC) : SETUP UNITCELL + DONE(0.0954487 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11364 SEC) : INIT PLANEWAVE + DONE(0.162332 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.4412 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651813e+02 0.000000e+00 2.155e-01 5.056e-01 + GE2 -4.664078e+02 -1.226464e+00 9.816e-02 4.303e-01 + GE3 -4.664120e+02 -4.210311e-03 6.296e-02 4.857e-01 + GE4 -4.664118e+02 1.882637e-04 2.027e-03 3.762e-01 + GE5 -4.664110e+02 8.001336e-04 9.025e-04 3.754e-01 + GE6 -4.664115e+02 -4.804311e-04 1.767e-04 3.671e-01 + GE7 -4.664113e+02 1.794049e-04 3.892e-05 3.573e-01 + GE8 -4.664114e+02 -6.286419e-05 1.629e-05 3.534e-01 + GE9 -4.664114e+02 1.882539e-05 1.630e-06 3.523e-01 + GE10 -4.664114e+02 -2.943930e-06 2.474e-07 3.532e-01 + GE11 -4.664114e+02 -3.463614e-07 9.914e-08 2.950e-01 +E_delta_band = -7.03960152e-02 Ry = -9.57786923e-01 eV +E_delta_NN= -1.94755322e-01 Ry = -2.64978210e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5203 11 0.59 1e+02 % + Run_lcao lcao_line 6.5102 1 6.5 1e+02 % + Potential init_pot 0.28465 2 0.14 4.4 % + PW_Basis recip2real 0.26999 16 0.017 4.1 % + PW_Basis gathers_scatterp 0.1176 16 0.0074 1.8 % + Potential v_of_rho 0.88313 13 0.068 14 % + XC_Functional v_xc 0.25232 14 0.018 3.9 % + H_Hartree_pw v_hartree 0.59286 13 0.046 9.1 % + PW_Basis real2recip 0.56078 38 0.015 8.6 % + PW_Basis gatherp_scatters 0.21819 38 0.0057 3.3 % + ORB_control set_orb_tables 1.1143 1 1.1 17 % + ORB_gen_tables gen_tables 1.1143 1 1.1 17 % + ORB_table_phi init_Table 0.48567 1 0.49 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.48069 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18948 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18796 56 0.0034 2.9 % + ORB_table_alpha init_Table_Alpha 0.2556 1 0.26 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25372 66 0.0038 3.9 % + LOOP_ions opt_ions 4.8782 1 4.9 75 % + ESolver_KS_LCAO Run 4.3126 1 4.3 66 % + HSolverLCAO solve 2.3283 11 0.21 36 % + HamiltLCAO updateHk 1.2096 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.1747 11 0.11 18 % + Gint_interface cal_gint 2.2196 23 0.097 34 % + Gint_Gamma distri_vl 2.0729 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.7113 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9412 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9412 6 0.32 30 % + ElecStateLCAO psiToRho 1.1052 11 0.1 17 % + Charge mix_rho 0.65947 10 0.066 10 % + LOOP_ions force_stress 0.56539 1 0.57 8.7 % + Force_Stress_LCAO getForceStress 0.56536 1 0.57 8.7 % + Force_LCAO_gamma ftable_gamma 0.35245 1 0.35 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.34575 1 0.35 5.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:53 2022 + FINISH Time : Wed Sep 28 11:12:59 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/234/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d28a148d9fac91b6ca49ca93a59bb77855337a91 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.61871 0.770141 0.164276 +H 0.571506 0.806928 0.132649 +H 0.617136 0.806106 0.221863 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f5f0228ba0225cd853f58e25283aa3361044e4b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0855 2 + 2 -12.2932 2 + 3 -9.52399 2 + 4 -6.70799 2 + 5 0.925364 0 + 6 3.79803 0 + 7 11.1482 0 + 8 11.4383 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..01dec644815f114c760e52903ef61eec7737203d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:55 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.3238694254 21.5639388933 4.59971991891 0 0 0 0 + tauc_H1 16.0021808274 22.5939802307 3.71417934815 0 0 0 0 + tauc_H2 17.2797944782 22.5709715072 6.21215897693 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0869586085463 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0873773558583 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105625513524 (SEC) + + DONE : INIT CHARGE Time : 0.150102315872 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.43148 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 0 81 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00131 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729 + + Density error is 0.20906073219 + + Energy Rydberg eV + E_KohnSham -34.188432979 -465.157494206 + E_Harris -34.3689134457 -467.61305693 + E_Fermi -0.383784285203 -5.22165308162 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00131619270232 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103020667924 + + Density error is 0.0984020492961 + + Energy Rydberg eV + E_KohnSham -34.2754782305 -466.34180561 + E_Harris -34.2828427623 -466.442005205 + E_Fermi -0.196891694489 -2.67884893393 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00123494549294 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989168716295 + + Density error is 0.0636110603175 + + Energy Rydberg eV + E_KohnSham -34.2759944576 -466.34882924 + E_Harris -34.2806802276 -466.412582412 + E_Fermi -0.191624169266 -2.60718057654 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110298232208 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000956701469433 + + Density error is 0.00184964792578 + + Energy Rydberg eV + E_KohnSham -34.2758633573 -466.347045528 + E_Harris -34.2758629507 -466.347039997 + E_Fermi -0.156241861305 -2.12577957988 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110412674372 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957440154064 + + Density error is 0.00100618467751 + + Energy Rydberg eV + E_KohnSham -34.2758363898 -466.346678617 + E_Harris -34.2758374224 -466.346692666 + E_Fermi -0.156588886352 -2.13050109787 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110198835524 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957135475925 + + Density error is 0.00012298186882 + + Energy Rydberg eV + E_KohnSham -34.2758454118 -466.346801367 + E_Harris -34.2758455713 -466.346803538 + E_Fermi -0.155985171569 -2.12228713684 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110205436518 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957263964259 + + Density error is 2.51955534803e-05 + + Energy Rydberg eV + E_KohnSham -34.2758439064 -466.346780886 + E_Harris -34.2758439076 -466.346780903 + E_Fermi -0.155976068364 -2.12216328138 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110199250602 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957198425303 + + Density error is 8.48210158175e-06 + + Energy Rydberg eV + E_KohnSham -34.2758450574 -466.346796546 + E_Harris -34.2758450577 -466.346796549 + E_Fermi -0.155981436491 -2.12223631851 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110198641012 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957202337017 + + Density error is 1.75664366704e-06 + + Energy Rydberg eV + E_KohnSham -34.2758443657 -466.346787135 + E_Harris -34.2758443657 -466.346787135 + E_Fermi -0.155973325174 -2.12212595837 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011019835011 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957204608515 + + Density error is 2.35206794055e-07 + + Energy Rydberg eV + E_KohnSham -34.2758444776 -466.346788657 + E_Harris -34.2758444776 -466.346788657 + E_Fermi -0.155971781764 -2.12210495921 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110198393621 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957205113195 + + Density error is 5.43655988661e-08 + + Energy Rydberg eV + E_KohnSham -34.2758444993 -466.346788952 + E_Harris -34.2758444993 -466.346788952 + E_band -7.88062657393 -107.221425216 + E_one_elec -68.5543961264 -932.730410268 + E_Hartree +35.676040155 +485.397428185 + E_xc -8.15112505381 -110.901745842 + E_Ewald +6.87939265561 +93.5989388957 + E_demet -3.81976969442e-57 -5.19706328918e-56 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193575297161 -2.63372703343 + E_Fermi -0.155971666924 -2.12210339672 + + charge density convergence is achieved + final etot is -466.346788952 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0855 2.00000 + 2 -12.2932 2.00000 + 3 -9.52399 2.00000 + 4 -6.70799 2.00000 + 5 0.925364 0.00000 + 6 3.79803 0.00000 + 7 11.1482 0.00000 + 8 11.4383 0.00000 + + EFERMI = -2.122103396723450 eV + OUT.ABACUS/ final etot is -466.3467889522847 eV + correction force for each atom along direction 1 is -0.000141408 + correction force for each atom along direction 2 is 0.000180116 + correction force for each atom along direction 3 is 1.58798e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.1850359 +1.8311819 +0.73833978 + H1 +0.73113876 -0.88305170 -0.038752408 + H2 +0.45389715 -0.94813016 -0.69958737 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3467889522847 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9309 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9218 1 6.9 1.e+02% + Potential init_pot 0.28296 2 0.14 4.1% + PW_Basis recip2real 0.28256 16 0.018 4.1% + PW_Basis gathers_scatterp 0.12050 16 0.0075 1.7% + Potential v_of_rho 1.0192 13 0.078 15.% + XC_Functional v_xc 0.30424 14 0.022 4.4% + H_Hartree_pw v_hartree 0.67239 13 0.052 9.7% + PW_Basis real2recip 0.69464 38 0.018 10.% + PW_Basis gatherp_scatters 0.25906 38 0.0068 3.7% + ORB_control set_orb_tables 1.0935 1 1.1 16.% + ORB_gen_tables gen_tables 1.0935 1 1.1 16.% + ORB_table_phi init_Table 0.47419 1 0.47 6.8% + ORB_table_phi cal_ST_Phi12_R 0.46903 126 0.0037 6.8% + ORB_table_beta init_Table_Beta 0.18222 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18074 56 0.0032 2.6% + ORB_table_alpha init_Table_Alpha 0.24763 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24567 66 0.0037 3.5% + LOOP_ions opt_ions 5.3182 1 5.3 77.% + ESolver_KS_LCAO Run 4.7414 1 4.7 68.% + HSolverLCAO solve 2.2821 11 0.21 33.% + HamiltLCAO updateHk 1.2447 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2167 11 0.11 18.% + Gint_interface cal_gint 2.1104 23 0.092 30.% + Gint_Gamma distri_vl 2.2718 6 0.38 33.% + LCAO_Deepks cal_projected_DM 5.1541 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1257 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.1258 6 0.35 31.% + ElecStateLCAO psiToRho 1.0136 11 0.092 15.% + Charge mix_rho 0.90344 10 0.090 13.% + LOOP_ions force_stress 0.57663 1 0.58 8.3% + Force_Stress_LCAO getForceStress 0.57660 1 0.58 8.3% + Force_LCAO_gamma ftable_gamma 0.35777 1 0.36 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.34971 1 0.35 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:55 2022 + Finish Time : Wed Sep 28 11:08:02 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..83cf6db7cd10ca9d448cdc00798465daa625c871 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123519 ima = 3.70317e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122958756095 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111330845363 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112213687545 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112420214593 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112411377191 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112416745704 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112415097712 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112416504187 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112416136781 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112416074585 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011241606179 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/STRU new file mode 100644 index 0000000000000000000000000000000000000000..859e117fe15916505c5ed30404aedc850fe89a9c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.676130574629 21.563938893289 4.599719918906 0 0 0 +H +0.0 +2 +-11.997819172640 22.593980230769 3.714179348130 0 0 0 +-10.720205521771 22.570971507134 6.212158976923 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/conv new file mode 100644 index 0000000000000000000000000000000000000000..521b21c7c198f12d543444920519b41df23a04de --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/conv @@ -0,0 +1 @@ +235 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..fd7eae8ade59605420584c0e73c73d67f3a5d39c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.756763548 0.01255497301 1.241703669 1.319056104 1.468490996 0.009799708369 0.01538184799 0.0393141525 +-4.731949561e-18 0.0007012961057 0.002668766336 0.01267912199 0.0429558221 -6.575930221e-19 2.380367101e-06 6.770959437e-06 +0.001562295275 0.006053521018 + +H atom_index 1 n_descriptor 18 +1.203012986 0.03664234106 0.09645261627 0.1290401475 0.3029077999 0.02104700481 0.02545832154 0.04003076875 +-2.767494132e-17 3.934521357e-05 0.08864809963 0.1100693015 0.1137314087 3.021670719e-18 4.440113078e-06 0.01436825723 +0.02462053742 0.02834765961 + +H atom_index 2 n_descriptor 18 +1.198100982 0.0367885371 0.09491661322 0.1270255678 0.3010064633 0.02080250893 0.02516795641 0.04022810834 +1.962723283e-17 3.893995567e-05 0.08741516329 0.1082961867 0.1134636039 6.107153212e-19 4.632893682e-06 0.01451375309 +0.02441429847 0.02808264697 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..b6c91ecde6a60e776e6fbd7f527c2df75e751c72 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:55 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0869816 SEC) : SETUP UNITCELL + DONE(0.0873949 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105644 SEC) : INIT PLANEWAVE + DONE(0.150238 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.43155 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651575e+02 0.000000e+00 2.091e-01 5.285e-01 + GE2 -4.663418e+02 -1.184311e+00 9.840e-02 4.834e-01 + GE3 -4.663488e+02 -7.023630e-03 6.361e-02 5.524e-01 + GE4 -4.663470e+02 1.783712e-03 1.850e-03 4.095e-01 + GE5 -4.663467e+02 3.669118e-04 1.006e-03 4.079e-01 + GE6 -4.663468e+02 -1.227508e-04 1.230e-04 4.112e-01 + GE7 -4.663468e+02 2.048137e-05 2.520e-05 3.936e-01 + GE8 -4.663468e+02 -1.565942e-05 8.482e-06 3.923e-01 + GE9 -4.663468e+02 9.410581e-06 1.757e-06 3.907e-01 + GE10 -4.663468e+02 -1.522273e-06 2.352e-07 3.925e-01 + GE11 -4.663468e+02 -2.950755e-07 5.437e-08 3.175e-01 +E_delta_band = -6.78191675e-02 Ry = -9.22727111e-01 eV +E_delta_NN= -1.93575297e-01 Ry = -2.63372703e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9309 11 0.63 1e+02 % + Run_lcao lcao_line 6.9218 1 6.9 1e+02 % + Potential init_pot 0.28296 2 0.14 4.1 % + PW_Basis recip2real 0.28256 16 0.018 4.1 % + PW_Basis gathers_scatterp 0.1205 16 0.0075 1.7 % + Potential v_of_rho 1.0192 13 0.078 15 % + XC_Functional v_xc 0.30424 14 0.022 4.4 % + H_Hartree_pw v_hartree 0.67239 13 0.052 9.7 % + PW_Basis real2recip 0.69464 38 0.018 10 % + PW_Basis gatherp_scatters 0.25906 38 0.0068 3.7 % + ORB_control set_orb_tables 1.0935 1 1.1 16 % + ORB_gen_tables gen_tables 1.0935 1 1.1 16 % + ORB_table_phi init_Table 0.47419 1 0.47 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.46903 126 0.0037 6.8 % + ORB_table_beta init_Table_Beta 0.18222 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18074 56 0.0032 2.6 % + ORB_table_alpha init_Table_Alpha 0.24763 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24567 66 0.0037 3.5 % + LOOP_ions opt_ions 5.3182 1 5.3 77 % + ESolver_KS_LCAO Run 4.7414 1 4.7 68 % + HSolverLCAO solve 2.2821 11 0.21 33 % + HamiltLCAO updateHk 1.2447 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.2167 11 0.11 18 % + Gint_interface cal_gint 2.1104 23 0.092 30 % + Gint_Gamma distri_vl 2.2718 6 0.38 33 % + LCAO_Deepks cal_projected_DM 5.1541 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.1257 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.1258 6 0.35 31 % + ElecStateLCAO psiToRho 1.0136 11 0.092 15 % + Charge mix_rho 0.90344 10 0.09 13 % + LOOP_ions force_stress 0.57663 1 0.58 8.3 % + Force_Stress_LCAO getForceStress 0.5766 1 0.58 8.3 % + Force_LCAO_gamma ftable_gamma 0.35777 1 0.36 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.34971 1 0.35 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:55 2022 + FINISH Time : Wed Sep 28 11:08:02 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/235/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fe68ef381d98757f610d624cf2f32e80827a3fc5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.632703 0.781078 0.168308 +H 0.635555 0.73091 0.127954 +H 0.58686 0.767189 0.213465 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d3326aea552401f7d3f82281ade2fa7bb9fa0722 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2873 2 + 2 -13.2452 2 + 3 -8.96872 2 + 4 -6.74275 2 + 5 1.35978 0 + 6 4.52857 0 + 7 11.0659 0 + 8 11.301 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..94f1b643a7001273890b1142f1e4e03c4f8bf331 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:24 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.7156883681 21.8701774449 4.71262519767 0 0 0 0 + tauc_H1 17.7955363606 20.4654692336 3.58270349551 0 0 0 0 + tauc_H2 16.4320726844 21.4812876944 5.97701507686 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0879831156236 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0886487881151 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.10668099883 (SEC) + + DONE : INIT CHARGE Time : 0.151675866761 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.43259 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000576 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134 + + Density error is 0.216081611802 + + Energy Rydberg eV + E_KohnSham -34.190209785 -465.181668891 + E_Harris -34.3840099865 -467.818455905 + E_Fermi -0.408138279406 -5.55300617184 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000860935559034 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013316313967 + + Density error is 0.0978761794497 + + Energy Rydberg eV + E_KohnSham -34.2801570006 -466.405463543 + E_Harris -34.2868166505 -466.496072729 + E_Fermi -0.216296538699 -2.94286538398 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000831353278687 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125031463493 + + Density error is 0.0627306320091 + + Energy Rydberg eV + E_KohnSham -34.2804200628 -466.409042687 + E_Harris -34.2847048475 -466.467340174 + E_Fermi -0.204197990829 -2.77825619543 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000798750670763 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112029797993 + + Density error is 0.00205405621235 + + Energy Rydberg eV + E_KohnSham -34.2804255147 -466.409116865 + E_Harris -34.2804279819 -466.409150432 + E_Fermi -0.168781394093 -2.29638867605 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00080020710576 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112000663972 + + Density error is 0.000876497719311 + + Energy Rydberg eV + E_KohnSham -34.2803648724 -466.408291784 + E_Harris -34.2803661639 -466.408309356 + E_Fermi -0.167908967127 -2.28451869822 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000799529043038 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111842359846 + + Density error is 0.000182228504833 + + Energy Rydberg eV + E_KohnSham -34.2804031412 -466.408812458 + E_Harris -34.2804032101 -466.408813395 + E_Fermi -0.167967155305 -2.285310389 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000799789891785 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111847001198 + + Density error is 4.11823304373e-05 + + Energy Rydberg eV + E_KohnSham -34.2803886637 -466.408615481 + E_Harris -34.2803886727 -466.408615604 + E_Fermi -0.167811239824 -2.28318905005 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000799721078828 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111842533767 + + Density error is 1.63918558867e-05 + + Energy Rydberg eV + E_KohnSham -34.2803935538 -466.408682014 + E_Harris -34.2803935549 -466.408682029 + E_Fermi -0.167856600201 -2.28380620965 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000799725186959 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111840726495 + + Density error is 1.65619796086e-06 + + Energy Rydberg eV + E_KohnSham -34.2803921144 -466.408662429 + E_Harris -34.2803921144 -466.40866243 + E_Fermi -0.167838995301 -2.28356668269 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000799726522017 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111840542682 + + Density error is 1.32184550266e-07 + + Energy Rydberg eV + E_KohnSham -34.2803923348 -466.408665429 + E_Harris -34.2803923348 -466.408665429 + E_Fermi -0.167837376745 -2.2835446611 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000799726859969 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111840591641 + + Density error is 3.86492617006e-08 + + Energy Rydberg eV + E_KohnSham -34.280392363 -466.408665812 + E_Harris -34.280392363 -466.408665812 + E_band -7.97370501921 -108.487822432 + E_one_elec -69.3994022602 -944.227308533 + E_Hartree +36.096567477 +491.118995929 + E_xc -8.21865755729 -111.82057269 + E_Ewald +7.36523195658 +100.209121701 + E_demet -1.58089528109e-80 -2.15091837641e-79 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194939703732 -2.65229073719 + E_Fermi -0.16783741162 -2.28354513561 + + charge density convergence is achieved + final etot is -466.408665812 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2873 2.00000 + 2 -13.2452 2.00000 + 3 -8.96872 2.00000 + 4 -6.74275 2.00000 + 5 1.35978 0.00000 + 6 4.52857 0.00000 + 7 11.0659 0.00000 + 8 11.3010 0.00000 + + EFERMI = -2.283545135607580 eV + OUT.ABACUS/ final etot is -466.4086658122815 eV + correction force for each atom along direction 1 is -2.62050e-05 + correction force for each atom along direction 2 is -5.08557e-05 + correction force for each atom along direction 3 is 3.01749e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.072303561 +1.0464106 +0.68429957 + H1 -0.10087323 -0.88964583 -0.53364731 + H2 +0.028569666 -0.15676476 -0.15065226 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4086658122815 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8641 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8535 1 6.9 1.e+02% + Potential init_pot 0.28277 2 0.14 4.1% + PW_Basis recip2real 0.28154 16 0.018 4.1% + PW_Basis gathers_scatterp 0.12202 16 0.0076 1.8% + Potential v_of_rho 1.0295 13 0.079 15.% + XC_Functional v_xc 0.31125 14 0.022 4.5% + H_Hartree_pw v_hartree 0.67511 13 0.052 9.8% + PW_Basis real2recip 0.69807 38 0.018 10.% + PW_Basis gatherp_scatters 0.25630 38 0.0067 3.7% + ORB_control set_orb_tables 1.0974 1 1.1 16.% + ORB_gen_tables gen_tables 1.0974 1 1.1 16.% + ORB_table_phi init_Table 0.47573 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47045 126 0.0037 6.9% + ORB_table_beta init_Table_Beta 0.18318 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18164 56 0.0032 2.6% + ORB_table_alpha init_Table_Alpha 0.24933 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24731 66 0.0037 3.6% + LOOP_ions opt_ions 5.2475 1 5.2 76.% + ESolver_KS_LCAO Run 4.7148 1 4.7 69.% + HSolverLCAO solve 2.2393 11 0.20 33.% + HamiltLCAO updateHk 1.1921 11 0.11 17.% + LCAO_Hamilt cal_Hgamma 1.1645 11 0.11 17.% + Gint_interface cal_gint 2.0242 23 0.088 29.% + Gint_Gamma distri_vl 2.2770 6 0.38 33.% + LCAO_Deepks cal_projected_DM 5.0989 13 0.39 74.% + LCAO_gen_fixedH add_v_delta 2.1278 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.1279 6 0.35 31.% + ElecStateLCAO psiToRho 1.0310 11 0.094 15.% + Charge mix_rho 0.90515 10 0.091 13.% + LOOP_ions force_stress 0.53256 1 0.53 7.8% + Force_Stress_LCAO getForceStress 0.53253 1 0.53 7.8% + Force_LCAO_gamma ftable_gamma 0.31300 1 0.31 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.30486 1 0.30 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:24 2022 + Finish Time : Wed Sep 28 11:03:31 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ad04b2d8081a3329a4413140a47f2ed2de8f3402 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123647 ima = 3.6937e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123328501954 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112442698313 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011292768982 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113170245111 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011311938404 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113149985879 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001131411706 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011314414197 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113143499729 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113143430664 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113143426301 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ed486dd6767bcbbf289590b7427703574fbb27a5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.284311631898 21.870177444867 4.712625197643 0 0 0 +H +0.0 +2 +-10.204463639339 20.465469233590 3.582703495496 0 0 0 +-11.567927315610 21.481287694414 5.977015076861 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/conv new file mode 100644 index 0000000000000000000000000000000000000000..d4d025265cbf76ebeadfa0dab097c15f4d7fdf47 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/conv @@ -0,0 +1 @@ +236 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..294b2e4c5a69de3cf3c8b6cf60dbe5fb983f58f3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746514604 0.01267095465 1.279432923 1.370452482 1.469364397 0.008090234941 0.01958448115 0.03894531303 +-9.398793469e-19 0.001131417865 0.002502401994 0.01242491897 0.04435845466 1.375513052e-20 1.780274332e-06 5.395260732e-06 +0.001714882436 0.005802802963 + +H atom_index 1 n_descriptor 18 +1.265738909 0.03336656354 0.1137767021 0.1580919158 0.3268951637 0.02270576996 0.02930631894 0.03666328854 +-2.926553881e-17 4.413668076e-05 0.105349545 0.1160026361 0.135779415 -4.136332801e-18 3.426599976e-06 0.01300272924 +0.02678731079 0.03150206492 + +H atom_index 2 n_descriptor 18 +1.234909304 0.03444206382 0.1031243374 0.1437487016 0.3171840047 0.02132646171 0.02752314884 0.037583207 +-6.455471701e-17 4.142614197e-05 0.09814027484 0.114338406 0.1234074274 -1.429552577e-18 4.988339327e-06 0.01318214 +0.02565437617 0.03013062751 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5383545ba90c022bbc5410af8967cfffaf1e0d9b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:24 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0880062 SEC) : SETUP UNITCELL + DONE(0.0886662 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106701 SEC) : INIT PLANEWAVE + DONE(0.151813 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.432659 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651817e+02 0.000000e+00 2.161e-01 5.188e-01 + GE2 -4.664055e+02 -1.223795e+00 9.788e-02 4.816e-01 + GE3 -4.664090e+02 -3.579144e-03 6.273e-02 5.542e-01 + GE4 -4.664091e+02 -7.417783e-05 2.054e-03 4.112e-01 + GE5 -4.664083e+02 8.250808e-04 8.765e-04 4.098e-01 + GE6 -4.664088e+02 -5.206736e-04 1.822e-04 4.031e-01 + GE7 -4.664086e+02 1.969766e-04 4.118e-05 3.962e-01 + GE8 -4.664087e+02 -6.653346e-05 1.639e-05 3.904e-01 + GE9 -4.664087e+02 1.958502e-05 1.656e-06 3.867e-01 + GE10 -4.664087e+02 -2.999816e-06 1.322e-07 3.877e-01 + GE11 -4.664087e+02 -3.830367e-07 3.865e-08 3.128e-01 +E_delta_band = -7.08077246e-02 Ry = -9.63388517e-01 eV +E_delta_NN= -1.94939704e-01 Ry = -2.65229074e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8641 11 0.62 1e+02 % + Run_lcao lcao_line 6.8535 1 6.9 1e+02 % + Potential init_pot 0.28277 2 0.14 4.1 % + PW_Basis recip2real 0.28154 16 0.018 4.1 % + PW_Basis gathers_scatterp 0.12202 16 0.0076 1.8 % + Potential v_of_rho 1.0295 13 0.079 15 % + XC_Functional v_xc 0.31125 14 0.022 4.5 % + H_Hartree_pw v_hartree 0.67511 13 0.052 9.8 % + PW_Basis real2recip 0.69807 38 0.018 10 % + PW_Basis gatherp_scatters 0.2563 38 0.0067 3.7 % + ORB_control set_orb_tables 1.0974 1 1.1 16 % + ORB_gen_tables gen_tables 1.0974 1 1.1 16 % + ORB_table_phi init_Table 0.47573 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47045 126 0.0037 6.9 % + ORB_table_beta init_Table_Beta 0.18318 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18164 56 0.0032 2.6 % + ORB_table_alpha init_Table_Alpha 0.24933 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24731 66 0.0037 3.6 % + LOOP_ions opt_ions 5.2475 1 5.2 76 % + ESolver_KS_LCAO Run 4.7148 1 4.7 69 % + HSolverLCAO solve 2.2393 11 0.2 33 % + HamiltLCAO updateHk 1.1921 11 0.11 17 % + LCAO_Hamilt cal_Hgamma 1.1645 11 0.11 17 % + Gint_interface cal_gint 2.0242 23 0.088 29 % + Gint_Gamma distri_vl 2.277 6 0.38 33 % + LCAO_Deepks cal_projected_DM 5.0989 13 0.39 74 % + LCAO_gen_fixedH add_v_delta 2.1278 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.1279 6 0.35 31 % + ElecStateLCAO psiToRho 1.031 11 0.094 15 % + Charge mix_rho 0.90515 10 0.091 13 % + LOOP_ions force_stress 0.53256 1 0.53 7.8 % + Force_Stress_LCAO getForceStress 0.53253 1 0.53 7.8 % + Force_LCAO_gamma ftable_gamma 0.313 1 0.31 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.30486 1 0.3 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:24 2022 + FINISH Time : Wed Sep 28 11:03:31 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/236/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..468fbcef3eec293ae2f41feb909c58548f41335f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.63931 0.770953 0.172726 +H 0.705011 0.77674 0.177393 +H 0.634094 0.756203 0.11005 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e1d4af4e75d251d12cff5c6605da9342c5dcfcf0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4066 2 + 2 -12.843 2 + 3 -9.34933 2 + 4 -6.77162 2 + 5 1.29243 0 + 6 4.43747 0 + 7 11.0618 0 + 8 11.3349 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fd645b259e612f9ee046c4d8a78818a32e283e36 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:06 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.900693764 21.5866907363 4.83632367796 0 0 0 0 + tauc_H1 19.7403148805 21.7487201851 4.9670091443 0 0 0 0 + tauc_H2 17.7546247498 21.1736742178 3.0813934273 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0879059019582 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0883345703618 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106394880137 (SEC) + + DONE : INIT CHARGE Time : 0.154797094256 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.434927 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00091 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000627 + + Density error is 0.215020475898 + + Energy Rydberg eV + E_KohnSham -34.1882801775 -465.155415235 + E_Harris -34.3809593477 -467.776949835 + E_Fermi -0.408532213842 -5.5583659248 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00133856765278 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000854499397345 + + Density error is 0.0978195386671 + + Energy Rydberg eV + E_KohnSham -34.2794112179 -466.395316649 + E_Harris -34.2862861033 -466.488854262 + E_Fermi -0.216423670042 -2.94459509464 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00128143227128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000820012012822 + + Density error is 0.0628966116827 + + Energy Rydberg eV + E_KohnSham -34.2798383279 -466.401127778 + E_Harris -34.2842913369 -466.461714074 + E_Fermi -0.206160517059 -2.80495773463 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120972487837 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000782857839932 + + Density error is 0.00195440232569 + + Energy Rydberg eV + E_KohnSham -34.2798134269 -466.400788982 + E_Harris -34.279814054 -466.400797515 + E_Fermi -0.170275728326 -2.31672013633 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121364893044 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785366263303 + + Density error is 0.00103946529291 + + Energy Rydberg eV + E_KohnSham -34.2797426075 -466.399825435 + E_Harris -34.2797443411 -466.399849022 + E_Fermi -0.169719740193 -2.3091555297 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121201420147 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784439555707 + + Density error is 9.76636058264e-05 + + Energy Rydberg eV + E_KohnSham -34.2797850076 -466.400402318 + E_Harris -34.2797850091 -466.400402339 + E_Fermi -0.169647947627 -2.30817874174 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121188389328 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784403946054 + + Density error is 4.15770442377e-05 + + Energy Rydberg eV + E_KohnSham -34.2797725935 -466.400233416 + E_Harris -34.2797726031 -466.400233547 + E_Fermi -0.169533160754 -2.30661698621 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012118233127 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784358171193 + + Density error is 9.70061268991e-06 + + Energy Rydberg eV + E_KohnSham -34.2797744811 -466.400259098 + E_Harris -34.2797744816 -466.400259104 + E_Fermi -0.169582280459 -2.30728529408 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012118340057 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784370034924 + + Density error is 4.58091031496e-07 + + Energy Rydberg eV + E_KohnSham -34.2797732071 -466.400241765 + E_Harris -34.2797732071 -466.400241765 + E_Fermi -0.169571993088 -2.30714532721 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121183292083 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784369756118 + + Density error is 1.53309991092e-07 + + Energy Rydberg eV + E_KohnSham -34.2797734202 -466.400244663 + E_Harris -34.2797734202 -466.400244663 + E_Fermi -0.169571772147 -2.30714232116 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012118331092 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784369879058 + + Density error is 2.84036553185e-08 + + Energy Rydberg eV + E_KohnSham -34.2797734175 -466.400244627 + E_Harris -34.2797734175 -466.400244627 + E_band -7.99232919338 -108.741217322 + E_one_elec -69.3618764076 -943.716743115 + E_Hartree +36.0651949676 +490.69215104 + E_xc -8.21367296881 -111.752753884 + E_Ewald +7.35473351596 +100.066283089 + E_demet -1.14131002077e-78 -1.5528319467e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194983035151 -2.65288029139 + E_Fermi -0.169571678191 -2.30714104281 + + charge density convergence is achieved + final etot is -466.400244627 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4066 2.00000 + 2 -12.8430 2.00000 + 3 -9.34933 2.00000 + 4 -6.77162 2.00000 + 5 1.29243 0.00000 + 6 4.43747 0.00000 + 7 11.0618 0.00000 + 8 11.3349 0.00000 + + EFERMI = -2.307141042813214 eV + OUT.ABACUS/ final etot is -466.4002446271202 eV + correction force for each atom along direction 1 is 0.000119538 + correction force for each atom along direction 2 is 0.000138579 + correction force for each atom along direction 3 is -0.000103313 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.59177487 +0.20389257 +0.66975657 + H1 -0.11826765 +0.070581969 +0.36118620 + H2 -0.47350722 -0.27447454 -1.0309428 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4002446271202 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6422 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6318 1 6.6 1.e+02% + Potential init_pot 0.28542 2 0.14 4.3% + PW_Basis recip2real 0.27863 16 0.017 4.2% + PW_Basis gathers_scatterp 0.13076 16 0.0082 2.0% + Potential v_of_rho 0.83996 13 0.065 13.% + XC_Functional v_xc 0.22199 14 0.016 3.3% + H_Hartree_pw v_hartree 0.58084 13 0.045 8.7% + PW_Basis real2recip 0.55551 38 0.015 8.4% + PW_Basis gatherp_scatters 0.21631 38 0.0057 3.3% + ORB_control set_orb_tables 1.0959 1 1.1 16.% + ORB_gen_tables gen_tables 1.0959 1 1.1 16.% + ORB_table_phi init_Table 0.48233 1 0.48 7.3% + ORB_table_phi cal_ST_Phi12_R 0.47742 126 0.0038 7.2% + ORB_table_beta init_Table_Beta 0.18699 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18554 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25376 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.25186 66 0.0038 3.8% + LOOP_ions opt_ions 5.0240 1 5.0 76.% + ESolver_KS_LCAO Run 4.4634 1 4.5 67.% + HSolverLCAO solve 2.5443 11 0.23 38.% + HamiltLCAO updateHk 1.3077 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.2793 11 0.12 19.% + Gint_interface cal_gint 2.4469 23 0.11 37.% + Gint_Gamma distri_vl 2.1444 6 0.36 32.% + LCAO_Deepks cal_projected_DM 4.8466 13 0.37 73.% + LCAO_gen_fixedH add_v_delta 2.0102 6 0.34 30.% + LCAO_DESCRIPTOR add_v_delta 2.0102 6 0.34 30.% + ElecStateLCAO psiToRho 1.2226 11 0.11 18.% + Charge mix_rho 0.65978 10 0.066 9.9% + LOOP_ions force_stress 0.56038 1 0.56 8.4% + Force_Stress_LCAO getForceStress 0.56036 1 0.56 8.4% + Force_LCAO_gamma ftable_gamma 0.35630 1 0.36 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.34949 1 0.35 5.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:06 2022 + Finish Time : Wed Sep 28 11:02:13 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..09a9fa79bddd52b1ab5e29453412fc2aa40ee90a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123737 ima = 3.68086e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122896256936 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011153408413 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112161109043 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112437152584 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112374722039 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112407608032 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240543502 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240814888 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240762073 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112407621925 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112407614827 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/STRU new file mode 100644 index 0000000000000000000000000000000000000000..6853630ed8d215e837415dbf3a3d586b945a14ec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.099306236012 21.586690736247 4.836323677943 0 0 0 +H +0.0 +2 +-8.259685119473 21.748720185042 4.967009144310 0 0 0 +-10.245375250144 21.173674217792 3.081393427289 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/conv new file mode 100644 index 0000000000000000000000000000000000000000..4d7cff9162ff4c3276e0507e3f395721b3cb1fdc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/conv @@ -0,0 +1 @@ +237 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d2a619c64fdd62dd00049e80f118eb0710ed5fd4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752810338 0.0127806609 1.273111019 1.357751642 1.46973991 0.009214829862 0.01730975779 0.03912659301 +2.456342893e-18 0.0009636257113 0.002796888806 0.01304487545 0.04676881469 -8.209602143e-20 2.608232705e-06 7.040415198e-06 +0.001597718152 0.006113020595 + +H atom_index 1 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:06 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087927 SEC) : SETUP UNITCELL + DONE(0.0883485 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.10642 SEC) : INIT PLANEWAVE + DONE(0.154943 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.434995 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651554e+02 0.000000e+00 2.150e-01 5.200e-01 + GE2 -4.663953e+02 -1.239901e+00 9.782e-02 4.427e-01 + GE3 -4.664011e+02 -5.811130e-03 6.290e-02 5.017e-01 + GE4 -4.664008e+02 3.387962e-04 1.954e-03 3.928e-01 + GE5 -4.663998e+02 9.635474e-04 1.039e-03 3.888e-01 + GE6 -4.664004e+02 -5.768836e-04 9.766e-05 3.685e-01 + GE7 -4.664002e+02 1.689023e-04 4.158e-05 3.702e-01 + GE8 -4.664003e+02 -2.568212e-05 9.701e-06 3.702e-01 + GE9 -4.664002e+02 1.733328e-05 4.581e-07 3.705e-01 + GE10 -4.664002e+02 -2.898454e-06 1.533e-07 3.675e-01 + GE11 -4.664002e+02 3.625876e-08 2.840e-08 3.094e-01 +E_delta_band = -7.08305105e-02 Ry = -9.63698535e-01 eV +E_delta_NN= -1.94983035e-01 Ry = -2.65288029e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6422 11 0.6 1e+02 % + Run_lcao lcao_line 6.6318 1 6.6 1e+02 % + Potential init_pot 0.28542 2 0.14 4.3 % + PW_Basis recip2real 0.27863 16 0.017 4.2 % + PW_Basis gathers_scatterp 0.13076 16 0.0082 2 % + Potential v_of_rho 0.83996 13 0.065 13 % + XC_Functional v_xc 0.22199 14 0.016 3.3 % + H_Hartree_pw v_hartree 0.58084 13 0.045 8.7 % + PW_Basis real2recip 0.55551 38 0.015 8.4 % + PW_Basis gatherp_scatters 0.21631 38 0.0057 3.3 % + ORB_control set_orb_tables 1.0959 1 1.1 16 % + ORB_gen_tables gen_tables 1.0959 1 1.1 16 % + ORB_table_phi init_Table 0.48233 1 0.48 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.47742 126 0.0038 7.2 % + ORB_table_beta init_Table_Beta 0.18699 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18554 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25376 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.25186 66 0.0038 3.8 % + LOOP_ions opt_ions 5.024 1 5 76 % + ESolver_KS_LCAO Run 4.4634 1 4.5 67 % + HSolverLCAO solve 2.5443 11 0.23 38 % + HamiltLCAO updateHk 1.3077 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.2793 11 0.12 19 % + Gint_interface cal_gint 2.4469 23 0.11 37 % + Gint_Gamma distri_vl 2.1444 6 0.36 32 % + LCAO_Deepks cal_projected_DM 4.8466 13 0.37 73 % + LCAO_gen_fixedH add_v_delta 2.0102 6 0.34 30 % + LCAO_DESCRIPTOR add_v_delta 2.0102 6 0.34 30 % + ElecStateLCAO psiToRho 1.2226 11 0.11 18 % + Charge mix_rho 0.65978 10 0.066 9.9 % + LOOP_ions force_stress 0.56038 1 0.56 8.4 % + Force_Stress_LCAO getForceStress 0.56036 1 0.56 8.4 % + Force_LCAO_gamma ftable_gamma 0.3563 1 0.36 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.34949 1 0.35 5.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:06 2022 + FINISH Time : Wed Sep 28 11:02:13 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/237/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..2b14c51143c82e63b1535f0022a310ad79621baf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.649753 0.777344 0.155552 +H 0.652395 0.791163 0.219484 +H 0.697671 0.730484 0.145152 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0e4af98ceb5e94a2c9db4bada99817d57bee378d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0751 2 + 2 -12.9473 2 + 3 -9.01721 2 + 4 -6.6952 2 + 5 1.12625 0 + 6 4.16222 0 + 7 11.1227 0 + 8 11.365 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1e514ba5d886dfb0bcaa3efa8c89e069e3d952ef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:02 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.1930875572 21.7656377452 4.35546489237 0 0 0 0 + tauc_H1 18.2670604882 22.1525749216 6.14554825961 0 0 0 0 + tauc_H2 19.5347826012 20.4535627169 4.06425692683 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0730190145842 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0849167395342 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.101101219747 (SEC) + + DONE : INIT CHARGE Time : 0.142438267399 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.389745 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00117 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126 + + Density error is 0.213142988098 + + Energy Rydberg eV + E_KohnSham -34.1907880055 -465.189535985 + E_Harris -34.3786682104 -467.745777313 + E_Fermi -0.393770957652 -5.35752873098 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00128337331118 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124745779687 + + Density error is 0.0984900642646 + + Energy Rydberg eV + E_KohnSham -34.2795771708 -466.397574553 + E_Harris -34.2865167205 -466.491991971 + E_Fermi -0.203487260581 -2.76858621432 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00121011125691 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117406213483 + + Density error is 0.063459424928 + + Energy Rydberg eV + E_KohnSham -34.2799253469 -466.402311732 + E_Harris -34.2843895755 -466.463050678 + E_Fermi -0.194999914712 -2.6531099496 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00108725673868 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105526354155 + + Density error is 0.00200821148979 + + Energy Rydberg eV + E_KohnSham -34.2798638077 -466.401474448 + E_Harris -34.2798661585 -466.401506433 + E_Fermi -0.159741096572 -2.17338911814 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00108571548939 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105409703919 + + Density error is 0.000891452052713 + + Energy Rydberg eV + E_KohnSham -34.2798223259 -466.40091006 + E_Harris -34.2798228942 -466.400917792 + E_Fermi -0.159390099522 -2.16861355829 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00108405480223 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105250067017 + + Density error is 0.000183895914159 + + Energy Rydberg eV + E_KohnSham -34.2798439948 -466.40120488 + E_Harris -34.2798438717 -466.401203205 + E_Fermi -0.159102120722 -2.16469540571 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00108425509002 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105270927174 + + Density error is 3.23244470307e-05 + + Energy Rydberg eV + E_KohnSham -34.2798362447 -466.401099434 + E_Harris -34.2798362487 -466.401099489 + E_Fermi -0.159045101143 -2.16391961454 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00108417902874 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105263723515 + + Density error is 1.44445834291e-05 + + Energy Rydberg eV + E_KohnSham -34.2798399212 -466.401149456 + E_Harris -34.279839922 -466.401149467 + E_Fermi -0.159069639409 -2.16425347476 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00108416819889 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105262763176 + + Density error is 2.3526653145e-06 + + Energy Rydberg eV + E_KohnSham -34.2798387678 -466.401133763 + E_Harris -34.2798387678 -466.401133763 + E_Fermi -0.159055450115 -2.16406041952 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00108416608559 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105262575819 + + Density error is 4.88961331124e-07 + + Energy Rydberg eV + E_KohnSham -34.2798389701 -466.401136516 + E_Harris -34.2798389701 -466.401136516 + E_Fermi -0.159053288342 -2.16403100709 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.001084166306 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105262586394 + + Density error is 1.82097288595e-07 + + Energy Rydberg eV + E_KohnSham -34.2798389905 -466.401136794 + E_Harris -34.2798389905 -466.401136794 + E_Fermi -0.159053091301 -2.16402832621 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00108416624331 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105262577911 + + Density error is 1.05068629923e-08 + + Energy Rydberg eV + E_KohnSham -34.2798389929 -466.401136826 + E_Harris -34.2798389929 -466.401136826 + E_band -7.89886716067 -107.46960113 + E_one_elec -68.893794867 -937.348167035 + E_Hartree +35.8556726895 +487.8414542 + E_xc -8.17999133658 -111.294491768 + E_Ewald +7.06342570301 +96.1028369606 + E_demet -3.59989071984e-66 -4.89790259672e-65 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19407030805 -2.64046200209 + E_Fermi -0.159052913078 -2.16402590136 + + charge density convergence is achieved + final etot is -466.401136826 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0751 2.00000 + 2 -12.9473 2.00000 + 3 -9.01721 2.00000 + 4 -6.69520 2.00000 + 5 1.12625 0.00000 + 6 4.16222 0.00000 + 7 11.1227 0.00000 + 8 11.3650 0.00000 + + EFERMI = -2.164025901358951 eV + OUT.ABACUS/ final etot is -466.4011368259280 eV + correction force for each atom along direction 1 is -2.09903e-05 + correction force for each atom along direction 2 is -6.15215e-05 + correction force for each atom along direction 3 is 8.90709e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.80661421 -0.90716623 -0.62063823 + H1 +0.11744609 -0.034038877 +0.28172848 + H2 -0.92406030 +0.94120510 +0.33890975 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4011368259280 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5674 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5598 1 7.6 1.e+02% + Potential init_pot 0.24688 2 0.12 3.3% + PW_Basis recip2real 0.28643 17 0.017 3.8% + PW_Basis gathers_scatterp 0.11859 17 0.0070 1.6% + Potential v_of_rho 0.99584 14 0.071 13.% + XC_Functional v_xc 0.29417 15 0.020 3.9% + H_Hartree_pw v_hartree 0.65982 14 0.047 8.7% + PW_Basis real2recip 0.65801 41 0.016 8.7% + PW_Basis gatherp_scatters 0.24516 41 0.0060 3.2% + ORB_control set_orb_tables 0.89379 1 0.89 12.% + ORB_gen_tables gen_tables 0.89378 1 0.89 12.% + ORB_table_phi init_Table 0.37671 1 0.38 5.0% + ORB_table_phi cal_ST_Phi12_R 0.37246 126 0.0030 4.9% + ORB_table_beta init_Table_Beta 0.15213 1 0.15 2.0% + ORB_table_beta VNL_PhiBeta_R 0.15083 56 0.0027 2.0% + ORB_table_alpha init_Table_Alpha 0.20702 1 0.21 2.7% + ORB_table_alpha S_PhiAlpha_R 0.20538 66 0.0031 2.7% + LOOP_ions opt_ions 6.2070 1 6.2 82.% + ESolver_KS_LCAO Run 5.6482 1 5.6 75.% + HSolverLCAO solve 3.2486 12 0.27 43.% + HamiltLCAO updateHk 1.5937 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.5585 12 0.13 21.% + Gint_interface cal_gint 3.1290 25 0.13 41.% + Gint_Gamma distri_vl 2.9237 6 0.49 39.% + LCAO_Deepks cal_projected_DM 6.0306 14 0.43 80.% + LCAO_gen_fixedH add_v_delta 2.7949 6 0.47 37.% + LCAO_DESCRIPTOR add_v_delta 2.7948 6 0.47 37.% + ElecStateLCAO psiToRho 1.6360 12 0.14 22.% + Charge mix_rho 0.84317 11 0.077 11.% + LOOP_ions force_stress 0.55862 1 0.56 7.4% + Force_Stress_LCAO getForceStress 0.55857 1 0.56 7.4% + Force_LCAO_gamma ftable_gamma 0.36212 1 0.36 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.35442 1 0.35 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:02 2022 + Finish Time : Wed Sep 28 11:09:10 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8aee0cba093926a21455f5d2f26d98bf63b689ff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123582 ima = 3.71114e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123525299509 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011228370163 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112946991223 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113153437518 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113127223803 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011314428923 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011313770567 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011314002276 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113139417627 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113139353282 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113139337583 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113139328088 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c1852166da0b75510f53996b5008b1b59b09077d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.806912442767 21.765637745200 4.355464892362 0 0 0 +H +0.0 +2 +-9.732939511786 22.152574921584 6.145548259620 0 0 0 +-8.465217398746 20.453562716888 4.064256926826 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/conv new file mode 100644 index 0000000000000000000000000000000000000000..d88cb4a146f83c7e48e28acc20012aa16f1a2ae7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/conv @@ -0,0 +1 @@ +238 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..df8f12e48c4c6984a5a14973cea3698763a02a6f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748297699 0.01250331187 1.256150524 1.35217406 1.468387615 0.008204877489 0.01863545055 0.03901739413 +2.378457771e-18 0.0009845278049 0.002420987351 0.01174035034 0.04244086329 5.168936849e-19 1.637954438e-06 5.072992418e-06 +0.001657348867 0.005826057803 + +H atom_index 1 n_descriptor 18 +1.244992149 0.03430066893 0.1059015214 0.148177117 0.3204527869 0.02169346442 0.02808932867 0.0375134816 +1.670845122e-17 4.02148702e-05 0.09871479795 0.1149796381 0.1270625955 2.563000172e-18 4.304378095e-06 0.01311976626 +0.02560709517 0.03055736216 + +H atom_index 2 n_descriptor 18 +1.19258983 0.03605209819 0.08938275043 0.1257249712 0.3019974256 0.01930410661 0.02503000994 0.03952768178 +-1.060763387e-17 3.582480499e-05 0.08499277038 0.1074287274 0.1132765138 8.842363035e-18 6.323634137e-06 0.01424311702 +0.02351136062 0.0279325376 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..2641bee798f874d302017a0bced7dbe84162a168 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/e_base.npy new file mode 100644 index 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TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:02 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.073037 SEC) : SETUP UNITCELL + DONE(0.0849272 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.101113 SEC) : INIT PLANEWAVE + DONE(0.14254 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.38979 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651895e+02 0.000000e+00 2.131e-01 5.413e-01 + GE2 -4.663976e+02 -1.208039e+00 9.849e-02 5.222e-01 + GE3 -4.664023e+02 -4.737179e-03 6.346e-02 5.857e-01 + GE4 -4.664015e+02 8.372844e-04 2.008e-03 4.581e-01 + GE5 -4.664009e+02 5.643878e-04 8.915e-04 4.570e-01 + GE6 -4.664012e+02 -2.948197e-04 1.839e-04 4.534e-01 + GE7 -4.664011e+02 1.054457e-04 3.232e-05 4.400e-01 + GE8 -4.664011e+02 -5.002148e-05 1.444e-05 4.386e-01 + GE9 -4.664011e+02 1.569281e-05 2.353e-06 4.384e-01 + GE10 -4.664011e+02 -2.752883e-06 4.890e-07 4.361e-01 + GE11 -4.664011e+02 -2.777384e-07 1.821e-07 4.404e-01 + GE12 -4.664011e+02 -3.219950e-08 1.051e-08 3.693e-01 +E_delta_band = -6.89191263e-02 Ry = -9.37692819e-01 eV +E_delta_NN= -1.94070308e-01 Ry = -2.64046200e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5674 11 0.69 1e+02 % + Run_lcao lcao_line 7.5598 1 7.6 1e+02 % + Potential init_pot 0.24688 2 0.12 3.3 % + PW_Basis recip2real 0.28643 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.11859 17 0.007 1.6 % + Potential v_of_rho 0.99584 14 0.071 13 % + XC_Functional v_xc 0.29417 15 0.02 3.9 % + H_Hartree_pw v_hartree 0.65982 14 0.047 8.7 % + PW_Basis real2recip 0.65801 41 0.016 8.7 % + PW_Basis gatherp_scatters 0.24516 41 0.006 3.2 % + ORB_control set_orb_tables 0.89379 1 0.89 12 % + ORB_gen_tables gen_tables 0.89378 1 0.89 12 % + ORB_table_phi init_Table 0.37671 1 0.38 5 % + ORB_table_phi cal_ST_Phi12_R 0.37246 126 0.003 4.9 % + ORB_table_beta init_Table_Beta 0.15213 1 0.15 2 % + ORB_table_beta VNL_PhiBeta_R 0.15083 56 0.0027 2 % + ORB_table_alpha init_Table_Alpha 0.20702 1 0.21 2.7 % + ORB_table_alpha S_PhiAlpha_R 0.20538 66 0.0031 2.7 % + LOOP_ions opt_ions 6.207 1 6.2 82 % + ESolver_KS_LCAO Run 5.6482 1 5.6 75 % + HSolverLCAO solve 3.2486 12 0.27 43 % + HamiltLCAO updateHk 1.5937 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.5585 12 0.13 21 % + Gint_interface cal_gint 3.129 25 0.13 41 % + Gint_Gamma distri_vl 2.9237 6 0.49 39 % + LCAO_Deepks cal_projected_DM 6.0306 14 0.43 80 % + LCAO_gen_fixedH add_v_delta 2.7949 6 0.47 37 % + LCAO_DESCRIPTOR add_v_delta 2.7948 6 0.47 37 % + ElecStateLCAO psiToRho 1.636 12 0.14 22 % + Charge mix_rho 0.84317 11 0.077 11 % + LOOP_ions force_stress 0.55862 1 0.56 7.4 % + Force_Stress_LCAO getForceStress 0.55857 1 0.56 7.4 % + Force_LCAO_gamma ftable_gamma 0.36212 1 0.36 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.35442 1 0.35 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:02 2022 + FINISH Time : Wed Sep 28 11:09:10 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/238/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..35a468663add01ada8e115d093e00014c776aa72 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.658986 0.778604 0.146258 +H 0.624116 0.822386 0.180382 +H 0.638829 0.723541 0.172512 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f6ce123610b3a408c6a7b42a9c4ddf3fe6999102 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4563 2 + 2 -12.9798 2 + 3 -9.28835 2 + 4 -6.7822 2 + 5 1.36747 0 + 6 4.55659 0 + 7 11.0449 0 + 8 11.3113 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..75554b71d21b467287712bc2117f28f8f1513818 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/running_scf.log @@ -0,0 +1,756 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:04 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.4515968352 21.8008999717 4.09521386405 0 0 0 0 + tauc_H1 17.4752379771 23.0268022678 5.05069066156 0 0 0 0 + tauc_H2 17.8872026951 20.259147391 4.83033219996 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0863418974695 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0984000059816 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116697449683 (SEC) + + DONE : INIT CHARGE Time : 0.167021436671 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441964 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00147 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909 + + Density error is 0.214622692323 + + Energy Rydberg eV + E_KohnSham -34.1911634751 -465.194644511 + E_Harris -34.3825991967 -467.799261125 + E_Fermi -0.411796342819 -5.60277667789 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00139059012896 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001145472608 + + Density error is 0.0974103703464 + + Energy Rydberg eV + E_KohnSham -34.2796587927 -466.398685076 + E_Harris -34.2863470477 -466.489683454 + E_Fermi -0.221630438787 -3.01543681775 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127556305598 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010973740881 + + Density error is 0.0622839655644 + + Energy Rydberg eV + E_KohnSham -34.2798199047 -466.400877118 + E_Harris -34.2841298411 -466.45951681 + E_Fermi -0.208596696866 -2.83810366135 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107621160312 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103529036632 + + Density error is 0.00197201387111 + + Energy Rydberg eV + E_KohnSham -34.2798369562 -466.401109115 + E_Harris -34.2798375114 -466.40111667 + E_Fermi -0.172896736504 -2.35238078206 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107398176619 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103824826941 + + Density error is 0.000834601937732 + + Energy Rydberg eV + E_KohnSham -34.2797733394 -466.400243565 + E_Harris -34.279775382 -466.400271355 + E_Fermi -0.171931895604 -2.33925344815 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010722778901 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103694324866 + + Density error is 9.64362130136e-05 + + Energy Rydberg eV + E_KohnSham -34.2798198339 -466.400876154 + E_Harris -34.2798198403 -466.400876241 + E_Fermi -0.17210419712 -2.34159773055 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107193933076 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103691380456 + + Density error is 4.01060342599e-05 + + Energy Rydberg eV + E_KohnSham -34.2798049662 -466.400673869 + E_Harris -34.2798049749 -466.400673987 + E_Fermi -0.171984332216 -2.33996688487 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107198327873 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103686688674 + + Density error is 9.35168585154e-06 + + Energy Rydberg eV + E_KohnSham -34.2798072644 -466.400705137 + E_Harris -34.2798072648 -466.400705142 + E_Fermi -0.172032983749 -2.34062882293 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107196698082 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103687441564 + + Density error is 5.83642505058e-07 + + Energy Rydberg eV + E_KohnSham -34.2798060526 -466.40068865 + E_Harris -34.2798060526 -466.40068865 + E_Fermi -0.172022769387 -2.3404898494 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107196643231 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103687401943 + + Density error is 8.37027256061e-08 + + Energy Rydberg eV + E_KohnSham -34.2798062357 -466.400691142 + E_Harris -34.2798062357 -466.400691142 + E_band -8.01233548967 -109.013416947 + E_one_elec -69.5147986973 -945.797357607 + E_Hartree +36.139601085 +491.704498203 + E_xc -8.22571927131 -111.916652238 + E_Ewald +7.4449552003 +101.293812079 + E_demet -2.58489703404e-83 -3.51693284063e-82 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195256402818 -2.65659964931 + E_Fermi -0.172022425614 -2.34048517213 + + charge density convergence is achieved + final etot is -466.400691142 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4563 2.00000 + 2 -12.9798 2.00000 + 3 -9.28835 2.00000 + 4 -6.78220 2.00000 + 5 1.36747 0.00000 + 6 4.55659 0.00000 + 7 11.0449 0.00000 + 8 11.3113 0.00000 + + EFERMI = -2.340485172128956 eV + OUT.ABACUS/ final etot is -466.4006911417680 eV + correction force for each atom along direction 1 is -0.000189517 + correction force for each atom along direction 2 is 2.33211e-05 + correction force for each atom along direction 3 is 0.000189222 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.27370888 +0.91019786 -0.37023285 + H1 -0.027932080 +0.40396654 -0.0024141148 + H2 -0.24577680 -1.3141644 +0.37264696 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4006911417680 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2969 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2879 1 6.3 1.e+02% + Potential init_pot 0.28185 2 0.14 4.5% + PW_Basis recip2real 0.25107 15 0.017 4.0% + PW_Basis gathers_scatterp 0.10777 15 0.0072 1.7% + Potential v_of_rho 0.80676 12 0.067 13.% + XC_Functional v_xc 0.22568 13 0.017 3.6% + H_Hartree_pw v_hartree 0.54663 12 0.046 8.7% + PW_Basis real2recip 0.50857 35 0.015 8.1% + PW_Basis gatherp_scatters 0.19405 35 0.0055 3.1% + ORB_control set_orb_tables 1.1057 1 1.1 18.% + ORB_gen_tables gen_tables 1.1057 1 1.1 18.% + ORB_table_phi init_Table 0.48509 1 0.49 7.7% + ORB_table_phi cal_ST_Phi12_R 0.48023 126 0.0038 7.6% + ORB_table_beta init_Table_Beta 0.18903 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18752 56 0.0033 3.0% + ORB_table_alpha init_Table_Alpha 0.25122 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.24934 66 0.0038 4.0% + LOOP_ions opt_ions 4.6585 1 4.7 74.% + ESolver_KS_LCAO Run 4.0865 1 4.1 65.% + HSolverLCAO solve 2.2981 10 0.23 36.% + HamiltLCAO updateHk 1.1853 10 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.1547 10 0.12 18.% + Gint_interface cal_gint 2.2099 21 0.11 35.% + Gint_Gamma distri_vl 2.1395 5 0.43 34.% + LCAO_Deepks cal_projected_DM 4.4823 12 0.37 71.% + LCAO_gen_fixedH add_v_delta 2.0062 5 0.40 32.% + LCAO_DESCRIPTOR add_v_delta 2.0062 5 0.40 32.% + ElecStateLCAO psiToRho 1.1002 10 0.11 17.% + Charge mix_rho 0.59460 9 0.066 9.4% + LOOP_ions force_stress 0.57190 1 0.57 9.1% + Force_Stress_LCAO getForceStress 0.57187 1 0.57 9.1% + Force_LCAO_gamma ftable_gamma 0.36189 1 0.36 5.7% + Force_LCAO_gamma cal_fvl_dphi 0.35503 1 0.36 5.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:04 2022 + Finish Time : Wed Sep 28 11:10:10 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8b9bb55769f78471a7b0737c2231f24f51b8fc83 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/OUT.ABACUS/warning.log @@ -0,0 +1,70 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012397 ima = 3.69426e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012255631943 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111688981866 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112161434244 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112418603083 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112353813086 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112390327005 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112387096843 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112389660628 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112389190854 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112389171051 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5d406320fb6797a7da7854f0d55016f2f3fd439f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.548403164822 21.800899971756 4.095213864052 0 0 0 +H +0.0 +2 +-10.524762022947 23.026802267836 5.050690661552 0 0 0 +-10.112797304888 20.259147391025 4.830332199975 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/conv new file mode 100644 index 0000000000000000000000000000000000000000..e8c1a004d306b28c7207c2bb45b0ac3f0a694965 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/conv @@ -0,0 +1 @@ +239 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9a30115ec96b6e088b4a57814c706b4aa28d5172 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751680599 0.01280368582 1.280113899 1.365006021 1.47000846 0.009041683183 0.01786212934 0.03909229597 +3.413046766e-18 0.001032813926 0.00279195953 0.01306494411 0.04722939792 5.160548231e-19 2.551322213e-06 6.910734483e-06 +0.001612753335 0.006080927011 + +H atom_index 1 n_descriptor 18 +1.24597391 0.03468812495 0.1081813605 0.1477340944 0.3187294475 0.02255628392 0.02802028383 0.03778923164 +-5.531491093e-17 4.989242552e-05 0.1021957836 0.1148178637 0.1268417541 -5.676666205e-18 3.996068961e-06 0.01334372678 +0.02668757164 0.03057011223 + +H atom_index 2 n_descriptor 18 +1.274835217 0.03372083494 0.1186339905 0.1615594307 0.3278435087 0.02394239398 0.02969846778 0.037016419 +-5.920570545e-18 5.268929672e-05 0.1073767221 0.1179926827 0.1387089555 1.27899351e-18 2.339997033e-06 0.01330897826 +0.02771589921 0.03182493415 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/dm_eig.npy new file mode 100644 index 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..10f867ca22e79447f75579179e7b6c4aeccd30f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/log.scf @@ -0,0 +1,100 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:04 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0863639 SEC) : SETUP UNITCELL + DONE(0.0984185 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116717 SEC) : INIT PLANEWAVE + DONE(0.167152 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.442029 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651946e+02 0.000000e+00 2.146e-01 5.230e-01 + GE2 -4.663987e+02 -1.204041e+00 9.741e-02 4.442e-01 + GE3 -4.664009e+02 -2.192042e-03 6.228e-02 5.026e-01 + GE4 -4.664011e+02 -2.319972e-04 1.972e-03 3.905e-01 + GE5 -4.664002e+02 8.655505e-04 8.346e-04 3.912e-01 + GE6 -4.664009e+02 -6.325892e-04 9.644e-05 3.653e-01 + GE7 -4.664007e+02 2.022847e-04 4.011e-05 3.691e-01 + GE8 -4.664007e+02 -3.126805e-05 9.352e-06 3.657e-01 + GE9 -4.664007e+02 1.648717e-05 5.836e-07 3.635e-01 + GE10 -4.664007e+02 -2.491785e-06 8.370e-08 3.101e-01 +E_delta_band = -7.14118504e-02 Ry = -9.71608070e-01 eV +E_delta_NN= -1.95256403e-01 Ry = -2.65659965e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2969 11 0.57 1e+02 % + Run_lcao lcao_line 6.2879 1 6.3 1e+02 % + Potential init_pot 0.28185 2 0.14 4.5 % + PW_Basis recip2real 0.25107 15 0.017 4 % + PW_Basis gathers_scatterp 0.10777 15 0.0072 1.7 % + Potential v_of_rho 0.80676 12 0.067 13 % + XC_Functional v_xc 0.22568 13 0.017 3.6 % + H_Hartree_pw v_hartree 0.54663 12 0.046 8.7 % + PW_Basis real2recip 0.50857 35 0.015 8.1 % + PW_Basis gatherp_scatters 0.19405 35 0.0055 3.1 % + ORB_control set_orb_tables 1.1057 1 1.1 18 % + ORB_gen_tables gen_tables 1.1057 1 1.1 18 % + ORB_table_phi init_Table 0.48509 1 0.49 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.48023 126 0.0038 7.6 % + ORB_table_beta init_Table_Beta 0.18903 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18752 56 0.0033 3 % + ORB_table_alpha init_Table_Alpha 0.25122 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.24934 66 0.0038 4 % + LOOP_ions opt_ions 4.6585 1 4.7 74 % + ESolver_KS_LCAO Run 4.0865 1 4.1 65 % + HSolverLCAO solve 2.2981 10 0.23 36 % + HamiltLCAO updateHk 1.1853 10 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.1547 10 0.12 18 % + Gint_interface cal_gint 2.2099 21 0.11 35 % + Gint_Gamma distri_vl 2.1395 5 0.43 34 % + LCAO_Deepks cal_projected_DM 4.4823 12 0.37 71 % + LCAO_gen_fixedH add_v_delta 2.0062 5 0.4 32 % + LCAO_DESCRIPTOR add_v_delta 2.0062 5 0.4 32 % + ElecStateLCAO psiToRho 1.1002 10 0.11 17 % + Charge mix_rho 0.5946 9 0.066 9.4 % + LOOP_ions force_stress 0.5719 1 0.57 9.1 % + Force_Stress_LCAO getForceStress 0.57187 1 0.57 9.1 % + Force_LCAO_gamma ftable_gamma 0.36189 1 0.36 5.7 % + Force_LCAO_gamma cal_fvl_dphi 0.35503 1 0.36 5.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:04 2022 + FINISH Time : Wed Sep 28 11:10:10 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/239/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..0ab5d11be04adefa66a18fde24a45eba511ac717 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.51103 0.355661 0.432194 +H 0.568479 0.351913 0.395541 +H 0.500104 0.295061 0.452355 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2b7949d05e0bdb4338774fac7aeaa26c1ea92a2d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1136 2 + 2 -12.9382 2 + 3 -9.0487 2 + 4 -6.70326 2 + 5 1.12351 0 + 6 4.20303 0 + 7 11.1153 0 + 8 11.3569 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..09836da46fe9cbfd78b8d6cbbc9bfa7002c7bc37 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:59 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.3088447666 9.95850024783 12.1014413815 0 0 0 0 + tauc_H1 15.9174084634 9.85355008114 11.0751366477 0 0 0 0 + tauc_H2 14.0029013768 8.26171579537 12.6659371303 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870136356539 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100663960814 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119461993469 (SEC) + + DONE : INIT CHARGE Time : 0.168197977105 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448159 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00156 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000763 + + Density error is 0.213205940076 + + Energy Rydberg eV + E_KohnSham -34.1899333676 -465.177908039 + E_Harris -34.3780665154 -467.737590833 + E_Fermi -0.395189283429 -5.37682604317 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00139741801413 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972895162 + + Density error is 0.0984831678761 + + Energy Rydberg eV + E_KohnSham -34.2785954708 -466.384217839 + E_Harris -34.2855103224 -466.478299222 + E_Fermi -0.205488587579 -2.79581566504 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012887976277 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00093471974697 + + Density error is 0.0634030620483 + + Energy Rydberg eV + E_KohnSham -34.2789074219 -466.388462153 + E_Harris -34.2833630453 -466.449084018 + E_Fermi -0.196528326832 -2.67390506332 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109078309778 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000886384901731 + + Density error is 0.00200513607227 + + Energy Rydberg eV + E_KohnSham -34.2788522221 -466.387711121 + E_Harris -34.2788545057 -466.387742191 + E_Fermi -0.161169073262 -2.19281773774 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108944808474 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000886206999917 + + Density error is 0.000882059922796 + + Energy Rydberg eV + E_KohnSham -34.2788115999 -466.387158427 + E_Harris -34.2788120714 -466.387164843 + E_Fermi -0.16082108286 -2.18808308542 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108692033747 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000885686521664 + + Density error is 0.000170456127348 + + Energy Rydberg eV + E_KohnSham -34.2788318505 -466.387433951 + E_Harris -34.2788318565 -466.387434033 + E_Fermi -0.160549977133 -2.18439450278 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108682252267 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000885913439304 + + Density error is 3.19845836214e-05 + + Energy Rydberg eV + E_KohnSham -34.2788255588 -466.387348348 + E_Harris -34.2788255631 -466.387348407 + E_Fermi -0.160473699025 -2.18335668588 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108678977751 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000885849219717 + + Density error is 1.44797091969e-05 + + Energy Rydberg eV + E_KohnSham -34.278828708 -466.387391194 + E_Harris -34.2788287089 -466.387391207 + E_Fermi -0.160498892773 -2.1836994644 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108676635632 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000885849385075 + + Density error is 1.63858963116e-06 + + Energy Rydberg eV + E_KohnSham -34.2788274975 -466.387374725 + E_Harris -34.2788274975 -466.387374725 + E_Fermi -0.160484053239 -2.18349756219 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108676258344 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000885849983582 + + Density error is 3.03536769817e-07 + + Energy Rydberg eV + E_KohnSham -34.2788277264 -466.387377839 + E_Harris -34.2788277264 -466.387377839 + E_Fermi -0.160482862595 -2.18348136264 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108676264006 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0008858506634 + + Density error is 7.08214860911e-08 + + Energy Rydberg eV + E_KohnSham -34.2788277482 -466.387378135 + E_Harris -34.2788277482 -466.387378135 + E_band -7.90899588789 -107.607409534 + E_one_elec -68.9430569658 -938.018412274 + E_Hartree +35.877675424 +488.140816761 + E_xc -8.18367997565 -111.344678277 + E_Ewald +7.09527362399 +96.5361501553 + E_demet -8.11824718802e-67 -1.1045441953e-65 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194194606817 -2.64215317359 + E_Fermi -0.160482739605 -2.18347968928 + + charge density convergence is achieved + final etot is -466.387378135 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1136 2.00000 + 2 -12.9382 2.00000 + 3 -9.04870 2.00000 + 4 -6.70326 2.00000 + 5 1.12351 0.00000 + 6 4.20303 0.00000 + 7 11.1153 0.00000 + 8 11.3569 0.00000 + + EFERMI = -2.183479689282855 eV + OUT.ABACUS/ final etot is -466.3873781353601 eV + correction force for each atom along direction 1 is 5.08359e-05 + correction force for each atom along direction 2 is -0.000110505 + correction force for each atom along direction 3 is -0.000113170 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.4002727 +0.79609645 -1.0895559 + H1 -1.3404717 -1.3510910e-06 +0.87669039 + H2 -0.059800956 -0.79609510 +0.21286554 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3873781353601 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9026 11 0.54 1.0e+02% + Run_lcao lcao_line 5.8929 1 5.9 1.e+02% + Potential init_pot 0.27940 2 0.14 4.7% + PW_Basis recip2real 0.26319 16 0.016 4.5% + PW_Basis gathers_scatterp 0.11884 16 0.0074 2.0% + Potential v_of_rho 0.87472 13 0.067 15.% + XC_Functional v_xc 0.24951 14 0.018 4.2% + H_Hartree_pw v_hartree 0.59047 13 0.045 10.% + PW_Basis real2recip 0.56503 38 0.015 9.6% + PW_Basis gatherp_scatters 0.22672 38 0.0060 3.8% + ORB_control set_orb_tables 1.1161 1 1.1 19.% + ORB_gen_tables gen_tables 1.1161 1 1.1 19.% + ORB_table_phi init_Table 0.48760 1 0.49 8.3% + ORB_table_phi cal_ST_Phi12_R 0.48274 126 0.0038 8.2% + ORB_table_beta init_Table_Beta 0.19034 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18882 56 0.0034 3.2% + ORB_table_alpha init_Table_Alpha 0.25953 1 0.26 4.4% + ORB_table_alpha S_PhiAlpha_R 0.25759 66 0.0039 4.4% + LOOP_ions opt_ions 4.2533 1 4.3 72.% + ESolver_KS_LCAO Run 3.7582 1 3.8 64.% + HSolverLCAO solve 1.7739 11 0.16 30.% + HamiltLCAO updateHk 0.95416 11 0.087 16.% + LCAO_Hamilt cal_Hgamma 0.92539 11 0.084 16.% + Gint_interface cal_gint 0.11361 23 0.0049 1.9% + Gint_Gamma distri_vl_value 0.53118 11 0.048 9.0% + Gint_Gamma distri_vl 1.8188 6 0.30 31.% + LCAO_Deepks cal_projected_DM 3.9230 13 0.30 66.% + LCAO_gen_fixedH add_v_delta 1.6870 6 0.28 29.% + LCAO_DESCRIPTOR add_v_delta 1.6870 6 0.28 29.% + ElecStateLCAO psiToRho 0.80216 11 0.073 14.% + Charge mix_rho 0.66443 10 0.066 11.% + LOOP_ions force_stress 0.49495 1 0.49 8.4% + Force_Stress_LCAO getForceStress 0.49493 1 0.49 8.4% + Force_LCAO_gamma ftable_gamma 0.28508 1 0.29 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:59 2022 + Finish Time : Wed Sep 28 11:11:05 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4eab92701516cfe1e140ef61964720e61a3adcc8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123895 ima = 3.6589e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123415922472 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112235961882 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112881389358 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113091621128 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113065877453 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113080813083 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113075754904 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113078157245 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011307748721 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113077423556 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113077410861 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e973de04a4409a8786fa42517037bd6772239b7b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.691155233431 9.958500247844 12.101441381549 0 0 0 +H +0.0 +2 +-12.082591536555 9.853550081143 11.075136647723 0 0 0 +-13.997098623205 8.261715795356 12.665937130300 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/conv new file mode 100644 index 0000000000000000000000000000000000000000..bf99cbe4ab7af81d3b656381f8aa819ddacc2421 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/conv @@ -0,0 +1 @@ +24 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..2ca7a84ff1f111901a4d4a7dd0dc4c7bbe749958 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748835282 0.01251365905 1.255614274 1.355035466 1.468584325 0.008323743708 0.01853368508 0.03904039111 +1.153658536e-18 0.0009850877665 0.002460402125 0.01179188741 0.04296103945 2.349542705e-19 1.696815891e-06 5.239529446e-06 +0.001642698242 0.005838710127 + +H atom_index 1 n_descriptor 18 +1.18370515 0.03636006888 0.08686548345 0.1220913162 0.2983239749 0.01894582275 0.02449234745 0.03993470828 +2.002794773e-18 3.594201476e-05 0.08287143692 0.1042293374 0.112795578 3.741995311e-18 6.6157414e-06 0.01455732061 +0.02319374417 0.02743915484 + +H atom_index 2 n_descriptor 18 +1.260274958 0.03382128539 0.111278422 0.1552075255 0.3250876255 0.02244876621 0.02895804824 0.0371022888 +-1.675752638e-17 4.246527431e-05 0.1025166344 0.1156658987 0.1331344149 -3.683176742e-18 3.534720492e-06 0.01306260855 +0.02622812849 0.0312298938 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..17b12f4a31084610e711fc07b7e44a82aa445751 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:59 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870342 SEC) : SETUP UNITCELL + DONE(0.100681 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119483 SEC) : INIT PLANEWAVE + DONE(0.16834 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448223 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651779e+02 0.000000e+00 2.132e-01 4.536e-01 + GE2 -4.663842e+02 -1.206310e+00 9.848e-02 3.790e-01 + GE3 -4.663885e+02 -4.244313e-03 6.340e-02 4.329e-01 + GE4 -4.663877e+02 7.510316e-04 2.005e-03 3.275e-01 + GE5 -4.663872e+02 5.526939e-04 8.821e-04 3.231e-01 + GE6 -4.663874e+02 -2.755243e-04 1.705e-04 3.178e-01 + GE7 -4.663873e+02 8.560295e-05 3.198e-05 3.092e-01 + GE8 -4.663874e+02 -4.284591e-05 1.448e-05 3.038e-01 + GE9 -4.663874e+02 1.646971e-05 1.639e-06 3.031e-01 + GE10 -4.663874e+02 -3.114261e-06 3.035e-07 3.038e-01 + GE11 -4.663874e+02 -2.965408e-07 7.082e-08 2.438e-01 +E_delta_band = -6.91547521e-02 Ry = -9.40898673e-01 eV +E_delta_NN= -1.94194607e-01 Ry = -2.64215317e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9026 11 0.54 1e+02 % + Run_lcao lcao_line 5.8929 1 5.9 1e+02 % + Potential init_pot 0.2794 2 0.14 4.7 % + PW_Basis recip2real 0.26319 16 0.016 4.5 % + PW_Basis gathers_scatterp 0.11884 16 0.0074 2 % + Potential v_of_rho 0.87472 13 0.067 15 % + XC_Functional v_xc 0.24951 14 0.018 4.2 % + H_Hartree_pw v_hartree 0.59047 13 0.045 10 % + PW_Basis real2recip 0.56503 38 0.015 9.6 % + PW_Basis gatherp_scatters 0.22672 38 0.006 3.8 % + ORB_control set_orb_tables 1.1161 1 1.1 19 % + ORB_gen_tables gen_tables 1.1161 1 1.1 19 % + ORB_table_phi init_Table 0.4876 1 0.49 8.3 % + ORB_table_phi cal_ST_Phi12_R 0.48274 126 0.0038 8.2 % + ORB_table_beta init_Table_Beta 0.19034 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18882 56 0.0034 3.2 % + ORB_table_alpha init_Table_Alpha 0.25953 1 0.26 4.4 % + ORB_table_alpha S_PhiAlpha_R 0.25759 66 0.0039 4.4 % + LOOP_ions opt_ions 4.2533 1 4.3 72 % + ESolver_KS_LCAO Run 3.7582 1 3.8 64 % + HSolverLCAO solve 1.7739 11 0.16 30 % + HamiltLCAO updateHk 0.95416 11 0.087 16 % + LCAO_Hamilt cal_Hgamma 0.92539 11 0.084 16 % + Gint_interface cal_gint 0.11361 23 0.0049 1.9 % + Gint_Gamma distri_vl_value 0.53118 11 0.048 9 % + Gint_Gamma distri_vl 1.8188 6 0.3 31 % + LCAO_Deepks cal_projected_DM 3.923 13 0.3 66 % + LCAO_gen_fixedH add_v_delta 1.687 6 0.28 29 % + LCAO_DESCRIPTOR add_v_delta 1.687 6 0.28 29 % + ElecStateLCAO psiToRho 0.80216 11 0.073 14 % + Charge mix_rho 0.66443 10 0.066 11 % + LOOP_ions force_stress 0.49495 1 0.49 8.4 % + Force_Stress_LCAO getForceStress 0.49493 1 0.49 8.4 % + Force_LCAO_gamma ftable_gamma 0.28508 1 0.29 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:59 2022 + FINISH Time : Wed Sep 28 11:11:05 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/24/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..6510716d4270154f8f5a64f602683a5cc2b0e904 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.665418 0.786086 0.146765 +H 0.653913 0.824753 0.094793 +H 0.619394 0.74039 0.144756 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8fd9dd0bf0e9c74775536ebcc83a32283f92cace --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2888 2 + 2 -13.1289 2 + 3 -9.05662 2 + 4 -6.74421 2 + 5 1.32987 0 + 6 4.46686 0 + 7 11.0711 0 + 8 11.3164 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c093caa9cf44df61c83afa7108379012e219bdf4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:38 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.6316947201 22.0104070809 4.10942249309 0 0 0 0 + tauc_H1 18.3095624511 23.093085613 2.65420528685 0 0 0 0 + tauc_H2 17.3430307645 20.7309142851 4.05317617147 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0878962331964 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0893631785459 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107690585458 (SEC) + + DONE : INIT CHARGE Time : 0.157832883859 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438815 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00126 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133 + + Density error is 0.215017727383 + + Energy Rydberg eV + E_KohnSham -34.1917541417 -465.202680942 + E_Harris -34.3835139609 -467.811707131 + E_Fermi -0.406470664828 -5.5303171115 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00132903536231 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130020299692 + + Density error is 0.097871461355 + + Energy Rydberg eV + E_KohnSham -34.2809155516 -466.415784159 + E_Harris -34.2876069349 -466.506825099 + E_Fermi -0.215280315783 -2.92903896189 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012412772886 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121836053942 + + Density error is 0.0627422980238 + + Energy Rydberg eV + E_KohnSham -34.2811453526 -466.418910761 + E_Harris -34.285463898 -466.477667587 + E_Fermi -0.20350517752 -2.76882998677 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010916198089 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108766408467 + + Density error is 0.00200987680129 + + Energy Rydberg eV + E_KohnSham -34.2811425161 -466.418872169 + E_Harris -34.2811444162 -466.418898021 + E_Fermi -0.168050231975 -2.28644070508 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109033527935 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108781708131 + + Density error is 0.000860183443411 + + Energy Rydberg eV + E_KohnSham -34.2810845001 -466.41808282 + E_Harris -34.281085695 -466.418099078 + E_Fermi -0.167246411267 -2.27550416328 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010886115475 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108617315113 + + Density error is 0.000170485096017 + + Energy Rydberg eV + E_KohnSham -34.2811228119 -466.41860408 + E_Harris -34.2811228883 -466.418605119 + E_Fermi -0.167286175656 -2.27604518555 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108863629353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108625369729 + + Density error is 3.81912252471e-05 + + Energy Rydberg eV + E_KohnSham -34.2811080212 -466.418402842 + E_Harris -34.281108029 -466.418402948 + E_Fermi -0.167147955465 -2.27416460337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108860865881 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108622693716 + + Density error is 1.6177202112e-05 + + Energy Rydberg eV + E_KohnSham -34.2811127234 -466.418466819 + E_Harris -34.2811127244 -466.418466832 + E_Fermi -0.167191139391 -2.27475215083 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108858176102 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108620852248 + + Density error is 1.68705852603e-06 + + Energy Rydberg eV + E_KohnSham -34.2811113513 -466.418448151 + E_Harris -34.2811113513 -466.418448151 + E_Fermi -0.167173485574 -2.27451195832 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108858000223 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108620577767 + + Density error is 2.75081048293e-07 + + Energy Rydberg eV + E_KohnSham -34.2811115663 -466.418451075 + E_Harris -34.2811115663 -466.418451075 + E_Fermi -0.167172083647 -2.27449288413 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108858057881 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108620627742 + + Density error is 9.32845384423e-08 + + Energy Rydberg eV + E_KohnSham -34.2811115906 -466.418451406 + E_Harris -34.2811115906 -466.418451406 + E_band -7.96997886551 -108.43712551 + E_one_elec -69.3375439626 -943.385683217 + E_Hartree +36.0640641722 +490.676765779 + E_xc -8.21345088742 -111.749732312 + E_Ewald +7.33006349929 +99.7306302922 + E_demet -7.16335150191e-79 -9.74623972028e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194860871956 -2.65121817585 + E_Fermi -0.167172010186 -2.27449188464 + + charge density convergence is achieved + final etot is -466.418451406 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2888 2.00000 + 2 -13.1289 2.00000 + 3 -9.05662 2.00000 + 4 -6.74421 2.00000 + 5 1.32987 0.00000 + 6 4.46686 0.00000 + 7 11.0711 0.00000 + 8 11.3164 0.00000 + + EFERMI = -2.274491884639136 eV + OUT.ABACUS/ final etot is -466.4184514061770 eV + correction force for each atom along direction 1 is -0.000148740 + correction force for each atom along direction 2 is 3.11713e-05 + correction force for each atom along direction 3 is 8.68221e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.57790579 +0.51242319 +0.098477673 + H1 -0.053326855 -0.046445735 -0.014187277 + H2 -0.52457893 -0.46597746 -0.084290396 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4184514061770 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6048 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5944 1 7.6 1.e+02% + Potential init_pot 0.28418 2 0.14 3.7% + PW_Basis recip2real 0.28628 16 0.018 3.8% + PW_Basis gathers_scatterp 0.12139 16 0.0076 1.6% + Potential v_of_rho 1.0078 13 0.078 13.% + XC_Functional v_xc 0.30011 14 0.021 3.9% + H_Hartree_pw v_hartree 0.66718 13 0.051 8.8% + PW_Basis real2recip 0.65094 38 0.017 8.6% + PW_Basis gatherp_scatters 0.24991 38 0.0066 3.3% + ORB_control set_orb_tables 1.0942 1 1.1 14.% + ORB_gen_tables gen_tables 1.0942 1 1.1 14.% + ORB_table_phi init_Table 0.47681 1 0.48 6.3% + ORB_table_phi cal_ST_Phi12_R 0.47170 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18385 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18227 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24797 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24603 66 0.0037 3.2% + LOOP_ions opt_ions 5.9817 1 6.0 79.% + ESolver_KS_LCAO Run 5.3651 1 5.4 71.% + HSolverLCAO solve 3.0730 11 0.28 40.% + HamiltLCAO updateHk 1.5585 11 0.14 20.% + LCAO_Hamilt cal_Hgamma 1.5267 11 0.14 20.% + Gint_interface cal_gint 2.9522 23 0.13 39.% + Gint_Gamma distri_vl 2.5763 6 0.43 34.% + LCAO_Deepks cal_projected_DM 5.8004 13 0.45 76.% + LCAO_gen_fixedH add_v_delta 2.4311 6 0.41 32.% + LCAO_DESCRIPTOR add_v_delta 2.4312 6 0.41 32.% + ElecStateLCAO psiToRho 1.4991 11 0.14 20.% + Charge mix_rho 0.77783 10 0.078 10.% + LOOP_ions force_stress 0.61642 1 0.62 8.1% + Force_Stress_LCAO getForceStress 0.61639 1 0.62 8.1% + Force_LCAO_gamma ftable_gamma 0.39703 1 0.40 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.38910 1 0.39 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:38 2022 + Finish Time : Wed Sep 28 11:07:46 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1f77f05b934ef99902363a5c563ca2fa79951e46 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123737 ima = 3.70324e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123144261794 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112227402756 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112734292692 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112973933144 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112923752436 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112955195312 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112946438635 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112949245379 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112948625968 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112948559836 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112948549606 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4e28bf9380d0aab999d8a000f6debb6786910b74 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.368305279967 22.010407080929 4.109422493118 0 0 0 +H +0.0 +2 +-9.690437548860 23.093085612954 2.654205286842 0 0 0 +-10.656969235496 20.730914285080 4.053176171497 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/conv new file mode 100644 index 0000000000000000000000000000000000000000..cdf9169aaa99be05877806d33953a286a3a0f651 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/conv @@ -0,0 +1 @@ +240 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d08eb3863db94393d94457be60838017485d2317 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748119835 0.0126835017 1.276007922 1.365286316 1.469329423 0.008323456087 0.01896970622 0.03899140908 +-1.33833486e-18 0.001086016714 0.00255803891 0.01241414067 0.04479507719 -2.442366564e-19 1.929547726e-06 5.693915282e-06 +0.00167561974 0.00589896761 + +H atom_index 1 n_descriptor 18 +1.237500652 0.03453984491 0.1039618925 0.1445361855 0.3174265627 0.0215605157 0.02762217054 0.03768055861 +-1.44417996e-17 4.333732821e-05 0.09860784539 0.1144760732 0.1240614288 2.443386066e-18 4.830636185e-06 0.01323651299 +0.02579017067 0.03021510933 + +H atom_index 2 n_descriptor 18 +1.257608817 0.03384152091 0.1108687414 0.1538220524 0.3239030011 0.0224802207 0.02879054061 0.03704823993 +4.594863552e-17 4.516119753e-05 0.1035124487 0.1153839905 0.1320850664 -7.826891268e-18 3.782623203e-06 0.01307348667 +0.026538118 0.03112808812 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0ef1d4bf4f4cadd14d5247707482555da106f42e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:38 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0879204 SEC) : SETUP UNITCELL + DONE(0.0893815 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107712 SEC) : INIT PLANEWAVE + DONE(0.157959 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438884 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652027e+02 0.000000e+00 2.150e-01 5.859e-01 + GE2 -4.664158e+02 -1.213103e+00 9.787e-02 5.347e-01 + GE3 -4.664189e+02 -3.126602e-03 6.274e-02 6.040e-01 + GE4 -4.664189e+02 3.859221e-05 2.010e-03 4.699e-01 + GE5 -4.664181e+02 7.893486e-04 8.602e-04 4.677e-01 + GE6 -4.664186e+02 -5.212599e-04 1.705e-04 4.586e-01 + GE7 -4.664184e+02 2.012377e-04 3.819e-05 4.571e-01 + GE8 -4.664185e+02 -6.397635e-05 1.618e-05 4.496e-01 + GE9 -4.664184e+02 1.866809e-05 1.687e-06 4.486e-01 + GE10 -4.664185e+02 -2.924551e-06 2.751e-07 4.484e-01 + GE11 -4.664185e+02 -3.309435e-07 9.328e-08 3.787e-01 +E_delta_band = -7.06164599e-02 Ry = -9.60786227e-01 eV +E_delta_NN= -1.94860872e-01 Ry = -2.65121818e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6048 11 0.69 1e+02 % + Run_lcao lcao_line 7.5944 1 7.6 1e+02 % + Potential init_pot 0.28418 2 0.14 3.7 % + PW_Basis recip2real 0.28628 16 0.018 3.8 % + PW_Basis gathers_scatterp 0.12139 16 0.0076 1.6 % + Potential v_of_rho 1.0078 13 0.078 13 % + XC_Functional v_xc 0.30011 14 0.021 3.9 % + H_Hartree_pw v_hartree 0.66718 13 0.051 8.8 % + PW_Basis real2recip 0.65094 38 0.017 8.6 % + PW_Basis gatherp_scatters 0.24991 38 0.0066 3.3 % + ORB_control set_orb_tables 1.0942 1 1.1 14 % + ORB_gen_tables gen_tables 1.0942 1 1.1 14 % + ORB_table_phi init_Table 0.47681 1 0.48 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.4717 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18385 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18227 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24797 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24603 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9817 1 6 79 % + ESolver_KS_LCAO Run 5.3651 1 5.4 71 % + HSolverLCAO solve 3.073 11 0.28 40 % + HamiltLCAO updateHk 1.5585 11 0.14 20 % + LCAO_Hamilt cal_Hgamma 1.5267 11 0.14 20 % + Gint_interface cal_gint 2.9522 23 0.13 39 % + Gint_Gamma distri_vl 2.5763 6 0.43 34 % + LCAO_Deepks cal_projected_DM 5.8004 13 0.45 76 % + LCAO_gen_fixedH add_v_delta 2.4311 6 0.41 32 % + LCAO_DESCRIPTOR add_v_delta 2.4312 6 0.41 32 % + ElecStateLCAO psiToRho 1.4991 11 0.14 20 % + Charge mix_rho 0.77783 10 0.078 10 % + LOOP_ions force_stress 0.61642 1 0.62 8.1 % + Force_Stress_LCAO getForceStress 0.61639 1 0.62 8.1 % + Force_LCAO_gamma ftable_gamma 0.39703 1 0.4 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.3891 1 0.39 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:38 2022 + FINISH Time : Wed Sep 28 11:07:46 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/240/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b1ce0e6df1b2f93664f36eaf70941515c300a4b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.681985 0.804698 0.138623 +H 0.725086 0.818715 0.0935863 +H 0.690608 0.739335 0.147565 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..373a3c3b073e1bf37aa3ac7a0962dc5318154214 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3701 2 + 2 -13.0241 2 + 3 -9.18866 2 + 4 -6.76198 2 + 5 1.31881 0 + 6 4.49767 0 + 7 11.0598 0 + 8 11.3136 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4115c7f4944e1756ad6ad68b18fd33f416c79e83 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:26 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.0955916376 22.5315571307 3.88144010762 0 0 0 0 + tauc_H1 20.3024085799 22.9240089278 2.62041733861 0 0 0 0 + tauc_H2 19.3370197021 20.7013905946 4.13182776447 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0738949162098 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.087437206474 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103817243732 (SEC) + + DONE : INIT CHARGE Time : 0.144994843218 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.391166 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00161 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0007 + + Density error is 0.21469682196 + + Energy Rydberg eV + E_KohnSham -34.1905967614 -465.186933975 + E_Harris -34.3819888804 -467.790957346 + E_Fermi -0.408795532783 -5.5619485628 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00143926575192 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000977728811769 + + Density error is 0.0976369669696 + + Energy Rydberg eV + E_KohnSham -34.2794109828 -466.39531345 + E_Harris -34.2861221835 -466.48662402 + E_Fermi -0.218225840014 -2.96911487502 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00131811434919 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946876451524 + + Density error is 0.0624764732988 + + Energy Rydberg eV + E_KohnSham -34.2796107794 -466.398031822 + E_Harris -34.2839381496 -466.456908714 + E_Fermi -0.206005799857 -2.80285269911 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110235535712 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914485382552 + + Density error is 0.00198750397805 + + Energy Rydberg eV + E_KohnSham -34.2796135992 -466.398070187 + E_Harris -34.2796149916 -466.398089131 + E_Fermi -0.170395709582 -2.31835256507 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109879675839 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000915137329295 + + Density error is 0.000831608625344 + + Energy Rydberg eV + E_KohnSham -34.2795567564 -466.397296801 + E_Harris -34.2795580103 -466.397313862 + E_Fermi -0.169585383574 -2.30732751412 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109691811075 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914510529907 + + Density error is 0.000145684648951 + + Energy Rydberg eV + E_KohnSham -34.2795953459 -466.397821838 + E_Harris -34.2795953893 -466.397822428 + E_Fermi -0.169645755902 -2.30814892179 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109677595206 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009148350711 + + Density error is 3.84200106951e-05 + + Energy Rydberg eV + E_KohnSham -34.2795813676 -466.397631654 + E_Harris -34.279581375 -466.397631755 + E_Fermi -0.16952070403 -2.30644750379 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109677106375 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914726772035 + + Density error is 1.96488451085e-05 + + Energy Rydberg eV + E_KohnSham -34.2795853969 -466.397686476 + E_Harris -34.2795853987 -466.3976865 + E_Fermi -0.169563099777 -2.30702432751 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109673727514 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914740503017 + + Density error is 2.70787024962e-06 + + Energy Rydberg eV + E_KohnSham -34.2795838321 -466.397665186 + E_Harris -34.2795838321 -466.397665186 + E_Fermi -0.169543848593 -2.30676240171 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109672966511 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00091474313026 + + Density error is 2.51680633411e-07 + + Energy Rydberg eV + E_KohnSham -34.2795841266 -466.397669193 + E_Harris -34.2795841266 -466.397669193 + E_Fermi -0.169540932359 -2.30672272431 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109672974476 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914743436316 + + Density error is 1.05433043116e-07 + + Energy Rydberg eV + E_KohnSham -34.2795841725 -466.397669816 + E_Harris -34.2795841725 -466.397669816 + E_Fermi -0.169540888055 -2.30672212153 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109672954899 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914743614199 + + Density error is 1.04405537744e-08 + + Energy Rydberg eV + E_KohnSham -34.2795841738 -466.397669834 + E_Harris -34.2795841738 -466.397669834 + E_band -7.98855150715 -108.689819264 + E_one_elec -69.3998264565 -944.233080019 + E_Hartree +36.0886634611 +491.011456276 + E_xc -8.21761469424 -111.80638381 + E_Ewald +7.37329644431 +100.318844686 + E_demet -9.06705192935e-80 -1.23363570301e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195043556301 -2.65370372388 + E_Fermi -0.169540808226 -2.3067210354 + + charge density convergence is achieved + final etot is -466.397669834 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3701 2.00000 + 2 -13.0241 2.00000 + 3 -9.18866 2.00000 + 4 -6.76198 2.00000 + 5 1.31881 0.00000 + 6 4.49767 0.00000 + 7 11.0598 0.00000 + 8 11.3136 0.00000 + + EFERMI = -2.306721035399418 eV + OUT.ABACUS/ final etot is -466.3976698337635 eV + correction force for each atom along direction 1 is -1.59999e-05 + correction force for each atom along direction 2 is -5.19334e-05 + correction force for each atom along direction 3 is 4.32276e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.91132799 -0.94765029 +1.1243806 + H1 +1.0617070 +0.48203318 -1.1457326 + H2 -0.15037901 +0.46561711 +0.021351935 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3976698337635 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8167 11 0.71 1.0e+02% + Run_lcao lcao_line 7.8092 1 7.8 1.e+02% + Potential init_pot 0.24451 2 0.12 3.1% + PW_Basis recip2real 0.27315 17 0.016 3.5% + PW_Basis gathers_scatterp 0.11442 17 0.0067 1.5% + Potential v_of_rho 0.98282 14 0.070 13.% + XC_Functional v_xc 0.29602 15 0.020 3.8% + H_Hartree_pw v_hartree 0.64698 14 0.046 8.3% + PW_Basis real2recip 0.64265 41 0.016 8.2% + PW_Basis gatherp_scatters 0.23801 41 0.0058 3.0% + ORB_control set_orb_tables 0.90134 1 0.90 12.% + ORB_gen_tables gen_tables 0.90134 1 0.90 12.% + ORB_table_phi init_Table 0.37631 1 0.38 4.8% + ORB_table_phi cal_ST_Phi12_R 0.37211 126 0.0030 4.8% + ORB_table_beta init_Table_Beta 0.15601 1 0.16 2.0% + ORB_table_beta VNL_PhiBeta_R 0.15463 56 0.0028 2.0% + ORB_table_alpha init_Table_Alpha 0.21150 1 0.21 2.7% + ORB_table_alpha S_PhiAlpha_R 0.20977 66 0.0032 2.7% + LOOP_ions opt_ions 6.4461 1 6.4 82.% + ESolver_KS_LCAO Run 5.8838 1 5.9 75.% + HSolverLCAO solve 3.5385 12 0.29 45.% + HamiltLCAO updateHk 1.7502 12 0.15 22.% + LCAO_Hamilt cal_Hgamma 1.7190 12 0.14 22.% + Gint_interface cal_gint 3.4348 25 0.14 44.% + Gint_Gamma distri_vl 3.0454 6 0.51 39.% + LCAO_Deepks cal_projected_DM 6.2736 14 0.45 80.% + LCAO_gen_fixedH add_v_delta 2.9162 6 0.49 37.% + LCAO_DESCRIPTOR add_v_delta 2.9161 6 0.49 37.% + ElecStateLCAO psiToRho 1.7701 12 0.15 23.% + Charge mix_rho 0.82432 11 0.075 11.% + LOOP_ions force_stress 0.56220 1 0.56 7.2% + Force_Stress_LCAO getForceStress 0.56217 1 0.56 7.2% + Force_LCAO_gamma ftable_gamma 0.36863 1 0.37 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.36120 1 0.36 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:26 2022 + Finish Time : Wed Sep 28 11:02:34 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..9a87c1c51f9bcd400b085d5ce4dee6e237608eb7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123798 ima = 3.66398e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122885073838 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112010175767 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112509799795 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112754995706 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112702910787 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112734022492 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112727207224 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112730222843 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112729330997 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112729215746 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112729207772 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112729203507 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1f52558b2324a8742a7cec9cb268c8fec24bedda --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.904408362386 22.531557130684 3.881440107614 0 0 0 +H +0.0 +2 +-7.697591420118 22.924008927765 2.620417338625 0 0 0 +-8.662980297904 20.701390594570 4.131827764462 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/conv new file mode 100644 index 0000000000000000000000000000000000000000..e298dddb0ef4fd01ef93038d91f7fd18b79560f1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/conv @@ -0,0 +1 @@ +241 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..58c333dceabcbe8c51f477a7718185fe26deb38e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750324588 0.01272205202 1.274492221 1.36578273 1.469675267 0.008747349892 0.01830344926 0.03906183745 +-1.650804271e-18 0.001048000917 0.002683108199 0.01264809923 0.04608646376 5.286279684e-19 2.224362741e-06 6.309090727e-06 +0.001627499095 0.005990874674 + +H atom_index 1 n_descriptor 18 +1.281485668 0.03330984045 0.1202283744 0.1651245868 0.3303446177 0.0239052925 0.03011068785 0.03674926855 +2.037091934e-17 5.060108318e-05 0.1074483902 0.1188031372 0.1417300061 1.431345005e-17 2.244005242e-06 0.01330690163 +0.02760386827 0.03208874373 + +H atom_index 2 n_descriptor 18 +1.223086851 0.03527943415 0.09972646659 0.137763347 0.3115836058 0.02116426395 0.02671677279 0.03844594481 +-6.136297099e-18 4.509351155e-05 0.09533375934 0.1139956477 0.1181580579 -7.559707157e-18 5.414905207e-06 0.01361188843 +0.02546753127 0.02947900221 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ebb3676cf822c398e0ddf809fece221a41549068 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:26 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0739103 SEC) : SETUP UNITCELL + DONE(0.0874503 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103833 SEC) : INIT PLANEWAVE + DONE(0.145098 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.391209 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651869e+02 0.000000e+00 2.147e-01 5.608e-01 + GE2 -4.663953e+02 -1.208379e+00 9.764e-02 5.368e-01 + GE3 -4.663980e+02 -2.718372e-03 6.248e-02 5.983e-01 + GE4 -4.663981e+02 -3.836506e-05 1.988e-03 4.787e-01 + GE5 -4.663973e+02 7.733860e-04 8.316e-04 4.762e-01 + GE6 -4.663978e+02 -5.250369e-04 1.457e-04 4.724e-01 + GE7 -4.663976e+02 1.901837e-04 3.842e-05 4.696e-01 + GE8 -4.663977e+02 -5.482174e-05 1.965e-05 4.626e-01 + GE9 -4.663977e+02 2.129039e-05 2.708e-06 4.577e-01 + GE10 -4.663977e+02 -4.007079e-06 2.517e-07 4.611e-01 + GE11 -4.663977e+02 -6.233210e-07 1.054e-07 4.604e-01 + GE12 -4.663977e+02 -1.781514e-08 1.044e-08 3.957e-01 +E_delta_band = -7.09406278e-02 Ry = -9.65196758e-01 eV +E_delta_NN= -1.95043556e-01 Ry = -2.65370372e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8167 11 0.71 1e+02 % + Run_lcao lcao_line 7.8092 1 7.8 1e+02 % + Potential init_pot 0.24451 2 0.12 3.1 % + PW_Basis recip2real 0.27315 17 0.016 3.5 % + PW_Basis gathers_scatterp 0.11442 17 0.0067 1.5 % + Potential v_of_rho 0.98282 14 0.07 13 % + XC_Functional v_xc 0.29602 15 0.02 3.8 % + H_Hartree_pw v_hartree 0.64698 14 0.046 8.3 % + PW_Basis real2recip 0.64265 41 0.016 8.2 % + PW_Basis gatherp_scatters 0.23801 41 0.0058 3 % + ORB_control set_orb_tables 0.90134 1 0.9 12 % + ORB_gen_tables gen_tables 0.90134 1 0.9 12 % + ORB_table_phi init_Table 0.37631 1 0.38 4.8 % + ORB_table_phi cal_ST_Phi12_R 0.37211 126 0.003 4.8 % + ORB_table_beta init_Table_Beta 0.15601 1 0.16 2 % + ORB_table_beta VNL_PhiBeta_R 0.15463 56 0.0028 2 % + ORB_table_alpha init_Table_Alpha 0.2115 1 0.21 2.7 % + ORB_table_alpha S_PhiAlpha_R 0.20977 66 0.0032 2.7 % + LOOP_ions opt_ions 6.4461 1 6.4 82 % + ESolver_KS_LCAO Run 5.8838 1 5.9 75 % + HSolverLCAO solve 3.5385 12 0.29 45 % + HamiltLCAO updateHk 1.7502 12 0.15 22 % + LCAO_Hamilt cal_Hgamma 1.719 12 0.14 22 % + Gint_interface cal_gint 3.4348 25 0.14 44 % + Gint_Gamma distri_vl 3.0454 6 0.51 39 % + LCAO_Deepks cal_projected_DM 6.2736 14 0.45 80 % + LCAO_gen_fixedH add_v_delta 2.9162 6 0.49 37 % + LCAO_DESCRIPTOR add_v_delta 2.9161 6 0.49 37 % + ElecStateLCAO psiToRho 1.7701 12 0.15 23 % + Charge mix_rho 0.82432 11 0.075 11 % + LOOP_ions force_stress 0.5622 1 0.56 7.2 % + Force_Stress_LCAO getForceStress 0.56217 1 0.56 7.2 % + Force_LCAO_gamma ftable_gamma 0.36863 1 0.37 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.3612 1 0.36 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:26 2022 + FINISH Time : Wed Sep 28 11:02:34 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/241/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..54ca8c99d358878405e2143bf2a062abc19c6b76 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.697734 0.81385 0.14301 +H 0.75208 0.852988 0.14345 +H 0.678507 0.810127 0.202629 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9fe1c06087231c8b4eb5cc2426c0f90fa7710de7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3775 2 + 2 -13.2309 2 + 3 -9.03318 2 + 4 -6.76025 2 + 5 1.34964 0 + 6 4.61998 0 + 7 11.0483 0 + 8 11.279 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9df602ded9fce8faad539246db82af641f1ead89 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:39 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.536552083 22.7878044275 4.00427792463 0 0 0 0 + tauc_H1 21.0582478909 23.8836656791 4.01658647299 0 0 0 0 + tauc_H2 18.9981929112 22.6835499126 5.67361502696 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0730323427387 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0734052393477 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0898208272722 (SEC) + + DONE : INIT CHARGE Time : 0.133471102588 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.377941 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000792 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000918 + + Density error is 0.217214782391 + + Energy Rydberg eV + E_KohnSham -34.1847039729 -465.106758475 + E_Harris -34.3817190986 -467.787286776 + E_Fermi -0.413218701602 -5.62212886194 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118470984145 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110118652536 + + Density error is 0.0980621697545 + + Energy Rydberg eV + E_KohnSham -34.2763651653 -466.353872977 + E_Harris -34.2830619424 -466.444987304 + E_Fermi -0.220145801966 -2.99523729751 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113659350947 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104672946066 + + Density error is 0.0628297246357 + + Energy Rydberg eV + E_KohnSham -34.2766870765 -466.358252803 + E_Harris -34.280994442 -466.416857518 + E_Fermi -0.207960096024 -2.82944226255 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107361350394 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967066198594 + + Density error is 0.00205426243827 + + Energy Rydberg eV + E_KohnSham -34.2766955364 -466.358367906 + E_Harris -34.2766979575 -466.358400846 + E_Fermi -0.17226691011 -2.34381155435 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107679610993 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009687171138 + + Density error is 0.000917539744885 + + Energy Rydberg eV + E_KohnSham -34.2766293278 -466.357467093 + E_Harris -34.2766305398 -466.357483583 + E_Fermi -0.171416703969 -2.33224390636 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107566082934 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967558660292 + + Density error is 0.000174433395983 + + Energy Rydberg eV + E_KohnSham -34.2766686336 -466.358001875 + E_Harris -34.2766687138 -466.358002966 + E_Fermi -0.171461020178 -2.33284685931 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107587051746 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967705827076 + + Density error is 4.44198185528e-05 + + Energy Rydberg eV + E_KohnSham -34.2766538834 -466.357801188 + E_Harris -34.2766538937 -466.357801329 + E_Fermi -0.171308585431 -2.33077287818 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107580844655 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967656222873 + + Density error is 1.80349587507e-05 + + Energy Rydberg eV + E_KohnSham -34.2766589213 -466.357869732 + E_Harris -34.2766589225 -466.357869748 + E_Fermi -0.171356645392 -2.3314267675 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107580905603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967650411925 + + Density error is 3.02879845035e-06 + + Energy Rydberg eV + E_KohnSham -34.2766574061 -466.357849117 + E_Harris -34.2766574062 -466.357849118 + E_Fermi -0.171338787281 -2.33118379543 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107580626096 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967647567147 + + Density error is 3.01698721284e-07 + + Energy Rydberg eV + E_KohnSham -34.2766575904 -466.357851624 + E_Harris -34.2766575904 -466.357851624 + E_Fermi -0.171335499984 -2.33113906946 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107580703834 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967648281773 + + Density error is 1.63374719413e-07 + + Energy Rydberg eV + E_KohnSham -34.276657642 -466.357852327 + E_Harris -34.276657642 -466.357852327 + E_Fermi -0.171335504105 -2.33113912553 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107580727479 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967648463327 + + Density error is 1.05280461708e-08 + + Energy Rydberg eV + E_KohnSham -34.2766576405 -466.357852306 + E_Harris -34.2766576405 -466.357852306 + E_band -7.99692091038 -108.803690837 + E_one_elec -69.5152839955 -945.803960428 + E_Hartree +36.1487456275 +491.828916086 + E_xc -8.22751341275 -111.941062785 + E_Ewald +7.44129948375 +101.244073503 + E_demet -3.89159491075e-82 -5.2947865094e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195247286955 -2.65647562163 + E_Fermi -0.171335351978 -2.33113705574 + + charge density convergence is achieved + final etot is -466.357852306 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3775 2.00000 + 2 -13.2309 2.00000 + 3 -9.03318 2.00000 + 4 -6.76025 2.00000 + 5 1.34964 0.00000 + 6 4.61998 0.00000 + 7 11.0483 0.00000 + 8 11.2790 0.00000 + + EFERMI = -2.331137055738609 eV + OUT.ABACUS/ final etot is -466.3578523055109 eV + correction force for each atom along direction 1 is -1.29748e-05 + correction force for each atom along direction 2 is -5.20440e-05 + correction force for each atom along direction 3 is 4.17841e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.4392580 +0.58633321 -2.6322012 + H1 -0.71677215 -0.49750176 +0.097306285 + H2 -0.72248585 -0.088831450 +2.5348949 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3578523055109 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6873 11 0.70 1.0e+02% + Run_lcao lcao_line 7.6801 1 7.7 1.e+02% + Potential init_pot 0.24430 2 0.12 3.2% + PW_Basis recip2real 0.27090 17 0.016 3.5% + PW_Basis gathers_scatterp 0.11165 17 0.0066 1.5% + Potential v_of_rho 0.98386 14 0.070 13.% + XC_Functional v_xc 0.29439 15 0.020 3.8% + H_Hartree_pw v_hartree 0.64950 14 0.046 8.4% + PW_Basis real2recip 0.65155 41 0.016 8.5% + PW_Basis gatherp_scatters 0.23937 41 0.0058 3.1% + ORB_control set_orb_tables 0.89377 1 0.89 12.% + ORB_gen_tables gen_tables 0.89377 1 0.89 12.% + ORB_table_phi init_Table 0.37380 1 0.37 4.9% + ORB_table_phi cal_ST_Phi12_R 0.36956 126 0.0029 4.8% + ORB_table_beta init_Table_Beta 0.15439 1 0.15 2.0% + ORB_table_beta VNL_PhiBeta_R 0.15310 56 0.0027 2.0% + ORB_table_alpha init_Table_Alpha 0.20720 1 0.21 2.7% + ORB_table_alpha S_PhiAlpha_R 0.20558 66 0.0031 2.7% + LOOP_ions opt_ions 6.3384 1 6.3 82.% + ESolver_KS_LCAO Run 5.7777 1 5.8 75.% + HSolverLCAO solve 3.4349 12 0.29 45.% + HamiltLCAO updateHk 1.7013 12 0.14 22.% + LCAO_Hamilt cal_Hgamma 1.6688 12 0.14 22.% + Gint_interface cal_gint 3.3258 25 0.13 43.% + Gint_Gamma distri_vl 2.9952 6 0.50 39.% + LCAO_Deepks cal_projected_DM 6.1679 14 0.44 80.% + LCAO_gen_fixedH add_v_delta 2.8678 6 0.48 37.% + LCAO_DESCRIPTOR add_v_delta 2.8678 6 0.48 37.% + ElecStateLCAO psiToRho 1.7164 12 0.14 22.% + Charge mix_rho 0.82893 11 0.075 11.% + LOOP_ions force_stress 0.56057 1 0.56 7.3% + Force_Stress_LCAO getForceStress 0.56054 1 0.56 7.3% + Force_LCAO_gamma ftable_gamma 0.36626 1 0.37 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.35850 1 0.36 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:39 2022 + Finish Time : Wed Sep 28 11:12:47 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4e4999ddf1492598d540f63a8e8e75119cdd6dc7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123961 ima = 3.69365e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123345718455 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011228779049 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112792527274 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113057773866 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011300323221 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113035195702 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113026119272 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113029292076 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113028669007 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113028541253 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113028536938 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113028529136 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3641c10744bdcef9a6b3c8e20d61080da5321e89 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.463447917029 22.787804427434 4.004277924622 0 0 0 +H +0.0 +2 +-6.941752109116 23.883665679078 4.016586472998 0 0 0 +-9.001807088817 22.683549912573 5.673615026959 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/conv new file mode 100644 index 0000000000000000000000000000000000000000..8ea17c05757e5a45f4c405f81c75cb2483c95efb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/conv @@ -0,0 +1 @@ +242 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..90bb025886f67b53b7f91b44df215050055a3bfe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747746238 0.01266614756 1.277561274 1.377876108 1.469836404 0.008365567244 0.01942584444 0.0390024299 +5.213074245e-18 0.001137790423 0.002592324066 0.0124943532 0.04556273133 5.213607805e-19 1.901406947e-06 5.715742557e-06 +0.00167483953 0.005806967018 + +H atom_index 1 n_descriptor 18 +1.210422697 0.03537886322 0.09533023206 0.1329013653 0.3082212917 0.02030955123 0.02605628016 0.03861143459 +3.314124105e-18 4.145100204e-05 0.09195374597 0.1135653228 0.113968864 9.27648767e-18 6.130617319e-06 0.01373707862 +0.02481236674 0.02890277313 + +H atom_index 2 n_descriptor 18 +1.304148011 0.03227102418 0.1285532838 0.1774796106 0.3371413111 0.02452277261 0.0314464152 0.03630965998 +-1.643969677e-17 4.99344866e-05 0.1078954626 0.1245918804 0.1522145098 8.390161083e-19 1.425816315e-06 0.01373787142 +0.02814708713 0.03291125916 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c77863a2f53bd330b1330a593d027995ed2451d8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:39 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0730482 SEC) : SETUP UNITCELL + DONE(0.0734148 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0898353 SEC) : INIT PLANEWAVE + DONE(0.133575 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.377984 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651068e+02 0.000000e+00 2.172e-01 5.517e-01 + GE2 -4.663539e+02 -1.247115e+00 9.806e-02 5.288e-01 + GE3 -4.663583e+02 -4.379826e-03 6.283e-02 5.906e-01 + GE4 -4.663584e+02 -1.151025e-04 2.054e-03 4.728e-01 + GE5 -4.663575e+02 9.008129e-04 9.175e-04 4.702e-01 + GE6 -4.663580e+02 -5.347823e-04 1.744e-04 4.652e-01 + GE7 -4.663578e+02 2.006871e-04 4.442e-05 4.597e-01 + GE8 -4.663579e+02 -6.854454e-05 1.803e-05 4.478e-01 + GE9 -4.663578e+02 2.061500e-05 3.029e-06 4.489e-01 + GE10 -4.663579e+02 -2.506572e-06 3.017e-07 4.511e-01 + GE11 -4.663579e+02 -7.030610e-07 1.634e-07 4.547e-01 + GE12 -4.663579e+02 2.142370e-08 1.053e-08 3.828e-01 +E_delta_band = -7.13419436e-02 Ry = -9.70656939e-01 eV +E_delta_NN= -1.95247287e-01 Ry = -2.65647562e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6873 11 0.7 1e+02 % + Run_lcao lcao_line 7.6801 1 7.7 1e+02 % + Potential init_pot 0.2443 2 0.12 3.2 % + PW_Basis recip2real 0.2709 17 0.016 3.5 % + PW_Basis gathers_scatterp 0.11165 17 0.0066 1.5 % + Potential v_of_rho 0.98386 14 0.07 13 % + XC_Functional v_xc 0.29439 15 0.02 3.8 % + H_Hartree_pw v_hartree 0.6495 14 0.046 8.4 % + PW_Basis real2recip 0.65155 41 0.016 8.5 % + PW_Basis gatherp_scatters 0.23937 41 0.0058 3.1 % + ORB_control set_orb_tables 0.89377 1 0.89 12 % + ORB_gen_tables gen_tables 0.89377 1 0.89 12 % + ORB_table_phi init_Table 0.3738 1 0.37 4.9 % + ORB_table_phi cal_ST_Phi12_R 0.36956 126 0.0029 4.8 % + ORB_table_beta init_Table_Beta 0.15439 1 0.15 2 % + ORB_table_beta VNL_PhiBeta_R 0.1531 56 0.0027 2 % + ORB_table_alpha init_Table_Alpha 0.2072 1 0.21 2.7 % + ORB_table_alpha S_PhiAlpha_R 0.20558 66 0.0031 2.7 % + LOOP_ions opt_ions 6.3384 1 6.3 82 % + ESolver_KS_LCAO Run 5.7777 1 5.8 75 % + HSolverLCAO solve 3.4349 12 0.29 45 % + HamiltLCAO updateHk 1.7013 12 0.14 22 % + LCAO_Hamilt cal_Hgamma 1.6688 12 0.14 22 % + Gint_interface cal_gint 3.3258 25 0.13 43 % + Gint_Gamma distri_vl 2.9952 6 0.5 39 % + LCAO_Deepks cal_projected_DM 6.1679 14 0.44 80 % + LCAO_gen_fixedH add_v_delta 2.8678 6 0.48 37 % + LCAO_DESCRIPTOR add_v_delta 2.8678 6 0.48 37 % + ElecStateLCAO psiToRho 1.7164 12 0.14 22 % + Charge mix_rho 0.82893 11 0.075 11 % + LOOP_ions force_stress 0.56057 1 0.56 7.3 % + Force_Stress_LCAO getForceStress 0.56054 1 0.56 7.3 % + Force_LCAO_gamma ftable_gamma 0.36626 1 0.37 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.3585 1 0.36 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:39 2022 + FINISH Time : Wed Sep 28 11:12:47 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/242/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..cc8bf89ddda97bb92266fa2b7166b794eaa3e564 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.696038 0.82388 0.163416 +H 0.718424 0.858523 0.212175 +H 0.635057 0.801625 0.185316 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..822c567039587222155271abad137c8dff4a9d22 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1959 2 + 2 -12.947 2 + 3 -9.09809 2 + 4 -6.72026 2 + 5 1.14075 0 + 6 4.3002 0 + 7 11.0984 0 + 8 11.338 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c2d731934ffb44037a4ce9fcf01e7b16eae66db4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:41 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.4890501629 23.0686467486 4.57564421851 0 0 0 0 + tauc_H1 20.115858757 24.0386331596 5.94090651943 0 0 0 0 + tauc_H2 17.7815960385 22.4454913263 5.1888374891 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0875971572837 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0987286385171 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117083811082 (SEC) + + DONE : INIT CHARGE Time : 0.166704445392 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451111 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00076 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00156 + + Density error is 0.214460175262 + + Energy Rydberg eV + E_KohnSham -34.1864008073 -465.129845091 + E_Harris -34.3777384559 -467.733127354 + E_Fermi -0.40003374841 -5.44273837067 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109813698408 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133194874816 + + Density error is 0.098541186212 + + Energy Rydberg eV + E_KohnSham -34.2768778404 -466.36084828 + E_Harris -34.283818171 -466.455276321 + E_Fermi -0.20892587449 -2.8425823527 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105447213816 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123627601635 + + Density error is 0.0634008523745 + + Energy Rydberg eV + E_KohnSham -34.2772782466 -466.366296085 + E_Harris -34.2817465116 -466.42708995 + E_Fermi -0.199899023642 -2.71976574616 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000999627528328 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106065218365 + + Density error is 0.00199364353608 + + Energy Rydberg eV + E_KohnSham -34.2772276289 -466.365607396 + E_Harris -34.2772293655 -466.365631024 + E_Fermi -0.16430828858 -2.23552895331 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00099944514738 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105858371389 + + Density error is 0.000946339342961 + + Energy Rydberg eV + E_KohnSham -34.2771756001 -466.364899507 + E_Harris -34.2771764926 -466.364911652 + E_Fermi -0.16393208141 -2.23041039218 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000998557897975 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105609379803 + + Density error is 0.000165661054888 + + Energy Rydberg eV + E_KohnSham -34.2772014605 -466.365251356 + E_Harris -34.277201493 -466.365251799 + E_Fermi -0.163685261489 -2.22705223488 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00099881170963 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105611188588 + + Density error is 3.85891729267e-05 + + Energy Rydberg eV + E_KohnSham -34.2771925001 -466.365129444 + E_Harris -34.2771925067 -466.365129534 + E_Fermi -0.163605397165 -2.225965625 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000998702180542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105606322577 + + Density error is 1.55189462816e-05 + + Energy Rydberg eV + E_KohnSham -34.2771963752 -466.365182167 + E_Harris -34.2771963762 -466.365182181 + E_Fermi -0.16363608125 -2.22638310339 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000998703439495 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105603768215 + + Density error is 2.38864007584e-06 + + Energy Rydberg eV + E_KohnSham -34.2771950287 -466.365163847 + E_Harris -34.2771950287 -466.365163848 + E_Fermi -0.163620554991 -2.22617185779 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000998705998846 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105603483658 + + Density error is 5.15505768458e-07 + + Energy Rydberg eV + E_KohnSham -34.2771952281 -466.36516656 + E_Harris -34.2771952281 -466.36516656 + E_Fermi -0.163618545685 -2.22614451979 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000998706841864 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105603487352 + + Density error is 1.78894238278e-07 + + Energy Rydberg eV + E_KohnSham -34.2771952581 -466.365166968 + E_Harris -34.2771952581 -466.365166968 + E_Fermi -0.163618326324 -2.22614153522 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000998707064107 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105603463871 + + Density error is 1.17606313212e-08 + + Energy Rydberg eV + E_KohnSham -34.2771952615 -466.365167015 + E_Harris -34.2771952615 -466.365167015 + E_band -7.93215057168 -107.922445169 + E_one_elec -69.0689327843 -939.731040645 + E_Hartree +35.9353255892 +488.925187498 + E_xc -8.19321546555 -111.474415273 + E_Ewald +7.17440393603 +97.6127732836 + E_demet -3.67048874143e-69 -4.99395613283e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19447303599 -2.64594139683 + E_Fermi -0.163618153819 -2.22613918818 + + charge density convergence is achieved + final etot is -466.365167015 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1959 2.00000 + 2 -12.9470 2.00000 + 3 -9.09809 2.00000 + 4 -6.72026 2.00000 + 5 1.14075 0.00000 + 6 4.30020 0.00000 + 7 11.0984 0.00000 + 8 11.3380 0.00000 + + EFERMI = -2.226139188182565 eV + OUT.ABACUS/ final etot is -466.3651670145669 eV + correction force for each atom along direction 1 is -6.93878e-05 + correction force for each atom along direction 2 is -2.85631e-06 + correction force for each atom along direction 3 is 0.000109911 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -2.1056913 -1.4591793 -0.72346567 + H1 +0.55896233 +0.88673223 +1.2623379 + H2 +1.5467289 +0.57244707 -0.53887222 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3651670145669 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.0231 11 0.73 1.0e+02% + Run_lcao lcao_line 8.0133 1 8.0 1.e+02% + Potential init_pot 0.28580 2 0.14 3.6% + PW_Basis recip2real 0.30549 17 0.018 3.8% + PW_Basis gathers_scatterp 0.12766 17 0.0075 1.6% + Potential v_of_rho 1.0724 14 0.077 13.% + XC_Functional v_xc 0.30867 15 0.021 3.8% + H_Hartree_pw v_hartree 0.71813 14 0.051 9.0% + PW_Basis real2recip 0.69328 41 0.017 8.6% + PW_Basis gatherp_scatters 0.26171 41 0.0064 3.3% + ORB_control set_orb_tables 1.1091 1 1.1 14.% + ORB_gen_tables gen_tables 1.1091 1 1.1 14.% + ORB_table_phi init_Table 0.48085 1 0.48 6.0% + ORB_table_phi cal_ST_Phi12_R 0.47555 126 0.0038 5.9% + ORB_table_beta init_Table_Beta 0.18978 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18810 56 0.0034 2.3% + ORB_table_alpha init_Table_Alpha 0.25183 1 0.25 3.1% + ORB_table_alpha S_PhiAlpha_R 0.24982 66 0.0038 3.1% + LOOP_ions opt_ions 6.3747 1 6.4 79.% + ESolver_KS_LCAO Run 5.7732 1 5.8 72.% + HSolverLCAO solve 3.2960 12 0.27 41.% + HamiltLCAO updateHk 1.6648 12 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.6276 12 0.14 20.% + Gint_interface cal_gint 3.1427 25 0.13 39.% + Gint_Gamma distri_vl 2.9983 6 0.50 37.% + LCAO_Deepks cal_projected_DM 6.1938 14 0.44 77.% + LCAO_gen_fixedH add_v_delta 2.8546 6 0.48 36.% + LCAO_DESCRIPTOR add_v_delta 2.8547 6 0.48 36.% + ElecStateLCAO psiToRho 1.6134 12 0.13 20.% + Charge mix_rho 0.85115 11 0.077 11.% + LOOP_ions force_stress 0.60128 1 0.60 7.5% + Force_Stress_LCAO getForceStress 0.60125 1 0.60 7.5% + Force_LCAO_gamma ftable_gamma 0.38076 1 0.38 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.37266 1 0.37 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:41 2022 + Finish Time : Wed Sep 28 11:06:49 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e9362a757c64bd596df8f69e4101cc4ec9a133b1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123644 ima = 3.69621e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123466056654 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112154794883 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112816267961 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113055574755 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113020443021 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113040947797 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113034289686 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113037059934 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113036440309 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113036351102 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113036333095 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011303632392 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c0f02f64d1edc1975486b9bc33f4b436a56fb0d9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.510949837144 23.068646748557 4.575644218485 0 0 0 +H +0.0 +2 +-7.884141243057 24.038633159551 5.940906519452 0 0 0 +-10.218403961499 22.445491326337 5.188837489102 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/conv new file mode 100644 index 0000000000000000000000000000000000000000..aabbfc9e2cf2b399ade51bbb3c50aeaa765665cf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/conv @@ -0,0 +1 @@ +243 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..286b608c1dd597a86c239c0ca8aa51c14ab4a837 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749564651 0.01254501688 1.256909363 1.361213958 1.468969529 0.008514403217 0.01844731133 0.03906685348 +-5.129631834e-18 0.0009971281566 0.002535026025 0.01195159509 0.0439913608 -5.597862077e-20 1.817115888e-06 5.551667312e-06 +0.001624056274 0.005857940829 + +H atom_index 1 n_descriptor 18 +1.281373424 0.03318921619 0.1192509181 0.1654148947 0.3310461648 0.02353449943 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:41 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087622 SEC) : SETUP UNITCELL + DONE(0.09875 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.117104 SEC) : INIT PLANEWAVE + DONE(0.166825 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451176 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651298e+02 0.000000e+00 2.145e-01 5.860e-01 + GE2 -4.663608e+02 -1.231003e+00 9.854e-02 5.387e-01 + GE3 -4.663663e+02 -5.447805e-03 6.340e-02 6.004e-01 + GE4 -4.663656e+02 6.886885e-04 1.994e-03 4.661e-01 + GE5 -4.663649e+02 7.078885e-04 9.463e-04 4.645e-01 + GE6 -4.663653e+02 -3.518489e-04 1.657e-04 4.601e-01 + GE7 -4.663651e+02 1.219123e-04 3.859e-05 4.473e-01 + GE8 -4.663652e+02 -5.272343e-05 1.552e-05 4.427e-01 + GE9 -4.663652e+02 1.832020e-05 2.389e-06 4.430e-01 + GE10 -4.663652e+02 -2.712981e-06 5.155e-07 4.436e-01 + GE11 -4.663652e+02 -4.079643e-07 1.789e-07 4.429e-01 + GE12 -4.663652e+02 -4.632787e-08 1.176e-08 3.757e-01 +E_delta_band = -6.96964992e-02 Ry = -9.48269519e-01 eV +E_delta_NN= -1.94473036e-01 Ry = -2.64594140e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.0231 11 0.73 1e+02 % + Run_lcao lcao_line 8.0133 1 8 1e+02 % + Potential init_pot 0.2858 2 0.14 3.6 % + PW_Basis recip2real 0.30549 17 0.018 3.8 % + PW_Basis gathers_scatterp 0.12766 17 0.0075 1.6 % + Potential v_of_rho 1.0724 14 0.077 13 % + XC_Functional v_xc 0.30867 15 0.021 3.8 % + H_Hartree_pw v_hartree 0.71813 14 0.051 9 % + PW_Basis real2recip 0.69328 41 0.017 8.6 % + PW_Basis gatherp_scatters 0.26171 41 0.0064 3.3 % + ORB_control set_orb_tables 1.1091 1 1.1 14 % + ORB_gen_tables gen_tables 1.1091 1 1.1 14 % + ORB_table_phi init_Table 0.48085 1 0.48 6 % + ORB_table_phi cal_ST_Phi12_R 0.47555 126 0.0038 5.9 % + ORB_table_beta init_Table_Beta 0.18978 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.1881 56 0.0034 2.3 % + ORB_table_alpha init_Table_Alpha 0.25183 1 0.25 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.24982 66 0.0038 3.1 % + LOOP_ions opt_ions 6.3747 1 6.4 79 % + ESolver_KS_LCAO Run 5.7732 1 5.8 72 % + HSolverLCAO solve 3.296 12 0.27 41 % + HamiltLCAO updateHk 1.6648 12 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.6276 12 0.14 20 % + Gint_interface cal_gint 3.1427 25 0.13 39 % + Gint_Gamma distri_vl 2.9983 6 0.5 37 % + LCAO_Deepks cal_projected_DM 6.1938 14 0.44 77 % + LCAO_gen_fixedH add_v_delta 2.8546 6 0.48 36 % + LCAO_DESCRIPTOR add_v_delta 2.8547 6 0.48 36 % + ElecStateLCAO psiToRho 1.6134 12 0.13 20 % + Charge mix_rho 0.85115 11 0.077 11 % + LOOP_ions force_stress 0.60128 1 0.6 7.5 % + Force_Stress_LCAO getForceStress 0.60125 1 0.6 7.5 % + Force_LCAO_gamma ftable_gamma 0.38076 1 0.38 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.37266 1 0.37 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:41 2022 + FINISH Time : Wed Sep 28 11:06:49 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/243/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a50c6ea7d8b17bf1c16f54f3f66c14e5b76aed4b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.680408 0.842264 0.18623 +H 0.697379 0.860287 0.246739 +H 0.644784 0.788862 0.19039 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..719877c3bfa24f77e250bb94862a483f1653c765 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.315 2 + 2 -13.3349 2 + 3 -8.92599 2 + 4 -6.74885 2 + 5 1.40546 0 + 6 4.60164 0 + 7 11.0559 0 + 8 11.2855 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c802737d95779d3ce47d2ee7db7bccf13d7f6812 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:44 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.0514218426 23.5833828169 5.21444074985 0 0 0 0 + tauc_H1 19.5266033458 24.0880473376 6.9086822145 0 0 0 0 + tauc_H2 18.0539496847 22.0881422911 5.33092859854 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0884954673488 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0890163273277 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107202016155 (SEC) + + DONE : INIT CHARGE Time : 0.156742541918 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438019 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00148 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123 + + Density error is 0.216613186082 + + Energy Rydberg eV + E_KohnSham -34.1897617941 -465.175573663 + E_Harris -34.3847174765 -467.828081801 + E_Fermi -0.410635513706 -5.58698278755 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00144770834157 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00136395676142 + + Density error is 0.0978500210469 + + Energy Rydberg eV + E_KohnSham -34.2797338588 -466.399706403 + E_Harris -34.2863382628 -466.48956393 + E_Fermi -0.21866284662 -2.97506065493 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00134332021781 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129163604625 + + Density error is 0.0626079761586 + + Energy Rydberg eV + E_KohnSham -34.2799566599 -466.402737768 + E_Harris -34.2841915643 -466.460356598 + E_Fermi -0.205701003598 -2.79870573325 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116467184668 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117938032459 + + Density error is 0.00207218374154 + + Energy Rydberg eV + E_KohnSham -34.2799768501 -466.40301247 + E_Harris -34.279979743 -466.403051829 + E_Fermi -0.17032953651 -2.31745223423 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116245518685 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117925669158 + + Density error is 0.000864442757799 + + Energy Rydberg eV + E_KohnSham -34.2799136953 -466.402153204 + E_Harris -34.2799150937 -466.402172231 + E_Fermi -0.169308755671 -2.30356379842 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116071081882 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011778756672 + + Density error is 0.000195813462327 + + Energy Rydberg eV + E_KohnSham -34.2799558959 -466.402727374 + E_Harris -34.279956006 -466.40272887 + E_Fermi -0.16946577835 -2.30570020156 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116061639554 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117804068428 + + Density error is 4.1995424995e-05 + + Energy Rydberg eV + E_KohnSham -34.2799391788 -466.402499925 + E_Harris -34.2799391883 -466.402500054 + E_Fermi -0.16928407553 -2.30322800787 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116060893521 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117798456705 + + Density error is 1.65286447267e-05 + + Energy Rydberg eV + E_KohnSham -34.2799446455 -466.402574303 + E_Harris -34.2799446466 -466.402574318 + E_Fermi -0.169332557226 -2.30388763519 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116057294635 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117796442663 + + Density error is 1.54260598642e-06 + + Energy Rydberg eV + E_KohnSham -34.2799432172 -466.40255487 + E_Harris -34.2799432172 -466.40255487 + E_Fermi -0.169314384263 -2.30364037935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116057017708 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117796396776 + + Density error is 1.21411843833e-07 + + Energy Rydberg eV + E_KohnSham -34.2799434294 -466.402557757 + E_Harris -34.2799434294 -466.402557757 + E_Fermi -0.169312945854 -2.30362080878 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116057068046 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117796452939 + + Density error is 3.10317711982e-08 + + Energy Rydberg eV + E_KohnSham -34.2799434562 -466.402558122 + E_Harris -34.2799434562 -466.402558122 + E_band -7.98558568808 -108.649467225 + E_one_elec -69.4941435988 -945.516330573 + E_Hartree +36.1429013124 +491.7494001 + E_xc -8.22608797839 -111.921668755 + E_Ewald +7.42132921807 +100.9723641 + E_demet -2.30865643508e-83 -3.14108822414e-82 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19509041781 -2.65434130742 + E_Fermi -0.169312977609 -2.30362124083 + + charge density convergence is achieved + final etot is -466.402558122 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3150 2.00000 + 2 -13.3349 2.00000 + 3 -8.92599 2.00000 + 4 -6.74885 2.00000 + 5 1.40546 0.00000 + 6 4.60164 0.00000 + 7 11.0559 0.00000 + 8 11.2855 0.00000 + + EFERMI = -2.303621240830404 eV + OUT.ABACUS/ final etot is -466.4025581221290 eV + correction force for each atom along direction 1 is -8.66395e-05 + correction force for each atom along direction 2 is 3.50932e-05 + correction force for each atom along direction 3 is 0.000139206 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.64854024 +1.0475838 -0.63404390 + H1 -0.069836179 -0.14405689 +0.30194240 + H2 -0.57870406 -0.90352695 +0.33210150 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4025581221290 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3202 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3093 1 7.3 1.e+02% + Potential init_pot 0.28379 2 0.14 3.9% + PW_Basis recip2real 0.28333 16 0.018 3.9% + PW_Basis gathers_scatterp 0.11819 16 0.0074 1.6% + Potential v_of_rho 0.99816 13 0.077 14.% + XC_Functional v_xc 0.29624 14 0.021 4.0% + H_Hartree_pw v_hartree 0.66069 13 0.051 9.0% + PW_Basis real2recip 0.64057 38 0.017 8.8% + PW_Basis gatherp_scatters 0.24113 38 0.0063 3.3% + ORB_control set_orb_tables 1.0967 1 1.1 15.% + ORB_gen_tables gen_tables 1.0967 1 1.1 15.% + ORB_table_phi init_Table 0.47400 1 0.47 6.5% + ORB_table_phi cal_ST_Phi12_R 0.46886 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18553 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18393 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.25002 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24806 66 0.0038 3.4% + LOOP_ions opt_ions 5.6976 1 5.7 78.% + ESolver_KS_LCAO Run 5.1065 1 5.1 70.% + HSolverLCAO solve 2.8310 11 0.26 39.% + HamiltLCAO updateHk 1.4462 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4135 11 0.13 19.% + Gint_interface cal_gint 2.6821 23 0.12 37.% + Gint_Gamma distri_vl 2.4604 6 0.41 34.% + LCAO_Deepks cal_projected_DM 5.5251 13 0.43 75.% + LCAO_gen_fixedH add_v_delta 2.3155 6 0.39 32.% + LCAO_DESCRIPTOR add_v_delta 2.3155 6 0.39 32.% + ElecStateLCAO psiToRho 1.3683 11 0.12 19.% + Charge mix_rho 0.77673 10 0.078 11.% + LOOP_ions force_stress 0.59097 1 0.59 8.1% + Force_Stress_LCAO getForceStress 0.59094 1 0.59 8.1% + Force_LCAO_gamma ftable_gamma 0.36886 1 0.37 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.36089 1 0.36 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:44 2022 + Finish Time : Wed Sep 28 11:05:51 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..340ce46e2c5e75e61def690a10a02a51ee5b0770 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123514 ima = 3.69969e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123341261896 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112567151825 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113007183106 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011325299156 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113197566347 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113232026324 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113221764043 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113224715322 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113224104604 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113224039454 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113224035186 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3789414788b89c3e0f9e76c10d7e4b025cd5860d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.948578157338 23.583382816889 5.214440749825 0 0 0 +H +0.0 +2 +-8.473396654222 24.088047337562 6.908682214497 0 0 0 +-9.946050315261 22.088142291084 5.330928598561 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/conv new file mode 100644 index 0000000000000000000000000000000000000000..c77e4c0ac8c8cd12c679039199fb1ecafb92c3b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/conv @@ -0,0 +1 @@ +244 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..452c9013d85c86978fca8d3d9bbc0709a8797ff4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745604764 0.01268785362 1.28444585 1.374653149 1.469527476 0.007986990374 0.0199727947 0.03891893993 +4.548202509e-18 0.00116919613 0.002487921039 0.01255391519 0.0443772858 -5.080874195e-20 1.73877673e-06 5.312541139e-06 +0.001741034539 0.005751241958 + +H atom_index 1 n_descriptor 18 +1.243989241 0.03401270721 0.1063557781 0.1480500365 0.320419815 0.02171300259 0.02807689585 0.03715637494 +5.091339849e-18 4.170920933e-05 0.1009030346 0.1145623273 0.1271755987 6.039351632e-18 4.56508254e-06 0.01302776144 +0.02605660887 0.03057679476 + +H atom_index 2 n_descriptor 18 +1.267404767 0.03319531948 0.1145726015 0.1590994492 0.3276031111 0.02274582817 0.02942575643 0.03651441307 +3.174514034e-17 4.37478082e-05 0.1059637345 0.1162146262 0.1366805754 4.773214409e-18 3.367059623e-06 0.01297348685 +0.02690025182 0.03158914078 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..98bbd3ebc024937fd8243459b7ea83eea7b2cb8f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:44 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0885171 SEC) : SETUP UNITCELL + DONE(0.0890303 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107223 SEC) : INIT PLANEWAVE + DONE(0.156874 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438091 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651756e+02 0.000000e+00 2.166e-01 5.663e-01 + GE2 -4.663997e+02 -1.224133e+00 9.785e-02 5.141e-01 + GE3 -4.664027e+02 -3.031366e-03 6.261e-02 5.822e-01 + GE4 -4.664030e+02 -2.747017e-04 2.072e-03 4.445e-01 + GE5 -4.664022e+02 8.592663e-04 8.644e-04 4.450e-01 + GE6 -4.664027e+02 -5.741698e-04 1.958e-04 4.373e-01 + GE7 -4.664025e+02 2.274481e-04 4.200e-05 4.322e-01 + GE8 -4.664026e+02 -7.437795e-05 1.653e-05 4.188e-01 + GE9 -4.664026e+02 1.943315e-05 1.543e-06 4.231e-01 + GE10 -4.664026e+02 -2.886826e-06 1.214e-07 4.232e-01 + GE11 -4.664026e+02 -3.650412e-07 3.103e-08 3.572e-01 +E_delta_band = -7.11480083e-02 Ry = -9.68018314e-01 eV +E_delta_NN= -1.95090418e-01 Ry = -2.65434131e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3202 11 0.67 1e+02 % + Run_lcao lcao_line 7.3093 1 7.3 1e+02 % + Potential init_pot 0.28379 2 0.14 3.9 % + PW_Basis recip2real 0.28333 16 0.018 3.9 % + PW_Basis gathers_scatterp 0.11819 16 0.0074 1.6 % + Potential v_of_rho 0.99816 13 0.077 14 % + XC_Functional v_xc 0.29624 14 0.021 4 % + H_Hartree_pw v_hartree 0.66069 13 0.051 9 % + PW_Basis real2recip 0.64057 38 0.017 8.8 % + PW_Basis gatherp_scatters 0.24113 38 0.0063 3.3 % + ORB_control set_orb_tables 1.0967 1 1.1 15 % + ORB_gen_tables gen_tables 1.0967 1 1.1 15 % + ORB_table_phi init_Table 0.474 1 0.47 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.46886 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18553 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18393 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.25002 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24806 66 0.0038 3.4 % + LOOP_ions opt_ions 5.6976 1 5.7 78 % + ESolver_KS_LCAO Run 5.1065 1 5.1 70 % + HSolverLCAO solve 2.831 11 0.26 39 % + HamiltLCAO updateHk 1.4462 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4135 11 0.13 19 % + Gint_interface cal_gint 2.6821 23 0.12 37 % + Gint_Gamma distri_vl 2.4604 6 0.41 34 % + LCAO_Deepks cal_projected_DM 5.5251 13 0.43 75 % + LCAO_gen_fixedH add_v_delta 2.3155 6 0.39 32 % + LCAO_DESCRIPTOR add_v_delta 2.3155 6 0.39 32 % + ElecStateLCAO psiToRho 1.3683 11 0.12 19 % + Charge mix_rho 0.77673 10 0.078 11 % + LOOP_ions force_stress 0.59097 1 0.59 8.1 % + Force_Stress_LCAO getForceStress 0.59094 1 0.59 8.1 % + Force_LCAO_gamma ftable_gamma 0.36886 1 0.37 5 % + Force_LCAO_gamma cal_fvl_dphi 0.36089 1 0.36 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:44 2022 + FINISH Time : Wed Sep 28 11:05:51 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/244/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e0ac08d1a4dad31e7c91b2b2f2107a190c31a862 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.664241 0.865669 0.191868 +H 0.699513 0.869831 0.248332 +H 0.630473 0.809301 0.192749 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..083a17488b60a3ff4bdb0a3d9d7c682d203638d7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0861 2 + 2 -13.1369 2 + 3 -8.88537 2 + 4 -6.69615 2 + 5 1.2059 0 + 6 4.27649 0 + 7 11.1123 0 + 8 11.3443 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4b71ee83dc215320f2f35038ab3e69ac9cc51098 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:59 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.5987398933 24.238730266 5.37229588337 0 0 0 0 + tauc_H1 19.5863637815 24.3552739265 6.95330619437 0 0 0 0 + tauc_H2 17.6532307059 22.6604262817 5.39697492159 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0880788604217 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0951862942121 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.113434137384 (SEC) + + DONE : INIT CHARGE Time : 0.161777295052 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44541 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00143 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111 + + Density error is 0.214178109471 + + Energy Rydberg eV + E_KohnSham -34.1913445455 -465.1971081 + E_Harris -34.3809802696 -467.777234492 + E_Fermi -0.396608244335 -5.39613199673 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00136618736851 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124253484658 + + Density error is 0.0984666252907 + + Energy Rydberg eV + E_KohnSham -34.2801152991 -466.404896165 + E_Harris -34.2869107216 -466.497352632 + E_Fermi -0.206117863872 -2.80437740825 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00127014290229 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118002545577 + + Density error is 0.063276844162 + + Energy Rydberg eV + E_KohnSham -34.2803918138 -466.40865834 + E_Harris -34.2847657473 -466.468168758 + E_Fermi -0.19628019975 -2.67052912117 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00110071981797 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108197756501 + + Density error is 0.00206658318509 + + Energy Rydberg eV + E_KohnSham -34.2803553311 -466.408161968 + E_Harris -34.2803592665 -466.408215511 + E_Fermi -0.161129447498 -2.19227860157 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109877309461 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108047272516 + + Density error is 0.000862341844484 + + Energy Rydberg eV + E_KohnSham -34.2803116605 -466.407567799 + E_Harris -34.2803120996 -466.407573773 + E_Fermi -0.160563312207 -2.18457593576 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109671800965 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107926520499 + + Density error is 0.00019119477385 + + Energy Rydberg eV + E_KohnSham -34.2803368884 -466.407911042 + E_Harris -34.2803369283 -466.407911585 + E_Fermi -0.160392468336 -2.18225148565 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109672013411 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107944845093 + + Density error is 3.4128609118e-05 + + Energy Rydberg eV + E_KohnSham -34.2803275256 -466.407783654 + E_Harris -34.280327531 -466.407783728 + E_Fermi -0.160289812189 -2.18085477712 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109668294112 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107937648089 + + Density error is 1.57104594254e-05 + + Energy Rydberg eV + E_KohnSham -34.2803317582 -466.407841242 + E_Harris -34.2803317593 -466.407841257 + E_Fermi -0.160322022781 -2.18129302471 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109665976912 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107936556334 + + Density error is 1.72635154282e-06 + + Energy Rydberg eV + E_KohnSham -34.2803304662 -466.407823663 + E_Harris -34.2803304662 -466.407823664 + E_Fermi -0.160305659608 -2.18107039232 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109665639524 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107936529052 + + Density error is 2.7643967413e-07 + + Energy Rydberg eV + E_KohnSham -34.2803307046 -466.407826908 + E_Harris -34.2803307046 -466.407826908 + E_Fermi -0.160304100615 -2.18104918113 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109665659179 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107936578101 + + Density error is 7.90056070536e-08 + + Energy Rydberg eV + E_KohnSham -34.2803307246 -466.407827179 + E_Harris -34.2803307246 -466.407827179 + E_band -7.90911503286 -107.609030584 + E_one_elec -69.0236166711 -939.114483294 + E_Hartree +35.9223405238 +488.748516619 + E_xc -8.19041664531 -111.43633537 + E_Ewald +7.1362831968 +97.0941140182 + E_demet -5.89433117457e-70 -8.01964898732e-69 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.1942108932 -2.64237476119 + E_Fermi -0.160303993669 -2.18104772606 + + charge density convergence is achieved + final etot is -466.407827179 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0861 2.00000 + 2 -13.1369 2.00000 + 3 -8.88537 2.00000 + 4 -6.69615 2.00000 + 5 1.20590 0.00000 + 6 4.27649 0.00000 + 7 11.1123 0.00000 + 8 11.3443 0.00000 + + EFERMI = -2.181047726060307 eV + OUT.ABACUS/ final etot is -466.4078271794267 eV + correction force for each atom along direction 1 is -1.78671e-05 + correction force for each atom along direction 2 is 1.60131e-06 + correction force for each atom along direction 3 is 0.000142631 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.36881929 +0.39872104 +0.22655670 + H1 -0.49469160 -0.32710143 -0.51399640 + H2 +0.12587230 -0.071619615 +0.28743970 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4078271794267 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4252 11 0.58 1.0e+02% + Run_lcao lcao_line 6.4150 1 6.4 1.e+02% + Potential init_pot 0.28985 2 0.14 4.5% + PW_Basis recip2real 0.27572 16 0.017 4.3% + PW_Basis gathers_scatterp 0.12032 16 0.0075 1.9% + Potential v_of_rho 0.88610 13 0.068 14.% + XC_Functional v_xc 0.24927 14 0.018 3.9% + H_Hartree_pw v_hartree 0.59790 13 0.046 9.3% + PW_Basis real2recip 0.56321 38 0.015 8.8% + PW_Basis gatherp_scatters 0.22068 38 0.0058 3.4% + ORB_control set_orb_tables 1.1073 1 1.1 17.% + ORB_gen_tables gen_tables 1.1073 1 1.1 17.% + ORB_table_phi init_Table 0.48201 1 0.48 7.5% + ORB_table_phi cal_ST_Phi12_R 0.47710 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18966 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18817 56 0.0034 2.9% + ORB_table_alpha init_Table_Alpha 0.25246 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25061 66 0.0038 3.9% + LOOP_ions opt_ions 4.7829 1 4.8 74.% + ESolver_KS_LCAO Run 4.2357 1 4.2 66.% + HSolverLCAO solve 2.2549 11 0.20 35.% + HamiltLCAO updateHk 1.1698 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1367 11 0.10 18.% + Gint_interface cal_gint 2.1348 23 0.093 33.% + Gint_Gamma distri_vl 2.0330 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.6192 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9041 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9041 6 0.32 30.% + ElecStateLCAO psiToRho 1.0708 11 0.097 17.% + Charge mix_rho 0.65982 10 0.066 10.% + LOOP_ions force_stress 0.54703 1 0.55 8.5% + Force_Stress_LCAO getForceStress 0.54700 1 0.55 8.5% + Force_LCAO_gamma ftable_gamma 0.33674 1 0.34 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.33012 1 0.33 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:59 2022 + Finish Time : Wed Sep 28 11:02:06 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..dea2fc67b9542e0f2bedee78a8752f906a649098 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123503 ima = 3.67574e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123632727972 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112622573059 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011319945251 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113403900382 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113372803736 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011339252121 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113385047841 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113387629231 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113386941505 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113386882781 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113386870153 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c4639f3c789f805e387d36925f94d6821d147b94 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.401260106706 24.238730265992 5.372295883372 0 0 0 +H +0.0 +2 +-8.413636218497 24.355273926466 6.953306194352 0 0 0 +-10.346769294129 22.660426281684 5.396974921567 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/conv new file mode 100644 index 0000000000000000000000000000000000000000..476253316312c67a8c44576adf14cc8c97e39fdb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/conv @@ -0,0 +1 @@ +245 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..fa49e8d78d298bf416df6abd85d96bd42276c7d3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745639558 0.01252439474 1.264904418 1.359536989 1.468420041 0.007820246177 0.01956390668 0.03892452991 +-1.27452735e-18 0.001056288396 0.002350655264 0.0118864354 0.04193651781 1.403353268e-19 1.492926102e-06 4.729085206e-06 +0.001730418346 0.005712901415 + +H atom_index 1 n_descriptor 18 +1.214512471 0.03508247755 0.09626307514 0.1353537822 0.3110869753 0.02020657909 0.02640128257 0.03834481343 +1.803073526e-17 3.555849028e-05 0.09135832327 0.1140348322 0.1159439962 -1.513161081e-18 5.562387609e-06 0.01349130842 +0.02445403445 0.02915437468 + +H atom_index 2 n_descriptor 18 +1.236630519 0.03431481173 0.1033548896 0.1449954235 0.3185989369 0.02119238885 0.0276876954 0.03751344063 +-2.437560349e-17 3.733612154e-05 0.09724844163 0.1145940676 0.1243532023 2.338929598e-18 4.704382751e-06 0.01308451725 +0.02532423132 0.03023102699 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..345ebb887c0963d940eab38a70474570dd858cb8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:59 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0881068 SEC) : SETUP UNITCELL + DONE(0.0952071 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.113455 SEC) : INIT PLANEWAVE + DONE(0.161907 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445471 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651971e+02 0.000000e+00 2.142e-01 4.965e-01 + GE2 -4.664049e+02 -1.207788e+00 9.847e-02 4.237e-01 + GE3 -4.664087e+02 -3.762176e-03 6.328e-02 4.742e-01 + GE4 -4.664082e+02 4.963723e-04 2.067e-03 3.696e-01 + GE5 -4.664076e+02 5.941693e-04 8.623e-04 3.692e-01 + GE6 -4.664079e+02 -3.432433e-04 1.912e-04 3.645e-01 + GE7 -4.664078e+02 1.273881e-04 3.413e-05 3.540e-01 + GE8 -4.664078e+02 -5.758850e-05 1.571e-05 3.434e-01 + GE9 -4.664078e+02 1.757911e-05 1.726e-06 3.468e-01 + GE10 -4.664078e+02 -3.244209e-06 2.764e-07 3.454e-01 + GE11 -4.664078e+02 -2.718488e-07 7.901e-08 2.871e-01 +E_delta_band = -6.92897644e-02 Ry = -9.42735609e-01 eV +E_delta_NN= -1.94210893e-01 Ry = -2.64237476e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4252 11 0.58 1e+02 % + Run_lcao lcao_line 6.415 1 6.4 1e+02 % + Potential init_pot 0.28985 2 0.14 4.5 % + PW_Basis recip2real 0.27572 16 0.017 4.3 % + PW_Basis gathers_scatterp 0.12032 16 0.0075 1.9 % + Potential v_of_rho 0.8861 13 0.068 14 % + XC_Functional v_xc 0.24927 14 0.018 3.9 % + H_Hartree_pw v_hartree 0.5979 13 0.046 9.3 % + PW_Basis real2recip 0.56321 38 0.015 8.8 % + PW_Basis gatherp_scatters 0.22068 38 0.0058 3.4 % + ORB_control set_orb_tables 1.1073 1 1.1 17 % + ORB_gen_tables gen_tables 1.1073 1 1.1 17 % + ORB_table_phi init_Table 0.48201 1 0.48 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.4771 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18966 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18817 56 0.0034 2.9 % + ORB_table_alpha init_Table_Alpha 0.25246 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25061 66 0.0038 3.9 % + LOOP_ions opt_ions 4.7829 1 4.8 74 % + ESolver_KS_LCAO Run 4.2357 1 4.2 66 % + HSolverLCAO solve 2.2549 11 0.2 35 % + HamiltLCAO updateHk 1.1698 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1367 11 0.1 18 % + Gint_interface cal_gint 2.1348 23 0.093 33 % + Gint_Gamma distri_vl 2.033 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.6192 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9041 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9041 6 0.32 30 % + ElecStateLCAO psiToRho 1.0708 11 0.097 17 % + Charge mix_rho 0.65982 10 0.066 10 % + LOOP_ions force_stress 0.54703 1 0.55 8.5 % + Force_Stress_LCAO getForceStress 0.547 1 0.55 8.5 % + Force_LCAO_gamma ftable_gamma 0.33674 1 0.34 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.33012 1 0.33 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:59 2022 + FINISH Time : Wed Sep 28 11:02:06 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/245/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..386061cab4a83aeacd7232b3bb9af42313b6ace8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.647642 0.878701 0.179016 +H 0.687112 0.86687 0.23081 +H 0.60433 0.831337 0.183086 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..be7950eb2776df6742196203f0e7d02a44947e91 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3627 2 + 2 -13.0124 2 + 3 -9.19518 2 + 4 -6.76119 2 + 5 1.32383 0 + 6 4.48102 0 + 7 11.0617 0 + 8 11.3188 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b65da499148d88e62803df05599c33e162941e8b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:03 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.1339868642 24.6036330993 5.01245485042 0 0 0 0 + tauc_H1 19.2391326642 24.2723508151 6.46268799681 0 0 0 0 + tauc_H2 16.921240906 23.2774466283 5.12640989183 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0863948081747 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0962693843177 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11456758326 (SEC) + + DONE : INIT CHARGE Time : 0.164435671235 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445737 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133 + + Density error is 0.215220226144 + + Energy Rydberg eV + E_KohnSham -34.1900306963 -465.179232264 + E_Harris -34.3825596269 -467.79872275 + E_Fermi -0.408178412513 -5.55355221077 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00134326278248 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133456282238 + + Density error is 0.0978359847365 + + Energy Rydberg eV + E_KohnSham -34.2800826229 -466.404451582 + E_Harris -34.286839057 -466.496377584 + E_Fermi -0.216993184996 -2.95234374311 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00125497800476 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012468498241 + + Density error is 0.0627295187345 + + Energy Rydberg eV + E_KohnSham -34.2803991381 -466.408757992 + E_Harris -34.2847662185 -466.468175169 + E_Fermi -0.205604593964 -2.79739401288 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00110970937551 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110072563415 + + Density error is 0.00198269457739 + + Energy Rydberg eV + E_KohnSham -34.2803913717 -466.408652326 + E_Harris -34.2803922645 -466.408664472 + E_Fermi -0.16991195291 -2.31177071788 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00111017334633 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011005197622 + + Density error is 0.000915791944761 + + Energy Rydberg eV + E_KohnSham -34.2803274047 -466.40778201 + E_Harris -34.2803289743 -466.407803366 + E_Fermi -0.169182290559 -2.30184315229 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00110832863066 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109868575548 + + Density error is 0.000128549822675 + + Energy Rydberg eV + E_KohnSham -34.2803677365 -466.408330752 + E_Harris -34.2803677597 -466.408331067 + E_Fermi -0.169191871453 -2.30197350704 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00110829024109 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109862745845 + + Density error is 4.03008475201e-05 + + Energy Rydberg eV + E_KohnSham -34.2803539769 -466.408143543 + E_Harris -34.2803539859 -466.408143665 + E_Fermi -0.169071535218 -2.30033624857 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00110826493602 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109859122772 + + Density error is 1.39341806123e-05 + + Energy Rydberg eV + E_KohnSham -34.2803574673 -466.408191033 + E_Harris -34.2803574681 -466.408191043 + E_Fermi -0.169115242614 -2.30093091821 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00110824791882 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109857096321 + + Density error is 1.62328688716e-06 + + Energy Rydberg eV + E_KohnSham -34.2803560966 -466.408172382 + E_Harris -34.2803560966 -466.408172382 + E_Fermi -0.169100251189 -2.3007269494 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00110824546528 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109857005463 + + Density error is 1.71396499343e-07 + + Energy Rydberg eV + E_KohnSham -34.2803562823 -466.408174909 + E_Harris -34.2803562823 -466.408174909 + E_Fermi -0.169098868066 -2.30070813105 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00110824594095 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109857066266 + + Density error is 5.49160993306e-08 + + Energy Rydberg eV + E_KohnSham -34.2803563112 -466.408175302 + E_Harris -34.2803563112 -466.408175302 + E_band -7.98658104575 -108.663009761 + E_one_elec -69.3855652056 -944.039045747 + E_Hartree +36.0817358945 +490.917201896 + E_xc -8.21642826523 -111.790241615 + E_Ewald +7.36402795605 +100.192740434 + E_demet -9.9959488304e-80 -1.3600186101e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195005210465 -2.65318200201 + E_Fermi -0.169098881062 -2.30070830786 + + charge density convergence is achieved + final etot is -466.408175302 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3627 2.00000 + 2 -13.0124 2.00000 + 3 -9.19518 2.00000 + 4 -6.76119 2.00000 + 5 1.32383 0.00000 + 6 4.48102 0.00000 + 7 11.0617 0.00000 + 8 11.3188 0.00000 + + EFERMI = -2.300708307860702 eV + OUT.ABACUS/ final etot is -466.4081753022726 eV + correction force for each atom along direction 1 is 3.76525e-05 + correction force for each atom along direction 2 is -0.000139594 + correction force for each atom along direction 3 is 9.23330e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.97296473 +0.72746917 +0.24429799 + H1 -0.058546158 +0.15033377 -0.20857179 + H2 -0.91441858 -0.87780295 -0.035726202 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4081753022726 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2509 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2422 1 7.2 1.e+02% + Potential init_pot 0.28375 2 0.14 3.9% + PW_Basis recip2real 0.28525 16 0.018 3.9% + PW_Basis gathers_scatterp 0.12553 16 0.0078 1.7% + Potential v_of_rho 0.98350 13 0.076 14.% + XC_Functional v_xc 0.28585 14 0.020 3.9% + H_Hartree_pw v_hartree 0.65606 13 0.050 9.0% + PW_Basis real2recip 0.65201 38 0.017 9.0% + PW_Basis gatherp_scatters 0.24630 38 0.0065 3.4% + ORB_control set_orb_tables 1.1047 1 1.1 15.% + ORB_gen_tables gen_tables 1.1047 1 1.1 15.% + ORB_table_phi init_Table 0.47695 1 0.48 6.6% + ORB_table_phi cal_ST_Phi12_R 0.47174 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18519 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18365 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.25719 1 0.26 3.5% + ORB_table_alpha S_PhiAlpha_R 0.25520 66 0.0039 3.5% + LOOP_ions opt_ions 5.6137 1 5.6 77.% + ESolver_KS_LCAO Run 5.0298 1 5.0 69.% + HSolverLCAO solve 2.7619 11 0.25 38.% + HamiltLCAO updateHk 1.4094 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.3817 11 0.13 19.% + Gint_interface cal_gint 2.6141 23 0.11 36.% + Gint_Gamma distri_vl 2.4133 6 0.40 33.% + LCAO_Deepks cal_projected_DM 5.4391 13 0.42 75.% + LCAO_gen_fixedH add_v_delta 2.2678 6 0.38 31.% + LCAO_DESCRIPTOR add_v_delta 2.2678 6 0.38 31.% + ElecStateLCAO psiToRho 1.3362 11 0.12 18.% + Charge mix_rho 0.78668 10 0.079 11.% + LOOP_ions force_stress 0.58369 1 0.58 8.0% + Force_Stress_LCAO getForceStress 0.58366 1 0.58 8.0% + Force_LCAO_gamma ftable_gamma 0.36714 1 0.37 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.35909 1 0.36 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:03 2022 + Finish Time : Wed Sep 28 11:02:10 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0279d6bbebbc1e3c6e5de3cf36bee7f5a0e4447d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012374 ima = 3.69564e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122990325622 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111916076762 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112463695241 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112721700748 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112666138957 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112698074375 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112692295339 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112695194986 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112694641234 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112694568758 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112694562984 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ad6f7e4d3deef9b9a536881f4ac790e44c3a6d1c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.866013135795 24.603633099325 5.012454850405 0 0 0 +H +0.0 +2 +-8.760867335802 24.272350815088 6.462687996814 0 0 0 +-11.078759093967 23.277446628294 5.126409891846 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/conv new file mode 100644 index 0000000000000000000000000000000000000000..50134ddbad657101dc645d4cee66b4a18aa4adc2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/conv @@ -0,0 +1 @@ +246 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0720270bd2bb98090e084833b020859e2058e071 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750393898 0.01273283018 1.275202219 1.363804904 1.4696281 0.008749516429 0.01823149841 0.03906044859 +-6.506675869e-19 0.001042330741 0.002682662521 0.0126689431 0.0460329745 -2.03542679e-19 2.244314484e-06 6.332694267e-06 +0.00162877417 0.006008630253 + +H atom_index 1 n_descriptor 18 +1.230922068 0.03503034547 0.102325285 0.1411657302 0.3142658617 0.02155059045 0.0271726925 0.03816633974 +-1.942763855e-17 4.58693633e-05 0.09739346076 0.114260831 0.1211206048 -4.299667627e-18 5.006925294e-06 0.01346876137 +0.02578477703 0.02986268348 + +H atom_index 2 n_descriptor 18 +1.272402651 0.03362033401 0.1168559311 0.1605536426 0.3276375221 0.02350275004 0.0295865934 0.03692746788 +1.46493781e-17 4.979058562e-05 0.1064932997 0.1171830436 0.1378358075 5.515904846e-18 2.721779357e-06 0.01321784614 +0.02730873822 0.03172703827 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..28b62e0c9363dfbfd8abc252c1a8b81b0591c20d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:03 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0864176 SEC) : SETUP UNITCELL + DONE(0.0962888 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.114589 SEC) : INIT PLANEWAVE + DONE(0.164576 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445797 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651792e+02 0.000000e+00 2.152e-01 5.561e-01 + GE2 -4.664045e+02 -1.225219e+00 9.784e-02 5.079e-01 + GE3 -4.664088e+02 -4.306410e-03 6.273e-02 5.753e-01 + GE4 -4.664087e+02 1.056669e-04 1.983e-03 4.393e-01 + GE5 -4.664078e+02 8.703156e-04 9.158e-04 4.389e-01 + GE6 -4.664083e+02 -5.487423e-04 1.285e-04 4.289e-01 + GE7 -4.664081e+02 1.872089e-04 4.030e-05 4.232e-01 + GE8 -4.664082e+02 -4.748916e-05 1.393e-05 4.183e-01 + GE9 -4.664082e+02 1.865016e-05 1.623e-06 4.150e-01 + GE10 -4.664082e+02 -2.526356e-06 1.714e-07 4.142e-01 + GE11 -4.664082e+02 -3.935593e-07 5.492e-08 3.498e-01 +E_delta_band = -7.08785196e-02 Ry = -9.64351732e-01 eV +E_delta_NN= -1.95005210e-01 Ry = -2.65318200e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2509 11 0.66 1e+02 % + Run_lcao lcao_line 7.2422 1 7.2 1e+02 % + Potential init_pot 0.28375 2 0.14 3.9 % + PW_Basis recip2real 0.28525 16 0.018 3.9 % + PW_Basis gathers_scatterp 0.12553 16 0.0078 1.7 % + Potential v_of_rho 0.9835 13 0.076 14 % + XC_Functional v_xc 0.28585 14 0.02 3.9 % + H_Hartree_pw v_hartree 0.65606 13 0.05 9 % + PW_Basis real2recip 0.65201 38 0.017 9 % + PW_Basis gatherp_scatters 0.2463 38 0.0065 3.4 % + ORB_control set_orb_tables 1.1047 1 1.1 15 % + ORB_gen_tables gen_tables 1.1047 1 1.1 15 % + ORB_table_phi init_Table 0.47695 1 0.48 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.47174 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.18519 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18365 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.25719 1 0.26 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.2552 66 0.0039 3.5 % + LOOP_ions opt_ions 5.6137 1 5.6 77 % + ESolver_KS_LCAO Run 5.0298 1 5 69 % + HSolverLCAO solve 2.7619 11 0.25 38 % + HamiltLCAO updateHk 1.4094 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.3817 11 0.13 19 % + Gint_interface cal_gint 2.6141 23 0.11 36 % + Gint_Gamma distri_vl 2.4133 6 0.4 33 % + LCAO_Deepks cal_projected_DM 5.4391 13 0.42 75 % + LCAO_gen_fixedH add_v_delta 2.2678 6 0.38 31 % + LCAO_DESCRIPTOR add_v_delta 2.2678 6 0.38 31 % + ElecStateLCAO psiToRho 1.3362 11 0.12 18 % + Charge mix_rho 0.78668 10 0.079 11 % + LOOP_ions force_stress 0.58369 1 0.58 8 % + Force_Stress_LCAO getForceStress 0.58366 1 0.58 8 % + Force_LCAO_gamma ftable_gamma 0.36714 1 0.37 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.35909 1 0.36 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:03 2022 + FINISH Time : Wed Sep 28 11:02:10 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/246/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..7aa9ddd4bdcff6dd022625470b0b11667daa97d9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.636289 0.886415 0.179023 +H 0.643129 0.855789 0.236687 +H 0.5865 0.855694 0.148757 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c6638d12f1fd419b767152d95cac53ed74c01c9f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2176 2 + 2 -13.0666 2 + 3 -9.04737 2 + 4 -6.72841 2 + 5 1.27183 0 + 6 4.36227 0 + 7 11.0885 0 + 8 11.335 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0924743cc85e69b9df41465df20a85e9ff36c6de --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:27 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.8160938612 24.8196199694 5.01263681839 0 0 0 0 + tauc_H1 18.0076033871 23.9620928467 6.62723155179 0 0 0 0 + tauc_H2 16.4219869339 23.9594276527 4.16519755482 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.073229782644 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0849431267307 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.101156031969 (SEC) + + DONE : INIT CHARGE Time : 0.143175801062 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.38651 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00087 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00143 + + Density error is 0.214713777776 + + Energy Rydberg eV + E_KohnSham -34.1915261022 -465.199578305 + E_Harris -34.3825408297 -467.798467001 + E_Fermi -0.402169003091 -5.47179000102 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0010945504842 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00136185356869 + + Density error is 0.0982127902903 + + Energy Rydberg eV + E_KohnSham -34.2811598876 -466.41910852 + E_Harris -34.2879434633 -466.511403802 + E_Fermi -0.210915068769 -2.86964672933 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104339940432 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127304069113 + + Density error is 0.0630825271749 + + Energy Rydberg eV + E_KohnSham -34.2814936275 -466.423649285 + E_Harris -34.2858727624 -466.483230471 + E_Fermi -0.200583102139 -2.7290731116 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000972782701811 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112519930545 + + Density error is 0.0020038745178 + + Energy Rydberg eV + E_KohnSham -34.2814677073 -466.423296622 + E_Harris -34.2814696815 -466.423323483 + E_Fermi -0.165157557755 -2.24708385323 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000973961050828 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112464909692 + + Density error is 0.00090640620211 + + Energy Rydberg eV + E_KohnSham -34.2814121636 -466.422540911 + E_Harris -34.2814130514 -466.42255299 + E_Fermi -0.164545457216 -2.23875579816 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000972872418745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112271486748 + + Density error is 0.000175248185165 + + Energy Rydberg eV + E_KohnSham -34.2814450525 -466.422988388 + E_Harris -34.2814451048 -466.422989099 + E_Fermi -0.164452024035 -2.2374845745 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00097309586972 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011227758112 + + Density error is 3.69584691157e-05 + + Energy Rydberg eV + E_KohnSham -34.2814327429 -466.422820907 + E_Harris -34.2814327496 -466.422820999 + E_Fermi -0.164335860339 -2.23590408635 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000973034708638 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112273557985 + + Density error is 1.56683731982e-05 + + Energy Rydberg eV + E_KohnSham -34.2814371163 -466.422880411 + E_Harris -34.2814371173 -466.422880424 + E_Fermi -0.164373359497 -2.23641428856 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000973031166388 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011227140145 + + Density error is 1.75910645814e-06 + + Energy Rydberg eV + E_KohnSham -34.2814357999 -466.4228625 + E_Harris -34.2814357999 -466.4228625 + E_Fermi -0.164356789244 -2.23618883871 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000973030764905 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112271129112 + + Density error is 1.39733776602e-07 + + Energy Rydberg eV + E_KohnSham -34.2814360016 -466.422865244 + E_Harris -34.2814360016 -466.422865244 + E_Fermi -0.164355052068 -2.23616520321 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000973031244238 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112271182834 + + Density error is 3.41136538941e-08 + + Energy Rydberg eV + E_KohnSham -34.281436032 -466.422865658 + E_Harris -34.281436032 -466.422865658 + E_band -7.94666680136 -108.119948606 + E_one_elec -69.1915684228 -941.399584107 + E_Hartree +35.9954020737 +489.742570003 + E_xc -8.20234030231 -111.598565046 + E_Ewald +7.24161838442 +98.5272727696 + E_demet -7.49801373214e-75 -1.02015710439e-73 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194588797862 -2.64751641789 + E_Fermi -0.164355071353 -2.23616546559 + + charge density convergence is achieved + final etot is -466.422865658 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2176 2.00000 + 2 -13.0666 2.00000 + 3 -9.04737 2.00000 + 4 -6.72841 2.00000 + 5 1.27183 0.00000 + 6 4.36227 0.00000 + 7 11.0885 0.00000 + 8 11.3350 0.00000 + + EFERMI = -2.236165465594912 eV + OUT.ABACUS/ final etot is -466.4228656582202 eV + correction force for each atom along direction 1 is -0.000115844 + correction force for each atom along direction 2 is -0.000153251 + correction force for each atom along direction 3 is 5.87091e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.020038045 +0.13114663 -0.16984290 + H1 -0.053814776 -0.10427845 +0.075782466 + H2 +0.033776731 -0.026868179 +0.094060430 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4228656582202 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5966 11 0.60 1.0e+02% + Run_lcao lcao_line 6.5890 1 6.6 1.e+02% + Potential init_pot 0.24046 2 0.12 3.6% + PW_Basis recip2real 0.24599 16 0.015 3.7% + PW_Basis gathers_scatterp 0.10281 16 0.0064 1.6% + Potential v_of_rho 0.90465 13 0.070 14.% + XC_Functional v_xc 0.27827 14 0.020 4.2% + H_Hartree_pw v_hartree 0.58973 13 0.045 8.9% + PW_Basis real2recip 0.60040 38 0.016 9.1% + PW_Basis gatherp_scatters 0.22742 38 0.0060 3.4% + ORB_control set_orb_tables 0.89866 1 0.90 14.% + ORB_gen_tables gen_tables 0.89865 1 0.90 14.% + ORB_table_phi init_Table 0.37639 1 0.38 5.7% + ORB_table_phi cal_ST_Phi12_R 0.37215 126 0.0030 5.6% + ORB_table_beta init_Table_Beta 0.15513 1 0.16 2.4% + ORB_table_beta VNL_PhiBeta_R 0.15381 56 0.0027 2.3% + ORB_table_alpha init_Table_Alpha 0.20935 1 0.21 3.2% + ORB_table_alpha S_PhiAlpha_R 0.20768 66 0.0031 3.1% + LOOP_ions opt_ions 5.2345 1 5.2 79.% + ESolver_KS_LCAO Run 4.6951 1 4.7 71.% + HSolverLCAO solve 2.5435 11 0.23 39.% + HamiltLCAO updateHk 1.2984 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.2717 11 0.12 19.% + Gint_interface cal_gint 2.4341 23 0.11 37.% + Gint_Gamma distri_vl 2.2516 6 0.38 34.% + LCAO_Deepks cal_projected_DM 5.0836 13 0.39 77.% + LCAO_gen_fixedH add_v_delta 2.1223 6 0.35 32.% + LCAO_DESCRIPTOR add_v_delta 2.1223 6 0.35 32.% + ElecStateLCAO psiToRho 1.2289 11 0.11 19.% + Charge mix_rho 0.76005 10 0.076 12.% + LOOP_ions force_stress 0.53917 1 0.54 8.2% + Force_Stress_LCAO getForceStress 0.53914 1 0.54 8.2% + Force_LCAO_gamma ftable_gamma 0.34669 1 0.35 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.33918 1 0.34 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:27 2022 + Finish Time : Wed Sep 28 11:05:33 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..63a14ed27d73dd0847aea320422e4a4a5ea31653 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123769 ima = 3.69572e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123305249883 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112171234399 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112748676713 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112981181526 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112937796437 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112964376167 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112956434013 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112959157472 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112958544663 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011295846802 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112958462372 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e6464887fc7e66aa6b3b29a1e253bc03eda7251b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.183906138798 24.819619969397 5.012636818370 0 0 0 +H +0.0 +2 +-9.992396612861 23.962092846657 6.627231551795 0 0 0 +-11.578013066073 23.959427652709 4.165197554838 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/conv new file mode 100644 index 0000000000000000000000000000000000000000..98212880f14cb3a2e393b785200dd76d41627f20 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/conv @@ -0,0 +1 @@ +247 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..74dee6560c45da9e07e47a4730702ff1ffe16d67 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748182069 0.01263745704 1.270313377 1.360084266 1.468993394 0.008279140662 0.01882133427 0.03899512784 +-1.872446129e-18 0.001051260626 0.002514476095 0.01221519549 0.04403070429 -1.633041904e-19 1.846985477e-06 5.510793864e-06 +0.001671932658 0.005891365685 + +H atom_index 1 n_descriptor 18 +1.240781707 0.03443930846 0.1048939226 0.1460771629 0.3186665271 0.02165195841 0.02782109878 0.03760055678 +1.738540871e-17 4.245440609e-05 0.09886210556 0.1146761707 0.1253445497 1.080279838e-17 4.61370276e-06 0.01318774779 +0.025768569 0.03036468281 + +H atom_index 2 n_descriptor 18 +1.235903066 0.03460879087 0.1032611672 0.1438753744 0.3170397706 0.02142815787 0.02753633713 0.03776965973 +2.717465329e-17 4.202197374e-05 0.09759506551 0.1145220509 0.1234341267 7.416722405e-20 4.851399917e-06 0.01325226908 +0.02558188759 0.03013447594 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..237f395f8438b1473e5d42fd69edeaa72b439326 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..1a9b3a4749fe44c1fb6c04100bd635a8094e5876 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:27 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0732452 SEC) : SETUP UNITCELL + DONE(0.0849534 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.101167 SEC) : INIT PLANEWAVE + DONE(0.143279 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.386554 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651996e+02 0.000000e+00 2.147e-01 5.036e-01 + GE2 -4.664191e+02 -1.219530e+00 9.821e-02 4.714e-01 + GE3 -4.664236e+02 -4.540765e-03 6.308e-02 5.357e-01 + GE4 -4.664233e+02 3.526625e-04 2.004e-03 4.114e-01 + GE5 -4.664225e+02 7.557111e-04 9.064e-04 4.100e-01 + GE6 -4.664230e+02 -4.474772e-04 1.752e-04 4.067e-01 + GE7 -4.664228e+02 1.674813e-04 3.696e-05 3.977e-01 + GE8 -4.664229e+02 -5.950372e-05 1.567e-05 3.900e-01 + GE9 -4.664229e+02 1.791070e-05 1.759e-06 3.939e-01 + GE10 -4.664229e+02 -2.744397e-06 1.397e-07 3.962e-01 + GE11 -4.664229e+02 -4.138034e-07 3.411e-08 3.252e-01 +E_delta_band = -7.00410328e-02 Ry = -9.52957140e-01 eV +E_delta_NN= -1.94588798e-01 Ry = -2.64751642e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5966 11 0.6 1e+02 % + Run_lcao lcao_line 6.589 1 6.6 1e+02 % + Potential init_pot 0.24046 2 0.12 3.6 % + PW_Basis recip2real 0.24599 16 0.015 3.7 % + PW_Basis gathers_scatterp 0.10281 16 0.0064 1.6 % + Potential v_of_rho 0.90465 13 0.07 14 % + XC_Functional v_xc 0.27827 14 0.02 4.2 % + H_Hartree_pw v_hartree 0.58973 13 0.045 8.9 % + PW_Basis real2recip 0.6004 38 0.016 9.1 % + PW_Basis gatherp_scatters 0.22742 38 0.006 3.4 % + ORB_control set_orb_tables 0.89866 1 0.9 14 % + ORB_gen_tables gen_tables 0.89865 1 0.9 14 % + ORB_table_phi init_Table 0.37639 1 0.38 5.7 % + ORB_table_phi cal_ST_Phi12_R 0.37215 126 0.003 5.6 % + ORB_table_beta init_Table_Beta 0.15513 1 0.16 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.15381 56 0.0027 2.3 % + ORB_table_alpha init_Table_Alpha 0.20935 1 0.21 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.20768 66 0.0031 3.1 % + LOOP_ions opt_ions 5.2345 1 5.2 79 % + ESolver_KS_LCAO Run 4.6951 1 4.7 71 % + HSolverLCAO solve 2.5435 11 0.23 39 % + HamiltLCAO updateHk 1.2984 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.2717 11 0.12 19 % + Gint_interface cal_gint 2.4341 23 0.11 37 % + Gint_Gamma distri_vl 2.2516 6 0.38 34 % + LCAO_Deepks cal_projected_DM 5.0836 13 0.39 77 % + LCAO_gen_fixedH add_v_delta 2.1223 6 0.35 32 % + LCAO_DESCRIPTOR add_v_delta 2.1223 6 0.35 32 % + ElecStateLCAO psiToRho 1.2289 11 0.11 19 % + Charge mix_rho 0.76005 10 0.076 12 % + LOOP_ions force_stress 0.53917 1 0.54 8.2 % + Force_Stress_LCAO getForceStress 0.53914 1 0.54 8.2 % + Force_LCAO_gamma ftable_gamma 0.34669 1 0.35 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.33918 1 0.34 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:27 2022 + FINISH Time : Wed Sep 28 11:05:33 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/247/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..455b725546f48adf3a9e659a53f20a3899dd8461 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.639116 0.890921 0.19536 +H 0.618171 0.861228 0.249634 +H 0.591515 0.881223 0.152576 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..73d4eae8625b50b9035eb62399ad0147f7938e54 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3669 2 + 2 -13.117 2 + 3 -9.12605 2 + 4 -6.76226 2 + 5 1.3716 0 + 6 4.53626 0 + 7 11.0559 0 + 8 11.3072 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..5261f1f8c94ea5fb80bfe733c20e6a8649d78905 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:56 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.8952585583 24.9457771425 5.4700812903 0 0 0 0 + tauc_H1 17.3087791828 24.1143820325 6.98974558138 0 0 0 0 + tauc_H2 16.5624061906 24.6742450012 4.2721248479 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.087441616514 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0878838489593 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105889806552 (SEC) + + DONE : INIT CHARGE Time : 0.155440285198 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437208 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00077 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134 + + Density error is 0.216084590367 + + Energy Rydberg eV + E_KohnSham -34.1897339842 -465.17519529 + E_Harris -34.3841049401 -467.819747815 + E_Fermi -0.410782385032 -5.58898107446 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.001170644283 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124335578671 + + Density error is 0.0978760762331 + + Energy Rydberg eV + E_KohnSham -34.2806309295 -466.411911677 + E_Harris -34.2873507175 -466.503339082 + E_Fermi -0.217929800312 -2.96508704824 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00112610129235 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116015356378 + + Density error is 0.062770826477 + + Energy Rydberg eV + E_KohnSham -34.2809715338 -466.416545836 + E_Harris -34.2853096091 -466.475568378 + E_Fermi -0.206276494437 -2.80653568781 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107206129603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102689825863 + + Density error is 0.00200702249092 + + Energy Rydberg eV + E_KohnSham -34.2809707395 -466.416535029 + E_Harris -34.2809725674 -466.416559898 + E_Fermi -0.170618222586 -2.3213800098 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107529090465 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010276175943 + + Density error is 0.000945718984539 + + Energy Rydberg eV + E_KohnSham -34.280901517 -466.415593208 + E_Harris -34.2809033005 -466.415617474 + E_Fermi -0.169794891481 -2.31017801543 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107401261211 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102587323286 + + Density error is 0.000138437657882 + + Energy Rydberg eV + E_KohnSham -34.2809448074 -466.416182204 + E_Harris -34.280944837 -466.416182607 + E_Fermi -0.169853516467 -2.31097564928 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107415461267 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102581334378 + + Density error is 4.02616231995e-05 + + Energy Rydberg eV + E_KohnSham -34.2809298697 -466.415978967 + E_Harris -34.2809298786 -466.415979088 + E_Fermi -0.169721382963 -2.30917788073 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0010740774714 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102580280737 + + Density error is 1.62065718657e-05 + + Energy Rydberg eV + E_KohnSham -34.2809336184 -466.41602997 + E_Harris -34.2809336195 -466.416029985 + E_Fermi -0.169768622461 -2.30982060708 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107408336891 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102579012135 + + Density error is 2.07167733256e-06 + + Energy Rydberg eV + E_KohnSham -34.2809321876 -466.416010503 + E_Harris -34.2809321876 -466.416010504 + E_Fermi -0.169751760809 -2.30959119254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107408299411 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102578584011 + + Density error is 2.12808610096e-07 + + Energy Rydberg eV + E_KohnSham -34.2809324016 -466.416013414 + E_Harris -34.2809324016 -466.416013414 + E_Fermi -0.169749618149 -2.30956204015 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107408371383 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102578630838 + + Density error is 9.83087159686e-08 + + Energy Rydberg eV + E_KohnSham -34.2809324365 -466.41601389 + E_Harris -34.2809324365 -466.41601389 + E_band -7.99257848026 -108.744609044 + E_one_elec -69.4534379197 -944.962501397 + E_Hartree +36.1163142663 +491.38766478 + E_xc -8.22194518097 -111.865303105 + E_Ewald +7.40212895771 +100.711131156 + E_demet -3.74382536365e-82 -5.09373572625e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195097721436 -2.65444067835 + E_Fermi -0.169749633247 -2.30956224557 + + charge density convergence is achieved + final etot is -466.41601389 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3669 2.00000 + 2 -13.1170 2.00000 + 3 -9.12605 2.00000 + 4 -6.76226 2.00000 + 5 1.37160 0.00000 + 6 4.53626 0.00000 + 7 11.0559 0.00000 + 8 11.3072 0.00000 + + EFERMI = -2.309562245568340 eV + OUT.ABACUS/ final etot is -466.4160138900963 eV + correction force for each atom along direction 1 is 2.51025e-06 + correction force for each atom along direction 2 is -5.80607e-05 + correction force for each atom along direction 3 is 6.97467e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.71052091 +0.27588217 +0.25286298 + H1 -0.096871882 -0.16554395 +0.33610060 + H2 -0.61364902 -0.11033822 -0.58896358 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4160138900963 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0613 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0513 1 7.1 1.e+02% + Potential init_pot 0.28293 2 0.14 4.0% + PW_Basis recip2real 0.28336 16 0.018 4.0% + PW_Basis gathers_scatterp 0.12092 16 0.0076 1.7% + Potential v_of_rho 0.99916 13 0.077 14.% + XC_Functional v_xc 0.29212 14 0.021 4.1% + H_Hartree_pw v_hartree 0.66424 13 0.051 9.4% + PW_Basis real2recip 0.65106 38 0.017 9.2% + PW_Basis gatherp_scatters 0.25088 38 0.0066 3.6% + ORB_control set_orb_tables 1.1023 1 1.1 16.% + ORB_gen_tables gen_tables 1.1023 1 1.1 16.% + ORB_table_phi init_Table 0.47600 1 0.48 6.7% + ORB_table_phi cal_ST_Phi12_R 0.47091 126 0.0037 6.7% + ORB_table_beta init_Table_Beta 0.18739 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18586 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.25266 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.25069 66 0.0038 3.6% + LOOP_ions opt_ions 5.4348 1 5.4 77.% + ESolver_KS_LCAO Run 4.8492 1 4.8 69.% + HSolverLCAO solve 2.5527 11 0.23 36.% + HamiltLCAO updateHk 1.3245 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2915 11 0.12 18.% + Gint_interface cal_gint 2.3985 23 0.10 34.% + Gint_Gamma distri_vl 2.3417 6 0.39 33.% + LCAO_Deepks cal_projected_DM 5.2687 13 0.41 75.% + LCAO_gen_fixedH add_v_delta 2.1966 6 0.37 31.% + LCAO_DESCRIPTOR add_v_delta 2.1966 6 0.37 31.% + ElecStateLCAO psiToRho 1.2116 11 0.11 17.% + Charge mix_rho 0.78694 10 0.079 11.% + LOOP_ions force_stress 0.58550 1 0.59 8.3% + Force_Stress_LCAO getForceStress 0.58545 1 0.59 8.3% + Force_LCAO_gamma ftable_gamma 0.36513 1 0.37 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.35713 1 0.36 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:56 2022 + Finish Time : Wed Sep 28 11:11:03 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2f0a17c9b854a364f379b27abc324fa9b85b83db --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123525 ima = 3.69055e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123128042624 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112054041782 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112583550658 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112847619289 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112787797684 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112822101767 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112815850156 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112818792244 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011281814981 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112818062568 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112818056632 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/STRU new file mode 100644 index 0000000000000000000000000000000000000000..50598c3f35fe6a58304b44034b80dd4f8350b4e7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.104741441725 24.945777142500 5.470081290287 0 0 0 +H +0.0 +2 +-10.691220817246 24.114382032467 6.989745581389 0 0 0 +-11.437593809411 24.674245001216 4.272124847874 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/conv new file mode 100644 index 0000000000000000000000000000000000000000..be0259bcc106323ee0ae6e4074bc0568bf7e115c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/conv @@ -0,0 +1 @@ +248 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f7588a6c0a077ce6ecf2132532b769390c715d6b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749122087 0.01274036161 1.280127923 1.367117316 1.469681312 0.008540148974 0.01871587747 0.03902090122 +3.733721215e-18 0.001090153636 0.002642790017 0.01265991439 0.04586354402 1.795180729e-19 2.13416548e-06 6.105656218e-06 +0.00165613379 0.00596262774 + +H atom_index 1 n_descriptor 18 +1.249038535 0.03425580426 0.1081998376 0.149537364 0.3206765822 0.02226599005 0.02825733824 0.0373915794 +-8.105281813e-19 4.675066558e-05 0.1021043842 0.1148897897 0.1284274309 8.362571e-18 4.193968402e-06 0.01317822756 +0.02643489858 0.03073560961 + +H atom_index 2 n_descriptor 18 +1.261925041 0.03381323801 0.1127447702 0.1556160324 0.3247431968 0.02286282343 0.0290050101 0.03702314006 +9.963458822e-18 4.795908495e-05 0.1049251987 0.1157864851 0.1336599954 2.779981833e-18 3.475440275e-06 0.01312954879 +0.0269023341 0.03130345164 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ba37a96673358b982e6f175d9fa078ea0388c646 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:56 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087464 SEC) : SETUP UNITCELL + DONE(0.0878995 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105909 SEC) : INIT PLANEWAVE + DONE(0.155585 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.437273 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651752e+02 0.000000e+00 2.161e-01 5.494e-01 + GE2 -4.664119e+02 -1.236716e+00 9.788e-02 4.901e-01 + GE3 -4.664165e+02 -4.634159e-03 6.277e-02 5.566e-01 + GE4 -4.664165e+02 1.080659e-05 2.007e-03 4.212e-01 + GE5 -4.664156e+02 9.418214e-04 9.457e-04 4.202e-01 + GE6 -4.664162e+02 -5.889959e-04 1.384e-04 4.139e-01 + GE7 -4.664160e+02 2.032371e-04 4.026e-05 4.112e-01 + GE8 -4.664160e+02 -5.100353e-05 1.621e-05 3.945e-01 + GE9 -4.664160e+02 1.946672e-05 2.072e-06 3.993e-01 + GE10 -4.664160e+02 -2.910976e-06 2.128e-07 4.000e-01 + GE11 -4.664160e+02 -4.758085e-07 9.831e-08 3.302e-01 +E_delta_band = -7.11051616e-02 Ry = -9.67435355e-01 eV +E_delta_NN= -1.95097721e-01 Ry = -2.65444068e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0613 11 0.64 1e+02 % + Run_lcao lcao_line 7.0513 1 7.1 1e+02 % + Potential init_pot 0.28293 2 0.14 4 % + PW_Basis recip2real 0.28336 16 0.018 4 % + PW_Basis gathers_scatterp 0.12092 16 0.0076 1.7 % + Potential v_of_rho 0.99916 13 0.077 14 % + XC_Functional v_xc 0.29212 14 0.021 4.1 % + H_Hartree_pw v_hartree 0.66424 13 0.051 9.4 % + PW_Basis real2recip 0.65106 38 0.017 9.2 % + PW_Basis gatherp_scatters 0.25088 38 0.0066 3.6 % + ORB_control set_orb_tables 1.1023 1 1.1 16 % + ORB_gen_tables gen_tables 1.1023 1 1.1 16 % + ORB_table_phi init_Table 0.476 1 0.48 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.47091 126 0.0037 6.7 % + ORB_table_beta init_Table_Beta 0.18739 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18586 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.25266 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.25069 66 0.0038 3.6 % + LOOP_ions opt_ions 5.4348 1 5.4 77 % + ESolver_KS_LCAO Run 4.8492 1 4.8 69 % + HSolverLCAO solve 2.5527 11 0.23 36 % + HamiltLCAO updateHk 1.3245 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2915 11 0.12 18 % + Gint_interface cal_gint 2.3985 23 0.1 34 % + Gint_Gamma distri_vl 2.3417 6 0.39 33 % + LCAO_Deepks cal_projected_DM 5.2687 13 0.41 75 % + LCAO_gen_fixedH add_v_delta 2.1966 6 0.37 31 % + LCAO_DESCRIPTOR add_v_delta 2.1966 6 0.37 31 % + ElecStateLCAO psiToRho 1.2116 11 0.11 17 % + Charge mix_rho 0.78694 10 0.079 11 % + LOOP_ions force_stress 0.5855 1 0.59 8.3 % + Force_Stress_LCAO getForceStress 0.58545 1 0.59 8.3 % + Force_LCAO_gamma ftable_gamma 0.36513 1 0.37 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.35713 1 0.36 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:56 2022 + FINISH Time : Wed Sep 28 11:11:03 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/248/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..79b8ec505f27956dcf36ee58a2d3c386ce804b5b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.623572 0.897674 0.219451 +H 0.621957 0.831036 0.225083 +H 0.616907 0.907554 0.154417 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b3cdb222da6fa323139df8ebbc5ab3a735bd05df --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1356 2 + 2 -12.8608 2 + 3 -9.13641 2 + 4 -6.71168 2 + 5 1.15641 0 + 6 4.16727 0 + 7 11.1142 0 + 8 11.3696 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..bc93b60eec739cffff93b4e5991267dc1f4b4dc7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:29 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.460029176 25.1348763798 6.14463117969 0 0 0 0 + tauc_H1 17.4147866285 23.2689979438 6.30231838726 0 0 0 0 + tauc_H2 17.2733888959 25.4115145983 4.32368492893 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.124028082307 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.124393020388 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.142771398491 (SEC) + + DONE : INIT CHARGE Time : 0.221477738887 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.562622 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000548 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000912 + + Density error is 0.212033231059 + + Energy Rydberg eV + E_KohnSham -34.1938917533 -465.23176464 + E_Harris -34.3793398766 -467.754915801 + E_Fermi -0.394311614506 -5.36488474486 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000807116844508 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125877432567 + + Density error is 0.0980858101509 + + Energy Rydberg eV + E_KohnSham -34.2809333898 -466.416026859 + E_Harris -34.2877935616 -466.509364286 + E_Fermi -0.205968565492 -2.80234609958 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000776278701107 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121146265198 + + Density error is 0.0630015152735 + + Energy Rydberg eV + E_KohnSham -34.2811602693 -466.419113714 + E_Harris -34.2855920998 -466.479411862 + E_Fermi -0.196471823021 -2.67313628953 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000740347144656 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115821401245 + + Density error is 0.00196465868067 + + Energy Rydberg eV + E_KohnSham -34.281110494 -466.418436486 + E_Harris -34.2811119705 -466.418456574 + E_Fermi -0.161185030844 -2.19303485178 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00074066335609 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116026642079 + + Density error is 0.000797176262677 + + Energy Rydberg eV + E_KohnSham -34.2810749567 -466.417952976 + E_Harris -34.2810753299 -466.417958053 + E_Fermi -0.160797465522 -2.18776175505 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000740238559635 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115945153227 + + Density error is 0.000158512892786 + + Energy Rydberg eV + E_KohnSham -34.2810957782 -466.418236268 + E_Harris -34.2810957893 -466.418236419 + E_Fermi -0.160566306613 -2.18461667675 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000740378230908 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115962964662 + + Density error is 2.83706965156e-05 + + Energy Rydberg eV + E_KohnSham -34.2810889817 -466.418143796 + E_Harris -34.2810889846 -466.418143835 + E_Fermi -0.160499274508 -2.18370465818 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000740334130773 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115955825264 + + Density error is 1.47166075448e-05 + + Energy Rydberg eV + E_KohnSham -34.2810918999 -466.418183501 + E_Harris -34.281091901 -466.418183515 + E_Fermi -0.160521941021 -2.18401305191 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000740341969092 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115957089918 + + Density error is 2.25416655028e-06 + + Energy Rydberg eV + E_KohnSham -34.2810907648 -466.418168056 + E_Harris -34.2810907648 -466.418168056 + E_Fermi -0.160508279466 -2.18382717691 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000740340631255 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115956646706 + + Density error is 5.08417732174e-07 + + Energy Rydberg eV + E_KohnSham -34.2810910243 -466.418171587 + E_Harris -34.2810910243 -466.418171587 + E_Fermi -0.16050637087 -2.18380120913 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000740341459377 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115956773958 + + Density error is 1.6825888016e-07 + + Energy Rydberg eV + E_KohnSham -34.2810910344 -466.418171725 + E_Harris -34.2810910344 -466.418171725 + E_Fermi -0.160506128883 -2.18379791673 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000740341692064 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011595680125 + + Density error is 1.08103125439e-08 + + Energy Rydberg eV + E_KohnSham -34.2810910387 -466.418171783 + E_Harris -34.2810910387 -466.418171783 + E_band -7.91499808908 -107.689073671 + E_one_elec -68.9471439198 -938.074018135 + E_Hartree +35.8764695989 +488.124410669 + E_xc -8.18331310394 -111.339686732 + E_Ewald +7.09793211679 +96.5723208056 + E_demet -4.11896448772e-68 -5.60413868926e-67 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194189658828 -2.64208585274 + E_Fermi -0.160505966678 -2.18379570982 + + charge density convergence is achieved + final etot is -466.418171783 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1356 2.00000 + 2 -12.8608 2.00000 + 3 -9.13641 2.00000 + 4 -6.71168 2.00000 + 5 1.15641 0.00000 + 6 4.16727 0.00000 + 7 11.1142 0.00000 + 8 11.3696 0.00000 + + EFERMI = -2.183795709821482 eV + OUT.ABACUS/ final etot is -466.4181717828122 eV + correction force for each atom along direction 1 is 0.000153698 + correction force for each atom along direction 2 is -2.71040e-05 + correction force for each atom along direction 3 is -9.58267e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.031219597 -0.71679608 -0.14531447 + H1 +0.016948435 +0.70587436 -0.022638830 + H2 +0.014271162 +0.010921714 +0.16795330 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4181717828122 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9057 11 0.72 1.0e+02% + Run_lcao lcao_line 7.8924 1 7.9 1.e+02% + Potential init_pot 0.30022 2 0.15 3.8% + PW_Basis recip2real 0.31230 17 0.018 4.0% + PW_Basis gathers_scatterp 0.13437 17 0.0079 1.7% + Potential v_of_rho 1.0896 14 0.078 14.% + XC_Functional v_xc 0.30332 15 0.020 3.8% + H_Hartree_pw v_hartree 0.74123 14 0.053 9.4% + PW_Basis real2recip 0.70392 41 0.017 8.9% + PW_Basis gatherp_scatters 0.27060 41 0.0066 3.4% + ORB_control set_orb_tables 1.2003 1 1.2 15.% + ORB_gen_tables gen_tables 1.2003 1 1.2 15.% + ORB_table_phi init_Table 0.48380 1 0.48 6.1% + ORB_table_phi cal_ST_Phi12_R 0.47553 126 0.0038 6.0% + ORB_table_beta init_Table_Beta 0.19042 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18887 56 0.0034 2.4% + ORB_table_alpha init_Table_Alpha 0.25568 1 0.26 3.2% + ORB_table_alpha S_PhiAlpha_R 0.25347 66 0.0038 3.2% + LOOP_ions opt_ions 6.0281 1 6.0 76.% + ESolver_KS_LCAO Run 5.4532 1 5.5 69.% + HSolverLCAO solve 2.9023 12 0.24 37.% + HamiltLCAO updateHk 1.4991 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4654 12 0.12 19.% + Gint_interface cal_gint 2.6086 25 0.10 33.% + Gint_Gamma distri_vl 2.9213 6 0.49 37.% + LCAO_Deepks cal_projected_DM 5.8429 14 0.42 74.% + LCAO_gen_fixedH add_v_delta 2.7135 6 0.45 34.% + LCAO_DESCRIPTOR add_v_delta 2.7135 6 0.45 34.% + ElecStateLCAO psiToRho 1.3326 12 0.11 17.% + Charge mix_rho 0.92704 11 0.084 12.% + LOOP_ions force_stress 0.57469 1 0.57 7.3% + Force_Stress_LCAO getForceStress 0.57466 1 0.57 7.3% + Force_LCAO_gamma ftable_gamma 0.35386 1 0.35 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.34566 1 0.35 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:29 2022 + Finish Time : Wed Sep 28 11:01:37 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..7d3830e31dd491c38c8f029754a2d6f0ec1e8beb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123395 ima = 3.72131e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123117621487 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112120362406 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112733227434 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112933350371 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112908296477 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112923726956 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011291888277 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011292102426 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112920299639 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112920258421 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112920238687 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112920230117 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/STRU new file mode 100644 index 0000000000000000000000000000000000000000..581885edc7bad152aa4f5f8d68bf3a8390aceacc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.539970823957 25.134876379835 6.144631179689 0 0 0 +H +0.0 +2 +-10.585213371456 23.268997943794 6.302318387260 0 0 0 +-10.726611104117 25.411514598335 4.323684928953 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/conv new file mode 100644 index 0000000000000000000000000000000000000000..95785d64cb5bf798f2edffda93e0cef2f78b373c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/conv @@ -0,0 +1 @@ +249 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a0dcdd40d479de9a7d88001b4f0d3442a462ac60 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750105134 0.01257765071 1.25895823 1.348530477 1.468639885 0.008529722779 0.0179934981 0.03906925462 +4.025739885e-18 0.0009562291354 0.002518838055 0.01200946049 0.04346233326 7.040961374e-20 1.894220695e-06 5.60118912e-06 +0.001625223764 0.005949489418 + +H atom_index 1 n_descriptor 18 +1.21507775 0.03552849325 0.09658578306 0.1345359015 0.3093210839 0.02055814257 0.02627540092 0.03879744579 +-4.960877037e-19 4.028596806e-05 0.09126648644 0.1140617307 0.1151857838 6.469942896e-18 5.580247351e-06 0.01374761374 +0.02464291771 0.02906303811 + +H atom_index 2 n_descriptor 18 +1.232303491 0.03494910669 0.1021200662 0.1420064878 0.3153817571 0.02136210705 0.02728489396 0.03813894617 +-3.546226415e-18 4.180476189e-05 0.09579042726 0.1146135526 0.1217102551 -5.437268243e-18 4.821065857e-06 0.01339492312 +0.02532855739 0.02992178516 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..83e0dac118c21ee971a0643888426dacc1cdfbb6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:29 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.124051 SEC) : SETUP UNITCELL + DONE(0.124408 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.142795 SEC) : INIT PLANEWAVE + DONE(0.221612 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.562686 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652318e+02 0.000000e+00 2.120e-01 7.420e-01 + GE2 -4.664160e+02 -1.184262e+00 9.809e-02 4.991e-01 + GE3 -4.664191e+02 -3.086854e-03 6.300e-02 5.639e-01 + GE4 -4.664184e+02 6.772279e-04 1.965e-03 4.227e-01 + GE5 -4.664180e+02 4.835097e-04 7.972e-04 4.227e-01 + GE6 -4.664182e+02 -2.832919e-04 1.585e-04 4.166e-01 + GE7 -4.664181e+02 9.247222e-05 2.837e-05 3.991e-01 + GE8 -4.664182e+02 -3.970520e-05 1.472e-05 3.969e-01 + GE9 -4.664182e+02 1.544441e-05 2.254e-06 3.967e-01 + GE10 -4.664182e+02 -3.530330e-06 5.084e-07 3.995e-01 + GE11 -4.664182e+02 -1.380948e-07 1.683e-07 3.967e-01 + GE12 -4.664182e+02 -5.804373e-08 1.081e-08 3.289e-01 +E_delta_band = -6.91539282e-02 Ry = -9.40887462e-01 eV +E_delta_NN= -1.94189659e-01 Ry = -2.64208585e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9057 11 0.72 1e+02 % + Run_lcao lcao_line 7.8924 1 7.9 1e+02 % + Potential init_pot 0.30022 2 0.15 3.8 % + PW_Basis recip2real 0.3123 17 0.018 4 % + PW_Basis gathers_scatterp 0.13437 17 0.0079 1.7 % + Potential v_of_rho 1.0896 14 0.078 14 % + XC_Functional v_xc 0.30332 15 0.02 3.8 % + H_Hartree_pw v_hartree 0.74123 14 0.053 9.4 % + PW_Basis real2recip 0.70392 41 0.017 8.9 % + PW_Basis gatherp_scatters 0.2706 41 0.0066 3.4 % + ORB_control set_orb_tables 1.2003 1 1.2 15 % + ORB_gen_tables gen_tables 1.2003 1 1.2 15 % + ORB_table_phi init_Table 0.4838 1 0.48 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.47553 126 0.0038 6 % + ORB_table_beta init_Table_Beta 0.19042 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18887 56 0.0034 2.4 % + ORB_table_alpha init_Table_Alpha 0.25568 1 0.26 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.25347 66 0.0038 3.2 % + LOOP_ions opt_ions 6.0281 1 6 76 % + ESolver_KS_LCAO Run 5.4532 1 5.5 69 % + HSolverLCAO solve 2.9023 12 0.24 37 % + HamiltLCAO updateHk 1.4991 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.4654 12 0.12 19 % + Gint_interface cal_gint 2.6086 25 0.1 33 % + Gint_Gamma distri_vl 2.9213 6 0.49 37 % + LCAO_Deepks cal_projected_DM 5.8429 14 0.42 74 % + LCAO_gen_fixedH add_v_delta 2.7135 6 0.45 34 % + LCAO_DESCRIPTOR add_v_delta 2.7135 6 0.45 34 % + ElecStateLCAO psiToRho 1.3326 12 0.11 17 % + Charge mix_rho 0.92704 11 0.084 12 % + LOOP_ions force_stress 0.57469 1 0.57 7.3 % + Force_Stress_LCAO getForceStress 0.57466 1 0.57 7.3 % + Force_LCAO_gamma ftable_gamma 0.35386 1 0.35 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.34566 1 0.35 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:29 2022 + FINISH Time : Wed Sep 28 11:01:37 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/249/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ab9a3797bdb2edbce5e51a8320e08dcbbd87b290 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.51634 0.387706 0.435821 +H 0.558778 0.379646 0.388715 +H 0.513337 0.325168 0.456393 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0ce7e1752bbc3c82dddbcb05dfb737191f62cdee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.525 2 + 2 -12.8195 2 + 3 -9.44549 2 + 4 -6.79674 2 + 5 1.33491 0 + 6 4.55005 0 + 7 11.0396 0 + 8 11.3209 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0191c7db970e123eb626f4f944d0b0a3f292647e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:56 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.4575263327 10.8557578128 12.2029857776 0 0 0 0 + tauc_H1 15.6457838839 10.6301009846 10.8840131751 0 0 0 0 + tauc_H2 14.373446034 9.1047152976 12.7789999993 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0728785290914 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0873366434442 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103115484894 (SEC) + + DONE : INIT CHARGE Time : 0.144535812836 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.386963 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00155 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000753 + + Density error is 0.214396142297 + + Energy Rydberg eV + E_KohnSham -34.188579838 -465.159492324 + E_Harris -34.3800852111 -467.765056596 + E_Fermi -0.412771801957 -5.61604848035 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00139611094243 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107449017393 + + Density error is 0.097299118296 + + Energy Rydberg eV + E_KohnSham -34.2775786174 -466.37038284 + E_Harris -34.284342971 -466.462416592 + E_Fermi -0.22270221478 -3.03001907823 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127794440193 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103735105667 + + Density error is 0.0622799623216 + + Energy Rydberg eV + E_KohnSham -34.2778036922 -466.373445139 + E_Harris -34.2821738301 -466.432903916 + E_Fermi -0.210182753485 -2.85968306872 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010726370283 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000997038914564 + + Density error is 0.00196445684184 + + Energy Rydberg eV + E_KohnSham -34.2778117924 -466.373555349 + E_Harris -34.2778126965 -466.373567649 + E_Fermi -0.174268715571 -2.3710475149 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107031528694 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999546765502 + + Density error is 0.000860741322976 + + Energy Rydberg eV + E_KohnSham -34.2777488953 -466.372699589 + E_Harris -34.2777509001 -466.372726866 + E_Fermi -0.173458917492 -2.36002964681 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106859283518 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009983879166 + + Density error is 0.000107925782921 + + Energy Rydberg eV + E_KohnSham -34.2777938707 -466.37331151 + E_Harris -34.2777938884 -466.373311751 + E_Fermi -0.173559208285 -2.36139417305 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106846179898 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998484127018 + + Density error is 3.98786806131e-05 + + Energy Rydberg eV + E_KohnSham -34.2777793129 -466.373113442 + E_Harris -34.2777793208 -466.37311355 + E_Fermi -0.173452784631 -2.35994620495 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106845563577 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998371253871 + + Density error is 1.97917042146e-05 + + Energy Rydberg eV + E_KohnSham -34.2777819072 -466.373148739 + E_Harris -34.277781909 -466.373148764 + E_Fermi -0.173497080817 -2.36054888547 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106842318448 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00099838774557 + + Density error is 2.34559596752e-06 + + Energy Rydberg eV + E_KohnSham -34.2777803081 -466.373126982 + E_Harris -34.2777803081 -466.373126982 + E_Fermi -0.173476143097 -2.36026401318 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106842028353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998392122308 + + Density error is 5.88076588999e-07 + + Energy Rydberg eV + E_KohnSham -34.2777806152 -466.373131161 + E_Harris -34.2777806152 -466.373131161 + E_Fermi -0.173474695865 -2.36024432259 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106841936002 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998392663009 + + Density error is 1.44735070422e-07 + + Energy Rydberg eV + E_KohnSham -34.2777806418 -466.373131522 + E_Harris -34.2777806418 -466.373131522 + E_Fermi -0.17347427714 -2.36023862553 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106841905631 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00099839282336 + + Density error is 1.09844344549e-08 + + Energy Rydberg eV + E_KohnSham -34.2777806493 -466.373131624 + E_Harris -34.2777806493 -466.373131624 + E_band -8.02409781286 -109.173451564 + E_one_elec -69.5307716385 -946.01468062 + E_Hartree +36.1419039833 +491.735830742 + E_xc -8.22602291218 -111.920783484 + E_Ewald +7.46090666668 +101.510842913 + E_demet -9.29778062372e-83 -1.26502795237e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195305311072 -2.65726508024 + E_Fermi -0.173474115473 -2.36023642595 + + charge density convergence is achieved + final etot is -466.373131624 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5250 2.00000 + 2 -12.8195 2.00000 + 3 -9.44549 2.00000 + 4 -6.79674 2.00000 + 5 1.33491 0.00000 + 6 4.55005 0.00000 + 7 11.0396 0.00000 + 8 11.3209 0.00000 + + EFERMI = -2.360236425948395 eV + OUT.ABACUS/ final etot is -466.3731316244028 eV + correction force for each atom along direction 1 is -1.59705e-05 + correction force for each atom along direction 2 is -7.67060e-05 + correction force for each atom along direction 3 is 4.68265e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.76908461 -0.35018311 +0.98975815 + H1 +1.1317573 +0.32384632 -1.4036733 + H2 -0.36267265 +0.026336784 +0.41391516 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3731316244028 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1512 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1440 1 6.1 1.e+02% + Potential init_pot 0.24157 2 0.12 3.9% + PW_Basis recip2real 0.24395 17 0.014 4.0% + PW_Basis gathers_scatterp 0.11669 17 0.0069 1.9% + Potential v_of_rho 0.96185 14 0.069 16.% + XC_Functional v_xc 0.30506 15 0.020 5.0% + H_Hartree_pw v_hartree 0.62062 14 0.044 10.% + PW_Basis real2recip 0.65318 41 0.016 11.% + PW_Basis gatherp_scatters 0.28069 41 0.0068 4.6% + ORB_control set_orb_tables 0.89636 1 0.90 15.% + ORB_gen_tables gen_tables 0.89636 1 0.90 15.% + ORB_table_phi init_Table 0.37246 1 0.37 6.1% + ORB_table_phi cal_ST_Phi12_R 0.36824 126 0.0029 6.0% + ORB_table_beta init_Table_Beta 0.15595 1 0.16 2.5% + ORB_table_beta VNL_PhiBeta_R 0.15458 56 0.0028 2.5% + ORB_table_alpha init_Table_Alpha 0.21044 1 0.21 3.4% + ORB_table_alpha S_PhiAlpha_R 0.20879 66 0.0032 3.4% + LOOP_ions opt_ions 4.7898 1 4.8 78.% + ESolver_KS_LCAO Run 4.3232 1 4.3 70.% + HSolverLCAO solve 1.9542 12 0.16 32.% + HamiltLCAO updateHk 1.0455 12 0.087 17.% + LCAO_Hamilt cal_Hgamma 1.0203 12 0.085 17.% + Gint_interface cal_gint 0.14987 25 0.0060 2.4% + Gint_Gamma distri_vl_value 0.58622 12 0.049 9.5% + Gint_Gamma distri_vl 2.2592 6 0.38 37.% + LCAO_Deepks cal_projected_DM 4.4674 14 0.32 73.% + LCAO_gen_fixedH add_v_delta 2.1288 6 0.35 35.% + LCAO_DESCRIPTOR add_v_delta 2.1289 6 0.35 35.% + ElecStateLCAO psiToRho 0.88892 12 0.074 14.% + Charge mix_rho 0.83345 11 0.076 14.% + LOOP_ions force_stress 0.46646 1 0.47 7.6% + Force_Stress_LCAO getForceStress 0.46644 1 0.47 7.6% + Force_LCAO_gamma ftable_gamma 0.27631 1 0.28 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:56 2022 + Finish Time : Wed Sep 28 11:07:02 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e4a7cda515f5c826f562f51aacf56f85cbd325ea --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124017 ima = 3.69218e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122428672693 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111444853756 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111962089653 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112230929142 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112166512959 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112202517864 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112199361273 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112202459196 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112201557154 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112201467683 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112201442487 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112201435091 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/STRU new file mode 100644 index 0000000000000000000000000000000000000000..311735baf37d7bedbdbc0689dc5976f6b2396d8d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.542473667263 10.855757812799 12.202985777625 0 0 0 +H +0.0 +2 +-12.354216116061 10.630100984546 10.884013175070 0 0 0 +-13.626553966040 9.104715297591 12.778999999345 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/conv new file mode 100644 index 0000000000000000000000000000000000000000..b198e13f3172506ea257e6ab75fe165e5d2947ee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/conv @@ -0,0 +1 @@ +25 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..1110e158b2a99b4d13b730dde11ad287e55c958e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754067549 0.01285167946 1.278183428 1.361719503 1.47022805 0.009552971119 0.01699287186 0.03916016088 +4.166555061e-18 0.0009537756637 0.002924913681 0.01358204068 0.04809240419 9.120446786e-22 2.973489613e-06 7.725672595e-06 +0.001591467535 0.00615669597 + +H atom_index 1 n_descriptor 18 +1.283746804 0.03379317563 0.1240098438 0.1659906072 0.3299686637 0.02497283799 0.03019293838 0.03717069938 +8.228009419e-17 5.523484311e-05 0.1082979451 0.1208731255 0.1423888987 4.013583606e-18 1.300011851e-06 0.01351422484 +0.02842736032 0.03218397239 + +H atom_index 2 n_descriptor 18 +1.240061664 0.03522436451 0.1078504855 0.1449166893 0.3160450288 0.0227979898 0.02764584815 0.03831084538 +2.513615766e-17 5.106342999e-05 0.1018315199 0.1146254713 0.1243275747 6.425702106e-19 3.685281634e-06 0.01353242013 +0.02688416773 0.03028675315 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..143015ab00f3b8e5a1b79ef049abe7798f66b155 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:56 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.072894 SEC) : SETUP UNITCELL + DONE(0.0873491 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103128 SEC) : INIT PLANEWAVE + DONE(0.144641 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.387007 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651595e+02 0.000000e+00 2.144e-01 4.479e-01 + GE2 -4.663704e+02 -1.210891e+00 9.730e-02 4.070e-01 + GE3 -4.663734e+02 -3.062299e-03 6.228e-02 4.699e-01 + GE4 -4.663736e+02 -1.102099e-04 1.964e-03 3.472e-01 + GE5 -4.663727e+02 8.557598e-04 8.607e-04 3.439e-01 + GE6 -4.663733e+02 -6.119216e-04 1.079e-04 3.399e-01 + GE7 -4.663731e+02 1.980683e-04 3.988e-05 3.361e-01 + GE8 -4.663731e+02 -3.529730e-05 1.979e-05 3.242e-01 + GE9 -4.663731e+02 2.175745e-05 2.346e-06 3.290e-01 + GE10 -4.663731e+02 -4.178997e-06 5.881e-07 3.277e-01 + GE11 -4.663731e+02 -3.615136e-07 1.447e-07 3.365e-01 + GE12 -4.663731e+02 -1.019115e-07 1.098e-08 2.603e-01 +E_delta_band = -7.15085625e-02 Ry = -9.72923905e-01 eV +E_delta_NN= -1.95305311e-01 Ry = -2.65726508e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1512 11 0.56 1e+02 % + Run_lcao lcao_line 6.144 1 6.1 1e+02 % + Potential init_pot 0.24157 2 0.12 3.9 % + PW_Basis recip2real 0.24395 17 0.014 4 % + PW_Basis gathers_scatterp 0.11669 17 0.0069 1.9 % + Potential v_of_rho 0.96185 14 0.069 16 % + XC_Functional v_xc 0.30506 15 0.02 5 % + H_Hartree_pw v_hartree 0.62062 14 0.044 10 % + PW_Basis real2recip 0.65318 41 0.016 11 % + PW_Basis gatherp_scatters 0.28069 41 0.0068 4.6 % + ORB_control set_orb_tables 0.89636 1 0.9 15 % + ORB_gen_tables gen_tables 0.89636 1 0.9 15 % + ORB_table_phi init_Table 0.37246 1 0.37 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.36824 126 0.0029 6 % + ORB_table_beta init_Table_Beta 0.15595 1 0.16 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.15458 56 0.0028 2.5 % + ORB_table_alpha init_Table_Alpha 0.21044 1 0.21 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.20879 66 0.0032 3.4 % + LOOP_ions opt_ions 4.7898 1 4.8 78 % + ESolver_KS_LCAO Run 4.3232 1 4.3 70 % + HSolverLCAO solve 1.9542 12 0.16 32 % + HamiltLCAO updateHk 1.0455 12 0.087 17 % + LCAO_Hamilt cal_Hgamma 1.0203 12 0.085 17 % + Gint_interface cal_gint 0.14987 25 0.006 2.4 % + Gint_Gamma distri_vl_value 0.58622 12 0.049 9.5 % + Gint_Gamma distri_vl 2.2592 6 0.38 37 % + LCAO_Deepks cal_projected_DM 4.4674 14 0.32 73 % + LCAO_gen_fixedH add_v_delta 2.1288 6 0.35 35 % + LCAO_DESCRIPTOR add_v_delta 2.1289 6 0.35 35 % + ElecStateLCAO psiToRho 0.88892 12 0.074 14 % + Charge mix_rho 0.83345 11 0.076 14 % + LOOP_ions force_stress 0.46646 1 0.47 7.6 % + Force_Stress_LCAO getForceStress 0.46644 1 0.47 7.6 % + Force_LCAO_gamma ftable_gamma 0.27631 1 0.28 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:56 2022 + FINISH Time : Wed Sep 28 11:07:02 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/25/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..15f44ba3f77010e89ef07c7b241d15edf3d2fbcd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.609137 0.904903 0.243519 +H 0.618447 0.847873 0.272701 +H 0.637054 0.893253 0.184854 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..784617b1ee4a068a7090115901a0b43375794dec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.384 2 + 2 -12.8882 2 + 3 -9.30156 2 + 4 -6.767 2 + 5 1.29963 0 + 6 4.43675 0 + 7 11.0635 0 + 8 11.333 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..35018c94a011f8e00aca4f2ad31d0667ea69b631 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:12 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.0558345196 25.3372953348 6.81852813336 0 0 0 0 + tauc_H1 17.3165292903 23.7404442424 7.63563037204 0 0 0 0 + tauc_H2 17.8375146612 25.0110704214 5.17590274976 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0724490096228 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0727664539299 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0889629298617 (SEC) + + DONE : INIT CHARGE Time : 0.130136682154 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374076 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000547 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104 + + Density error is 0.214027891174 + + Energy Rydberg eV + E_KohnSham -34.1913891036 -465.197714344 + E_Harris -34.381508577 -467.784422483 + E_Fermi -0.406852367378 -5.53551044113 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000843389735903 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127294742634 + + Density error is 0.0976630465687 + + Energy Rydberg eV + E_KohnSham -34.2801223398 -466.404991958 + E_Harris -34.2868910358 -466.497084792 + E_Fermi -0.21701441274 -2.95263256139 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00081241948171 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012130752973 + + Density error is 0.0625811668029 + + Energy Rydberg eV + E_KohnSham -34.280371732 -466.408385114 + E_Harris -34.2847499413 -466.467953707 + E_Fermi -0.205496959642 -2.79592957281 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000781408515195 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113199551929 + + Density error is 0.00195195286721 + + Energy Rydberg eV + E_KohnSham -34.2803619802 -466.408252433 + E_Harris -34.280362696 -466.408262173 + E_Fermi -0.169803568993 -2.31029607904 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000783895997195 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113474272975 + + Density error is 0.000860286024084 + + Energy Rydberg eV + E_KohnSham -34.2803033308 -466.407454467 + E_Harris -34.2803047161 -466.407473315 + E_Fermi -0.16909746589 -2.30068905347 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000783029344296 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113322762941 + + Density error is 0.000102821038128 + + Energy Rydberg eV + E_KohnSham -34.2803429671 -466.407993747 + E_Harris -34.2803429714 -466.407993805 + E_Fermi -0.169111058117 -2.30087398519 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000783059897565 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113315766106 + + Density error is 3.66890645513e-05 + + Energy Rydberg eV + E_KohnSham -34.2803305154 -466.407824333 + E_Harris -34.280330523 -466.407824436 + E_Fermi -0.169005334249 -2.29943553818 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000783004691838 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113309605656 + + Density error is 1.16277347157e-05 + + Energy Rydberg eV + E_KohnSham -34.2803328647 -466.407856297 + E_Harris -34.2803328653 -466.407856305 + E_Fermi -0.169046516245 -2.29999584797 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000783017050262 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113310370816 + + Density error is 1.63207780515e-06 + + Energy Rydberg eV + E_KohnSham -34.2803316051 -466.407839158 + E_Harris -34.2803316051 -466.407839159 + E_Fermi -0.169034921829 -2.29983809786 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000783018094661 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113310303657 + + Density error is 1.1830517279e-07 + + Energy Rydberg eV + E_KohnSham -34.2803317884 -466.407841653 + E_Harris -34.2803317884 -466.407841653 + E_Fermi -0.16903326046 -2.29981549378 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000783018287892 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113310340671 + + Density error is 5.54703933762e-08 + + Energy Rydberg eV + E_KohnSham -34.2803318164 -466.407842034 + E_Harris -34.2803318164 -466.407842034 + E_band -7.98794413954 -108.681555603 + E_one_elec -69.3524535637 -943.588538747 + E_Hartree +36.0624007381 +490.654133597 + E_xc -8.21325353486 -111.747047193 + E_Ewald +7.34715218953 +99.9631338508 + E_demet -1.15556608283e-78 -1.5722283142e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194957234828 -2.65252925998 + E_Fermi -0.169033303129 -2.29981607431 + + charge density convergence is achieved + final etot is -466.407842034 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3840 2.00000 + 2 -12.8882 2.00000 + 3 -9.30156 2.00000 + 4 -6.76700 2.00000 + 5 1.29963 0.00000 + 6 4.43675 0.00000 + 7 11.0635 0.00000 + 8 11.3330 0.00000 + + EFERMI = -2.299816074311870 eV + OUT.ABACUS/ final etot is -466.4078420339276 eV + correction force for each atom along direction 1 is 4.73367e-05 + correction force for each atom along direction 2 is -1.19203e-05 + correction force for each atom along direction 3 is -8.91978e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.083020975 +0.45832694 -0.62532280 + H1 -0.0026606906 -0.74210919 +0.68641329 + H2 -0.080360285 +0.28378225 -0.061090492 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4078420339276 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2241 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2171 1 6.2 1.e+02% + Potential init_pot 0.24437 2 0.12 3.9% + PW_Basis recip2real 0.25182 16 0.016 4.0% + PW_Basis gathers_scatterp 0.10692 16 0.0067 1.7% + Potential v_of_rho 0.90044 13 0.069 14.% + XC_Functional v_xc 0.26369 14 0.019 4.2% + H_Hartree_pw v_hartree 0.59756 13 0.046 9.6% + PW_Basis real2recip 0.60106 38 0.016 9.7% + PW_Basis gatherp_scatters 0.22670 38 0.0060 3.6% + ORB_control set_orb_tables 0.89791 1 0.90 14.% + ORB_gen_tables gen_tables 0.89791 1 0.90 14.% + ORB_table_phi init_Table 0.37635 1 0.38 6.0% + ORB_table_phi cal_ST_Phi12_R 0.37207 126 0.0030 6.0% + ORB_table_beta init_Table_Beta 0.15535 1 0.16 2.5% + ORB_table_beta VNL_PhiBeta_R 0.15401 56 0.0028 2.5% + ORB_table_alpha init_Table_Alpha 0.20757 1 0.21 3.3% + ORB_table_alpha S_PhiAlpha_R 0.20591 66 0.0031 3.3% + LOOP_ions opt_ions 4.8749 1 4.9 78.% + ESolver_KS_LCAO Run 4.3647 1 4.4 70.% + HSolverLCAO solve 2.2211 11 0.20 36.% + HamiltLCAO updateHk 1.1565 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.1283 11 0.10 18.% + Gint_interface cal_gint 2.0737 23 0.090 33.% + Gint_Gamma distri_vl 2.1028 6 0.35 34.% + LCAO_Deepks cal_projected_DM 4.7364 13 0.36 76.% + LCAO_gen_fixedH add_v_delta 1.9733 6 0.33 32.% + LCAO_DESCRIPTOR add_v_delta 1.9734 6 0.33 32.% + ElecStateLCAO psiToRho 1.0478 11 0.095 17.% + Charge mix_rho 0.75553 10 0.076 12.% + LOOP_ions force_stress 0.51008 1 0.51 8.2% + Force_Stress_LCAO getForceStress 0.51003 1 0.51 8.2% + Force_LCAO_gamma ftable_gamma 0.31400 1 0.31 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.30665 1 0.31 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:12 2022 + Finish Time : Wed Sep 28 11:05:18 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..bbcb68d7c751f6044f241601d8ef9880c15af4e5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123562 ima = 3.67995e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122742967154 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111753785324 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112297555635 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112546687459 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112491938551 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112522533492 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011251919954 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112521846872 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112521311926 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112521243726 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112521240509 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8cddf1cb1a6cd0f68bc7eef60eb4b3042ad5695c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.944165480466 25.337295334751 6.818528133377 0 0 0 +H +0.0 +2 +-10.683470709691 23.740444242409 7.635630372055 0 0 0 +-10.162485338797 25.011070421362 5.175902749739 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/conv new file mode 100644 index 0000000000000000000000000000000000000000..ea56e03dc59cad7543b0af33c3ebd6879af106e8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/conv @@ -0,0 +1 @@ +250 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7e87d665da800693e7e3b72a343013e5481a17c0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752084088 0.01276450372 1.27347624 1.358606015 1.469679027 0.009060576616 0.01756515648 0.03911026349 +2.089870916e-18 0.0009849533778 0.002756464491 0.01289660804 0.04647608607 4.678708496e-19 2.487549406e-06 6.798050474e-06 +0.001605400917 0.006088405799 + +H atom_index 1 n_descriptor 18 +1.264421304 0.03411672961 0.1147753527 0.1564612157 0.3247412468 0.02344412506 0.02909623629 0.03731778119 +1.901409305e-17 5.048755797e-05 0.1054303997 0.1164080076 0.1342850711 -5.487637969e-19 2.842409006e-06 0.01326225326 +0.02722401307 0.03138382008 + +H atom_index 2 n_descriptor 18 +1.236419065 0.03506338368 0.1049215084 0.1434034872 0.3155624648 0.02209298733 0.02745969855 0.03818231457 +-2.43903535e-17 4.781225122e-05 0.09916833909 0.1145124918 0.1230191722 1.972605364e-18 4.415359249e-06 0.0134705116 +0.02618824705 0.03010815638 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9567ffe1cfee61e73140a27bedca8d9baa6e66fa Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:12 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0724647 SEC) : SETUP UNITCELL + DONE(0.0727757 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0889753 SEC) : INIT PLANEWAVE + DONE(0.130241 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374124 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651977e+02 0.000000e+00 2.140e-01 4.727e-01 + GE2 -4.664050e+02 -1.207278e+00 9.766e-02 4.428e-01 + GE3 -4.664084e+02 -3.393156e-03 6.258e-02 5.062e-01 + GE4 -4.664083e+02 1.326807e-04 1.952e-03 3.829e-01 + GE5 -4.664075e+02 7.979657e-04 8.603e-04 3.812e-01 + GE6 -4.664080e+02 -5.392794e-04 1.028e-04 3.717e-01 + GE7 -4.664078e+02 1.694141e-04 3.669e-05 3.652e-01 + GE8 -4.664079e+02 -3.196442e-05 1.163e-05 3.577e-01 + GE9 -4.664078e+02 1.713865e-05 1.632e-06 3.646e-01 + GE10 -4.664078e+02 -2.494964e-06 1.183e-07 3.690e-01 + GE11 -4.664078e+02 -3.805614e-07 5.547e-08 2.975e-01 +E_delta_band = -7.07795894e-02 Ry = -9.63005717e-01 eV +E_delta_NN= -1.94957235e-01 Ry = -2.65252926e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2241 11 0.57 1e+02 % + Run_lcao lcao_line 6.2171 1 6.2 1e+02 % + Potential init_pot 0.24437 2 0.12 3.9 % + PW_Basis recip2real 0.25182 16 0.016 4 % + PW_Basis gathers_scatterp 0.10692 16 0.0067 1.7 % + Potential v_of_rho 0.90044 13 0.069 14 % + XC_Functional v_xc 0.26369 14 0.019 4.2 % + H_Hartree_pw v_hartree 0.59756 13 0.046 9.6 % + PW_Basis real2recip 0.60106 38 0.016 9.7 % + PW_Basis gatherp_scatters 0.2267 38 0.006 3.6 % + ORB_control set_orb_tables 0.89791 1 0.9 14 % + ORB_gen_tables gen_tables 0.89791 1 0.9 14 % + ORB_table_phi init_Table 0.37635 1 0.38 6 % + ORB_table_phi cal_ST_Phi12_R 0.37207 126 0.003 6 % + ORB_table_beta init_Table_Beta 0.15535 1 0.16 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.15401 56 0.0028 2.5 % + ORB_table_alpha init_Table_Alpha 0.20757 1 0.21 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.20591 66 0.0031 3.3 % + LOOP_ions opt_ions 4.8749 1 4.9 78 % + ESolver_KS_LCAO Run 4.3647 1 4.4 70 % + HSolverLCAO solve 2.2211 11 0.2 36 % + HamiltLCAO updateHk 1.1565 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.1283 11 0.1 18 % + Gint_interface cal_gint 2.0737 23 0.09 33 % + Gint_Gamma distri_vl 2.1028 6 0.35 34 % + LCAO_Deepks cal_projected_DM 4.7364 13 0.36 76 % + LCAO_gen_fixedH add_v_delta 1.9733 6 0.33 32 % + LCAO_DESCRIPTOR add_v_delta 1.9734 6 0.33 32 % + ElecStateLCAO psiToRho 1.0478 11 0.095 17 % + Charge mix_rho 0.75553 10 0.076 12 % + LOOP_ions force_stress 0.51008 1 0.51 8.2 % + Force_Stress_LCAO getForceStress 0.51003 1 0.51 8.2 % + Force_LCAO_gamma ftable_gamma 0.314 1 0.31 5 % + Force_LCAO_gamma cal_fvl_dphi 0.30665 1 0.31 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:12 2022 + FINISH Time : Wed Sep 28 11:05:18 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/250/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a81d71b368092f0c4f4d2e226fd4bb0c9c52ca14 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.593898 0.909739 0.261573 +H 0.61399 0.856373 0.293045 +H 0.649123 0.939729 0.243475 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..5283004413cb9e360a7fd28826c6b1021b6ce36c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.321 2 + 2 -13.0928 2 + 3 -9.10878 2 + 4 -6.7518 2 + 5 1.33952 0 + 6 4.47833 0 + 7 11.0665 0 + 8 11.3167 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a7353723df6e22cdaf19a2ec4232d1bc8e319c33 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:25 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.6291309892 25.4726935651 7.3240512517 0 0 0 0 + tauc_H1 17.1917321383 23.9784543549 8.20525985134 0 0 0 0 + tauc_H2 18.1754308558 26.3124046035 6.81729920611 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0869778352325 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.097281538359 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11538075667 (SEC) + + DONE : INIT CHARGE Time : 0.164472590496 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447125 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 4 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000672 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00146 + + Density error is 0.214988056082 + + Energy Rydberg eV + E_KohnSham -34.1917476727 -465.202592927 + E_Harris -34.3835791796 -467.812594476 + E_Fermi -0.407774012573 -5.54805006731 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000824740136535 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124001654458 + + Density error is 0.0978176161282 + + Energy Rydberg eV + E_KohnSham -34.2810369082 -466.417435299 + E_Harris -34.2877366818 -466.508590396 + E_Fermi -0.216264083175 -2.94242380392 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000793066157081 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114642501716 + + Density error is 0.0626773584161 + + Energy Rydberg eV + E_KohnSham -34.2812746602 -466.420670081 + E_Harris -34.2856006771 -466.479528561 + E_Fermi -0.204433203219 -2.78145642418 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000756784683198 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000990001288407 + + Density error is 0.001999390607 + + Energy Rydberg eV + E_KohnSham -34.2812736866 -466.420656836 + E_Harris -34.2812747152 -466.420670831 + E_Fermi -0.168907841697 -2.29810908396 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000757837482481 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989545120493 + + Density error is 0.00087163288773 + + Energy Rydberg eV + E_KohnSham -34.2812131329 -466.41983296 + E_Harris -34.2812147509 -466.419854974 + E_Fermi -0.168102909658 -2.28715742173 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000757211688927 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000987794777205 + + Density error is 0.000146821957263 + + Energy Rydberg eV + E_KohnSham -34.2812527372 -466.420371805 + E_Harris -34.2812526157 -466.420370151 + E_Fermi -0.168149088872 -2.28778572217 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000757438991275 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000987701372889 + + Density error is 3.8316213984e-05 + + Energy Rydberg eV + E_KohnSham -34.2812386547 -466.420180201 + E_Harris -34.2812386628 -466.420180311 + E_Fermi -0.168018957403 -2.28601519271 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000757377899517 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000987706407627 + + Density error is 1.64700054723e-05 + + Energy Rydberg eV + E_KohnSham -34.2812426315 -466.420234309 + E_Harris -34.2812426327 -466.420234325 + E_Fermi -0.168063516359 -2.2866214484 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000757381767521 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000987689030313 + + Density error is 1.96123222123e-06 + + Energy Rydberg eV + E_KohnSham -34.281241189 -466.420214683 + E_Harris -34.2812411891 -466.420214683 + E_Fermi -0.168046222497 -2.28638615333 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000757383304358 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000987683771379 + + Density error is 3.07833024994e-07 + + Energy Rydberg eV + E_KohnSham -34.2812414329 -466.420218001 + E_Harris -34.2812414329 -466.420218001 + E_Fermi -0.168044356327 -2.28636076278 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000757383588971 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000987684111364 + + Density error is 1.11123301497e-07 + + Energy Rydberg eV + E_KohnSham -34.2812414591 -466.420218357 + E_Harris -34.2812414591 -466.420218357 + E_Fermi -0.16804426186 -2.2863594775 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000757383655107 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000987683994069 + + Density error is 1.00697710618e-08 + + Energy Rydberg eV + E_KohnSham -34.2812414617 -466.420218393 + E_Harris -34.2812414617 -466.420218393 + E_band -7.97818327761 -108.548752264 + E_one_elec -69.3681878547 -943.802614759 + E_Hartree +36.0766210748 +490.847611205 + E_xc -8.21548071687 -111.777349559 + E_Ewald +7.34997781208 +100.001578418 + E_demet -8.76331266532e-80 -1.19230985604e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194933719816 -2.65220932183 + E_Fermi -0.168044164274 -2.28635814977 + + charge density convergence is achieved + final etot is -466.420218393 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3210 2.00000 + 2 -13.0928 2.00000 + 3 -9.10878 2.00000 + 4 -6.75180 2.00000 + 5 1.33952 0.00000 + 6 4.47833 0.00000 + 7 11.0665 0.00000 + 8 11.3167 0.00000 + + EFERMI = -2.286358149774826 eV + OUT.ABACUS/ final etot is -466.4202183928991 eV + correction force for each atom along direction 1 is 7.34511e-05 + correction force for each atom along direction 2 is -6.46566e-05 + correction force for each atom along direction 3 is 1.88881e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.42572310 +0.28291481 -0.16586637 + H1 +0.15823038 -0.43474777 +0.25712954 + H2 +0.26749272 +0.15183296 -0.091263174 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4202183928991 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2808 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2718 1 7.3 1.e+02% + Potential init_pot 0.28340 2 0.14 3.9% + PW_Basis recip2real 0.30006 17 0.018 4.1% + PW_Basis gathers_scatterp 0.13324 17 0.0078 1.8% + Potential v_of_rho 1.0594 14 0.076 15.% + XC_Functional v_xc 0.30075 15 0.020 4.1% + H_Hartree_pw v_hartree 0.71397 14 0.051 9.8% + PW_Basis real2recip 0.70560 41 0.017 9.7% + PW_Basis gatherp_scatters 0.27482 41 0.0067 3.8% + ORB_control set_orb_tables 1.1051 1 1.1 15.% + ORB_gen_tables gen_tables 1.1051 1 1.1 15.% + ORB_table_phi init_Table 0.47903 1 0.48 6.6% + ORB_table_phi cal_ST_Phi12_R 0.47387 126 0.0038 6.5% + ORB_table_beta init_Table_Beta 0.18665 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18509 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.25282 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.25082 66 0.0038 3.4% + LOOP_ions opt_ions 5.6384 1 5.6 77.% + ESolver_KS_LCAO Run 5.0804 1 5.1 70.% + HSolverLCAO solve 2.5773 12 0.21 35.% + HamiltLCAO updateHk 1.3268 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2970 12 0.11 18.% + Gint_interface cal_gint 1.9207 25 0.077 26.% + Gint_Gamma distri_vl_value 0.17237 12 0.014 2.4% + Gint_Gamma distri_vl 2.6625 6 0.44 37.% + LCAO_Deepks cal_projected_DM 5.4447 14 0.39 75.% + LCAO_gen_fixedH add_v_delta 2.5169 6 0.42 35.% + LCAO_DESCRIPTOR add_v_delta 2.5170 6 0.42 35.% + ElecStateLCAO psiToRho 1.2202 12 0.10 17.% + Charge mix_rho 0.85112 11 0.077 12.% + LOOP_ions force_stress 0.55781 1 0.56 7.7% + Force_Stress_LCAO getForceStress 0.55778 1 0.56 7.7% + Force_LCAO_gamma ftable_gamma 0.34058 1 0.34 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.29743 1 0.30 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:25 2022 + Finish Time : Wed Sep 28 11:04:32 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..9f6085300cbec79c538bc50ab77a09663b30ae29 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123895 ima = 3.64847e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123041771346 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112069703906 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112581068415 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112825563593 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112772402398 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112803906342 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112797022349 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112799940318 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112799236561 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112799163912 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112799151774 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112799146774 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/STRU new file mode 100644 index 0000000000000000000000000000000000000000..373176022311d8206eab11a0c268d755d551eabe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.370869010853 25.472693565101 7.324051251682 0 0 0 +H +0.0 +2 +-10.808267861642 23.978454354903 8.205259851329 0 0 0 +-9.824569144165 26.312404603540 6.817299206117 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/conv new file mode 100644 index 0000000000000000000000000000000000000000..18caa9b147f1c717aba74d941eba05f6b532c62a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/conv @@ -0,0 +1 @@ +251 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..36da7de84079301fea91a0a862fad1ebbcc4878e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748946001 0.01271099224 1.276912919 1.364533902 1.469449921 0.008473868219 0.01870248218 0.03901216423 +-1.270758894e-18 0.001074618562 0.002606903831 0.01252422408 0.04532740124 -5.672429652e-19 2.055327612e-06 5.945979987e-06 +0.00165866764 0.005949715337 + +H atom_index 1 n_descriptor 18 +1.252987586 0.03410083089 0.1094241853 0.1514490544 0.3221039282 0.02238580717 0.02849650218 0.03726568373 +4.346562211e-17 4.612375603e-05 0.1026567802 0.1151309179 0.1300434414 4.44819343e-18 3.977494529e-06 0.01313664279 +0.02647225078 0.03091220055 + +H atom_index 2 n_descriptor 18 +1.247086591 0.03430489083 0.1073829477 0.1487125595 0.3202174497 0.02211349557 0.02815411868 0.037447183 +2.407422815e-17 4.557911749e-05 0.1012495342 0.1148365953 0.1276809457 6.996315405e-18 4.29662789e-06 0.01317797012 +0.02625420423 0.03064654333 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..485a85ac70a32f725d5f09b871ce1eb039b8b35d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:25 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870014 SEC) : SETUP UNITCELL + DONE(0.0973004 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115402 SEC) : INIT PLANEWAVE + DONE(0.164613 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447192 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652026e+02 0.000000e+00 2.150e-01 5.345e-01 + GE2 -4.664174e+02 -1.214842e+00 9.782e-02 4.756e-01 + GE3 -4.664207e+02 -3.234782e-03 6.268e-02 5.466e-01 + GE4 -4.664207e+02 1.324565e-05 1.999e-03 4.079e-01 + GE5 -4.664198e+02 8.238753e-04 8.716e-04 4.170e-01 + GE6 -4.664204e+02 -5.388443e-04 1.468e-04 3.946e-01 + GE7 -4.664202e+02 1.916034e-04 3.832e-05 3.885e-01 + GE8 -4.664202e+02 -5.410816e-05 1.647e-05 3.781e-01 + GE9 -4.664202e+02 1.962601e-05 1.961e-06 3.844e-01 + GE10 -4.664202e+02 -3.317674e-06 3.078e-07 3.885e-01 + GE11 -4.664202e+02 -3.561932e-07 1.111e-07 3.853e-01 + GE12 -4.664202e+02 -3.577664e-08 1.007e-08 3.169e-01 +E_delta_band = -7.07619428e-02 Ry = -9.62765624e-01 eV +E_delta_NN= -1.94933720e-01 Ry = -2.65220932e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2808 11 0.66 1e+02 % + Run_lcao lcao_line 7.2718 1 7.3 1e+02 % + Potential init_pot 0.2834 2 0.14 3.9 % + PW_Basis recip2real 0.30006 17 0.018 4.1 % + PW_Basis gathers_scatterp 0.13324 17 0.0078 1.8 % + Potential v_of_rho 1.0594 14 0.076 15 % + XC_Functional v_xc 0.30075 15 0.02 4.1 % + H_Hartree_pw v_hartree 0.71397 14 0.051 9.8 % + PW_Basis real2recip 0.7056 41 0.017 9.7 % + PW_Basis gatherp_scatters 0.27482 41 0.0067 3.8 % + ORB_control set_orb_tables 1.1051 1 1.1 15 % + ORB_gen_tables gen_tables 1.1051 1 1.1 15 % + ORB_table_phi init_Table 0.47903 1 0.48 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.47387 126 0.0038 6.5 % + ORB_table_beta init_Table_Beta 0.18665 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18509 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.25282 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.25082 66 0.0038 3.4 % + LOOP_ions opt_ions 5.6384 1 5.6 77 % + ESolver_KS_LCAO Run 5.0804 1 5.1 70 % + HSolverLCAO solve 2.5773 12 0.21 35 % + HamiltLCAO updateHk 1.3268 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.297 12 0.11 18 % + Gint_interface cal_gint 1.9207 25 0.077 26 % + Gint_Gamma distri_vl_value 0.17237 12 0.014 2.4 % + Gint_Gamma distri_vl 2.6625 6 0.44 37 % + LCAO_Deepks cal_projected_DM 5.4447 14 0.39 75 % + LCAO_gen_fixedH add_v_delta 2.5169 6 0.42 35 % + LCAO_DESCRIPTOR add_v_delta 2.517 6 0.42 35 % + ElecStateLCAO psiToRho 1.2202 12 0.1 17 % + Charge mix_rho 0.85112 11 0.077 12 % + LOOP_ions force_stress 0.55781 1 0.56 7.7 % + Force_Stress_LCAO getForceStress 0.55778 1 0.56 7.7 % + Force_LCAO_gamma ftable_gamma 0.34058 1 0.34 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.29743 1 0.3 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:25 2022 + FINISH Time : Wed Sep 28 11:04:32 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/251/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ef6d0bc0b98064dcc726209989356bcd5cbbcc2e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.586006 0.911623 0.273391 +H 0.632093 0.87485 0.302609 +H 0.564969 0.951115 0.322721 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e61754a175641ae09486160d0a19a179abc75e12 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1929 2 + 2 -12.8874 2 + 3 -9.16086 2 + 4 -6.72449 2 + 5 1.19877 0 + 6 4.24026 0 + 7 11.1014 0 + 8 11.3592 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9ad760da163fdc5215a52e585395959bd1384300 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:13 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.4081711304 25.5254328092 7.65495403033 0 0 0 0 + tauc_H1 17.6985949587 24.4958057613 8.47304734592 0 0 0 0 + tauc_H2 15.8191360169 26.6312212627 9.03620164609 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0868705789417 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100802143079 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11889484997 (SEC) + + DONE : INIT CHARGE Time : 0.166746202386 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44497 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 144 25 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00107 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000855 + + Density error is 0.213106444197 + + Energy Rydberg eV + E_KohnSham -34.1924588767 -465.212269354 + E_Harris -34.3804329981 -467.769788481 + E_Fermi -0.397973183633 -5.41470294861 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00124168510319 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107918426249 + + Density error is 0.0982306317474 + + Energy Rydberg eV + E_KohnSham -34.2810345242 -466.417402863 + E_Harris -34.2879043272 -466.510871328 + E_Fermi -0.20817561658 -2.83237457015 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00117227692327 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103323745179 + + Density error is 0.063078683151 + + Energy Rydberg eV + E_KohnSham -34.2813513216 -466.421713113 + E_Harris -34.2857903043 -466.482108571 + E_Fermi -0.19869271036 -2.70335301196 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00105950806863 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972586381794 + + Density error is 0.00195735353848 + + Energy Rydberg eV + E_KohnSham -34.2813057967 -466.421093716 + E_Harris -34.2813071135 -466.421111632 + E_Fermi -0.163250570081 -2.22113795485 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00105879343121 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972693273607 + + Density error is 0.000883623085031 + + Energy Rydberg eV + E_KohnSham -34.2812575559 -466.420437365 + E_Harris -34.2812582967 -466.420447444 + E_Fermi -0.162818645925 -2.21526132522 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00105726802824 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000971791492341 + + Density error is 0.000157883523153 + + Energy Rydberg eV + E_KohnSham -34.2812859439 -466.420823604 + E_Harris -34.2812859812 -466.420824112 + E_Fermi -0.162628125485 -2.21266916165 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00105742604781 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972018582258 + + Density error is 3.39454218339e-05 + + Energy Rydberg eV + E_KohnSham -34.28127564 -466.420683412 + E_Harris -34.2812756453 -466.420683484 + E_Fermi -0.162548248386 -2.21158237796 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00105735756052 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000971936632342 + + Density error is 1.46256172662e-05 + + Energy Rydberg eV + E_KohnSham -34.2812793311 -466.420733632 + E_Harris -34.2812793319 -466.420733644 + E_Fermi -0.162579070099 -2.21200172888 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00105734415299 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000971933984789 + + Density error is 1.91190886213e-06 + + Energy Rydberg eV + E_KohnSham -34.2812780948 -466.420716812 + E_Harris -34.2812780948 -466.420716812 + E_Fermi -0.162563871572 -2.21179494232 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00105734411186 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000971935799821 + + Density error is 3.44520326422e-07 + + Energy Rydberg eV + E_KohnSham -34.2812782953 -466.42071954 + E_Harris -34.2812782953 -466.42071954 + E_Fermi -0.162562178588 -2.21177190809 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00105734460894 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000971936394334 + + Density error is 1.13279956194e-07 + + Energy Rydberg eV + E_KohnSham -34.2812783203 -466.42071988 + E_Harris -34.2812783203 -466.42071988 + E_Fermi -0.162562051491 -2.21177017884 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00105734460592 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00097193648869 + + Density error is 1.03609024516e-08 + + Energy Rydberg eV + E_KohnSham -34.2812783235 -466.420719924 + E_Harris -34.2812783235 -466.420719924 + E_band -7.93281266958 -107.931453473 + E_one_elec -69.0526470107 -939.509461329 + E_Hartree +35.9255146249 +488.791702482 + E_xc -8.19119670509 -111.446948628 + E_Ewald +7.16186665264 +97.4421947921 + E_demet -6.75532018704e-71 -9.19108463582e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194383322389 -2.64472078066 + E_Fermi -0.162561948744 -2.21176878091 + + charge density convergence is achieved + final etot is -466.420719924 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1929 2.00000 + 2 -12.8874 2.00000 + 3 -9.16086 2.00000 + 4 -6.72449 2.00000 + 5 1.19877 0.00000 + 6 4.24026 0.00000 + 7 11.1014 0.00000 + 8 11.3592 0.00000 + + EFERMI = -2.211768780906136 eV + OUT.ABACUS/ final etot is -466.4207199236394 eV + correction force for each atom along direction 1 is 2.08914e-05 + correction force for each atom along direction 2 is 9.00831e-05 + correction force for each atom along direction 3 is 7.49302e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.17218309 +0.34592555 +0.45469300 + H1 +0.061719366 -0.078221640 -0.034592776 + H2 +0.11046372 -0.26770391 -0.42010022 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4207199236394 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5738 11 0.60 1.0e+02% + Run_lcao lcao_line 6.5638 1 6.6 1.e+02% + Potential init_pot 0.28464 2 0.14 4.3% + PW_Basis recip2real 0.28230 17 0.017 4.3% + PW_Basis gathers_scatterp 0.12577 17 0.0074 1.9% + Potential v_of_rho 0.92667 14 0.066 14.% + XC_Functional v_xc 0.25895 15 0.017 3.9% + H_Hartree_pw v_hartree 0.63052 14 0.045 9.6% + PW_Basis real2recip 0.60325 41 0.015 9.2% + PW_Basis gatherp_scatters 0.23925 41 0.0058 3.6% + ORB_control set_orb_tables 1.1075 1 1.1 17.% + ORB_gen_tables gen_tables 1.1075 1 1.1 17.% + ORB_table_phi init_Table 0.48421 1 0.48 7.4% + ORB_table_phi cal_ST_Phi12_R 0.47932 126 0.0038 7.3% + ORB_table_beta init_Table_Beta 0.18870 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18722 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25528 1 0.26 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25342 66 0.0038 3.9% + LOOP_ions opt_ions 4.9356 1 4.9 75.% + ESolver_KS_LCAO Run 4.3899 1 4.4 67.% + HSolverLCAO solve 2.2577 12 0.19 34.% + HamiltLCAO updateHk 1.1744 12 0.098 18.% + LCAO_Hamilt cal_Hgamma 1.1437 12 0.095 17.% + Gint_interface cal_gint 1.1550 25 0.046 18.% + Gint_Gamma distri_vl_value 0.35782 12 0.030 5.4% + Gint_Gamma distri_vl 2.2849 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.6634 14 0.33 71.% + LCAO_gen_fixedH add_v_delta 2.1536 6 0.36 33.% + LCAO_DESCRIPTOR add_v_delta 2.1536 6 0.36 33.% + ElecStateLCAO psiToRho 1.0630 12 0.089 16.% + Charge mix_rho 0.71158 11 0.065 11.% + LOOP_ions force_stress 0.54547 1 0.55 8.3% + Force_Stress_LCAO getForceStress 0.54544 1 0.55 8.3% + Force_LCAO_gamma ftable_gamma 0.33267 1 0.33 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.21415 1 0.21 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:13 2022 + Finish Time : Wed Sep 28 11:11:20 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..088df18a21b23737af1719c845523691b7529dbb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123398 ima = 3.68624e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123188970055 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112050412096 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112675999922 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011290036667 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112863941692 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112886670992 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112880055237 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112882571081 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112881972764 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011288190072 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112881886961 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112881881561 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b8496e2553808f1b89a0dab8b5832a44bd5cc5b3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.591828869644 25.525432809203 7.654954030347 0 0 0 +H +0.0 +2 +-10.301405041277 24.495805761295 8.473047345907 0 0 0 +-12.180863983152 26.631221262721 9.036201646112 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/conv new file mode 100644 index 0000000000000000000000000000000000000000..2dd02ac6b0bc40703da4ddc376e9e6025b7551ad --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/conv @@ -0,0 +1 @@ +252 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b30c6cde67788dca52390f71d04fdf8b5348202d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750310727 0.01262432164 1.263056549 1.351657949 1.468870791 0.008604568483 0.01798557912 0.03906752545 +3.915578062e-18 0.0009727623064 0.002565304237 0.01219130987 0.04414276762 -1.852522622e-19 2.000004733e-06 5.823485825e-06 +0.00162475552 0.00597849626 + +H atom_index 1 n_descriptor 18 +1.239472048 0.0347305542 0.104721571 0.1451292778 0.3175953816 0.02178229356 0.02769207827 0.03789568174 +-1.864848639e-17 4.362358871e-05 0.09813073711 0.1147852188 0.1244527382 -4.077932815e-18 4.482530074e-06 0.0133077775 +0.02574247271 0.03026359367 + +H atom_index 2 n_descriptor 18 +1.221791874 0.03533085373 0.09891475994 0.1373180377 0.3114881194 0.020952922 0.02665623043 0.03854518575 +2.606429431e-18 4.202674493e-05 0.09351768906 0.11420594 0.1176505775 7.509773883e-20 5.32756067e-06 0.01361643572 +0.02504975958 0.02940069591 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..70905bb530974cc8448ab7bb11d95845f5124598 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:13 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0868923 SEC) : SETUP UNITCELL + DONE(0.100821 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118917 SEC) : INIT PLANEWAVE + DONE(0.16687 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44504 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652123e+02 0.000000e+00 2.131e-01 4.823e-01 + GE2 -4.664174e+02 -1.205134e+00 9.823e-02 4.059e-01 + GE3 -4.664217e+02 -4.310250e-03 6.308e-02 4.643e-01 + GE4 -4.664211e+02 6.193975e-04 1.957e-03 3.503e-01 + GE5 -4.664204e+02 6.563507e-04 8.836e-04 3.530e-01 + GE6 -4.664208e+02 -3.862386e-04 1.579e-04 3.468e-01 + GE7 -4.664207e+02 1.401914e-04 3.395e-05 3.305e-01 + GE8 -4.664207e+02 -5.021986e-05 1.463e-05 3.307e-01 + GE9 -4.664207e+02 1.682081e-05 1.912e-06 3.296e-01 + GE10 -4.664207e+02 -2.728199e-06 3.445e-07 3.307e-01 + GE11 -4.664207e+02 -3.407222e-07 1.133e-07 3.311e-01 + GE12 -4.664207e+02 -4.317784e-08 1.036e-08 2.705e-01 +E_delta_band = -6.95674371e-02 Ry = -9.46513540e-01 eV +E_delta_NN= -1.94383322e-01 Ry = -2.64472078e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5738 11 0.6 1e+02 % + Run_lcao lcao_line 6.5638 1 6.6 1e+02 % + Potential init_pot 0.28464 2 0.14 4.3 % + PW_Basis recip2real 0.2823 17 0.017 4.3 % + PW_Basis gathers_scatterp 0.12577 17 0.0074 1.9 % + Potential v_of_rho 0.92667 14 0.066 14 % + XC_Functional v_xc 0.25895 15 0.017 3.9 % + H_Hartree_pw v_hartree 0.63052 14 0.045 9.6 % + PW_Basis real2recip 0.60325 41 0.015 9.2 % + PW_Basis gatherp_scatters 0.23925 41 0.0058 3.6 % + ORB_control set_orb_tables 1.1075 1 1.1 17 % + ORB_gen_tables gen_tables 1.1075 1 1.1 17 % + ORB_table_phi init_Table 0.48421 1 0.48 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.47932 126 0.0038 7.3 % + ORB_table_beta init_Table_Beta 0.1887 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18722 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25528 1 0.26 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25342 66 0.0038 3.9 % + LOOP_ions opt_ions 4.9356 1 4.9 75 % + ESolver_KS_LCAO Run 4.3899 1 4.4 67 % + HSolverLCAO solve 2.2577 12 0.19 34 % + HamiltLCAO updateHk 1.1744 12 0.098 18 % + LCAO_Hamilt cal_Hgamma 1.1437 12 0.095 17 % + Gint_interface cal_gint 1.155 25 0.046 18 % + Gint_Gamma distri_vl_value 0.35782 12 0.03 5.4 % + Gint_Gamma distri_vl 2.2849 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.6634 14 0.33 71 % + LCAO_gen_fixedH add_v_delta 2.1536 6 0.36 33 % + LCAO_DESCRIPTOR add_v_delta 2.1536 6 0.36 33 % + ElecStateLCAO psiToRho 1.063 12 0.089 16 % + Charge mix_rho 0.71158 11 0.065 11 % + LOOP_ions force_stress 0.54547 1 0.55 8.3 % + Force_Stress_LCAO getForceStress 0.54544 1 0.55 8.3 % + Force_LCAO_gamma ftable_gamma 0.33267 1 0.33 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.21415 1 0.21 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:13 2022 + FINISH Time : Wed Sep 28 11:11:20 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/252/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ad309dc02f2d1af1cdd0c8ccb5c3734b195fa8c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.569267 0.920038 0.276301 +H 0.630779 0.899264 0.275235 +H 0.543619 0.872828 0.313065 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bc6708bda7eea8e1bd49c03534a26a9a534e4652 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4879 2 + 2 -12.8348 2 + 3 -9.41346 2 + 4 -6.78946 2 + 5 1.33712 0 + 6 4.51495 0 + 7 11.0463 0 + 8 11.3277 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b65656a90beb423634636e5100f9d85954f18bfa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:36 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.9394869469 25.761069729 7.73643886607 0 0 0 0 + tauc_H1 17.661816065 25.179387222 7.70658890299 0 0 0 0 + tauc_H2 15.2213425598 24.4391816624 8.76581590851 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0875989308751 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.097831541841 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116227145255 (SEC) + + DONE : INIT CHARGE Time : 0.165684259039 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447366 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00123 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000829 + + Density error is 0.214842333675 + + Energy Rydberg eV + E_KohnSham -34.1889331776 -465.164299757 + E_Harris -34.3811363484 -467.779358054 + E_Fermi -0.411412566406 -5.59755513192 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00128410854247 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989883675971 + + Density error is 0.0975308549925 + + Energy Rydberg eV + E_KohnSham -34.2789166265 -466.388587387 + E_Harris -34.2857116153 -466.481037953 + E_Fermi -0.220474293266 -2.99970665094 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00119873430221 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000939451322383 + + Density error is 0.0625255215118 + + Energy Rydberg eV + E_KohnSham -34.2792421591 -466.393016486 + E_Harris -34.2836435864 -466.452900976 + E_Fermi -0.208820596885 -2.84114997739 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0010607583822 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00086689303547 + + Density error is 0.00195766865525 + + Energy Rydberg eV + E_KohnSham -34.2792386187 -466.392968316 + E_Harris -34.2792394934 -466.392980217 + E_Fermi -0.172900612282 -2.35243351473 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00106144538097 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000868670714364 + + Density error is 0.000954406444967 + + Energy Rydberg eV + E_KohnSham -34.2791694887 -466.392027754 + E_Harris -34.2791715534 -466.392055845 + E_Fermi -0.172166561219 -2.34244623765 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00105970508916 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00086728887971 + + Density error is 9.88561287784e-05 + + Energy Rydberg eV + E_KohnSham -34.2792160616 -466.39266141 + E_Harris -34.2792162291 -466.39266369 + E_Fermi -0.172216066597 -2.34311979286 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00105956984727 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867098889591 + + Density error is 4.05387977253e-05 + + Energy Rydberg eV + E_KohnSham -34.2792022531 -466.392473536 + E_Harris -34.2792022619 -466.392473657 + E_Fermi -0.172109121272 -2.34166472707 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00105954860117 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867064926198 + + Density error is 1.55516039968e-05 + + Energy Rydberg eV + E_KohnSham -34.2792037664 -466.392494126 + E_Harris -34.2792037675 -466.392494141 + E_Fermi -0.172160243448 -2.34236027996 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00105954061327 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867073932326 + + Density error is 2.40840680352e-06 + + Energy Rydberg eV + E_KohnSham -34.279202369 -466.392475114 + E_Harris -34.2792023691 -466.392475114 + E_Fermi -0.172145595599 -2.34216098574 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00105953941668 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867076571861 + + Density error is 4.57415796091e-07 + + Energy Rydberg eV + E_KohnSham -34.2792026099 -466.392478391 + E_Harris -34.2792026099 -466.392478391 + E_Fermi -0.172143636804 -2.34213433497 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00105953927626 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867076976525 + + Density error is 1.16322326867e-07 + + Energy Rydberg eV + E_KohnSham -34.2792026426 -466.392478836 + E_Harris -34.2792026426 -466.392478836 + E_Fermi -0.17214335477 -2.3421304977 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00105953914994 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00086707698323 + + Density error is 1.05103990355e-08 + + Energy Rydberg eV + E_KohnSham -34.2792026489 -466.392478921 + E_Harris -34.2792026489 -466.392478921 + E_band -8.01511250367 -109.051200161 + E_one_elec -69.4855179568 -945.398972694 + E_Hartree +36.121552635 +491.458936443 + E_xc -8.22266238777 -111.875061204 + E_Ewald +7.43130932556 +101.108150428 + E_demet -4.52912063391e-82 -6.16218475505e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195204939281 -2.65589945197 + E_Fermi -0.172143224752 -2.34212872872 + + charge density convergence is achieved + final etot is -466.392478921 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4879 2.00000 + 2 -12.8348 2.00000 + 3 -9.41346 2.00000 + 4 -6.78946 2.00000 + 5 1.33712 0.00000 + 6 4.51495 0.00000 + 7 11.0463 0.00000 + 8 11.3277 0.00000 + + EFERMI = -2.342128728716956 eV + OUT.ABACUS/ final etot is -466.3924789214078 eV + correction force for each atom along direction 1 is 7.60057e-05 + correction force for each atom along direction 2 is -1.06512e-05 + correction force for each atom along direction 3 is -2.47523e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.20672998 +0.19755707 -0.080253019 + H1 +0.93233401 +0.11138770 -0.29301807 + H2 -0.72560403 -0.30894477 +0.37327109 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3924789214078 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0937 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0840 1 7.1 1.e+02% + Potential init_pot 0.28375 2 0.14 4.0% + PW_Basis recip2real 0.28494 17 0.017 4.0% + PW_Basis gathers_scatterp 0.12927 17 0.0076 1.8% + Potential v_of_rho 1.0324 14 0.074 15.% + XC_Functional v_xc 0.29844 15 0.020 4.2% + H_Hartree_pw v_hartree 0.69133 14 0.049 9.7% + PW_Basis real2recip 0.69254 41 0.017 9.8% + PW_Basis gatherp_scatters 0.27096 41 0.0066 3.8% + ORB_control set_orb_tables 1.0986 1 1.1 15.% + ORB_gen_tables gen_tables 1.0986 1 1.1 15.% + ORB_table_phi init_Table 0.47879 1 0.48 6.7% + ORB_table_phi cal_ST_Phi12_R 0.47361 126 0.0038 6.7% + ORB_table_beta init_Table_Beta 0.18610 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18452 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.24642 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24447 66 0.0037 3.4% + LOOP_ions opt_ions 5.4610 1 5.5 77.% + ESolver_KS_LCAO Run 4.8954 1 4.9 69.% + HSolverLCAO solve 2.4234 12 0.20 34.% + HamiltLCAO updateHk 1.2664 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2372 12 0.10 17.% + Gint_interface cal_gint 1.4333 25 0.057 20.% + Gint_Gamma distri_vl_value 0.30094 12 0.025 4.2% + Gint_Gamma distri_vl 2.5636 6 0.43 36.% + LCAO_Deepks cal_projected_DM 5.2083 14 0.37 73.% + LCAO_gen_fixedH add_v_delta 2.4176 6 0.40 34.% + LCAO_DESCRIPTOR add_v_delta 2.4176 6 0.40 34.% + ElecStateLCAO psiToRho 1.1326 12 0.094 16.% + Charge mix_rho 0.84566 11 0.077 12.% + LOOP_ions force_stress 0.56541 1 0.57 8.0% + Force_Stress_LCAO getForceStress 0.56538 1 0.57 8.0% + Force_LCAO_gamma ftable_gamma 0.34654 1 0.35 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.24193 1 0.24 3.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:36 2022 + Finish Time : Wed Sep 28 11:05:43 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..dccae001407167e5e0d643073629aa8bad7cd955 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123943 ima = 3.66602e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8.00000000000001 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122586966633 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111435262488 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111995471667 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011227194337 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112204297702 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112240786615 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112239777955 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112242584038 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112241850058 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112241751506 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112241730401 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112241724679 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/STRU new file mode 100644 index 0000000000000000000000000000000000000000..26d80f75a8b6ab76bf1d05c636d2552fb92ad614 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.060513053093 25.761069728985 7.736438866070 0 0 0 +H +0.0 +2 +-10.338183934998 25.179387221976 7.706588903006 0 0 0 +-12.778657440187 24.439181662445 8.765815908503 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/conv new file mode 100644 index 0000000000000000000000000000000000000000..d2f24401f00b245b813d2dade20f9becf02dc785 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/conv @@ -0,0 +1 @@ +253 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..fa73fe649e7f83cbe3e1e83ca92e69054276f10e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753587752 0.01284345605 1.278476357 1.359373182 1.470056478 0.009425781862 0.01709582609 0.0391406185 +-1.232079782e-18 0.0009613720406 0.002883127389 0.01343330936 0.04769414111 5.68419578e-19 2.871719412e-06 7.52149744e-06 +0.001596549103 0.006157127366 + +H atom_index 1 n_descriptor 18 +1.261101725 0.03445384587 0.1149411833 0.1547547016 0.3231489068 0.02371690131 0.02888273202 0.03759576739 +-4.651751769e-18 5.252215658e-05 0.1058796212 0.1163424554 0.1328113775 4.524545888e-18 2.619326874e-06 0.01334650151 +0.02753271098 0.0312458029 + +H atom_index 2 n_descriptor 18 +1.257420299 0.03457713008 0.1135947783 0.1529924254 0.321967088 0.02353476888 0.02866759098 0.03769895096 +-1.008007675e-17 5.216940411e-05 0.1052267833 0.1159254536 0.1312982876 2.410012998e-18 2.828169054e-06 0.01335599761 +0.02740114073 0.03108348668 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d50c0f74e79cad10a6be91c97fe6456346e028ef Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:36 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087622 SEC) : SETUP UNITCELL + DONE(0.09785 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116249 SEC) : INIT PLANEWAVE + DONE(0.165814 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447431 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651643e+02 0.000000e+00 2.148e-01 5.223e-01 + GE2 -4.663886e+02 -1.224288e+00 9.753e-02 4.590e-01 + GE3 -4.663930e+02 -4.429098e-03 6.253e-02 5.316e-01 + GE4 -4.663930e+02 4.817039e-05 1.958e-03 3.916e-01 + GE5 -4.663920e+02 9.405618e-04 9.544e-04 3.894e-01 + GE6 -4.663927e+02 -6.336567e-04 9.886e-05 3.792e-01 + GE7 -4.663925e+02 1.878743e-04 4.054e-05 3.739e-01 + GE8 -4.663925e+02 -2.059011e-05 1.555e-05 3.699e-01 + GE9 -4.663925e+02 1.901211e-05 2.408e-06 3.716e-01 + GE10 -4.663925e+02 -3.277073e-06 4.574e-07 3.706e-01 + GE11 -4.663925e+02 -4.447284e-07 1.163e-07 3.701e-01 + GE12 -4.663925e+02 -8.545322e-08 1.051e-08 3.034e-01 +E_delta_band = -7.13206744e-02 Ry = -9.70367557e-01 eV +E_delta_NN= -1.95204939e-01 Ry = -2.65589945e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0937 11 0.64 1e+02 % + Run_lcao lcao_line 7.084 1 7.1 1e+02 % + Potential init_pot 0.28375 2 0.14 4 % + PW_Basis recip2real 0.28494 17 0.017 4 % + PW_Basis gathers_scatterp 0.12927 17 0.0076 1.8 % + Potential v_of_rho 1.0324 14 0.074 15 % + XC_Functional v_xc 0.29844 15 0.02 4.2 % + H_Hartree_pw v_hartree 0.69133 14 0.049 9.7 % + PW_Basis real2recip 0.69254 41 0.017 9.8 % + PW_Basis gatherp_scatters 0.27096 41 0.0066 3.8 % + ORB_control set_orb_tables 1.0986 1 1.1 15 % + ORB_gen_tables gen_tables 1.0986 1 1.1 15 % + ORB_table_phi init_Table 0.47879 1 0.48 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.47361 126 0.0038 6.7 % + ORB_table_beta init_Table_Beta 0.1861 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18452 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.24642 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24447 66 0.0037 3.4 % + LOOP_ions opt_ions 5.461 1 5.5 77 % + ESolver_KS_LCAO Run 4.8954 1 4.9 69 % + HSolverLCAO solve 2.4234 12 0.2 34 % + HamiltLCAO updateHk 1.2664 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.2372 12 0.1 17 % + Gint_interface cal_gint 1.4333 25 0.057 20 % + Gint_Gamma distri_vl_value 0.30094 12 0.025 4.2 % + Gint_Gamma distri_vl 2.5636 6 0.43 36 % + LCAO_Deepks cal_projected_DM 5.2083 14 0.37 73 % + LCAO_gen_fixedH add_v_delta 2.4176 6 0.4 34 % + LCAO_DESCRIPTOR add_v_delta 2.4176 6 0.4 34 % + ElecStateLCAO psiToRho 1.1326 12 0.094 16 % + Charge mix_rho 0.84566 11 0.077 12 % + LOOP_ions force_stress 0.56541 1 0.57 8 % + Force_Stress_LCAO getForceStress 0.56538 1 0.57 8 % + Force_LCAO_gamma ftable_gamma 0.34654 1 0.35 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.24193 1 0.24 3.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:36 2022 + FINISH Time : Wed Sep 28 11:05:43 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/253/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9f62436de82cb8b95ec0607489d716c7e48d4b7c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.553382 0.940433 0.290045 +H 0.601214 0.988038 0.29057 +H 0.579964 0.883062 0.270409 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9eeea66e16c196503c96e9d18a7552f2dc937fae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9666 2 + 2 -13.0849 2 + 3 -8.82251 2 + 4 -6.66739 2 + 5 1.10647 0 + 6 4.13338 0 + 7 11.1395 0 + 8 11.3666 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b4423a8a5837ce447c8f90366e600cbaf32df7be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.4946930827 26.3321339702 8.12126768599 0 0 0 0 + tauc_H1 16.8339906144 27.6650573154 8.13596770467 0 0 0 0 + tauc_H2 16.2389974519 24.7257440728 7.57144126886 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870390893562 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.097093488095 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115385057525 (SEC) + + DONE : INIT CHARGE Time : 0.163519248813 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.444329 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000754 + + Density error is 0.212774530629 + + Energy Rydberg eV + E_KohnSham -34.1914780408 -465.198924396 + E_Harris -34.3781845677 -467.739197016 + E_Fermi -0.390695226179 -5.31568125743 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00104937151676 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000858436944282 + + Density error is 0.0986892162173 + + Energy Rydberg eV + E_KohnSham -34.2788464647 -466.387632787 + E_Harris -34.2857121976 -466.481045875 + E_Fermi -0.200676099916 -2.73033841128 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000987048490873 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00082475313294 + + Density error is 0.0634896810952 + + Energy Rydberg eV + E_KohnSham -34.2790515319 -466.390422869 + E_Harris -34.2834632033 -466.450446738 + E_Fermi -0.191712706205 -2.60838518339 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000887617644023 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00078348169393 + + Density error is 0.00209059479522 + + Energy Rydberg eV + E_KohnSham -34.2789967148 -466.389677044 + E_Harris -34.2790007874 -466.389732455 + E_Fermi -0.156754133108 -2.13274939532 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00088701569892 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783383560943 + + Density error is 0.000819958596727 + + Energy Rydberg eV + E_KohnSham -34.2789666328 -466.389267758 + E_Harris -34.2789671327 -466.38927456 + E_Fermi -0.156323071513 -2.12688450143 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000885718530323 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00078292510055 + + Density error is 0.000187788852487 + + Energy Rydberg eV + E_KohnSham -34.2789842937 -466.389508047 + E_Harris -34.2789840134 -466.389504233 + E_Fermi -0.156019745255 -2.12275753597 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0008859029851 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783138880206 + + Density error is 2.96895486968e-05 + + Energy Rydberg eV + E_KohnSham -34.2789781768 -466.389424822 + E_Harris -34.2789781801 -466.389424866 + E_Fermi -0.155979711577 -2.12221284984 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000885861240775 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783096002713 + + Density error is 1.383194176e-05 + + Energy Rydberg eV + E_KohnSham -34.2789816603 -466.389472218 + E_Harris -34.2789816612 -466.389472229 + E_Fermi -0.156001545195 -2.12250991146 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000885853184282 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783097565312 + + Density error is 1.37974892535e-06 + + Energy Rydberg eV + E_KohnSham -34.2789805698 -466.389457381 + E_Harris -34.2789805698 -466.389457381 + E_Fermi -0.155986537836 -2.12230572586 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000885852472419 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783097392392 + + Density error is 2.37919269759e-07 + + Energy Rydberg eV + E_KohnSham -34.2789807861 -466.389460323 + E_Harris -34.2789807861 -466.389460323 + E_Fermi -0.155985609068 -2.12229308933 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000885852642606 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783097812446 + + Density error is 3.47702964134e-08 + + Energy Rydberg eV + E_KohnSham -34.2789808017 -466.389460536 + E_Harris -34.2789808017 -466.389460536 + E_band -7.87044170407 -107.082852952 + E_one_elec -68.8041630578 -936.128663707 + E_Hartree +35.821192966 +487.372333495 + E_xc -8.17410818729 -111.214447416 + E_Ewald +7.00346916477 +95.2870864082 + E_demet -8.09624397327e-64 -1.10155050435e-62 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193792102128 -2.63667681634 + E_Fermi -0.155985480971 -2.12229134647 + + charge density convergence is achieved + final etot is -466.389460536 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9666 2.00000 + 2 -13.0849 2.00000 + 3 -8.82251 2.00000 + 4 -6.66739 2.00000 + 5 1.10647 0.00000 + 6 4.13338 0.00000 + 7 11.1395 0.00000 + 8 11.3666 0.00000 + + EFERMI = -2.122291346471455 eV + OUT.ABACUS/ final etot is -466.3894605362756 eV + correction force for each atom along direction 1 is 0.000158780 + correction force for each atom along direction 2 is -5.86740e-05 + correction force for each atom along direction 3 is -0.000124572 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.39040225 +0.63536160 +0.059196016 + H1 -0.60545537 -1.1392584 -0.13228997 + H2 +0.21505312 +0.50389681 +0.073093953 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3894605362756 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0788 11 0.55 1.0e+02% + Run_lcao lcao_line 6.0686 1 6.1 1.e+02% + Potential init_pot 0.28492 2 0.14 4.7% + PW_Basis recip2real 0.26501 16 0.017 4.4% + PW_Basis gathers_scatterp 0.11435 16 0.0071 1.9% + Potential v_of_rho 0.87929 13 0.068 14.% + XC_Functional v_xc 0.25151 14 0.018 4.1% + H_Hartree_pw v_hartree 0.58951 13 0.045 9.7% + PW_Basis real2recip 0.55886 38 0.015 9.2% + PW_Basis gatherp_scatters 0.21793 38 0.0057 3.6% + ORB_control set_orb_tables 1.1104 1 1.1 18.% + ORB_gen_tables gen_tables 1.1104 1 1.1 18.% + ORB_table_phi init_Table 0.48751 1 0.49 8.0% + ORB_table_phi cal_ST_Phi12_R 0.48257 126 0.0038 7.9% + ORB_table_beta init_Table_Beta 0.18683 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18535 56 0.0033 3.0% + ORB_table_alpha init_Table_Alpha 0.25643 1 0.26 4.2% + ORB_table_alpha S_PhiAlpha_R 0.25449 66 0.0039 4.2% + LOOP_ions opt_ions 4.4367 1 4.4 73.% + ESolver_KS_LCAO Run 3.9147 1 3.9 64.% + HSolverLCAO solve 1.9326 11 0.18 32.% + HamiltLCAO updateHk 1.0252 11 0.093 17.% + LCAO_Hamilt cal_Hgamma 0.99295 11 0.090 16.% + Gint_interface cal_gint 1.1373 23 0.049 19.% + Gint_Gamma distri_vl_value 0.23017 11 0.021 3.8% + Gint_Gamma distri_vl 1.8845 6 0.31 31.% + LCAO_Deepks cal_projected_DM 4.1982 13 0.32 69.% + LCAO_gen_fixedH add_v_delta 1.7541 6 0.29 29.% + LCAO_DESCRIPTOR add_v_delta 1.7541 6 0.29 29.% + ElecStateLCAO psiToRho 0.88951 11 0.081 15.% + Charge mix_rho 0.66149 10 0.066 11.% + LOOP_ions force_stress 0.52174 1 0.52 8.6% + Force_Stress_LCAO getForceStress 0.52172 1 0.52 8.6% + Force_LCAO_gamma ftable_gamma 0.30961 1 0.31 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.21667 1 0.22 3.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:17 2022 + Finish Time : Wed Sep 28 11:07:23 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..cc0123c7db2ebd591ba9bca9e43fc368259a5fc6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123293 ima = 3.68599e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123803138674 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112836249219 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011344270445 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011361878515 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113600834841 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113614061735 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113607770603 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113609906472 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113609291795 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113609243255 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011360922964 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3fe05d9b532268a89621761f00b6a2bd2daac98c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.505306917309 26.332133970158 8.121267685977 0 0 0 +H +0.0 +2 +-11.166009385641 27.665057315390 8.135967704684 0 0 0 +-11.761002548050 24.725744072864 7.571441268860 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/conv new file mode 100644 index 0000000000000000000000000000000000000000..cf003f10c959efdd07766990f04f417488603a0c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/conv @@ -0,0 +1 @@ +254 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..768ce2087aca4e144babb9c26757873c08ef1d3a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.744953108 0.01241690474 1.256018772 1.354020617 1.467891167 0.007647424833 0.01966178429 0.03891401356 +-1.985330057e-18 0.001015287134 0.002255129032 0.01157147866 0.04040957811 2.178706936e-19 1.316285271e-06 4.29821789e-06 +0.001742440874 0.005623931252 + +H atom_index 1 n_descriptor 18 +1.196268433 0.03563241925 0.09064733569 0.1281880643 0.3052020606 0.01928553949 0.02539444436 0.03906813498 +-8.678699578e-18 3.164245786e-05 0.08589637178 0.109568061 0.113597407 -5.479581935e-18 5.850661195e-06 0.01390719959 +0.02349545473 0.02824351185 + +H atom_index 2 n_descriptor 18 +1.224760702 0.03467162844 0.09938065446 0.1401299191 0.3152443529 0.02054588065 0.02704987878 0.03792051613 +1.479034095e-17 3.377607182e-05 0.0934422344 0.1144214427 0.1200428971 -1.48132723e-19 4.991162914e-06 0.01321999215 +0.02464841485 0.02968772016 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ea4ee110a5dfee3782c89e9ec87ab9f4bb3bb4ff Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870601 SEC) : SETUP UNITCELL + DONE(0.0971138 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115407 SEC) : INIT PLANEWAVE + DONE(0.163653 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444399 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651989e+02 0.000000e+00 2.128e-01 4.703e-01 + GE2 -4.663876e+02 -1.188708e+00 9.869e-02 3.957e-01 + GE3 -4.663904e+02 -2.790082e-03 6.349e-02 4.488e-01 + GE4 -4.663897e+02 7.458249e-04 2.091e-03 3.425e-01 + GE5 -4.663893e+02 4.092864e-04 8.200e-04 3.397e-01 + GE6 -4.663895e+02 -2.402891e-04 1.878e-04 3.318e-01 + GE7 -4.663894e+02 8.322515e-05 2.969e-05 3.207e-01 + GE8 -4.663895e+02 -4.739648e-05 1.383e-05 3.131e-01 + GE9 -4.663895e+02 1.483721e-05 1.380e-06 3.131e-01 + GE10 -4.663895e+02 -2.942453e-06 2.379e-07 3.177e-01 + GE11 -4.663895e+02 -2.128842e-07 3.477e-08 2.596e-01 +E_delta_band = -6.84204147e-02 Ry = -9.30907499e-01 eV +E_delta_NN= -1.93792102e-01 Ry = -2.63667682e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0788 11 0.55 1e+02 % + Run_lcao lcao_line 6.0686 1 6.1 1e+02 % + Potential init_pot 0.28492 2 0.14 4.7 % + PW_Basis recip2real 0.26501 16 0.017 4.4 % + PW_Basis gathers_scatterp 0.11435 16 0.0071 1.9 % + Potential v_of_rho 0.87929 13 0.068 14 % + XC_Functional v_xc 0.25151 14 0.018 4.1 % + H_Hartree_pw v_hartree 0.58951 13 0.045 9.7 % + PW_Basis real2recip 0.55886 38 0.015 9.2 % + PW_Basis gatherp_scatters 0.21793 38 0.0057 3.6 % + ORB_control set_orb_tables 1.1104 1 1.1 18 % + ORB_gen_tables gen_tables 1.1104 1 1.1 18 % + ORB_table_phi init_Table 0.48751 1 0.49 8 % + ORB_table_phi cal_ST_Phi12_R 0.48257 126 0.0038 7.9 % + ORB_table_beta init_Table_Beta 0.18683 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18535 56 0.0033 3 % + ORB_table_alpha init_Table_Alpha 0.25643 1 0.26 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.25449 66 0.0039 4.2 % + LOOP_ions opt_ions 4.4367 1 4.4 73 % + ESolver_KS_LCAO Run 3.9147 1 3.9 64 % + HSolverLCAO solve 1.9326 11 0.18 32 % + HamiltLCAO updateHk 1.0252 11 0.093 17 % + LCAO_Hamilt cal_Hgamma 0.99295 11 0.09 16 % + Gint_interface cal_gint 1.1373 23 0.049 19 % + Gint_Gamma distri_vl_value 0.23017 11 0.021 3.8 % + Gint_Gamma distri_vl 1.8845 6 0.31 31 % + LCAO_Deepks cal_projected_DM 4.1982 13 0.32 69 % + LCAO_gen_fixedH add_v_delta 1.7541 6 0.29 29 % + LCAO_DESCRIPTOR add_v_delta 1.7541 6 0.29 29 % + ElecStateLCAO psiToRho 0.88951 11 0.081 15 % + Charge mix_rho 0.66149 10 0.066 11 % + LOOP_ions force_stress 0.52174 1 0.52 8.6 % + Force_Stress_LCAO getForceStress 0.52172 1 0.52 8.6 % + Force_LCAO_gamma ftable_gamma 0.30961 1 0.31 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.21667 1 0.22 3.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:17 2022 + FINISH Time : Wed Sep 28 11:07:23 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/254/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..284004c5d4aeb8d21b74d0398f0ab343d103c10f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.549967 0.958966 0.292088 +H 0.562701 0.997306 0.341623 +H 0.576094 0.992569 0.242187 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..cf99521bbde0b6ef7f93cea12352e469445b42d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4705 2 + 2 -13.0309 2 + 3 -9.26148 2 + 4 -6.78473 2 + 5 1.388 0 + 6 4.59702 0 + 7 11.0398 0 + 8 11.3017 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..91abe645a2efeccdfe8b249c07bf825ce4198ff0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:06 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.3990768845 26.8510383737 8.17845011292 0 0 0 0 + tauc_H1 15.7556144711 27.9245731635 9.56545612028 0 0 0 0 + tauc_H2 16.130621106 27.7919192324 6.78124106658 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870283124315 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0897452927516 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107967198974 (SEC) + + DONE : INIT CHARGE Time : 0.157882918648 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437934 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000931 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101 + + Density error is 0.215653957296 + + Energy Rydberg eV + E_KohnSham -34.1893992757 -465.170641346 + E_Harris -34.3830308538 -467.805134122 + E_Fermi -0.413492489181 -5.62585393307 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0012367566096 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125981278462 + + Density error is 0.0974988721312 + + Energy Rydberg eV + E_KohnSham -34.2792360809 -466.392933787 + E_Harris -34.2859377159 -466.484114209 + E_Fermi -0.222303340569 -3.02459211617 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118694460469 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120321277057 + + Density error is 0.0623863217358 + + Energy Rydberg eV + E_KohnSham -34.2794937908 -466.39644011 + E_Harris -34.2838139832 -466.455219344 + E_Fermi -0.20952190388 -2.85069174858 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112430298159 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112642171842 + + Density error is 0.00198761686845 + + Energy Rydberg eV + E_KohnSham -34.2795092269 -466.396650129 + E_Harris -34.2795106636 -466.396669677 + E_Fermi -0.173741416355 -2.36387324102 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011281770715 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112893160905 + + Density error is 0.000888948132893 + + Energy Rydberg eV + E_KohnSham -34.2794402937 -466.395712246 + E_Harris -34.2794423452 -466.395740158 + E_Fermi -0.172781517775 -2.35081315082 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112661946075 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112742701048 + + Density error is 0.000105335908247 + + Energy Rydberg eV + E_KohnSham -34.2794884192 -466.396367026 + E_Harris -34.2794884348 -466.396367238 + E_Fermi -0.1729478856 -2.35307670121 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112660014404 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112747466452 + + Density error is 4.20950595247e-05 + + Energy Rydberg eV + E_KohnSham -34.2794724155 -466.396149284 + E_Harris -34.2794724252 -466.396149417 + E_Fermi -0.172821818469 -2.3513614699 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112654185674 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112740029617 + + Density error is 1.15766803251e-05 + + Energy Rydberg eV + E_KohnSham -34.2794752888 -466.396188378 + E_Harris -34.2794752893 -466.396188384 + E_Fermi -0.172871089942 -2.35203184268 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112654823177 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112739559451 + + Density error is 2.08297939211e-06 + + Energy Rydberg eV + E_KohnSham -34.2794740142 -466.396171035 + E_Harris -34.2794740142 -466.396171036 + E_Fermi -0.172859558951 -2.3518749555 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112654857926 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112739804208 + + Density error is 1.2435113567e-07 + + Energy Rydberg eV + E_KohnSham -34.2794741358 -466.396172691 + E_Harris -34.2794741358 -466.396172691 + E_Fermi -0.172857266392 -2.35184376364 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112654882818 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112739824035 + + Density error is 3.88261311903e-08 + + Energy Rydberg eV + E_KohnSham -34.279474182 -466.396173319 + E_Harris -34.279474182 -466.396173319 + E_band -8.01835017101 -109.095250885 + E_one_elec -69.5634679429 -946.459536664 + E_Hartree +36.1634968508 +492.029616776 + E_xc -8.22960961469 -111.969583075 + E_Ewald +7.47385710019 +101.6870426 + E_demet -1.04499734013e-84 -1.42179182206e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195347603818 -2.65784050258 + E_Fermi -0.172857370046 -2.35184517391 + + charge density convergence is achieved + final etot is -466.396173319 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4705 2.00000 + 2 -13.0309 2.00000 + 3 -9.26148 2.00000 + 4 -6.78473 2.00000 + 5 1.38800 0.00000 + 6 4.59702 0.00000 + 7 11.0398 0.00000 + 8 11.3017 0.00000 + + EFERMI = -2.351845173914428 eV + OUT.ABACUS/ final etot is -466.3961733192958 eV + correction force for each atom along direction 1 is 2.89048e-06 + correction force for each atom along direction 2 is 0.000178692 + correction force for each atom along direction 3 is -2.78276e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.23893270 -0.75385654 -1.0779140 + H1 +0.21205078 +0.80956529 +1.4157977 + H2 +0.026881917 -0.055708749 -0.33788371 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3961733192958 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9556 11 0.54 1.0e+02% + Run_lcao lcao_line 5.9464 1 5.9 1.e+02% + Potential init_pot 0.28621 2 0.14 4.8% + PW_Basis recip2real 0.26508 16 0.017 4.5% + PW_Basis gathers_scatterp 0.11310 16 0.0071 1.9% + Potential v_of_rho 0.87110 13 0.067 15.% + XC_Functional v_xc 0.24194 14 0.017 4.1% + H_Hartree_pw v_hartree 0.59299 13 0.046 10.% + PW_Basis real2recip 0.56207 38 0.015 9.4% + PW_Basis gatherp_scatters 0.21925 38 0.0058 3.7% + ORB_control set_orb_tables 1.1037 1 1.1 19.% + ORB_gen_tables gen_tables 1.1037 1 1.1 19.% + ORB_table_phi init_Table 0.48413 1 0.48 8.1% + ORB_table_phi cal_ST_Phi12_R 0.47920 126 0.0038 8.0% + ORB_table_beta init_Table_Beta 0.18686 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18538 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25582 1 0.26 4.3% + ORB_table_alpha S_PhiAlpha_R 0.25398 66 0.0038 4.3% + LOOP_ions opt_ions 4.3270 1 4.3 73.% + ESolver_KS_LCAO Run 3.8162 1 3.8 64.% + HSolverLCAO solve 1.8428 11 0.17 31.% + HamiltLCAO updateHk 0.98956 11 0.090 17.% + LCAO_Hamilt cal_Hgamma 0.95787 11 0.087 16.% + Gint_interface cal_gint 1.0188 23 0.044 17.% + Gint_Gamma distri_vl_value 0.24092 11 0.022 4.0% + Gint_Gamma distri_vl 1.8523 6 0.31 31.% + LCAO_Deepks cal_projected_DM 4.0949 13 0.31 69.% + LCAO_gen_fixedH add_v_delta 1.7213 6 0.29 29.% + LCAO_DESCRIPTOR add_v_delta 1.7212 6 0.29 29.% + ElecStateLCAO psiToRho 0.83442 11 0.076 14.% + Charge mix_rho 0.65850 10 0.066 11.% + LOOP_ions force_stress 0.51056 1 0.51 8.6% + Force_Stress_LCAO getForceStress 0.51053 1 0.51 8.6% + Force_LCAO_gamma ftable_gamma 0.29858 1 0.30 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.20572 1 0.21 3.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:06 2022 + Finish Time : Wed Sep 28 11:13:12 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8b19b19a6fc4027047e0f4340bcc2fc8b1ef05ca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124061 ima = 3.68246e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122738539726 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111790847204 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112279868904 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112550022537 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112483291835 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112521540101 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112517104122 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112519889795 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112519464786 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112519357904 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112519358998 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/STRU new file mode 100644 index 0000000000000000000000000000000000000000..557692be3a9f68248e16ed9ebda0839ca1d32239 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.600923115542 26.851038373699 8.178450112914 0 0 0 +H +0.0 +2 +-12.244385528876 27.924573163514 9.565456120266 0 0 0 +-11.869378894038 27.791919232371 6.781241066601 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/conv new file mode 100644 index 0000000000000000000000000000000000000000..b498b1ed278a37d30aa7bf24d5cef5a27df92542 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/conv @@ -0,0 +1 @@ +255 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..597ec47e0bd303e52d57b7c772195157d5aa215e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751223551 0.01280238222 1.281939957 1.367993733 1.47008788 0.008972729436 0.01809102714 0.03907798713 +4.273821331e-19 0.001058256324 0.002783858669 0.01304967006 0.04732258226 3.016871975e-19 2.506375333e-06 6.829157937e-06 +0.001618585193 0.006057346636 + +H atom_index 1 n_descriptor 18 +1.281565602 0.03343796842 0.1209859933 0.1649786752 0.3299032155 0.02418563253 0.03009080305 0.03683382262 +-1.022692148e-17 5.332081757e-05 0.1079704951 0.1193427356 0.1416442704 1.107236954e-18 2.063717512e-06 0.01336715835 +0.02792506669 0.03209421046 + +H atom_index 2 n_descriptor 18 +1.244769751 0.03466505224 0.1075754853 0.1472211543 0.318440775 0.02243173703 0.02795683556 0.03776286558 +1.064429878e-17 4.974963134e-05 0.1019858359 0.1147007274 0.1264256999 8.494558714e-18 4.167478854e-06 0.01333555548 +0.02662977846 0.03052031516 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c6b3bbc4b18286373b3d71eaf620851398544228 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..027719ca32ddf8f35bfa6f40cd259841eba4706e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..05fd69b2352731cc768f51121e4b9441de797129 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..17417258fe701d621a77c6d037a92e00fe764d20 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:06 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870499 SEC) : SETUP UNITCELL + DONE(0.0897625 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107986 SEC) : INIT PLANEWAVE + DONE(0.15802 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438007 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651706e+02 0.000000e+00 2.157e-01 4.612e-01 + GE2 -4.663929e+02 -1.222292e+00 9.750e-02 3.840e-01 + GE3 -4.663964e+02 -3.506323e-03 6.239e-02 4.415e-01 + GE4 -4.663967e+02 -2.100185e-04 1.988e-03 3.316e-01 + GE5 -4.663957e+02 9.378834e-04 8.889e-04 3.342e-01 + GE6 -4.663964e+02 -6.547806e-04 1.053e-04 3.150e-01 + GE7 -4.663961e+02 2.177418e-04 4.210e-05 3.145e-01 + GE8 -4.663962e+02 -3.909345e-05 1.158e-05 3.068e-01 + GE9 -4.663962e+02 1.734235e-05 2.083e-06 3.058e-01 + GE10 -4.663962e+02 -1.655520e-06 1.244e-07 3.093e-01 + GE11 -4.663962e+02 -6.283131e-07 3.883e-08 2.507e-01 +E_delta_band = -7.15970284e-02 Ry = -9.74127546e-01 eV +E_delta_NN= -1.95347604e-01 Ry = -2.65784050e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9556 11 0.54 1e+02 % + Run_lcao lcao_line 5.9464 1 5.9 1e+02 % + Potential init_pot 0.28621 2 0.14 4.8 % + PW_Basis recip2real 0.26508 16 0.017 4.5 % + PW_Basis gathers_scatterp 0.1131 16 0.0071 1.9 % + Potential v_of_rho 0.8711 13 0.067 15 % + XC_Functional v_xc 0.24194 14 0.017 4.1 % + H_Hartree_pw v_hartree 0.59299 13 0.046 10 % + PW_Basis real2recip 0.56207 38 0.015 9.4 % + PW_Basis gatherp_scatters 0.21925 38 0.0058 3.7 % + ORB_control set_orb_tables 1.1037 1 1.1 19 % + ORB_gen_tables gen_tables 1.1037 1 1.1 19 % + ORB_table_phi init_Table 0.48413 1 0.48 8.1 % + ORB_table_phi cal_ST_Phi12_R 0.4792 126 0.0038 8 % + ORB_table_beta init_Table_Beta 0.18686 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18538 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.25582 1 0.26 4.3 % + ORB_table_alpha S_PhiAlpha_R 0.25398 66 0.0038 4.3 % + LOOP_ions opt_ions 4.327 1 4.3 73 % + ESolver_KS_LCAO Run 3.8162 1 3.8 64 % + HSolverLCAO solve 1.8428 11 0.17 31 % + HamiltLCAO updateHk 0.98956 11 0.09 17 % + LCAO_Hamilt cal_Hgamma 0.95787 11 0.087 16 % + Gint_interface cal_gint 1.0188 23 0.044 17 % + Gint_Gamma distri_vl_value 0.24092 11 0.022 4 % + Gint_Gamma distri_vl 1.8523 6 0.31 31 % + LCAO_Deepks cal_projected_DM 4.0949 13 0.31 69 % + LCAO_gen_fixedH add_v_delta 1.7213 6 0.29 29 % + LCAO_DESCRIPTOR add_v_delta 1.7212 6 0.29 29 % + ElecStateLCAO psiToRho 0.83442 11 0.076 14 % + Charge mix_rho 0.6585 10 0.066 11 % + LOOP_ions force_stress 0.51056 1 0.51 8.6 % + Force_Stress_LCAO getForceStress 0.51053 1 0.51 8.6 % + Force_LCAO_gamma ftable_gamma 0.29858 1 0.3 5 % + Force_LCAO_gamma cal_fvl_dphi 0.20572 1 0.21 3.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:06 2022 + FINISH Time : Wed Sep 28 11:13:12 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/255/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9c1924763cbb0cb2d2eafc0580da2dd558e0f965 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.542523 0.981714 0.278147 +H 0.571813 0.965811 0.333796 +H 0.514677 0.0377339 0.292427 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..db775fb79410bc34a3db6b26172d2b988056f557 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4893 2 + 2 -13.1132 2 + 3 -9.21936 2 + 4 -6.78919 2 + 5 1.43382 0 + 6 4.6555 0 + 7 11.0317 0 + 8 11.2897 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a0f5ad0afbfbdee370ef2f9c75617fb026d49a56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:29 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.1906327612 27.4879817795 7.78812875755 0 0 0 0 + tauc_H1 16.0107655391 27.0427063734 9.3462956959 0 0 0 0 + tauc_H2 14.4109683656 1.05654998589 8.18796876013 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0867365316234 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0993560075449 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117443899965 (SEC) + + DONE : INIT CHARGE Time : 0.165878753648 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44639 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 144 25 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00155 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109 + + Density error is 0.216091259154 + + Energy Rydberg eV + E_KohnSham -34.1897267524 -465.175096895 + E_Harris -34.3841474975 -467.820326839 + E_Fermi -0.415455307748 -5.65255944971 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00148468015166 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130919933791 + + Density error is 0.0974282388383 + + Energy Rydberg eV + E_KohnSham -34.2795265552 -466.396885893 + E_Harris -34.2861787979 -466.487394298 + E_Fermi -0.224144661918 -3.04964457838 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00136876249417 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124466171232 + + Density error is 0.0622542139191 + + Energy Rydberg eV + E_KohnSham -34.2797405719 -466.39979774 + E_Harris -34.2840176033 -466.457989738 + E_Fermi -0.21060093034 -2.86537265672 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00117093935022 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114927570606 + + Density error is 0.00200861806664 + + Energy Rydberg eV + E_KohnSham -34.2797701292 -466.400199887 + E_Harris -34.2797714002 -466.40021718 + E_Fermi -0.174877428374 -2.37932947748 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116899205949 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011510385486 + + Density error is 0.000887368083512 + + Energy Rydberg eV + E_KohnSham -34.279697871 -466.399216764 + E_Harris -34.2797006864 -466.399255069 + E_Fermi -0.173767015556 -2.36422153601 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116731231333 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114953986875 + + Density error is 0.000102367272603 + + Energy Rydberg eV + E_KohnSham -34.2797491139 -466.39991396 + E_Harris -34.2797491218 -466.399914067 + E_Fermi -0.174014955305 -2.36759492937 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116704150927 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001149487272 + + Density error is 4.33530704571e-05 + + Energy Rydberg eV + E_KohnSham -34.2797325829 -466.399689044 + E_Harris -34.2797325932 -466.399689184 + E_Fermi -0.173886598999 -2.36584855223 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116706508167 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011494324227 + + Density error is 1.06451400492e-05 + + Energy Rydberg eV + E_KohnSham -34.2797351583 -466.399724084 + E_Harris -34.2797351588 -466.399724091 + E_Fermi -0.173938156706 -2.36655003082 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116704569878 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114942773655 + + Density error is 1.63147026731e-06 + + Energy Rydberg eV + E_KohnSham -34.2797338528 -466.399706322 + E_Harris -34.2797338528 -466.399706322 + E_Fermi -0.173927703735 -2.36640781085 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116704222833 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114942858264 + + Density error is 1.07482668387e-07 + + Energy Rydberg eV + E_KohnSham -34.2797340154 -466.399708535 + E_Harris -34.2797340154 -466.399708535 + E_Fermi -0.173925926835 -2.36638363489 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116704264839 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114942889159 + + Density error is 4.19623909325e-08 + + Energy Rydberg eV + E_KohnSham -34.2797340469 -466.399708963 + E_Harris -34.2797340469 -466.399708963 + E_band -8.02767725697 -109.2221524 + E_one_elec -69.6404405416 -947.506802596 + E_Hartree +36.2013357154 +492.54444094 + E_xc -8.23569413049 -112.05236716 + E_Ewald +7.51865726366 +102.296580095 + E_demet -2.34799686922e-87 -3.19461363076e-86 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195474909264 -2.65957258202 + E_Fermi -0.173926025105 -2.36638497192 + + charge density convergence is achieved + final etot is -466.399708963 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4893 2.00000 + 2 -13.1132 2.00000 + 3 -9.21936 2.00000 + 4 -6.78919 2.00000 + 5 1.43382 0.00000 + 6 4.65550 0.00000 + 7 11.0317 0.00000 + 8 11.2897 0.00000 + + EFERMI = -2.366384971916910 eV + OUT.ABACUS/ final etot is -466.3997089629424 eV + correction force for each atom along direction 1 is -3.55922e-05 + correction force for each atom along direction 2 is 0.000120587 + correction force for each atom along direction 3 is 0.000162211 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.24703036 -0.86100795 -0.72143557 + H1 +0.41634428 -0.34717662 +0.59008499 + H2 -0.66337464 +1.2081846 +0.13135058 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3997089629424 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9075 11 0.54 1.0e+02% + Run_lcao lcao_line 5.8979 1 5.9 1.e+02% + Potential init_pot 0.28743 2 0.14 4.9% + PW_Basis recip2real 0.26529 16 0.017 4.5% + PW_Basis gathers_scatterp 0.11228 16 0.0070 1.9% + Potential v_of_rho 0.85897 13 0.066 15.% + XC_Functional v_xc 0.23522 14 0.017 4.0% + H_Hartree_pw v_hartree 0.58673 13 0.045 9.9% + PW_Basis real2recip 0.55543 38 0.015 9.4% + PW_Basis gatherp_scatters 0.22094 38 0.0058 3.7% + ORB_control set_orb_tables 1.1015 1 1.1 19.% + ORB_gen_tables gen_tables 1.1015 1 1.1 19.% + ORB_table_phi init_Table 0.47821 1 0.48 8.1% + ORB_table_phi cal_ST_Phi12_R 0.47323 126 0.0038 8.0% + ORB_table_beta init_Table_Beta 0.18746 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18599 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25607 1 0.26 4.3% + ORB_table_alpha S_PhiAlpha_R 0.25418 66 0.0039 4.3% + LOOP_ions opt_ions 4.2734 1 4.3 72.% + ESolver_KS_LCAO Run 3.7680 1 3.8 64.% + HSolverLCAO solve 1.8135 11 0.16 31.% + HamiltLCAO updateHk 0.97757 11 0.089 17.% + LCAO_Hamilt cal_Hgamma 0.94653 11 0.086 16.% + Gint_interface cal_gint 0.84646 23 0.037 14.% + Gint_Gamma distri_vl_value 0.29351 11 0.027 5.0% + Gint_Gamma distri_vl 1.8299 6 0.30 31.% + LCAO_Deepks cal_projected_DM 4.0304 13 0.31 68.% + LCAO_gen_fixedH add_v_delta 1.6980 6 0.28 29.% + LCAO_DESCRIPTOR add_v_delta 1.6980 6 0.28 29.% + ElecStateLCAO psiToRho 0.81783 11 0.074 14.% + Charge mix_rho 0.65287 10 0.065 11.% + LOOP_ions force_stress 0.50525 1 0.51 8.6% + Force_Stress_LCAO getForceStress 0.50522 1 0.51 8.6% + Force_LCAO_gamma ftable_gamma 0.29238 1 0.29 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.18807 1 0.19 3.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:29 2022 + Finish Time : Wed Sep 28 11:08:35 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..bd24de8256d8d4616f360426dcfb9d8109fbf912 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124163 ima = 3.69942e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122718494841 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111861203525 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112309734868 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112582646509 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112511243977 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112551388288 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112547736343 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112550532736 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112550052201 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112549980311 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112549981008 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b44c8e288978859ed67bf5ca9dd9520529566dbf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.809367238841 27.487981779508 7.788128757538 0 0 0 +H +0.0 +2 +-11.989234460928 27.042706373392 9.346295695919 0 0 0 +-13.589031634409 29.056549985907 8.187968760157 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/conv new file mode 100644 index 0000000000000000000000000000000000000000..c7bd75f44bc1d35a75ce5980500cc1a902a39ec7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/conv @@ -0,0 +1 @@ +256 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0ee4d98985e36a7de393649b4767e1573fda8ce6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750435714 0.0128155591 1.286578312 1.371074813 1.470201997 0.008850652451 0.01843406313 0.039052911 +-5.704562852e-18 0.001099235931 0.002768237051 0.01306805828 0.04741699798 -3.867185169e-19 2.449161632e-06 6.711772472e-06 +0.001633454058 0.006031134273 + +H atom_index 1 n_descriptor 18 +1.2600292 0.03404163152 0.1127329687 0.1544304144 0.3235213481 0.02306598489 0.02885742362 0.0371963674 +-5.07168862e-18 5.114728436e-05 0.1055148919 0.1157153526 0.1326901608 2.865512015e-18 3.423988175e-06 0.01321226601 +0.02718674243 0.03121644735 + +H atom_index 2 n_descriptor 18 +1.275461913 0.03352703945 0.1184145792 0.1619629809 0.3282202599 0.02379314713 0.02974922429 0.03683798984 +3.916685823e-17 5.264637981e-05 0.1076646237 0.1180034763 0.1391320481 4.196180648e-18 2.531421109e-06 0.0132722529 +0.02772006171 0.03186016532 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4a507ffbe5fe82757417360e34c2013486cdbe08 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..370afa863de608c1046d0971414813ffe39594fc Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..7f7e19040a89e0a7a131ab914d349cbf14f5f098 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..6dd47825d9060447f1f2f9e803ce793c6d466dfc Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..3bd271c7a07c8ea24447558ecb6defb4e4e23f19 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:29 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0867582 SEC) : SETUP UNITCELL + DONE(0.0993733 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.117463 SEC) : INIT PLANEWAVE + DONE(0.166003 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446455 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651751e+02 0.000000e+00 2.161e-01 4.577e-01 + GE2 -4.663969e+02 -1.221789e+00 9.743e-02 3.798e-01 + GE3 -4.663998e+02 -2.911847e-03 6.225e-02 4.391e-01 + GE4 -4.664002e+02 -4.021470e-04 2.009e-03 3.319e-01 + GE5 -4.663992e+02 9.831227e-04 8.874e-04 3.290e-01 + GE6 -4.663999e+02 -6.971954e-04 1.024e-04 3.090e-01 + GE7 -4.663997e+02 2.249152e-04 4.335e-05 3.065e-01 + GE8 -4.663997e+02 -3.503980e-05 1.065e-05 3.036e-01 + GE9 -4.663997e+02 1.776262e-05 1.631e-06 3.022e-01 + GE10 -4.663997e+02 -2.212996e-06 1.075e-07 3.022e-01 + GE11 -4.663997e+02 -4.284361e-07 4.196e-08 2.452e-01 +E_delta_band = -7.18825553e-02 Ry = -9.78012339e-01 eV +E_delta_NN= -1.95474909e-01 Ry = -2.65957258e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9075 11 0.54 1e+02 % + Run_lcao lcao_line 5.8979 1 5.9 1e+02 % + Potential init_pot 0.28743 2 0.14 4.9 % + PW_Basis recip2real 0.26529 16 0.017 4.5 % + PW_Basis gathers_scatterp 0.11228 16 0.007 1.9 % + Potential v_of_rho 0.85897 13 0.066 15 % + XC_Functional v_xc 0.23522 14 0.017 4 % + H_Hartree_pw v_hartree 0.58673 13 0.045 9.9 % + PW_Basis real2recip 0.55543 38 0.015 9.4 % + PW_Basis gatherp_scatters 0.22094 38 0.0058 3.7 % + ORB_control set_orb_tables 1.1015 1 1.1 19 % + ORB_gen_tables gen_tables 1.1015 1 1.1 19 % + ORB_table_phi init_Table 0.47821 1 0.48 8.1 % + ORB_table_phi cal_ST_Phi12_R 0.47323 126 0.0038 8 % + ORB_table_beta init_Table_Beta 0.18746 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18599 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.25607 1 0.26 4.3 % + ORB_table_alpha S_PhiAlpha_R 0.25418 66 0.0039 4.3 % + LOOP_ions opt_ions 4.2734 1 4.3 72 % + ESolver_KS_LCAO Run 3.768 1 3.8 64 % + HSolverLCAO solve 1.8135 11 0.16 31 % + HamiltLCAO updateHk 0.97757 11 0.089 17 % + LCAO_Hamilt cal_Hgamma 0.94653 11 0.086 16 % + Gint_interface cal_gint 0.84646 23 0.037 14 % + Gint_Gamma distri_vl_value 0.29351 11 0.027 5 % + Gint_Gamma distri_vl 1.8299 6 0.3 31 % + LCAO_Deepks cal_projected_DM 4.0304 13 0.31 68 % + LCAO_gen_fixedH add_v_delta 1.698 6 0.28 29 % + LCAO_DESCRIPTOR add_v_delta 1.698 6 0.28 29 % + ElecStateLCAO psiToRho 0.81783 11 0.074 14 % + Charge mix_rho 0.65287 10 0.065 11 % + LOOP_ions force_stress 0.50525 1 0.51 8.6 % + Force_Stress_LCAO getForceStress 0.50522 1 0.51 8.6 % + Force_LCAO_gamma ftable_gamma 0.29238 1 0.29 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.18807 1 0.19 3.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:29 2022 + FINISH Time : Wed Sep 28 11:08:35 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/256/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..bea0d27cbeac7617a6124a145da3e5249193c4af --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.528596 0.00245623 0.267449 +H 0.580962 0.958276 0.269879 +H 0.504217 0.0010824 0.33103 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d17eaf98e1bb324236a402a399d5a109809d9235 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.8459 2 + 2 -12.6085 2 + 3 -9.09835 2 + 4 -6.64796 2 + 5 0.891379 0 + 6 3.72025 0 + 7 11.1821 0 + 8 11.4315 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a457ef68c815a19077f4b0affc18bad86c96e312 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:36 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.8007018789 0.0687744891111 7.48857395748 0 0 0 0 + tauc_H1 16.2669496916 26.8317331399 7.55661657829 0 0 0 0 + tauc_H2 14.1180782284 0.0303072589304 9.26884621727 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0875462493414 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0989365651699 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117408478257 (SEC) + + DONE : INIT CHARGE Time : 0.166391210099 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446564 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000637 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000841 + + Density error is 0.210182564531 + + Energy Rydberg eV + E_KohnSham -34.1892362027 -465.168422624 + E_Harris -34.3707155294 -467.637575536 + E_Fermi -0.377677712751 -5.13856890103 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000988608710689 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101156454773 + + Density error is 0.0992712956542 + + Energy Rydberg eV + E_KohnSham -34.2767312747 -466.358854151 + E_Harris -34.2841389837 -466.459641202 + E_Fermi -0.189450873046 -2.57761136451 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000952967891999 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000966605945957 + + Density error is 0.0642578957687 + + Energy Rydberg eV + E_KohnSham -34.2772529246 -466.365951562 + E_Harris -34.281922319 -466.429481932 + E_Fermi -0.185024604506 -2.51738889148 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000922748672968 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906257756892 + + Density error is 0.00198936240727 + + Energy Rydberg eV + E_KohnSham -34.2771154893 -466.364081659 + E_Harris -34.2771191374 -466.364131293 + E_Fermi -0.150098251027 -2.04219147379 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000922281437824 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904972009464 + + Density error is 0.000956680431067 + + Energy Rydberg eV + E_KohnSham -34.2770933255 -466.363780105 + E_Harris -34.2770935594 -466.363783287 + E_Fermi -0.150230890432 -2.0439961255 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000922089762818 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00090420168378 + + Density error is 0.0002028739124 + + Energy Rydberg eV + E_KohnSham -34.2770985495 -466.363851181 + E_Harris -34.2770985552 -466.363851258 + E_Fermi -0.149655994491 -2.03617426493 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000922275413372 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904367563876 + + Density error is 2.55850850887e-05 + + Energy Rydberg eV + E_KohnSham -34.2770982672 -466.36384734 + E_Harris -34.2770982683 -466.363847355 + E_Fermi -0.149685176318 -2.03657130406 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000922221939437 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904310077531 + + Density error is 9.31708409499e-06 + + Energy Rydberg eV + E_KohnSham -34.2770998562 -466.363868959 + E_Harris -34.2770998566 -466.363868964 + E_Fermi -0.149689215684 -2.03662626245 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00092222434729 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904308054302 + + Density error is 1.87208326127e-06 + + Energy Rydberg eV + E_KohnSham -34.2770991597 -466.363859484 + E_Harris -34.2770991598 -466.363859484 + E_Fermi -0.149680345807 -2.03650558159 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000922223605605 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904306900512 + + Density error is 4.0450696776e-07 + + Energy Rydberg eV + E_KohnSham -34.2770992884 -466.363861234 + E_Harris -34.2770992884 -466.363861234 + E_Fermi -0.149678841866 -2.03648511942 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00092222435238 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904307516021 + + Density error is 1.07621654581e-07 + + Energy Rydberg eV + E_KohnSham -34.2770992996 -466.363861387 + E_Harris -34.2770992996 -466.363861387 + E_Fermi -0.149678604559 -2.03648189069 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000922224579035 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904307674114 + + Density error is 1.08833233945e-08 + + Energy Rydberg eV + E_KohnSham -34.2770993049 -466.363861458 + E_Harris -34.2770993049 -466.363861458 + E_band -7.82035879356 -106.401439997 + E_one_elec -68.3384833927 -929.792766819 + E_Hartree +35.5892052638 +484.215978879 + E_xc -8.13744458244 -110.71561348 + E_Ewald +6.73584964913 +91.6459360994 + E_demet -5.94099111926e-53 -8.08313309894e-52 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193154499819 -2.62800179189 + E_Fermi -0.149678514266 -2.03648066219 + + charge density convergence is achieved + final etot is -466.363861458 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.8459 2.00000 + 2 -12.6085 2.00000 + 3 -9.09835 2.00000 + 4 -6.64796 2.00000 + 5 0.891379 0.00000 + 6 3.72025 0.00000 + 7 11.1821 0.00000 + 8 11.4315 0.00000 + + EFERMI = -2.036480662185245 eV + OUT.ABACUS/ final etot is -466.3638614580805 eV + correction force for each atom along direction 1 is 0.000109231 + correction force for each atom along direction 2 is -0.000165451 + correction force for each atom along direction 3 is 3.08186e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.76380374 -1.0934100 +1.3500412 + H1 -1.2981348 +1.0848822 -0.025285121 + H2 +0.53433109 +0.0085278248 -1.3247561 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3638614580805 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6882 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6785 1 6.7 1.e+02% + Potential init_pot 0.28362 2 0.14 4.2% + PW_Basis recip2real 0.29861 17 0.018 4.5% + PW_Basis gathers_scatterp 0.13264 17 0.0078 2.0% + Potential v_of_rho 1.0550 14 0.075 16.% + XC_Functional v_xc 0.30209 15 0.020 4.5% + H_Hartree_pw v_hartree 0.70976 14 0.051 11.% + PW_Basis real2recip 0.70502 41 0.017 11.% + PW_Basis gatherp_scatters 0.27564 41 0.0067 4.1% + ORB_control set_orb_tables 1.1046 1 1.1 17.% + ORB_gen_tables gen_tables 1.1046 1 1.1 17.% + ORB_table_phi init_Table 0.48015 1 0.48 7.2% + ORB_table_phi cal_ST_Phi12_R 0.47491 126 0.0038 7.1% + ORB_table_beta init_Table_Beta 0.18849 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18687 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.24957 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.24760 66 0.0038 3.7% + LOOP_ions opt_ions 5.0500 1 5.1 76.% + ESolver_KS_LCAO Run 4.5378 1 4.5 68.% + HSolverLCAO solve 2.0459 12 0.17 31.% + HamiltLCAO updateHk 1.0948 12 0.091 16.% + LCAO_Hamilt cal_Hgamma 1.0650 12 0.089 16.% + Gint_interface cal_gint 1.1623 25 0.046 17.% + Gint_Gamma distri_vl_value 0.23847 12 0.020 3.6% + Gint_Gamma distri_vl 2.3721 6 0.40 35.% + LCAO_Deepks cal_projected_DM 4.8331 14 0.35 72.% + LCAO_gen_fixedH add_v_delta 2.2273 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2274 6 0.37 33.% + ElecStateLCAO psiToRho 0.92850 12 0.077 14.% + Charge mix_rho 0.85282 11 0.078 13.% + LOOP_ions force_stress 0.51201 1 0.51 7.7% + Force_Stress_LCAO getForceStress 0.51198 1 0.51 7.7% + Force_LCAO_gamma ftable_gamma 0.29244 1 0.29 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.21111 1 0.21 3.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:36 2022 + Finish Time : Wed Sep 28 11:02:43 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c704f3f566dce44132a0d47dcdf0edfd122b04c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123505 ima = 3.67733e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123748334075 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112108468274 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112990634366 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113165918316 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113164643098 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113167603138 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113165503604 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011316687659 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113166477396 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011316643329 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113166414707 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113166409821 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e672638bbc2dce04931198c18355cfb2bc001c76 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.199298121052 28.068774489130 7.488573957504 0 0 0 +H +0.0 +2 +-11.733050308432 26.831733139858 7.556616578306 0 0 0 +-13.881921771591 28.030307258909 9.268846217267 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/conv new file mode 100644 index 0000000000000000000000000000000000000000..0e4da6ec257a80c222f5fd9ffc97460c7c8a3309 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/conv @@ -0,0 +1 @@ +257 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..1857c06f9a2bbdf9b7a597e5113b1363183232a4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750904232 0.0122989973 1.234322643 1.326643695 1.467528454 0.008465384239 0.01751221206 0.03914564239 +3.848387139e-18 0.0008257185685 0.002329146972 0.01114628373 0.04017180445 -4.238870505e-19 1.502965254e-06 4.703181444e-06 +0.001586182136 0.005811305822 + +H atom_index 1 n_descriptor 18 +1.178999417 0.03668100914 0.08519115674 0.1201259463 0.2962525297 0.01865056403 0.02418909085 0.04039707802 +-2.567247096e-17 3.290260709e-05 0.0797151327 0.1023073344 0.1128395755 -1.074440107e-18 6.250390312e-06 0.01479189177 +0.02254858798 0.02712056452 + +H atom_index 2 n_descriptor 18 +1.188802935 0.03639961577 0.08799615927 0.1239675031 0.3000976586 0.01910028858 0.02476210667 0.03999652738 +-1.662203821e-18 3.367129907e-05 0.0821623426 0.1057074954 0.1133814274 1.124822538e-18 6.021037305e-06 0.01447144547 +0.022963159 0.0276597888 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..11b90d04a99dee1c71681e1280293ed0b1ee446a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:36 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0875696 SEC) : SETUP UNITCELL + DONE(0.0989566 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11743 SEC) : INIT PLANEWAVE + DONE(0.166521 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446632 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651684e+02 0.000000e+00 2.102e-01 4.890e-01 + GE2 -4.663589e+02 -1.190432e+00 9.927e-02 4.286e-01 + GE3 -4.663660e+02 -7.097411e-03 6.426e-02 4.990e-01 + GE4 -4.663641e+02 1.869903e-03 1.989e-03 3.665e-01 + GE5 -4.663638e+02 3.015539e-04 9.567e-04 3.621e-01 + GE6 -4.663639e+02 -7.107636e-05 2.029e-04 3.588e-01 + GE7 -4.663638e+02 3.841237e-06 2.559e-05 3.382e-01 + GE8 -4.663639e+02 -2.161931e-05 9.317e-06 3.405e-01 + GE9 -4.663639e+02 9.475842e-06 1.872e-06 3.409e-01 + GE10 -4.663639e+02 -1.750183e-06 4.045e-07 3.401e-01 + GE11 -4.663639e+02 -1.531870e-07 1.076e-07 3.382e-01 + GE12 -4.663639e+02 -7.115451e-08 1.088e-08 2.737e-01 +E_delta_band = -6.69282572e-02 Ry = -9.10605655e-01 eV +E_delta_NN= -1.93154500e-01 Ry = -2.62800179e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6882 11 0.61 1e+02 % + Run_lcao lcao_line 6.6785 1 6.7 1e+02 % + Potential init_pot 0.28362 2 0.14 4.2 % + PW_Basis recip2real 0.29861 17 0.018 4.5 % + PW_Basis gathers_scatterp 0.13264 17 0.0078 2 % + Potential v_of_rho 1.055 14 0.075 16 % + XC_Functional v_xc 0.30209 15 0.02 4.5 % + H_Hartree_pw v_hartree 0.70976 14 0.051 11 % + PW_Basis real2recip 0.70502 41 0.017 11 % + PW_Basis gatherp_scatters 0.27564 41 0.0067 4.1 % + ORB_control set_orb_tables 1.1046 1 1.1 17 % + ORB_gen_tables gen_tables 1.1046 1 1.1 17 % + ORB_table_phi init_Table 0.48015 1 0.48 7.2 % + ORB_table_phi cal_ST_Phi12_R 0.47491 126 0.0038 7.1 % + ORB_table_beta init_Table_Beta 0.18849 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18687 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.24957 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.2476 66 0.0038 3.7 % + LOOP_ions opt_ions 5.05 1 5.1 76 % + ESolver_KS_LCAO Run 4.5378 1 4.5 68 % + HSolverLCAO solve 2.0459 12 0.17 31 % + HamiltLCAO updateHk 1.0948 12 0.091 16 % + LCAO_Hamilt cal_Hgamma 1.065 12 0.089 16 % + Gint_interface cal_gint 1.1623 25 0.046 17 % + Gint_Gamma distri_vl_value 0.23847 12 0.02 3.6 % + Gint_Gamma distri_vl 2.3721 6 0.4 35 % + LCAO_Deepks cal_projected_DM 4.8331 14 0.35 72 % + LCAO_gen_fixedH add_v_delta 2.2273 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2274 6 0.37 33 % + ElecStateLCAO psiToRho 0.9285 12 0.077 14 % + Charge mix_rho 0.85282 11 0.078 13 % + LOOP_ions force_stress 0.51201 1 0.51 7.7 % + Force_Stress_LCAO getForceStress 0.51198 1 0.51 7.7 % + Force_LCAO_gamma ftable_gamma 0.29244 1 0.29 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.21111 1 0.21 3.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:36 2022 + FINISH Time : Wed Sep 28 11:02:43 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/257/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..35b679a72d5b96b5b0907b92aa78b049f30f698d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.524909 0.0295395 0.272082 +H 0.554871 0.00409873 0.222976 +H 0.489688 0.979629 0.296967 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..4e89288bd24c2fb4c540ae0b1ce35b7628f38edf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4855 2 + 2 -13.1961 2 + 3 -9.14896 2 + 4 -6.78645 2 + 5 1.42733 0 + 6 4.69914 0 + 7 11.0281 0 + 8 11.2726 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e1b674a8c609745b7f5a5eeb5bc4e6b3220e5dd0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:11 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.6974465305 0.827104865835 7.61829577843 0 0 0 0 + tauc_H1 15.5363744821 0.114764316742 6.24332007658 0 0 0 0 + tauc_H2 13.7112599805 27.4295994804 8.3150704263 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.100493591815 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.10088625145 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11894584094 (SEC) + + DONE : INIT CHARGE Time : 0.162282012083 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44583 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00115 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111 + + Density error is 0.216981133843 + + Energy Rydberg eV + E_KohnSham -34.1869375499 -465.137147848 + E_Harris -34.3832275473 -467.807810274 + E_Fermi -0.417031614929 -5.67400620918 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00115016264558 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126788777248 + + Density error is 0.0975228572529 + + Energy Rydberg eV + E_KohnSham -34.2774434588 -466.368543913 + E_Harris -34.2840880027 -466.45894757 + E_Fermi -0.225024328717 -3.06161305918 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00107047130808 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120280863404 + + Density error is 0.0622882478149 + + Energy Rydberg eV + E_KohnSham -34.277681625 -466.37178433 + E_Harris -34.2819449142 -466.429789356 + E_Fermi -0.211337541547 -2.87539476636 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000943186683113 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110222086037 + + Density error is 0.00203447001824 + + Energy Rydberg eV + E_KohnSham -34.2777145862 -466.37223279 + E_Harris -34.2777167236 -466.37226187 + E_Fermi -0.175596284343 -2.3891100147 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000942175445457 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110215878382 + + Density error is 0.000884787619526 + + Energy Rydberg eV + E_KohnSham -34.2776439712 -466.371272024 + E_Harris -34.2776461668 -466.371301896 + E_Fermi -0.174504212826 -2.37425161943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000940972205647 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110079020216 + + Density error is 0.000153518172246 + + Energy Rydberg eV + E_KohnSham -34.2776925936 -466.371933566 + E_Harris -34.2776926703 -466.371934609 + E_Fermi -0.174739975796 -2.3774593392 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000941070793051 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110092962072 + + Density error is 4.57361385375e-05 + + Energy Rydberg eV + E_KohnSham -34.2776744535 -466.371686757 + E_Harris -34.2776744646 -466.371686908 + E_Fermi -0.174575817711 -2.37522585387 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000941039889614 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110085228468 + + Density error is 1.65646123815e-05 + + Energy Rydberg eV + E_KohnSham -34.2776791553 -466.371750727 + E_Harris -34.2776791562 -466.37175074 + E_Fermi -0.174627709059 -2.37593187189 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000941019073341 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110083763934 + + Density error is 2.92053650151e-06 + + Energy Rydberg eV + E_KohnSham -34.2776776917 -466.371730814 + E_Harris -34.2776776917 -466.371730815 + E_Fermi -0.174611281983 -2.37570837005 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000941016527039 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110083798546 + + Density error is 1.36184991819e-07 + + Energy Rydberg eV + E_KohnSham -34.2776778373 -466.371732796 + E_Harris -34.2776778373 -466.371732796 + E_Fermi -0.174607981143 -2.37566345983 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000941016668654 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110083830848 + + Density error is 6.70193456766e-08 + + Energy Rydberg eV + E_KohnSham -34.2776778943 -466.371733571 + E_Harris -34.2776778943 -466.371733571 + E_band -8.02854889184 -109.234011601 + E_one_elec -69.6715410981 -947.929947375 + E_Hartree +36.2184311463 +492.777036211 + E_xc -8.23869172269 -112.093151494 + E_Ewald +7.53768328832 +102.555442441 + E_demet -1.79033096552e-87 -2.43587024369e-86 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195551189381 -2.66061042626 + E_Fermi -0.174608016542 -2.37566394144 + + charge density convergence is achieved + final etot is -466.371733571 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4855 2.00000 + 2 -13.1961 2.00000 + 3 -9.14896 2.00000 + 4 -6.78645 2.00000 + 5 1.42733 0.00000 + 6 4.69914 0.00000 + 7 11.0281 0.00000 + 8 11.2726 0.00000 + + EFERMI = -2.375663941443040 eV + OUT.ABACUS/ final etot is -466.3717335705763 eV + correction force for each atom along direction 1 is -9.42178e-05 + correction force for each atom along direction 2 is -2.68374e-05 + correction force for each atom along direction 3 is 3.65340e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.2776904 +0.82823597 +1.9847343 + H1 +1.2397053 -0.95770837 -1.9908998 + H2 +0.037985116 +0.12947240 +0.0061655856 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3717335705763 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0025 11 0.64 1.0e+02% + Run_lcao lcao_line 6.9934 1 7.0 1.e+02% + Potential init_pot 0.28607 2 0.14 4.1% + PW_Basis recip2real 0.26761 16 0.017 3.8% + PW_Basis gathers_scatterp 0.12301 16 0.0077 1.8% + Potential v_of_rho 0.92218 13 0.071 13.% + XC_Functional v_xc 0.28254 14 0.020 4.0% + H_Hartree_pw v_hartree 0.59737 13 0.046 8.5% + PW_Basis real2recip 0.68286 38 0.018 9.8% + PW_Basis gatherp_scatters 0.27677 38 0.0073 4.0% + ORB_control set_orb_tables 1.0879 1 1.1 16.% + ORB_gen_tables gen_tables 1.0879 1 1.1 16.% + ORB_table_phi init_Table 0.47082 1 0.47 6.7% + ORB_table_phi cal_ST_Phi12_R 0.46563 126 0.0037 6.6% + ORB_table_beta init_Table_Beta 0.18282 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18126 56 0.0032 2.6% + ORB_table_alpha init_Table_Alpha 0.24731 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24535 66 0.0037 3.5% + LOOP_ions opt_ions 5.3822 1 5.4 77.% + ESolver_KS_LCAO Run 4.8313 1 4.8 69.% + HSolverLCAO solve 2.4583 11 0.22 35.% + HamiltLCAO updateHk 1.2844 11 0.12 18.% + LCAO_Hamilt cal_Hgamma 1.2570 11 0.11 18.% + Gint_interface cal_gint 1.8445 23 0.080 26.% + Gint_Gamma distri_vl_value 0.15602 11 0.014 2.2% + Gint_Gamma distri_vl 2.3289 6 0.39 33.% + LCAO_Deepks cal_projected_DM 5.1758 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1824 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1824 6 0.36 31.% + ElecStateLCAO psiToRho 1.1517 11 0.10 16.% + Charge mix_rho 0.89525 10 0.090 13.% + LOOP_ions force_stress 0.55070 1 0.55 7.9% + Force_Stress_LCAO getForceStress 0.55067 1 0.55 7.9% + Force_LCAO_gamma ftable_gamma 0.34561 1 0.35 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.28827 1 0.29 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:11 2022 + Finish Time : Wed Sep 28 11:12:18 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..65789f223bdd5c20f9e0f37714450114a5f5f97b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123842 ima = 3.66107e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012292906619 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112078168964 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112516933853 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112790726177 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112724182034 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112764128688 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755715161 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112758842499 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112758306873 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112758169611 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011275816613 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/STRU new file mode 100644 index 0000000000000000000000000000000000000000..67197b4227d6d15e517f18cc1c0de34cf7330f63 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.302553469492 28.827104865833 7.618295778443 0 0 0 +H +0.0 +2 +-12.463625517874 28.114764316729 6.243320076570 0 0 0 +-14.288740019538 27.429599480417 8.315070426314 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/conv new file mode 100644 index 0000000000000000000000000000000000000000..fdbaa87435ec87404f80dfcf1c4a427868695bc3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/conv @@ -0,0 +1 @@ +258 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..3d6a448d7dd901b54c9b0ba01937f0abfc0f8662 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749401625 0.01276741764 1.285232951 1.377433481 1.470273753 0.008692129592 0.01893084078 0.03903872105 +-4.197041469e-19 0.001136510803 0.002722712751 0.01290921226 0.04713294735 -1.806190227e-20 2.25662586e-06 6.378646025e-06 +0.001645882773 0.005936278321 + +H atom_index 1 n_descriptor 18 +1.302388323 0.03254396775 0.1284902978 0.1760928066 0.3360366284 0.02481837886 0.03129982272 0.03643871215 +4.46044809e-17 5.390436877e-05 0.1081897107 0.1248295081 0.1510956675 2.472322855e-18 1.309264199e-06 0.01376521445 +0.02843621816 0.03285076396 + +H atom_index 2 n_descriptor 18 +1.23464702 0.03475719413 0.1035507487 0.1429053889 0.3156698992 0.02169409846 0.02740568488 0.03785669943 +-4.687637255e-17 4.743082849e-05 0.09938688247 0.1141701943 0.122761469 -1.618490454e-18 5.01988272e-06 0.01336661328 +0.02611713223 0.03007266167 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..1ca93970cfe2d7dc849ec20a68b94b314b60a900 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..3935e44eb2a49412a4b61530717be9f1184e8696 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..fd7c78dd4df6c1d62a885fcf78a45d6149c09945 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..7265a420ec0e84b6fdc63a674b3428fddcb4925d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..582a040f81092d63bd15c9f85b41278026cd04ae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:11 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.100529 SEC) : SETUP UNITCELL + DONE(0.100902 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118966 SEC) : INIT PLANEWAVE + DONE(0.16242 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445893 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651371e+02 0.000000e+00 2.170e-01 5.308e-01 + GE2 -4.663685e+02 -1.231396e+00 9.752e-02 4.901e-01 + GE3 -4.663718e+02 -3.240418e-03 6.229e-02 5.615e-01 + GE4 -4.663722e+02 -4.484597e-04 2.034e-03 4.199e-01 + GE5 -4.663713e+02 9.607657e-04 8.848e-04 4.191e-01 + GE6 -4.663719e+02 -6.615418e-04 1.535e-04 4.134e-01 + GE7 -4.663717e+02 2.468093e-04 4.574e-05 4.071e-01 + GE8 -4.663718e+02 -6.397072e-05 1.656e-05 3.983e-01 + GE9 -4.663717e+02 1.991317e-05 2.921e-06 3.983e-01 + GE10 -4.663717e+02 -1.981911e-06 1.362e-07 3.971e-01 + GE11 -4.663717e+02 -7.744448e-07 6.702e-08 3.326e-01 +E_delta_band = -7.19916812e-02 Ry = -9.79497073e-01 eV +E_delta_NN= -1.95551189e-01 Ry = -2.66061043e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0025 11 0.64 1e+02 % + Run_lcao lcao_line 6.9934 1 7 1e+02 % + Potential init_pot 0.28607 2 0.14 4.1 % + PW_Basis recip2real 0.26761 16 0.017 3.8 % + PW_Basis gathers_scatterp 0.12301 16 0.0077 1.8 % + Potential v_of_rho 0.92218 13 0.071 13 % + XC_Functional v_xc 0.28254 14 0.02 4 % + H_Hartree_pw v_hartree 0.59737 13 0.046 8.5 % + PW_Basis real2recip 0.68286 38 0.018 9.8 % + PW_Basis gatherp_scatters 0.27677 38 0.0073 4 % + ORB_control set_orb_tables 1.0879 1 1.1 16 % + ORB_gen_tables gen_tables 1.0879 1 1.1 16 % + ORB_table_phi init_Table 0.47082 1 0.47 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.46563 126 0.0037 6.6 % + ORB_table_beta init_Table_Beta 0.18282 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18126 56 0.0032 2.6 % + ORB_table_alpha init_Table_Alpha 0.24731 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24535 66 0.0037 3.5 % + LOOP_ions opt_ions 5.3822 1 5.4 77 % + ESolver_KS_LCAO Run 4.8313 1 4.8 69 % + HSolverLCAO solve 2.4583 11 0.22 35 % + HamiltLCAO updateHk 1.2844 11 0.12 18 % + LCAO_Hamilt cal_Hgamma 1.257 11 0.11 18 % + Gint_interface cal_gint 1.8445 23 0.08 26 % + Gint_Gamma distri_vl_value 0.15602 11 0.014 2.2 % + Gint_Gamma distri_vl 2.3289 6 0.39 33 % + LCAO_Deepks cal_projected_DM 5.1758 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.1824 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1824 6 0.36 31 % + ElecStateLCAO psiToRho 1.1517 11 0.1 16 % + Charge mix_rho 0.89525 10 0.09 13 % + LOOP_ions force_stress 0.5507 1 0.55 7.9 % + Force_Stress_LCAO getForceStress 0.55067 1 0.55 7.9 % + Force_LCAO_gamma ftable_gamma 0.34561 1 0.35 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.28827 1 0.29 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:11 2022 + FINISH Time : Wed Sep 28 11:12:18 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/258/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..bc70b80684052a58bbb8c22e4e8c5a6325a74693 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.518997 0.0574972 0.281947 +H 0.541474 0.0690053 0.217613 +H 0.505192 0.995459 0.273924 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0f2ec2384a25dcde3043da123d20c16cf53a8503 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2897 2 + 2 -12.5165 2 + 3 -9.4811 2 + 4 -6.74489 2 + 5 1.02514 0 + 6 4.17553 0 + 7 11.0997 0 + 8 11.3692 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0f4a6ee2c403ca6991ac38098b32d0b23a965e11 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:29 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.5319046685 1.60992273148 7.89452261454 0 0 0 0 + tauc_H1 15.1612685409 1.93214977016 6.0931514613 0 0 0 0 + tauc_H2 14.1453751599 27.8728470845 7.66985906582 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0872073928936 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0876226168922 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105790899514 (SEC) + + DONE : INIT CHARGE Time : 0.155986676854 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.4337 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 341 ; sender_size of each process is: +144 144 49 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00089 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103 + + Density error is 0.21153533787 + + Energy Rydberg eV + E_KohnSham -34.1855415632 -465.118154475 + E_Harris -34.371503936 -467.648302359 + E_Fermi -0.396971573201 -5.40107533956 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00119687004316 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134033155934 + + Density error is 0.0980666555367 + + Energy Rydberg eV + E_KohnSham -34.2735917643 -466.31613892 + E_Harris -34.2806537517 -466.412222188 + E_Fermi -0.209807681017 -2.854579946 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00114601049187 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128076007023 + + Density error is 0.0630772464455 + + Energy Rydberg eV + E_KohnSham -34.2739174653 -466.320570309 + E_Harris -34.2784705525 -466.382518239 + E_Fermi -0.201133055052 -2.73655560485 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00108945366011 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012077077736 + + Density error is 0.0019006884598 + + Energy Rydberg eV + E_KohnSham -34.2738448702 -466.319582603 + E_Harris -34.2738446035 -466.319578974 + E_Fermi -0.165242550706 -2.24824024166 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00109074364605 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121045605146 + + Density error is 0.000842690431007 + + Energy Rydberg eV + E_KohnSham -34.273809404 -466.319100061 + E_Harris -34.2738097803 -466.319105181 + E_Fermi -0.165184145065 -2.24744559214 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00108992797739 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120945766529 + + Density error is 9.72189537182e-05 + + Energy Rydberg eV + E_KohnSham -34.273826626 -466.319334378 + E_Harris -34.2738266263 -466.319334381 + E_Fermi -0.164821366615 -2.24250973811 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00108994880775 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120940305162 + + Density error is 2.90744977626e-05 + + Energy Rydberg eV + E_KohnSham -34.2738227794 -466.319282043 + E_Harris -34.2738227826 -466.319282085 + E_Fermi -0.164765962934 -2.24175593236 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00108985738088 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120933977821 + + Density error is 1.03281239474e-05 + + Energy Rydberg eV + E_KohnSham -34.2738242833 -466.319302504 + E_Harris -34.2738242837 -466.31930251 + E_Fermi -0.164783378024 -2.24199287682 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00108986382256 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120934549443 + + Density error is 1.99732054488e-06 + + Energy Rydberg eV + E_KohnSham -34.2738233255 -466.319289472 + E_Harris -34.2738233255 -466.319289472 + E_Fermi -0.164773685455 -2.24186100265 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00108986850769 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120934563033 + + Density error is 2.66619147926e-07 + + Energy Rydberg eV + E_KohnSham -34.2738234628 -466.31929134 + E_Harris -34.2738234628 -466.31929134 + E_Fermi -0.164772269214 -2.2418417337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 341 + sender_size = 341 + last sender_buffer = 0.00108986900784 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120934618279 + + Density error is 8.31362730842e-08 + + Energy Rydberg eV + E_KohnSham -34.2738234986 -466.319291828 + E_Harris -34.2738234986 -466.319291828 + E_band -7.94257660312 -108.064298604 + E_one_elec -68.9757883018 -938.463744946 + E_Hartree +35.8773789481 +488.136782999 + E_xc -8.18388580005 -111.347478662 + E_Ewald +7.1333849707 +97.0546816291 + E_demet -2.83330966489e-65 -3.85491556409e-64 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194391958472 -2.6448382806 + E_Fermi -0.164772134821 -2.24183990519 + + charge density convergence is achieved + final etot is -466.319291828 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2897 2.00000 + 2 -12.5165 2.00000 + 3 -9.48110 2.00000 + 4 -6.74489 2.00000 + 5 1.02514 0.00000 + 6 4.17553 0.00000 + 7 11.0997 0.00000 + 8 11.3692 0.00000 + + EFERMI = -2.241839905191819 eV + OUT.ABACUS/ final etot is -466.3192918276991 eV + correction force for each atom along direction 1 is -4.57635e-05 + correction force for each atom along direction 2 is -0.000129252 + correction force for each atom along direction 3 is -0.000103795 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.0319223 +1.4295481 -2.1818026 + H1 -0.49489960 +0.21937794 +1.8297538 + H2 -0.53702269 -1.6489260 +0.35204876 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3192918276991 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0391 11 0.55 1.0e+02% + Run_lcao lcao_line 6.0289 1 6.0 1.e+02% + Potential init_pot 0.27998 2 0.14 4.6% + PW_Basis recip2real 0.27736 16 0.017 4.6% + PW_Basis gathers_scatterp 0.11912 16 0.0074 2.0% + Potential v_of_rho 0.98685 13 0.076 16.% + XC_Functional v_xc 0.28589 14 0.020 4.7% + H_Hartree_pw v_hartree 0.65706 13 0.051 11.% + PW_Basis real2recip 0.66204 38 0.017 11.% + PW_Basis gatherp_scatters 0.26121 38 0.0069 4.3% + ORB_control set_orb_tables 1.1088 1 1.1 18.% + ORB_gen_tables gen_tables 1.1088 1 1.1 18.% + ORB_table_phi init_Table 0.48392 1 0.48 8.0% + ORB_table_phi cal_ST_Phi12_R 0.47875 126 0.0038 7.9% + ORB_table_beta init_Table_Beta 0.18626 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18468 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25312 1 0.25 4.2% + ORB_table_alpha S_PhiAlpha_R 0.25118 66 0.0038 4.2% + LOOP_ions opt_ions 4.4089 1 4.4 73.% + ESolver_KS_LCAO Run 3.9390 1 3.9 65.% + HSolverLCAO solve 1.6635 11 0.15 28.% + HamiltLCAO updateHk 0.94636 11 0.086 16.% + LCAO_Hamilt cal_Hgamma 0.91867 11 0.084 15.% + Gint_interface cal_gint 1.2247 23 0.053 20.% + Gint_Gamma distri_vl 1.9385 6 0.32 32.% + LCAO_Deepks cal_projected_DM 4.2503 13 0.33 70.% + LCAO_gen_fixedH add_v_delta 1.7929 6 0.30 30.% + LCAO_DESCRIPTOR add_v_delta 1.7929 6 0.30 30.% + ElecStateLCAO psiToRho 0.69486 11 0.063 12.% + Charge mix_rho 0.77888 10 0.078 13.% + LOOP_ions force_stress 0.46969 1 0.47 7.8% + Force_Stress_LCAO getForceStress 0.46966 1 0.47 7.8% + Force_LCAO_gamma ftable_gamma 0.25395 1 0.25 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.22160 1 0.22 3.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:29 2022 + Finish Time : Wed Sep 28 11:05:35 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..14cc9fb9dbaa8e8a516afc041759355a2b76a1a7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/OUT.ABACUS/warning.log @@ -0,0 +1,73 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123944 ima = 3.68281e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 3 + 3 1 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122719113881 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111414230394 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112134914469 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112366359634 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112342509721 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112354471323 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112352487623 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112354469298 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112354005531 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112353907623 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112353894996 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1e4c1ad89768f07f9f51f76a44b8cb56acea6fa6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.468095331447 29.609922731478 7.894522614527 0 0 0 +H +0.0 +2 +-12.838731459143 29.932149770135 6.093151461293 0 0 0 +-13.854624840049 27.872847084547 7.669859065820 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/conv new file mode 100644 index 0000000000000000000000000000000000000000..12bd8f9dd65c4be39ce4afbefa2f7032a78b8399 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/conv @@ -0,0 +1 @@ +259 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..cb2e26d157c3806512b0b14cff6e6723ab38a1c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755691546 0.01263166194 1.247557458 1.347460819 1.469322283 0.009723632507 0.0161845386 0.03926284193 +-3.507267141e-18 0.0008022655657 0.002790640403 0.01287753814 0.04538642251 5.009968272e-19 2.54206278e-06 7.140660846e-06 +0.001556563181 0.006048785966 + +H atom_index 1 n_descriptor 18 +1.171032925 0.03741840236 0.08620935883 0.1163690347 0.2902174292 0.01936615896 0.02358489083 0.04116804461 +7.203550666e-19 3.979022952e-05 0.08183217038 0.09902618057 0.1115180922 5.560017461e-18 6.165704755e-06 0.01539394949 +0.02347059565 0.02660938897 + +H atom_index 2 n_descriptor 18 +1.28152574 0.03398561346 0.1232913417 0.1650122518 0.3297447919 0.02484829893 0.03007378105 0.03737413221 +7.742216752e-18 4.951241036e-05 0.1065822709 0.1197453433 0.1413226368 -4.108334639e-18 1.175814375e-06 0.01346726561 +0.02781077575 0.03207717249 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..cd6fd1102e26ee97c9ee2b356655df98515dbb1c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:29 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872325 SEC) : SETUP UNITCELL + DONE(0.0876395 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.10581 SEC) : INIT PLANEWAVE + DONE(0.156103 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.433762 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651182e+02 0.000000e+00 2.115e-01 4.676e-01 + GE2 -4.663161e+02 -1.197984e+00 9.807e-02 4.423e-01 + GE3 -4.663206e+02 -4.431389e-03 6.308e-02 4.720e-01 + GE4 -4.663196e+02 9.877062e-04 1.901e-03 3.332e-01 + GE5 -4.663191e+02 4.825419e-04 8.427e-04 3.333e-01 + GE6 -4.663193e+02 -2.343172e-04 9.722e-05 3.285e-01 + GE7 -4.663193e+02 5.233558e-05 2.907e-05 3.185e-01 + GE8 -4.663193e+02 -2.046091e-05 1.033e-05 3.106e-01 + GE9 -4.663193e+02 1.303189e-05 1.997e-06 3.116e-01 + GE10 -4.663193e+02 -1.867973e-06 2.666e-07 3.118e-01 + GE11 -4.663193e+02 -4.880889e-07 8.314e-08 2.465e-01 +E_delta_band = -6.94786429e-02 Ry = -9.45305432e-01 eV +E_delta_NN= -1.94391958e-01 Ry = -2.64483828e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0391 11 0.55 1e+02 % + Run_lcao lcao_line 6.0289 1 6 1e+02 % + Potential init_pot 0.27998 2 0.14 4.6 % + PW_Basis recip2real 0.27736 16 0.017 4.6 % + PW_Basis gathers_scatterp 0.11912 16 0.0074 2 % + Potential v_of_rho 0.98685 13 0.076 16 % + XC_Functional v_xc 0.28589 14 0.02 4.7 % + H_Hartree_pw v_hartree 0.65706 13 0.051 11 % + PW_Basis real2recip 0.66204 38 0.017 11 % + PW_Basis gatherp_scatters 0.26121 38 0.0069 4.3 % + ORB_control set_orb_tables 1.1088 1 1.1 18 % + ORB_gen_tables gen_tables 1.1088 1 1.1 18 % + ORB_table_phi init_Table 0.48392 1 0.48 8 % + ORB_table_phi cal_ST_Phi12_R 0.47875 126 0.0038 7.9 % + ORB_table_beta init_Table_Beta 0.18626 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18468 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.25312 1 0.25 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.25118 66 0.0038 4.2 % + LOOP_ions opt_ions 4.4089 1 4.4 73 % + ESolver_KS_LCAO Run 3.939 1 3.9 65 % + HSolverLCAO solve 1.6635 11 0.15 28 % + HamiltLCAO updateHk 0.94636 11 0.086 16 % + LCAO_Hamilt cal_Hgamma 0.91867 11 0.084 15 % + Gint_interface cal_gint 1.2247 23 0.053 20 % + Gint_Gamma distri_vl 1.9385 6 0.32 32 % + LCAO_Deepks cal_projected_DM 4.2503 13 0.33 70 % + LCAO_gen_fixedH add_v_delta 1.7929 6 0.3 30 % + LCAO_DESCRIPTOR add_v_delta 1.7929 6 0.3 30 % + ElecStateLCAO psiToRho 0.69486 11 0.063 12 % + Charge mix_rho 0.77888 10 0.078 13 % + LOOP_ions force_stress 0.46969 1 0.47 7.8 % + Force_Stress_LCAO getForceStress 0.46966 1 0.47 7.8 % + Force_LCAO_gamma ftable_gamma 0.25395 1 0.25 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.2216 1 0.22 3.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:29 2022 + FINISH Time : Wed Sep 28 11:05:35 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/259/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..914eb5097a5f71ac0fbc7315081b1ac4ad39d998 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.519604 0.408729 0.437607 +H 0.526302 0.402912 0.373258 +H 0.522524 0.348759 0.463734 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c82c523defdc8813f5fe8b49deb77ab217ae823c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2568 2 + 2 -13.2688 2 + 3 -8.92855 2 + 4 -6.73538 2 + 5 1.35407 0 + 6 4.51022 0 + 7 11.0717 0 + 8 11.3033 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..71018eb56448d3b91fb1a1324df34de2e995d38c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.5489227077 11.4444233605 12.2529987974 0 0 0 0 + tauc_H1 14.7364683869 11.2815232212 10.4512151676 0 0 0 0 + tauc_H2 14.6306676854 9.7652427256 12.9845414463 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0862592187634 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0983392396598 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11659115561 (SEC) + + DONE : INIT CHARGE Time : 0.166046403881 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449302 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00147 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000905 + + Density error is 0.215539478607 + + Energy Rydberg eV + E_KohnSham -34.1914429765 -465.198447323 + E_Harris -34.3840129711 -467.818496513 + E_Fermi -0.406484716116 -5.5305082891 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00133542314205 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124914933308 + + Density error is 0.0978893864406 + + Energy Rydberg eV + E_KohnSham -34.2804036504 -466.408819385 + E_Harris -34.287036497 -466.499063893 + E_Fermi -0.215557980661 -2.93281678636 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00123048685849 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120947203483 + + Density error is 0.0626549678822 + + Energy Rydberg eV + E_KohnSham -34.2805993102 -466.411481473 + E_Harris -34.2848588736 -466.469435807 + E_Fermi -0.203139537831 -2.76385520359 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105117314925 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116038604983 + + Density error is 0.00206278736994 + + Energy Rydberg eV + E_KohnSham -34.280608513 -466.411606684 + E_Harris -34.2806113023 -466.411644635 + E_Fermi -0.167867488701 -2.28395435529 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104855461836 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116090405053 + + Density error is 0.000831390390196 + + Energy Rydberg eV + E_KohnSham -34.280553038 -466.410851907 + E_Harris -34.2805541132 -466.410866537 + E_Fermi -0.166944037604 -2.27139015855 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104690623273 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116008190519 + + Density error is 0.000199952247744 + + Energy Rydberg eV + E_KohnSham -34.2805906502 -466.411363648 + E_Harris -34.2805907552 -466.411365077 + E_Fermi -0.167036013206 -2.2726415508 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104681595278 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116051961668 + + Density error is 4.02562617988e-05 + + Energy Rydberg eV + E_KohnSham -34.2805753989 -466.411156143 + E_Harris -34.2805754075 -466.41115626 + E_Fermi -0.166867382626 -2.27034721406 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104680628613 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116040197881 + + Density error is 1.7503535877e-05 + + Energy Rydberg eV + E_KohnSham -34.2805808657 -466.411230524 + E_Harris -34.280580867 -466.411230541 + E_Fermi -0.166912304426 -2.2709584065 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104677749726 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116040088748 + + Density error is 2.28139149726e-06 + + Energy Rydberg eV + E_KohnSham -34.2805793869 -466.411210403 + E_Harris -34.2805793869 -466.411210403 + E_Fermi -0.166894412183 -2.27071497005 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104677286887 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011604028025 + + Density error is 4.61721617893e-07 + + Energy Rydberg eV + E_KohnSham -34.2805796378 -466.411213817 + E_Harris -34.2805796378 -466.411213817 + E_Fermi -0.16689225909 -2.27068567571 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104677259201 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116040343096 + + Density error is 1.61077283003e-07 + + Energy Rydberg eV + E_KohnSham -34.2805796597 -466.411214115 + E_Harris -34.2805796597 -466.411214115 + E_Fermi -0.16689205421 -2.27068288818 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104677228705 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116040362771 + + Density error is 9.96495268697e-09 + + Energy Rydberg eV + E_KohnSham -34.280579663 -466.411214159 + E_Harris -34.280579663 -466.411214159 + E_band -7.9657067157 -108.37899993 + E_one_elec -69.3663960396 -943.778235864 + E_Hartree +36.0824817501 +490.927349782 + E_xc -8.21626030248 -111.787956365 + E_Ewald +7.34380087651 +99.9175368979 + E_demet -9.7888522922e-80 -1.33184168054e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194851474762 -2.65109032047 + E_Fermi -0.16689189876 -2.27068077318 + + charge density convergence is achieved + final etot is -466.411214159 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2568 2.00000 + 2 -13.2688 2.00000 + 3 -8.92855 2.00000 + 4 -6.73538 2.00000 + 5 1.35407 0.00000 + 6 4.51022 0.00000 + 7 11.0717 0.00000 + 8 11.3033 0.00000 + + EFERMI = -2.270680773178149 eV + OUT.ABACUS/ final etot is -466.4112141592641 eV + correction force for each atom along direction 1 is 3.47418e-05 + correction force for each atom along direction 2 is -0.000164789 + correction force for each atom along direction 3 is -4.96794e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.11799624 +0.55248312 +0.71613584 + H1 +0.079737638 -0.30735958 -0.54437692 + H2 +0.038258597 -0.24512354 -0.17175892 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4112141592641 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6261 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6177 1 6.6 1.e+02% + Potential init_pot 0.28518 2 0.14 4.3% + PW_Basis recip2real 0.28306 17 0.017 4.3% + PW_Basis gathers_scatterp 0.13097 17 0.0077 2.0% + Potential v_of_rho 1.0547 14 0.075 16.% + XC_Functional v_xc 0.31921 15 0.021 4.8% + H_Hartree_pw v_hartree 0.69163 14 0.049 10.% + PW_Basis real2recip 0.70271 41 0.017 11.% + PW_Basis gatherp_scatters 0.30701 41 0.0075 4.6% + ORB_control set_orb_tables 1.0866 1 1.1 16.% + ORB_gen_tables gen_tables 1.0866 1 1.1 16.% + ORB_table_phi init_Table 0.47146 1 0.47 7.1% + ORB_table_phi cal_ST_Phi12_R 0.46635 126 0.0037 7.0% + ORB_table_beta init_Table_Beta 0.18221 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18067 56 0.0032 2.7% + ORB_table_alpha init_Table_Alpha 0.24666 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.24477 66 0.0037 3.7% + LOOP_ions opt_ions 5.0003 1 5.0 75.% + ESolver_KS_LCAO Run 4.4971 1 4.5 68.% + HSolverLCAO solve 2.0145 12 0.17 30.% + HamiltLCAO updateHk 1.0831 12 0.090 16.% + LCAO_Hamilt cal_Hgamma 1.0536 12 0.088 16.% + Gint_interface cal_gint 0.16032 25 0.0064 2.4% + Gint_Gamma distri_vl_value 0.58605 12 0.049 8.8% + Gint_Gamma distri_vl 2.3508 6 0.39 35.% + LCAO_Deepks cal_projected_DM 4.6637 14 0.33 70.% + LCAO_gen_fixedH add_v_delta 2.2063 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2063 6 0.37 33.% + ElecStateLCAO psiToRho 0.90692 12 0.076 14.% + Charge mix_rho 0.84798 11 0.077 13.% + LOOP_ions force_stress 0.50300 1 0.50 7.6% + Force_Stress_LCAO getForceStress 0.50297 1 0.50 7.6% + Force_LCAO_gamma ftable_gamma 0.29260 1 0.29 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:48 2022 + Finish Time : Wed Sep 28 11:09:55 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8bb2ad252d675c1d849366184eaf6b00b7d80071 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123766 ima = 3.6787e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123287906173 + charge after normalized = 8.00000000000004 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112490467628 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112948876454 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113174913128 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113126451501 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113157465807 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113147204968 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113150212205 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113149485969 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113149417693 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113149401109 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113149393154 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/STRU new file mode 100644 index 0000000000000000000000000000000000000000..959739812fa25b290e9a30f874cc1a70a52bb569 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.451077292284 11.444423360506 12.252998797373 0 0 0 +H +0.0 +2 +-13.263531613158 11.281523221155 10.451215167571 0 0 0 +-13.369332314595 9.765242725619 12.984541446247 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/conv new file mode 100644 index 0000000000000000000000000000000000000000..70696c11f83cd15c9f82a5df24cb2452d8b5067d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/conv @@ -0,0 +1 @@ +26 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f6f08537642d9bc6f7dab90f40d7eb19ba8389c3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745819846 0.01265437118 1.279255254 1.369930828 1.469208199 0.007968194026 0.01977273485 0.0389187995 +9.657638545e-19 0.001134549623 0.002461057126 0.01238151155 0.04383445095 -1.958763691e-20 1.698369995e-06 5.214073993e-06 +0.001733846802 0.005764332032 + +H atom_index 1 n_descriptor 18 +1.253654021 0.03371078532 0.1095084464 0.152535647 0.323516988 0.02210529002 0.02863677559 0.03691511759 +-5.774422365e-18 4.183475506e-05 0.1027672374 0.1150535252 0.1309929365 -4.544811376e-19 4.048732349e-06 0.01296864497 +0.02629859022 0.03099992079 + +H atom_index 2 n_descriptor 18 +1.242014467 0.03412029868 0.1055181129 0.1471555256 0.3198335346 0.02158798487 0.02796322004 0.03727484601 +2.080611307e-17 4.083338169e-05 0.09990374122 0.1145644617 0.1263465592 -3.577365492e-19 4.620562001e-06 0.01305272029 +0.02586744344 0.03047751897 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c72dc1067c7f9e702c79d7f07011218aefcbd9af Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0862808 SEC) : SETUP UNITCELL + DONE(0.0983554 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116613 SEC) : INIT PLANEWAVE + DONE(0.166178 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449364 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651984e+02 0.000000e+00 2.155e-01 4.893e-01 + GE2 -4.664088e+02 -1.210372e+00 9.789e-02 4.293e-01 + GE3 -4.664115e+02 -2.662088e-03 6.265e-02 4.941e-01 + GE4 -4.664116e+02 -1.252105e-04 2.063e-03 3.614e-01 + GE5 -4.664109e+02 7.547763e-04 8.314e-04 3.584e-01 + GE6 -4.664114e+02 -5.117410e-04 2.000e-04 3.535e-01 + GE7 -4.664112e+02 2.075055e-04 4.026e-05 3.426e-01 + GE8 -4.664112e+02 -7.438072e-05 1.750e-05 3.353e-01 + GE9 -4.664112e+02 2.012045e-05 2.281e-06 3.323e-01 + GE10 -4.664112e+02 -3.413545e-06 4.617e-07 3.345e-01 + GE11 -4.664112e+02 -2.982184e-07 1.611e-07 3.362e-01 + GE12 -4.664112e+02 -4.420597e-08 9.965e-09 2.680e-01 +E_delta_band = -7.06455273e-02 Ry = -9.61181710e-01 eV +E_delta_NN= -1.94851475e-01 Ry = -2.65109032e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6261 11 0.6 1e+02 % + Run_lcao lcao_line 6.6177 1 6.6 1e+02 % + Potential init_pot 0.28518 2 0.14 4.3 % + PW_Basis recip2real 0.28306 17 0.017 4.3 % + PW_Basis gathers_scatterp 0.13097 17 0.0077 2 % + Potential v_of_rho 1.0547 14 0.075 16 % + XC_Functional v_xc 0.31921 15 0.021 4.8 % + H_Hartree_pw v_hartree 0.69163 14 0.049 10 % + PW_Basis real2recip 0.70271 41 0.017 11 % + PW_Basis gatherp_scatters 0.30701 41 0.0075 4.6 % + ORB_control set_orb_tables 1.0866 1 1.1 16 % + ORB_gen_tables gen_tables 1.0866 1 1.1 16 % + ORB_table_phi init_Table 0.47146 1 0.47 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.46635 126 0.0037 7 % + ORB_table_beta init_Table_Beta 0.18221 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18067 56 0.0032 2.7 % + ORB_table_alpha init_Table_Alpha 0.24666 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.24477 66 0.0037 3.7 % + LOOP_ions opt_ions 5.0003 1 5 75 % + ESolver_KS_LCAO Run 4.4971 1 4.5 68 % + HSolverLCAO solve 2.0145 12 0.17 30 % + HamiltLCAO updateHk 1.0831 12 0.09 16 % + LCAO_Hamilt cal_Hgamma 1.0536 12 0.088 16 % + Gint_interface cal_gint 0.16032 25 0.0064 2.4 % + Gint_Gamma distri_vl_value 0.58605 12 0.049 8.8 % + Gint_Gamma distri_vl 2.3508 6 0.39 35 % + LCAO_Deepks cal_projected_DM 4.6637 14 0.33 70 % + LCAO_gen_fixedH add_v_delta 2.2063 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2063 6 0.37 33 % + ElecStateLCAO psiToRho 0.90692 12 0.076 14 % + Charge mix_rho 0.84798 11 0.077 13 % + LOOP_ions force_stress 0.503 1 0.5 7.6 % + Force_Stress_LCAO getForceStress 0.50297 1 0.5 7.6 % + Force_LCAO_gamma ftable_gamma 0.2926 1 0.29 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:48 2022 + FINISH Time : Wed Sep 28 11:09:55 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/26/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..7c5bf9e4488b5d9ce2690b4baa2237f11b5cfb95 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.506866 0.0633852 0.287331 +H 0.504653 0.100074 0.233324 +H 0.528597 0.999425 0.285867 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e1abda55c16f5d2a1b376e1e54d304dc47d1fe3e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.8101 2 + 2 -13.6354 2 + 3 -8.22008 2 + 4 -6.61224 2 + 5 1.08011 0 + 6 4.34583 0 + 7 11.1516 0 + 8 11.3178 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b216d9d4aa0705eda68c33651764ba48a321554f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:20 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.1922463118 1.77478630574 8.04528088163 0 0 0 0 + tauc_H1 14.1302916408 2.80207317744 6.53306330557 0 0 0 0 + tauc_H2 14.8007251326 27.9839046496 8.00427656994 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0876788738813 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101905494187 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.120914670613 (SEC) + + DONE : INIT CHARGE Time : 0.169463551225 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.452053 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 100 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00149 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000918 + + Density error is 0.216498299285 + + Energy Rydberg eV + E_KohnSham -34.1779001768 -465.01418808 + E_Harris -34.3721221817 -467.656714023 + E_Fermi -0.39174727721 -5.32999514604 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00135528114053 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118046112423 + + Density error is 0.0990149425189 + + Energy Rydberg eV + E_KohnSham -34.2666251261 -466.221352945 + E_Harris -34.2733286684 -466.312559317 + E_Fermi -0.199731161722 -2.71748186758 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00125511322569 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114536195492 + + Density error is 0.063511701042 + + Energy Rydberg eV + E_KohnSham -34.2667435612 -466.222964337 + E_Harris -34.2709705028 -466.280474828 + E_Fermi -0.189306067779 -2.57564118776 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107107944427 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110023298418 + + Density error is 0.0025095726325 + + Energy Rydberg eV + E_KohnSham -34.2667229303 -466.22268364 + E_Harris -34.2667356828 -466.222857146 + E_Fermi -0.15507943485 -2.10996395658 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106441134404 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109735446624 + + Density error is 0.000764546827622 + + Energy Rydberg eV + E_KohnSham -34.2666990512 -466.222358748 + E_Harris -34.2666991785 -466.222360479 + E_Fermi -0.154151760585 -2.09734230069 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106235547905 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109677535658 + + Density error is 0.000205693519819 + + Energy Rydberg eV + E_KohnSham -34.266721737 -466.222667404 + E_Harris -34.2667217898 -466.222668122 + E_Fermi -0.15401311662 -2.09545595277 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106215060978 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109700058918 + + Density error is 2.95728719839e-05 + + Energy Rydberg eV + E_KohnSham -34.26671336 -466.222553429 + E_Harris -34.2667133645 -466.22255349 + E_Fermi -0.15389703062 -2.09387652171 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106213688064 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109690764063 + + Density error is 1.50102718481e-05 + + Energy Rydberg eV + E_KohnSham -34.2667175843 -466.222610904 + E_Harris -34.2667175853 -466.222610917 + E_Fermi -0.153929200274 -2.09431421231 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106210816124 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109691021857 + + Density error is 2.05537007479e-06 + + Energy Rydberg eV + E_KohnSham -34.2667164477 -466.222595439 + E_Harris -34.2667164477 -466.222595439 + E_Fermi -0.153913743239 -2.09410390856 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0010621027041 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109691035826 + + Density error is 3.88582809414e-07 + + Energy Rydberg eV + E_KohnSham -34.2667166947 -466.2225988 + E_Harris -34.2667166947 -466.2225988 + E_Fermi -0.153912125661 -2.09408190028 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106210257294 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109691070212 + + Density error is 1.61614560068e-07 + + Energy Rydberg eV + E_KohnSham -34.2667166976 -466.222598839 + E_Harris -34.2667166976 -466.222598839 + E_Fermi -0.153911996592 -2.0940801442 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106210229452 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109691086009 + + Density error is 8.68767772698e-09 + + Energy Rydberg eV + E_KohnSham -34.2667166982 -466.222598848 + E_Harris -34.2667166982 -466.222598848 + E_band -7.83168344057 -106.555519724 + E_one_elec -68.8923977109 -937.32915775 + E_Hartree +35.8906023322 +488.31669637 + E_xc -8.18304629011 -111.336056543 + E_Ewald +7.04345626688 +95.8311388434 + E_demet -9.07519512149e-62 -1.23474364114e-60 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193371646413 -2.63095622286 + E_Fermi -0.153911845376 -2.09407808681 + + charge density convergence is achieved + final etot is -466.222598848 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.8101 2.00000 + 2 -13.6354 2.00000 + 3 -8.22008 2.00000 + 4 -6.61224 2.00000 + 5 1.08011 0.00000 + 6 4.34583 0.00000 + 7 11.1516 0.00000 + 8 11.3178 0.00000 + + EFERMI = -2.094078086809602 eV + OUT.ABACUS/ final etot is -466.2225988476914 eV + correction force for each atom along direction 1 is 0.000120860 + correction force for each atom along direction 2 is -6.71364e-05 + correction force for each atom along direction 3 is -1.65193e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.063384388 -0.72286939 +1.6632341 + H1 +0.40078519 -0.85759613 -0.61910591 + H2 -0.33740081 +1.5804655 -1.0441282 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2225988476914 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8523 11 0.53 1.0e+02% + Run_lcao lcao_line 5.8431 1 5.8 1.e+02% + Potential init_pot 0.28624 2 0.14 4.9% + PW_Basis recip2real 0.28237 17 0.017 4.8% + PW_Basis gathers_scatterp 0.11972 17 0.0070 2.0% + Potential v_of_rho 0.93332 14 0.067 16.% + XC_Functional v_xc 0.25080 15 0.017 4.3% + H_Hartree_pw v_hartree 0.64149 14 0.046 11.% + PW_Basis real2recip 0.60043 41 0.015 10.% + PW_Basis gatherp_scatters 0.23389 41 0.0057 4.0% + ORB_control set_orb_tables 1.1176 1 1.1 19.% + ORB_gen_tables gen_tables 1.1176 1 1.1 19.% + ORB_table_phi init_Table 0.48633 1 0.49 8.3% + ORB_table_phi cal_ST_Phi12_R 0.48143 126 0.0038 8.2% + ORB_table_beta init_Table_Beta 0.19036 1 0.19 3.3% + ORB_table_beta VNL_PhiBeta_R 0.18884 56 0.0034 3.2% + ORB_table_alpha init_Table_Alpha 0.25731 1 0.26 4.4% + ORB_table_alpha S_PhiAlpha_R 0.25539 66 0.0039 4.4% + LOOP_ions opt_ions 4.1966 1 4.2 72.% + ESolver_KS_LCAO Run 3.7413 1 3.7 64.% + HSolverLCAO solve 1.6050 12 0.13 27.% + HamiltLCAO updateHk 0.88450 12 0.074 15.% + LCAO_Hamilt cal_Hgamma 0.84719 12 0.071 14.% + Gint_interface cal_gint 1.0313 25 0.041 18.% + Gint_Gamma distri_vl_value 0.12916 12 0.011 2.2% + Gint_Gamma distri_vl 1.9593 6 0.33 33.% + LCAO_Deepks cal_projected_DM 4.0219 14 0.29 69.% + LCAO_gen_fixedH add_v_delta 1.8277 6 0.30 31.% + LCAO_DESCRIPTOR add_v_delta 1.8276 6 0.30 31.% + ElecStateLCAO psiToRho 0.70365 12 0.059 12.% + Charge mix_rho 0.71942 11 0.065 12.% + LOOP_ions force_stress 0.45510 1 0.46 7.8% + Force_Stress_LCAO getForceStress 0.45507 1 0.46 7.8% + Force_LCAO_gamma ftable_gamma 0.24282 1 0.24 4.1% + Force_LCAO_gamma cal_fvl_dphi 0.19289 1 0.19 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:20 2022 + Finish Time : Wed Sep 28 11:11:26 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6484d09bff9fb9deb2eaa77a2f169446816bb841 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123122 ima = 3.68534e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00125043648948 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114483669181 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114954330453 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00115099082222 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00115075742988 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00115092381993 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011508468232 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00115086888638 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00115086229886 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00115086214665 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00115086204782 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00115086196998 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d4762ccfc3752a914c900c8ea10800772fc0d56e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.807753688215 29.774786305720 8.045280881613 0 0 0 +H +0.0 +2 +-13.869708359209 30.802073177456 6.533063305560 0 0 0 +-13.199274867405 27.983904649550 8.004276569915 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/conv new file mode 100644 index 0000000000000000000000000000000000000000..6ce392f57e09c128eee08ca29c2c62ac0b70b4a4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/conv @@ -0,0 +1 @@ +260 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..12c3c9c8b1098f5b7fc6628c36b1b5417290a7b7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.731980849 0.01224479989 1.268619576 1.378138717 1.466956648 0.006210263147 0.02359583504 0.03849430897 +8.094852353e-18 0.001051542722 0.001805132828 0.01272877258 0.03374199591 -9.947343174e-20 7.649108236e-07 2.669636407e-06 +0.002130558726 0.004657881945 + +H atom_index 1 n_descriptor 18 +1.227668245 0.03334219538 0.1074672367 0.146892505 0.322317324 0.02111652634 0.02793007372 0.03659982671 +3.204019755e-17 2.008473258e-05 0.09951085277 0.1143159777 0.1256989122 6.562940753e-18 3.125286577e-06 0.01241737005 +0.02540393184 0.03035210905 + +H atom_index 2 n_descriptor 18 +1.176512021 0.03516937998 0.09153861696 0.1256593311 0.3055619636 0.01903342555 0.02502485607 0.03868499237 +-2.09292668e-17 1.778038896e-05 0.08568035602 0.1071124898 0.1132719688 -3.523679369e-20 3.935554808e-06 0.01357526204 +0.02334423589 0.02786340511 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c4e70aca52102ecbc166cd5c833b47fa06c086a1 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:20 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0877036 SEC) : SETUP UNITCELL + DONE(0.101925 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.120937 SEC) : INIT PLANEWAVE + DONE(0.169597 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.452126 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650142e+02 0.000000e+00 2.165e-01 4.234e-01 + GE2 -4.662214e+02 -1.207165e+00 9.901e-02 3.549e-01 + GE3 -4.662230e+02 -1.611393e-03 6.351e-02 4.098e-01 + GE4 -4.662227e+02 2.806976e-04 2.510e-03 2.976e-01 + GE5 -4.662224e+02 3.248916e-04 7.645e-04 3.015e-01 + GE6 -4.662227e+02 -3.086558e-04 2.057e-04 2.906e-01 + GE7 -4.662226e+02 1.139748e-04 2.957e-05 2.783e-01 + GE8 -4.662226e+02 -5.747453e-05 1.501e-05 2.791e-01 + GE9 -4.662226e+02 1.546444e-05 2.055e-06 2.765e-01 + GE10 -4.662226e+02 -3.360586e-06 3.886e-07 2.750e-01 + GE11 -4.662226e+02 -3.888124e-08 1.616e-07 2.761e-01 + GE12 -4.662226e+02 -9.083130e-09 8.688e-09 2.170e-01 +E_delta_band = -6.80403501e-02 Ry = -9.25736455e-01 eV +E_delta_NN= -1.93371646e-01 Ry = -2.63095622e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8523 11 0.53 1e+02 % + Run_lcao lcao_line 5.8431 1 5.8 1e+02 % + Potential init_pot 0.28624 2 0.14 4.9 % + PW_Basis recip2real 0.28237 17 0.017 4.8 % + PW_Basis gathers_scatterp 0.11972 17 0.007 2 % + Potential v_of_rho 0.93332 14 0.067 16 % + XC_Functional v_xc 0.2508 15 0.017 4.3 % + H_Hartree_pw v_hartree 0.64149 14 0.046 11 % + PW_Basis real2recip 0.60043 41 0.015 10 % + PW_Basis gatherp_scatters 0.23389 41 0.0057 4 % + ORB_control set_orb_tables 1.1176 1 1.1 19 % + ORB_gen_tables gen_tables 1.1176 1 1.1 19 % + ORB_table_phi init_Table 0.48633 1 0.49 8.3 % + ORB_table_phi cal_ST_Phi12_R 0.48143 126 0.0038 8.2 % + ORB_table_beta init_Table_Beta 0.19036 1 0.19 3.3 % + ORB_table_beta VNL_PhiBeta_R 0.18884 56 0.0034 3.2 % + ORB_table_alpha init_Table_Alpha 0.25731 1 0.26 4.4 % + ORB_table_alpha S_PhiAlpha_R 0.25539 66 0.0039 4.4 % + LOOP_ions opt_ions 4.1966 1 4.2 72 % + ESolver_KS_LCAO Run 3.7413 1 3.7 64 % + HSolverLCAO solve 1.605 12 0.13 27 % + HamiltLCAO updateHk 0.8845 12 0.074 15 % + LCAO_Hamilt cal_Hgamma 0.84719 12 0.071 14 % + Gint_interface cal_gint 1.0313 25 0.041 18 % + Gint_Gamma distri_vl_value 0.12916 12 0.011 2.2 % + Gint_Gamma distri_vl 1.9593 6 0.33 33 % + LCAO_Deepks cal_projected_DM 4.0219 14 0.29 69 % + LCAO_gen_fixedH add_v_delta 1.8277 6 0.3 31 % + LCAO_DESCRIPTOR add_v_delta 1.8276 6 0.3 31 % + ElecStateLCAO psiToRho 0.70365 12 0.059 12 % + Charge mix_rho 0.71942 11 0.065 12 % + LOOP_ions force_stress 0.4551 1 0.46 7.8 % + Force_Stress_LCAO getForceStress 0.45507 1 0.46 7.8 % + Force_LCAO_gamma ftable_gamma 0.24282 1 0.24 4.1 % + Force_LCAO_gamma cal_fvl_dphi 0.19289 1 0.19 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:20 2022 + FINISH Time : Wed Sep 28 11:11:26 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/260/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..58344209fda3238d739e2d252092dcd30ef13e20 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.515425 0.0747871 0.303868 +H 0.470106 0.0807794 0.260111 +H 0.539592 0.021233 0.277666 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ee37a6d44397a173b3c7b0d695cf44ce92fb8e9a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.8286 2 + 2 -12.7308 2 + 3 -9.69985 2 + 4 -6.85795 2 + 5 1.43775 0 + 6 4.82251 0 + 7 10.9874 0 + 8 11.2963 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1f5356100086269a9cfde1cb844530e90e15eaab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:53 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.4319045552 2.09403949711 8.50831005927 0 0 0 0 + tauc_H1 13.1629557646 2.26182441842 7.28311902248 0 0 0 0 + tauc_H2 15.1085885215 0.5945248672 7.77465236561 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0888038473665 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0952728718823 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.113478708528 (SEC) + + DONE : INIT CHARGE Time : 0.162993912348 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441645 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 337 ; sender_size of each process is: +144 144 49 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000576 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000932 + + Density error is 0.216218025324 + + Energy Rydberg eV + E_KohnSham -34.1800192556 -465.043019625 + E_Harris -34.3765033643 -467.716323071 + E_Fermi -0.426070864189 -5.79699150475 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000759591481815 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118893640613 + + Density error is 0.0967205279449 + + Energy Rydberg eV + E_KohnSham -34.2706427312 -466.276015267 + E_Harris -34.2774385877 -466.368477638 + E_Fermi -0.234694726597 -3.19318557227 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000780995045405 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112979173386 + + Density error is 0.0616936041992 + + Energy Rydberg eV + E_KohnSham -34.2708761317 -466.279190844 + E_Harris -34.2752304295 -466.338434104 + E_Fermi -0.220215004698 -2.99617884898 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000837981418605 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010495144135 + + Density error is 0.00210616632487 + + Energy Rydberg eV + E_KohnSham -34.2709219868 -466.279814734 + E_Harris -34.2709259363 -466.27986847 + E_Fermi -0.183865575975 -2.50161949932 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000844606038747 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105373150998 + + Density error is 0.000891898905582 + + Energy Rydberg eV + E_KohnSham -34.2708530943 -466.278877403 + E_Harris -34.2708552118 -466.278906214 + E_Fermi -0.182944663331 -2.48908984 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00084375246675 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105177371761 + + Density error is 0.000207280137929 + + Energy Rydberg eV + E_KohnSham -34.2709022534 -466.279546248 + E_Harris -34.2709022566 -466.27954629 + E_Fermi -0.183145536629 -2.49182286142 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000843472399217 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105187311196 + + Density error is 4.28856783876e-05 + + Energy Rydberg eV + E_KohnSham -34.2708824927 -466.279277389 + E_Harris -34.2708825014 -466.279277507 + E_Fermi -0.182951149876 -2.48917809397 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000843413856736 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105178574901 + + Density error is 2.16725947581e-05 + + Energy Rydberg eV + E_KohnSham -34.2708883271 -466.279356771 + E_Harris -34.2708883289 -466.279356795 + E_Fermi -0.183000932011 -2.48985541466 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000843425698779 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105177825274 + + Density error is 1.90341339654e-06 + + Energy Rydberg eV + E_KohnSham -34.2708867359 -466.27933512 + E_Harris -34.2708867359 -466.279335121 + E_Fermi -0.182976419976 -2.48952191131 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000843429557468 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105178134151 + + Density error is 4.81749688403e-07 + + Energy Rydberg eV + E_KohnSham -34.2708870171 -466.279338947 + E_Harris -34.2708870171 -466.279338947 + E_Fermi -0.182975153496 -2.48950467996 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000843430129153 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105178202908 + + Density error is 1.56269174171e-07 + + Energy Rydberg eV + E_KohnSham -34.2708870382 -466.279339234 + E_Harris -34.2708870382 -466.279339234 + E_Fermi -0.182974939856 -2.48950177324 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000843430200693 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105178215785 + + Density error is 1.1194175836e-08 + + Energy Rydberg eV + E_KohnSham -34.270887042 -466.279339286 + E_Harris -34.270887042 -466.279339286 + E_band -8.10207783952 -110.234424257 + E_one_elec -69.9470171424 -951.677991241 + E_Hartree +36.3309425085 +494.307831826 + E_xc -8.25619899153 -112.331350107 + E_Ewald +7.7243079186 +105.094600799 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196044440152 -2.66732144728 + E_Fermi -0.182974771381 -2.48949948102 + + charge density convergence is achieved + final etot is -466.279339286 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.8286 2.00000 + 2 -12.7308 2.00000 + 3 -9.69985 2.00000 + 4 -6.85795 2.00000 + 5 1.43775 0.00000 + 6 4.82251 0.00000 + 7 10.9874 0.00000 + 8 11.2963 0.00000 + + EFERMI = -2.489499481024444 eV + OUT.ABACUS/ final etot is -466.2793392859792 eV + correction force for each atom along direction 1 is -7.28041e-06 + correction force for each atom along direction 2 is -5.08568e-05 + correction force for each atom along direction 3 is -1.58771e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.83516217 +0.21192721 +1.1253334 + H1 -2.1076577 +1.0892752 -1.2388952 + H2 +1.2724956 -1.3012024 +0.11356183 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2793392859792 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8741 11 0.53 1.0e+02% + Run_lcao lcao_line 5.8634 1 5.9 1.e+02% + Potential init_pot 0.28448 2 0.14 4.8% + PW_Basis recip2real 0.28428 17 0.017 4.8% + PW_Basis gathers_scatterp 0.12184 17 0.0072 2.1% + Potential v_of_rho 0.94325 14 0.067 16.% + XC_Functional v_xc 0.26578 15 0.018 4.5% + H_Hartree_pw v_hartree 0.63766 14 0.046 11.% + PW_Basis real2recip 0.59725 41 0.015 10.% + PW_Basis gatherp_scatters 0.23346 41 0.0057 4.0% + ORB_control set_orb_tables 1.0976 1 1.1 19.% + ORB_gen_tables gen_tables 1.0976 1 1.1 19.% + ORB_table_phi init_Table 0.48157 1 0.48 8.2% + ORB_table_phi cal_ST_Phi12_R 0.47660 126 0.0038 8.1% + ORB_table_beta init_Table_Beta 0.18523 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18369 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25299 1 0.25 4.3% + ORB_table_alpha S_PhiAlpha_R 0.25112 66 0.0038 4.3% + LOOP_ions opt_ions 4.2488 1 4.2 72.% + ESolver_KS_LCAO Run 3.7848 1 3.8 64.% + HSolverLCAO solve 1.6406 12 0.14 28.% + HamiltLCAO updateHk 0.89504 12 0.075 15.% + LCAO_Hamilt cal_Hgamma 0.85993 12 0.072 15.% + Gint_interface cal_gint 0.90785 25 0.036 15.% + Gint_Gamma distri_vl_value 0.18402 12 0.015 3.1% + Gint_Gamma distri_vl 1.9899 6 0.33 34.% + LCAO_Deepks cal_projected_DM 4.0498 14 0.29 69.% + LCAO_gen_fixedH add_v_delta 1.8616 6 0.31 32.% + LCAO_DESCRIPTOR add_v_delta 1.8616 6 0.31 32.% + ElecStateLCAO psiToRho 0.72596 12 0.060 12.% + Charge mix_rho 0.71250 11 0.065 12.% + LOOP_ions force_stress 0.46387 1 0.46 7.9% + Force_Stress_LCAO getForceStress 0.46384 1 0.46 7.9% + Force_LCAO_gamma ftable_gamma 0.25245 1 0.25 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.17917 1 0.18 3.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:53 2022 + Finish Time : Wed Sep 28 11:07:59 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..50b0ac2c43310620169e309938a5691704232998 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124234 ima = 3.65792e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122008649206 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111018048943 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111486060558 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111804116338 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011173041637 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111773318224 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111762640763 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111765747114 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111764958105 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111764892763 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111764875453 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111764867414 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e3f1a491dcea74034317b4a7708403f6c0d33442 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.568095444846 30.094039497116 8.508310059257 0 0 0 +H +0.0 +2 +-14.837044235427 30.261824418438 7.283119022453 0 0 0 +-12.891411478472 28.594524867186 7.774652365599 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/conv new file mode 100644 index 0000000000000000000000000000000000000000..48f48f25e7e3cee81b6ebc883c71c341c544dd85 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/conv @@ -0,0 +1 @@ +261 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8cbeed6839723231adea72c9395ecefb6933ce5e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.757209122 0.01303205703 1.293581853 1.368166238 1.471357156 0.01049149318 0.01612159669 0.03922280626 +-5.539612649e-18 0.000901654988 0.003270434795 0.01535122953 0.05107623034 2.152090519e-19 4.093681312e-06 9.752381269e-06 +0.001611811842 0.006223911152 + +H atom_index 1 n_descriptor 18 +1.29882713 0.03398191533 0.135410768 0.1742585326 0.3335553036 0.02708020818 0.03107690662 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:53 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0888306 SEC) : SETUP UNITCELL + DONE(0.0952907 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.113502 SEC) : INIT PLANEWAVE + DONE(0.16312 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.441712 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650430e+02 0.000000e+00 2.162e-01 4.319e-01 + GE2 -4.662760e+02 -1.232996e+00 9.672e-02 3.592e-01 + GE3 -4.662792e+02 -3.175577e-03 6.169e-02 4.127e-01 + GE4 -4.662798e+02 -6.238898e-04 2.106e-03 2.997e-01 + GE5 -4.662789e+02 9.373307e-04 8.919e-04 3.022e-01 + GE6 -4.662795e+02 -6.688445e-04 2.073e-04 2.947e-01 + GE7 -4.662793e+02 2.688590e-04 4.289e-05 2.939e-01 + GE8 -4.662794e+02 -7.938204e-05 2.167e-05 2.769e-01 + GE9 -4.662793e+02 2.165023e-05 1.903e-06 2.771e-01 + GE10 -4.662793e+02 -3.826783e-06 4.817e-07 2.783e-01 + GE11 -4.662793e+02 -2.866378e-07 1.563e-07 2.778e-01 + GE12 -4.662793e+02 -5.213055e-08 1.119e-08 2.191e-01 +E_delta_band = -7.31231050e-02 Ry = -9.94890883e-01 eV +E_delta_NN= -1.96044440e-01 Ry = -2.66732145e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8741 11 0.53 1e+02 % + Run_lcao lcao_line 5.8634 1 5.9 1e+02 % + Potential init_pot 0.28448 2 0.14 4.8 % + PW_Basis recip2real 0.28428 17 0.017 4.8 % + PW_Basis gathers_scatterp 0.12184 17 0.0072 2.1 % + Potential v_of_rho 0.94325 14 0.067 16 % + XC_Functional v_xc 0.26578 15 0.018 4.5 % + H_Hartree_pw v_hartree 0.63766 14 0.046 11 % + PW_Basis real2recip 0.59725 41 0.015 10 % + PW_Basis gatherp_scatters 0.23346 41 0.0057 4 % + ORB_control set_orb_tables 1.0976 1 1.1 19 % + ORB_gen_tables gen_tables 1.0976 1 1.1 19 % + ORB_table_phi init_Table 0.48157 1 0.48 8.2 % + ORB_table_phi cal_ST_Phi12_R 0.4766 126 0.0038 8.1 % + ORB_table_beta init_Table_Beta 0.18523 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18369 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.25299 1 0.25 4.3 % + ORB_table_alpha S_PhiAlpha_R 0.25112 66 0.0038 4.3 % + LOOP_ions opt_ions 4.2488 1 4.2 72 % + ESolver_KS_LCAO Run 3.7848 1 3.8 64 % + HSolverLCAO solve 1.6406 12 0.14 28 % + HamiltLCAO updateHk 0.89504 12 0.075 15 % + LCAO_Hamilt cal_Hgamma 0.85993 12 0.072 15 % + Gint_interface cal_gint 0.90785 25 0.036 15 % + Gint_Gamma distri_vl_value 0.18402 12 0.015 3.1 % + Gint_Gamma distri_vl 1.9899 6 0.33 34 % + LCAO_Deepks cal_projected_DM 4.0498 14 0.29 69 % + LCAO_gen_fixedH add_v_delta 1.8616 6 0.31 32 % + LCAO_DESCRIPTOR add_v_delta 1.8616 6 0.31 32 % + ElecStateLCAO psiToRho 0.72596 12 0.06 12 % + Charge mix_rho 0.7125 11 0.065 12 % + LOOP_ions force_stress 0.46387 1 0.46 7.9 % + Force_Stress_LCAO getForceStress 0.46384 1 0.46 7.9 % + Force_LCAO_gamma ftable_gamma 0.25245 1 0.25 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.17917 1 0.18 3.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:53 2022 + FINISH Time : Wed Sep 28 11:07:59 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/261/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c63980a7969faba26e9958c0c450b69d0f739c71 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.538482 0.0852914 0.309798 +H 0.473312 0.0841584 0.321699 +H 0.566498 0.0261136 0.311495 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..96271ec8727e85016c54a1feba6c21fc72b7e156 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0397 2 + 2 -13.4168 2 + 3 -8.62743 2 + 4 -6.68007 2 + 5 1.24511 0 + 6 4.39626 0 + 7 11.1107 0 + 8 11.3161 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a5bda8f6b40fec5b9cc150a3ae5bf2a069de28ad --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:29 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.0774900028 2.38815819626 8.67434536727 0 0 0 0 + tauc_H1 13.2527320057 2.35643400491 9.00757309091 0 0 0 0 + tauc_H2 15.8619500826 0.731181746029 8.72185662149 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0724696726827 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0727478943154 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0889921362453 (SEC) + + DONE : INIT CHARGE Time : 0.130201748732 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374679 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00144 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000833 + + Density error is 0.216149215787 + + Energy Rydberg eV + E_KohnSham -34.1873170571 -465.142311309 + E_Harris -34.3807274594 -467.773794833 + E_Fermi -0.399106745485 -5.43012584883 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00131749679416 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909535180847 + + Density error is 0.0984910215406 + + Energy Rydberg eV + E_KohnSham -34.2770871054 -466.363695475 + E_Harris -34.2837800219 -466.454757277 + E_Fermi -0.206903459936 -2.81506599104 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122115270931 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000864697770565 + + Density error is 0.0632060525792 + + Energy Rydberg eV + E_KohnSham -34.2773541469 -466.367328762 + E_Harris -34.2816342955 -466.425563171 + E_Fermi -0.196228743677 -2.66982902539 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010536728265 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000788801933581 + + Density error is 0.0022058814668 + + Energy Rydberg eV + E_KohnSham -34.2773373104 -466.36709969 + E_Harris -34.2773435434 -466.367184494 + E_Fermi -0.16131699661 -2.19483033814 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105114563759 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785614831774 + + Density error is 0.000862847367382 + + Energy Rydberg eV + E_KohnSham -34.2772917573 -466.366479907 + E_Harris -34.2772922107 -466.366486077 + E_Fermi -0.160533448827 -2.18416962364 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104927346783 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784765899497 + + Density error is 0.000213564842647 + + Energy Rydberg eV + E_KohnSham -34.2773197395 -466.366860625 + E_Harris -34.2773197844 -466.366861237 + E_Fermi -0.160442630418 -2.18293397579 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104911961866 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00078482687212 + + Density error is 3.66385183494e-05 + + Energy Rydberg eV + E_KohnSham -34.277309264 -466.366718099 + E_Harris -34.277309271 -466.366718194 + E_Fermi -0.160300431466 -2.1809992598 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104909663103 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784785582307 + + Density error is 1.77482799816e-05 + + Energy Rydberg eV + E_KohnSham -34.2773140418 -466.366783103 + E_Harris -34.2773140432 -466.366783123 + E_Fermi -0.160339811672 -2.18153505498 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104907221673 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784774696518 + + Density error is 1.8058685488e-06 + + Energy Rydberg eV + E_KohnSham -34.2773126116 -466.366763645 + E_Harris -34.2773126116 -466.366763645 + E_Fermi -0.160321415557 -2.181284763 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104906854822 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784774175295 + + Density error is 4.59825658016e-07 + + Energy Rydberg eV + E_KohnSham -34.2773129034 -466.366767616 + E_Harris -34.2773129034 -466.366767616 + E_Fermi -0.160319954153 -2.18126487957 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104906834234 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784774597608 + + Density error is 1.50185407232e-07 + + Energy Rydberg eV + E_KohnSham -34.2773129116 -466.366767727 + E_Harris -34.2773129116 -466.366767727 + E_Fermi -0.160319733901 -2.18126188289 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010490680541 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000784774615259 + + Density error is 9.98507642721e-09 + + Energy Rydberg eV + E_KohnSham -34.2773129156 -466.366767781 + E_Harris -34.2773129156 -466.366767781 + E_band -7.90316430996 -107.528066846 + E_one_elec -69.113661146 -940.339601227 + E_Hartree +35.9755807676 +489.472887298 + E_xc -8.19835582442 -111.544353444 + E_Ewald +7.18391170768 +97.7421331534 + E_demet -1.5663188079e-71 -2.1310860672e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194181800248 -2.64197893127 + E_Fermi -0.160319589366 -2.1812599164 + + charge density convergence is achieved + final etot is -466.366767781 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0397 2.00000 + 2 -13.4168 2.00000 + 3 -8.62743 2.00000 + 4 -6.68007 2.00000 + 5 1.24511 0.00000 + 6 4.39626 0.00000 + 7 11.1107 0.00000 + 8 11.3161 0.00000 + + EFERMI = -2.181259916399982 eV + OUT.ABACUS/ final etot is -466.3667677812643 eV + correction force for each atom along direction 1 is -1.91933e-05 + correction force for each atom along direction 2 is -3.61797e-05 + correction force for each atom along direction 3 is 0.000168664 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.023022660 +0.94879443 -0.10449251 + H1 +0.55316093 -0.64422509 -0.030267743 + H2 -0.57618359 -0.30456934 +0.13476025 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3667677812643 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1524 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1453 1 6.1 1.e+02% + Potential init_pot 0.24167 2 0.12 3.9% + PW_Basis recip2real 0.24477 17 0.014 4.0% + PW_Basis gathers_scatterp 0.11248 17 0.0066 1.8% + Potential v_of_rho 0.94266 14 0.067 15.% + XC_Functional v_xc 0.29516 15 0.020 4.8% + H_Hartree_pw v_hartree 0.60737 14 0.043 9.9% + PW_Basis real2recip 0.63439 41 0.015 10.% + PW_Basis gatherp_scatters 0.24692 41 0.0060 4.0% + ORB_control set_orb_tables 0.89632 1 0.90 15.% + ORB_gen_tables gen_tables 0.89632 1 0.90 15.% + ORB_table_phi init_Table 0.37711 1 0.38 6.1% + ORB_table_phi cal_ST_Phi12_R 0.37280 126 0.0030 6.1% + ORB_table_beta init_Table_Beta 0.15284 1 0.15 2.5% + ORB_table_beta VNL_PhiBeta_R 0.15156 56 0.0027 2.5% + ORB_table_alpha init_Table_Alpha 0.20804 1 0.21 3.4% + ORB_table_alpha S_PhiAlpha_R 0.20632 66 0.0031 3.4% + LOOP_ions opt_ions 4.8046 1 4.8 78.% + ESolver_KS_LCAO Run 4.3273 1 4.3 70.% + HSolverLCAO solve 1.9687 12 0.16 32.% + HamiltLCAO updateHk 1.0565 12 0.088 17.% + LCAO_Hamilt cal_Hgamma 1.0313 12 0.086 17.% + Gint_interface cal_gint 0.79397 25 0.032 13.% + Gint_Gamma distri_vl_value 0.36607 12 0.031 6.0% + Gint_Gamma distri_vl 2.2668 6 0.38 37.% + LCAO_Deepks cal_projected_DM 4.5537 14 0.33 74.% + LCAO_gen_fixedH add_v_delta 2.1386 6 0.36 35.% + LCAO_DESCRIPTOR add_v_delta 2.1387 6 0.36 35.% + ElecStateLCAO psiToRho 0.89447 12 0.075 15.% + Charge mix_rho 0.82748 11 0.075 13.% + LOOP_ions force_stress 0.47708 1 0.48 7.8% + Force_Stress_LCAO getForceStress 0.47705 1 0.48 7.8% + Force_LCAO_gamma ftable_gamma 0.27888 1 0.28 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.15295 1 0.15 2.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:29 2022 + Finish Time : Wed Sep 28 11:11:35 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1ff8d0072d6d953c1ecc03eb7fe37a1bdfc55bf3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123427 ima = 3.65749e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124121505586 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113237651039 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113749767632 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113949494176 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113914766664 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113936141907 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113927855427 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113930676424 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113929877834 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113929841771 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113929823924 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113929816689 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/STRU new file mode 100644 index 0000000000000000000000000000000000000000..98c70a831d992160ccfd0a69ebe272504696d88d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.922509997192 30.388158196274 8.674345367253 0 0 0 +H +0.0 +2 +-14.747267994275 30.356434004919 9.007573090899 0 0 0 +-12.138049917405 28.731181746030 8.721856621482 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/conv new file mode 100644 index 0000000000000000000000000000000000000000..01e88669da006b74272a4d83582cd1902ceb00a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/conv @@ -0,0 +1 @@ +262 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e83a132a1958bc8d382907acf4f334f9cca5acef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.740479346 0.0124768571 1.272842239 1.370670143 1.468188974 0.00715403521 0.02126715174 0.03875803039 +7.889968403e-19 0.001120899717 0.002166719178 0.01221072585 0.03968653118 2.071480736e-19 1.178944967e-06 3.950014722e-06 +0.001884121502 0.005370886807 + +H atom_index 1 n_descriptor 18 +1.218215152 0.03444715356 0.09909265469 0.1386815506 0.3148487896 0.02035005228 0.02685781703 0.03767047478 +-2.047260923e-18 2.997111281e-05 0.09377299704 0.1140956821 0.1188306842 2.004762413e-18 4.857266683e-06 0.01308329037 +0.02470161109 0.02952710718 + +H atom_index 2 n_descriptor 18 +1.235362158 0.03383223286 0.1046390373 0.1461939386 0.3204224502 0.02107803097 0.02784520962 0.03704094535 +1.256951723e-17 3.114390754e-05 0.09837766852 0.1144428659 0.1253700108 -5.593047264e-18 4.297339264e-06 0.01280746124 +0.02536803807 0.0303375934 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..273624c5cdcdcc2463d31b9d5aa55a21d5985b86 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:29 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0724856 SEC) : SETUP UNITCELL + DONE(0.0727567 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0890046 SEC) : INIT PLANEWAVE + DONE(0.130305 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374732 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651423e+02 0.000000e+00 2.161e-01 4.538e-01 + GE2 -4.663637e+02 -1.221384e+00 9.849e-02 4.122e-01 + GE3 -4.663673e+02 -3.633286e-03 6.321e-02 4.734e-01 + GE4 -4.663671e+02 2.290719e-04 2.206e-03 3.478e-01 + GE5 -4.663665e+02 6.197825e-04 8.628e-04 3.476e-01 + GE6 -4.663669e+02 -3.807180e-04 2.136e-04 3.435e-01 + GE7 -4.663667e+02 1.425263e-04 3.664e-05 3.358e-01 + GE8 -4.663668e+02 -6.500436e-05 1.775e-05 3.219e-01 + GE9 -4.663668e+02 1.945837e-05 1.806e-06 3.265e-01 + GE10 -4.663668e+02 -3.970814e-06 4.598e-07 3.250e-01 + GE11 -4.663668e+02 -1.113652e-07 1.502e-07 3.269e-01 + GE12 -4.663668e+02 -5.407902e-08 9.985e-09 2.597e-01 +E_delta_band = -6.93933798e-02 Ry = -9.44145369e-01 eV +E_delta_NN= -1.94181800e-01 Ry = -2.64197893e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1524 11 0.56 1e+02 % + Run_lcao lcao_line 6.1453 1 6.1 1e+02 % + Potential init_pot 0.24167 2 0.12 3.9 % + PW_Basis recip2real 0.24477 17 0.014 4 % + PW_Basis gathers_scatterp 0.11248 17 0.0066 1.8 % + Potential v_of_rho 0.94266 14 0.067 15 % + XC_Functional v_xc 0.29516 15 0.02 4.8 % + H_Hartree_pw v_hartree 0.60737 14 0.043 9.9 % + PW_Basis real2recip 0.63439 41 0.015 10 % + PW_Basis gatherp_scatters 0.24692 41 0.006 4 % + ORB_control set_orb_tables 0.89632 1 0.9 15 % + ORB_gen_tables gen_tables 0.89632 1 0.9 15 % + ORB_table_phi init_Table 0.37711 1 0.38 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.3728 126 0.003 6.1 % + ORB_table_beta init_Table_Beta 0.15284 1 0.15 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.15156 56 0.0027 2.5 % + ORB_table_alpha init_Table_Alpha 0.20804 1 0.21 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.20632 66 0.0031 3.4 % + LOOP_ions opt_ions 4.8046 1 4.8 78 % + ESolver_KS_LCAO Run 4.3273 1 4.3 70 % + HSolverLCAO solve 1.9687 12 0.16 32 % + HamiltLCAO updateHk 1.0565 12 0.088 17 % + LCAO_Hamilt cal_Hgamma 1.0313 12 0.086 17 % + Gint_interface cal_gint 0.79397 25 0.032 13 % + Gint_Gamma distri_vl_value 0.36607 12 0.031 6 % + Gint_Gamma distri_vl 2.2668 6 0.38 37 % + LCAO_Deepks cal_projected_DM 4.5537 14 0.33 74 % + LCAO_gen_fixedH add_v_delta 2.1386 6 0.36 35 % + LCAO_DESCRIPTOR add_v_delta 2.1387 6 0.36 35 % + ElecStateLCAO psiToRho 0.89447 12 0.075 15 % + Charge mix_rho 0.82748 11 0.075 13 % + LOOP_ions force_stress 0.47708 1 0.48 7.8 % + Force_Stress_LCAO getForceStress 0.47705 1 0.48 7.8 % + Force_LCAO_gamma ftable_gamma 0.27888 1 0.28 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.15295 1 0.15 2.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:29 2022 + FINISH Time : Wed Sep 28 11:11:35 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/262/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..bbcc6eb204a28272e6484143f0080aa9e2e8d94b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.564548 0.0950282 0.312676 +H 0.522724 0.0595484 0.34792 +H 0.565675 0.0602712 0.257827 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bb15d810ba1563388c5870cfddb8bb6aefa38748 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.445 2 + 2 -12.9067 2 + 3 -9.33349 2 + 4 -6.78028 2 + 5 1.34249 0 + 6 4.50702 0 + 7 11.0507 0 + 8 11.3238 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3b59b59a25a60d79c9f56a11754f12afe785a41c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:57 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.8073499853 2.6607894342 8.75491519983 0 0 0 0 + tauc_H1 14.6362597807 1.66735542712 9.74176558309 0 0 0 0 + tauc_H2 15.8389129771 1.6875922691 7.21914815844 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0729886280249 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0733087982898 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0891598385003 (SEC) + + DONE : INIT CHARGE Time : 0.132385329158 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.376021 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00131 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000794 + + Density error is 0.214786756798 + + Energy Rydberg eV + E_KohnSham -34.1902445351 -465.18214169 + E_Harris -34.3821444195 -467.793073565 + E_Fermi -0.41034619271 -5.58304637346 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00137126931425 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110529341405 + + Density error is 0.0975799386443 + + Energy Rydberg eV + E_KohnSham -34.2798359608 -466.401095572 + E_Harris -34.2865956492 -466.493065851 + E_Fermi -0.219567119137 -2.98736391371 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00128870301931 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106380807573 + + Density error is 0.0625355341204 + + Energy Rydberg eV + E_KohnSham -34.2801276967 -466.405064843 + E_Harris -34.284502085 -466.464581449 + E_Fermi -0.207732663668 -2.8263478866 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116035912023 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101665855321 + + Density error is 0.00195827939754 + + Energy Rydberg eV + E_KohnSham -34.2801263696 -466.405046787 + E_Harris -34.2801271076 -466.405056827 + E_Fermi -0.171931652412 -2.33925013935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116196713956 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102006438598 + + Density error is 0.000914169356213 + + Energy Rydberg eV + E_KohnSham -34.2800590982 -466.404131513 + E_Harris -34.280061111 -466.404158897 + E_Fermi -0.171126628229 -2.32829722344 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116007247063 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101868147992 + + Density error is 9.37491877613e-05 + + Energy Rydberg eV + E_KohnSham -34.2801058031 -466.404766965 + E_Harris -34.2801058059 -466.404767004 + E_Fermi -0.171213404744 -2.3294778785 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115987011212 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101863109645 + + Density error is 3.96456598636e-05 + + Energy Rydberg eV + E_KohnSham -34.2800911796 -466.404568002 + E_Harris -34.2800911879 -466.404568114 + E_Fermi -0.171100888803 -2.32794702059 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011598570001 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101857317811 + + Density error is 8.90389484164e-06 + + Energy Rydberg eV + E_KohnSham -34.2800930602 -466.404593588 + E_Harris -34.2800930605 -466.404593593 + E_Fermi -0.171147424702 -2.32858017397 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011598572407 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101858358053 + + Density error is 4.08756222201e-07 + + Energy Rydberg eV + E_KohnSham -34.280091895 -466.404577736 + E_Harris -34.280091895 -466.404577736 + E_Fermi -0.171137784948 -2.3284490184 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115985562788 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101858358799 + + Density error is 1.02842974261e-07 + + Energy Rydberg eV + E_KohnSham -34.2800920897 -466.404580385 + E_Harris -34.2800920897 -466.404580385 + E_Fermi -0.17113747896 -2.32844485521 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115985550681 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101858359062 + + Density error is 2.77298619779e-08 + + Energy Rydberg eV + E_KohnSham -34.2800920926 -466.404580425 + E_Harris -34.2800920926 -466.404580424 + E_band -8.00626830735 -108.930868697 + E_one_elec -69.459046153 -945.038805325 + E_Hartree +36.1117589491 +491.32568651 + E_xc -8.22117203354 -111.854783894 + E_Ewald +7.41231718218 +100.849749061 + E_demet -1.03412304242e-81 -1.406996581e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195151255665 -2.6551690489 + E_Fermi -0.171137573602 -2.32844614288 + + charge density convergence is achieved + final etot is -466.404580425 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4450 2.00000 + 2 -12.9067 2.00000 + 3 -9.33349 2.00000 + 4 -6.78028 2.00000 + 5 1.34249 0.00000 + 6 4.50702 0.00000 + 7 11.0507 0.00000 + 8 11.3238 0.00000 + + EFERMI = -2.328446142883593 eV + OUT.ABACUS/ final etot is -466.4045804245089 eV + correction force for each atom along direction 1 is -0.000176906 + correction force for each atom along direction 2 is -0.000153203 + correction force for each atom along direction 3 is -3.02207e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.094015819 +0.28421764 +0.22095694 + H1 -0.34557397 -0.092842746 +0.59732874 + H2 +0.25155815 -0.19137489 -0.81828568 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4045804245089 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9807 11 0.54 1.0e+02% + Run_lcao lcao_line 5.9735 1 6.0 1.e+02% + Potential init_pot 0.24193 2 0.12 4.0% + PW_Basis recip2real 0.23350 16 0.015 3.9% + PW_Basis gathers_scatterp 0.10322 16 0.0065 1.7% + Potential v_of_rho 0.86225 13 0.066 14.% + XC_Functional v_xc 0.25734 14 0.018 4.3% + H_Hartree_pw v_hartree 0.56989 13 0.044 9.5% + PW_Basis real2recip 0.59028 38 0.016 9.9% + PW_Basis gatherp_scatters 0.22511 38 0.0059 3.8% + ORB_control set_orb_tables 0.90198 1 0.90 15.% + ORB_gen_tables gen_tables 0.90198 1 0.90 15.% + ORB_table_phi init_Table 0.37894 1 0.38 6.3% + ORB_table_phi cal_ST_Phi12_R 0.37457 126 0.0030 6.3% + ORB_table_beta init_Table_Beta 0.15499 1 0.15 2.6% + ORB_table_beta VNL_PhiBeta_R 0.15367 56 0.0027 2.6% + ORB_table_alpha init_Table_Alpha 0.20936 1 0.21 3.5% + ORB_table_alpha S_PhiAlpha_R 0.20771 66 0.0031 3.5% + LOOP_ions opt_ions 4.6247 1 4.6 77.% + ESolver_KS_LCAO Run 4.1257 1 4.1 69.% + HSolverLCAO solve 1.9858 11 0.18 33.% + HamiltLCAO updateHk 1.0525 11 0.096 18.% + LCAO_Hamilt cal_Hgamma 1.0290 11 0.094 17.% + Gint_interface cal_gint 0.96464 23 0.042 16.% + Gint_Gamma distri_vl_value 0.31040 11 0.028 5.2% + Gint_Gamma distri_vl 1.9874 6 0.33 33.% + LCAO_Deepks cal_projected_DM 4.3718 13 0.34 73.% + LCAO_gen_fixedH add_v_delta 1.8567 6 0.31 31.% + LCAO_DESCRIPTOR add_v_delta 1.8565 6 0.31 31.% + ElecStateLCAO psiToRho 0.91635 11 0.083 15.% + Charge mix_rho 0.76405 10 0.076 13.% + LOOP_ions force_stress 0.49885 1 0.50 8.3% + Force_Stress_LCAO getForceStress 0.49883 1 0.50 8.3% + Force_LCAO_gamma ftable_gamma 0.30752 1 0.31 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.18261 1 0.18 3.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:57 2022 + Finish Time : Wed Sep 28 11:12:03 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1b49693346908ad5caf5878431b6b97c89863572 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123623 ima = 3.68204e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122670361884 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111597179349 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112136536051 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112402529295 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112337185463 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112373935655 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112371557471 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112374032405 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112373553617 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112373552672 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112373557208 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/STRU new file mode 100644 index 0000000000000000000000000000000000000000..84a6f3b89188c5a9abd8e46d44f12c875e01de99 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.192650014695 30.660789434209 8.754915199854 0 0 0 +H +0.0 +2 +-13.363740219284 29.667355427128 9.741765583098 0 0 0 +-12.161087022836 29.687592269114 7.219148158437 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/conv new file mode 100644 index 0000000000000000000000000000000000000000..abef17c5d42da5fc6874804b03904522b6f806c3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/conv @@ -0,0 +1 @@ +263 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e94fc661873c84038777986b28c0cfa541ac6f53 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752411006 0.01281036142 1.278129142 1.360923357 1.469920747 0.009167329424 0.01751945324 0.03911135746 +-4.65579489e-18 0.0009964858029 0.002811526221 0.01313488037 0.04717813819 8.630193397e-20 2.640798323e-06 7.078725973e-06 +0.00160498241 0.006115054827 + +H atom_index 1 n_descriptor 18 +1.254538523 0.03450168155 0.1116011662 0.151677117 0.3213655675 0.02310174324 0.02851164023 0.03762516287 +1.351842914e-17 5.087644912e-05 0.1041210245 0.1154831951 0.1302018147 -8.143598507e-18 3.321924113e-06 0.01331087317 +0.02705866668 0.03095415265 + +H atom_index 2 n_descriptor 18 +1.260054259 0.03431614866 0.1135892431 0.1542993562 0.323138997 0.02336984551 0.02883352211 0.03746803304 +-1.157572986e-17 5.14085188e-05 0.105213789 0.1159947887 0.132456081 3.165297923e-18 3.004295287e-06 0.01329125278 +0.02725787655 0.03119857892 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f31407f43533c0f78800e5bd71a4d4a0ea2bd971 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..b3e6d1048f7d60db3b813e5a70db5bcefac519b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:57 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0730048 SEC) : SETUP UNITCELL + DONE(0.0733192 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0891741 SEC) : INIT PLANEWAVE + DONE(0.132487 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.376064 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651821e+02 0.000000e+00 2.148e-01 4.567e-01 + GE2 -4.664011e+02 -1.218954e+00 9.758e-02 4.217e-01 + GE3 -4.664051e+02 -3.969271e-03 6.254e-02 4.878e-01 + GE4 -4.664050e+02 1.805648e-05 1.958e-03 3.584e-01 + GE5 -4.664041e+02 9.152739e-04 9.142e-04 3.593e-01 + GE6 -4.664048e+02 -6.354526e-04 9.375e-05 3.483e-01 + GE7 -4.664046e+02 1.989629e-04 3.965e-05 3.357e-01 + GE8 -4.664046e+02 -2.558592e-05 8.904e-06 3.444e-01 + GE9 -4.664046e+02 1.585260e-05 4.088e-07 3.401e-01 + GE10 -4.664046e+02 -2.648722e-06 1.028e-07 3.434e-01 + GE11 -4.664046e+02 -4.000460e-08 2.773e-08 2.759e-01 +E_delta_band = -7.12012183e-02 Ry = -9.68742273e-01 eV +E_delta_NN= -1.95151256e-01 Ry = -2.65516905e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9807 11 0.54 1e+02 % + Run_lcao lcao_line 5.9735 1 6 1e+02 % + Potential init_pot 0.24193 2 0.12 4 % + PW_Basis recip2real 0.2335 16 0.015 3.9 % + PW_Basis gathers_scatterp 0.10322 16 0.0065 1.7 % + Potential v_of_rho 0.86225 13 0.066 14 % + XC_Functional v_xc 0.25734 14 0.018 4.3 % + H_Hartree_pw v_hartree 0.56989 13 0.044 9.5 % + PW_Basis real2recip 0.59028 38 0.016 9.9 % + PW_Basis gatherp_scatters 0.22511 38 0.0059 3.8 % + ORB_control set_orb_tables 0.90198 1 0.9 15 % + ORB_gen_tables gen_tables 0.90198 1 0.9 15 % + ORB_table_phi init_Table 0.37894 1 0.38 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.37457 126 0.003 6.3 % + ORB_table_beta init_Table_Beta 0.15499 1 0.15 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.15367 56 0.0027 2.6 % + ORB_table_alpha init_Table_Alpha 0.20936 1 0.21 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.20771 66 0.0031 3.5 % + LOOP_ions opt_ions 4.6247 1 4.6 77 % + ESolver_KS_LCAO Run 4.1257 1 4.1 69 % + HSolverLCAO solve 1.9858 11 0.18 33 % + HamiltLCAO updateHk 1.0525 11 0.096 18 % + LCAO_Hamilt cal_Hgamma 1.029 11 0.094 17 % + Gint_interface cal_gint 0.96464 23 0.042 16 % + Gint_Gamma distri_vl_value 0.3104 11 0.028 5.2 % + Gint_Gamma distri_vl 1.9874 6 0.33 33 % + LCAO_Deepks cal_projected_DM 4.3718 13 0.34 73 % + LCAO_gen_fixedH add_v_delta 1.8567 6 0.31 31 % + LCAO_DESCRIPTOR add_v_delta 1.8565 6 0.31 31 % + ElecStateLCAO psiToRho 0.91635 11 0.083 15 % + Charge mix_rho 0.76405 10 0.076 13 % + LOOP_ions force_stress 0.49885 1 0.5 8.3 % + Force_Stress_LCAO getForceStress 0.49883 1 0.5 8.3 % + Force_LCAO_gamma ftable_gamma 0.30752 1 0.31 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.18261 1 0.18 3.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:57 2022 + FINISH Time : Wed Sep 28 11:12:03 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/263/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d3157d8e2e938961a8724e4c31b8de08f02dde69 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.592799 0.0946339 0.315024 +H 0.60483 0.047399 0.356471 +H 0.572759 0.0629435 0.259211 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9b556d84e7ccc19a09a501efdad8ee468e50db65 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.278 2 + 2 -13.0338 2 + 3 -9.10845 2 + 4 -6.74056 2 + 5 1.25749 0 + 6 4.41537 0 + 7 11.0778 0 + 8 11.3231 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..22e8d62ead78d5d35030cb6159bcc573806e429d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:43 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.5983735958 2.64974803942 8.82066035776 0 0 0 0 + tauc_H1 16.935235329 1.32717066052 9.98118139974 0 0 0 0 + tauc_H2 16.0372550649 1.76241819978 7.25791110191 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0732836107988 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0874069787874 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.10316312518 (SEC) + + DONE : INIT CHARGE Time : 0.14440889302 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.38687 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000996 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000922 + + Density error is 0.214428564249 + + Energy Rydberg eV + E_KohnSham -34.1900797079 -465.179899102 + E_Harris -34.3810240946 -467.777830762 + E_Fermi -0.404184615479 -5.49921381445 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00130361066536 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122494543552 + + Density error is 0.0979692468514 + + Energy Rydberg eV + E_KohnSham -34.2790806021 -466.39081839 + E_Harris -34.28584026 -466.482788254 + E_Fermi -0.214077966701 -2.91268016338 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00125106359192 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117785192868 + + Density error is 0.0628178542569 + + Energy Rydberg eV + E_KohnSham -34.2793373698 -466.394311893 + E_Harris -34.2837012961 -466.453686156 + E_Fermi -0.202913179136 -2.76077543555 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118249792635 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111841990886 + + Density error is 0.00199553264817 + + Energy Rydberg eV + E_KohnSham -34.2793219249 -466.394101756 + E_Harris -34.2793234214 -466.394122116 + E_Fermi -0.167382928475 -2.27736157519 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118466867296 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111911245539 + + Density error is 0.000843798044373 + + Energy Rydberg eV + E_KohnSham -34.279269759 -466.393392002 + E_Harris -34.2792706029 -466.393403484 + E_Fermi -0.166723839024 -2.26839420316 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118351275649 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111813737171 + + Density error is 0.000166050232678 + + Energy Rydberg eV + E_KohnSham -34.2793024412 -466.393836666 + E_Harris -34.2793025004 -466.393837471 + E_Fermi -0.166666048023 -2.26760791625 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118378284779 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111845785081 + + Density error is 4.0337082677e-05 + + Energy Rydberg eV + E_KohnSham -34.2792899785 -466.393667102 + E_Harris -34.2792899869 -466.393667216 + E_Fermi -0.166549072079 -2.26601637688 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118369811862 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111833822266 + + Density error is 1.54958377297e-05 + + Energy Rydberg eV + E_KohnSham -34.2792945031 -466.393728662 + E_Harris -34.279294504 -466.393728675 + E_Fermi -0.166587770607 -2.26654289737 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118369677906 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111833580466 + + Density error is 2.51367319948e-06 + + Energy Rydberg eV + E_KohnSham -34.2792931029 -466.393709612 + E_Harris -34.2792931029 -466.393709612 + E_Fermi -0.166572344788 -2.26633301834 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118369487735 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111833914142 + + Density error is 4.35090869926e-07 + + Energy Rydberg eV + E_KohnSham -34.2792932802 -466.393712024 + E_Harris -34.2792932802 -466.393712024 + E_Fermi -0.166570002041 -2.26630114363 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118369587539 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111833987831 + + Density error is 1.55448248022e-07 + + Energy Rydberg eV + E_KohnSham -34.2792933181 -466.39371254 + E_Harris -34.2792933181 -466.39371254 + E_Fermi -0.166569837181 -2.26629890059 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118369611986 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111834006425 + + Density error is 1.10347756585e-08 + + Energy Rydberg eV + E_KohnSham -34.2792933208 -466.393712576 + E_Harris -34.2792933208 -466.393712576 + E_band -7.96148622908 -108.321577264 + E_one_elec -69.2579275408 -942.302446226 + E_Hartree +36.0244709173 +490.13807191 + E_xc -8.20733839545 -111.666567592 + E_Ewald +7.28590609365 +99.1298379665 + E_demet -1.67392926857e-75 -2.27749761015e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194773849099 -2.65003416914 + E_Fermi -0.166569688966 -2.26629688403 + + charge density convergence is achieved + final etot is -466.393712576 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2780 2.00000 + 2 -13.0338 2.00000 + 3 -9.10845 2.00000 + 4 -6.74056 2.00000 + 5 1.25749 0.00000 + 6 4.41537 0.00000 + 7 11.0778 0.00000 + 8 11.3231 0.00000 + + EFERMI = -2.266296884030422 eV + OUT.ABACUS/ final etot is -466.3937125757163 eV + correction force for each atom along direction 1 is 0.000102082 + correction force for each atom along direction 2 is -0.000134322 + correction force for each atom along direction 3 is -7.32269e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.57154386 +0.65563229 -1.7983071 + H1 +0.28327298 -1.1189101 +0.98640633 + H2 +0.28827088 +0.46327778 +0.81190074 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3937125757163 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8005 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7935 1 6.8 1.e+02% + Potential init_pot 0.24378 2 0.12 3.6% + PW_Basis recip2real 0.24260 17 0.014 3.6% + PW_Basis gathers_scatterp 0.11586 17 0.0068 1.7% + Potential v_of_rho 0.94664 14 0.068 14.% + XC_Functional v_xc 0.30284 15 0.020 4.5% + H_Hartree_pw v_hartree 0.60827 14 0.043 8.9% + PW_Basis real2recip 0.64109 41 0.016 9.4% + PW_Basis gatherp_scatters 0.26358 41 0.0064 3.9% + ORB_control set_orb_tables 0.89502 1 0.90 13.% + ORB_gen_tables gen_tables 0.89501 1 0.90 13.% + ORB_table_phi init_Table 0.37329 1 0.37 5.5% + ORB_table_phi cal_ST_Phi12_R 0.36894 126 0.0029 5.4% + ORB_table_beta init_Table_Beta 0.15401 1 0.15 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15272 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.21037 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20866 66 0.0032 3.1% + LOOP_ions opt_ions 5.4426 1 5.4 80.% + ESolver_KS_LCAO Run 4.8942 1 4.9 72.% + HSolverLCAO solve 2.5305 12 0.21 37.% + HamiltLCAO updateHk 1.2951 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2700 12 0.11 19.% + Gint_interface cal_gint 1.1736 25 0.047 17.% + Gint_Gamma distri_vl_value 0.45263 12 0.038 6.7% + Gint_Gamma distri_vl 2.5471 6 0.42 37.% + LCAO_Deepks cal_projected_DM 5.1572 14 0.37 76.% + LCAO_gen_fixedH add_v_delta 2.4180 6 0.40 36.% + LCAO_DESCRIPTOR add_v_delta 2.4180 6 0.40 36.% + ElecStateLCAO psiToRho 1.2174 12 0.10 18.% + Charge mix_rho 0.82145 11 0.075 12.% + LOOP_ions force_stress 0.54827 1 0.55 8.1% + Force_Stress_LCAO getForceStress 0.54824 1 0.55 8.1% + Force_LCAO_gamma ftable_gamma 0.35005 1 0.35 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.20150 1 0.20 3.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:43 2022 + Finish Time : Wed Sep 28 11:03:50 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4a2cff59cdd2c277eee35f44849a95606bd054de --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123593 ima = 3.67432e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123152930149 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112204369547 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011274776203 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011298356333 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112940938987 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112967421508 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011295928265 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112962223369 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011296164666 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112961541482 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112961526752 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112961518971 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/STRU new file mode 100644 index 0000000000000000000000000000000000000000..6a9c1a06dc5b55e11b89980f8a50fd0cdd1b067c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.401626404150 30.649748039418 8.820660357775 0 0 0 +H +0.0 +2 +-11.064764671027 29.327170660503 9.981181399738 0 0 0 +-11.962744935093 29.762418199791 7.257911101883 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/conv new file mode 100644 index 0000000000000000000000000000000000000000..fe79bc910f6cc7d5952744c86b4b326a1bef9cf6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/conv @@ -0,0 +1 @@ +264 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..13bd531bb4003dbc29745a5aa763a6ef16735d13 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749258859 0.01264392852 1.268327706 1.364283316 1.469309002 0.008508701627 0.01859509575 0.03904196936 +-4.990561088e-19 0.001043689185 0.002584973883 0.01229781224 0.04488269293 -3.000275458e-19 1.964607891e-06 5.807840839e-06 +0.001642387404 0.005911261924 + +H atom_index 1 n_descriptor 18 +1.278623545 0.03325942146 0.1185388553 0.1639352505 0.330014646 0.02350994674 0.02997927217 0.03669999144 +-4.478557671e-17 4.758912995e-05 0.1067315916 0.1178655171 0.1406901026 7.4733582e-18 2.550645073e-06 0.01320768798 +0.02723239073 0.03198240751 + +H atom_index 2 n_descriptor 18 +1.20647072 0.03570054922 0.09403030197 0.1309891816 0.3062620765 0.02017849565 0.02578284672 0.03899799568 +-1.601653827e-17 4.10316335e-05 0.09007302482 0.1121841284 0.1135538107 -8.823331266e-18 6.135419307e-06 0.01392970197 +0.02451681317 0.02864775907 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d2109d153c755a9ddf8734dcc8e3387f365ea27f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:43 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.073299 SEC) : SETUP UNITCELL + DONE(0.0874203 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103175 SEC) : INIT PLANEWAVE + DONE(0.144505 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.386914 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651799e+02 0.000000e+00 2.144e-01 4.915e-01 + GE2 -4.663908e+02 -1.210919e+00 9.797e-02 4.552e-01 + GE3 -4.663943e+02 -3.493503e-03 6.282e-02 5.169e-01 + GE4 -4.663941e+02 2.101375e-04 1.996e-03 3.963e-01 + GE5 -4.663934e+02 7.097538e-04 8.438e-04 3.954e-01 + GE6 -4.663938e+02 -4.446639e-04 1.661e-04 3.923e-01 + GE7 -4.663937e+02 1.695632e-04 4.034e-05 3.812e-01 + GE8 -4.663937e+02 -6.155974e-05 1.550e-05 3.767e-01 + GE9 -4.663937e+02 1.905041e-05 2.514e-06 3.766e-01 + GE10 -4.663937e+02 -2.412237e-06 4.351e-07 3.770e-01 + GE11 -4.663937e+02 -5.156994e-07 1.554e-07 3.735e-01 + GE12 -4.663937e+02 -3.605787e-08 1.103e-08 3.085e-01 +E_delta_band = -7.03694537e-02 Ry = -9.57425535e-01 eV +E_delta_NN= -1.94773849e-01 Ry = -2.65003417e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8005 11 0.62 1e+02 % + Run_lcao lcao_line 6.7935 1 6.8 1e+02 % + Potential init_pot 0.24378 2 0.12 3.6 % + PW_Basis recip2real 0.2426 17 0.014 3.6 % + PW_Basis gathers_scatterp 0.11586 17 0.0068 1.7 % + Potential v_of_rho 0.94664 14 0.068 14 % + XC_Functional v_xc 0.30284 15 0.02 4.5 % + H_Hartree_pw v_hartree 0.60827 14 0.043 8.9 % + PW_Basis real2recip 0.64109 41 0.016 9.4 % + PW_Basis gatherp_scatters 0.26358 41 0.0064 3.9 % + ORB_control set_orb_tables 0.89502 1 0.9 13 % + ORB_gen_tables gen_tables 0.89501 1 0.9 13 % + ORB_table_phi init_Table 0.37329 1 0.37 5.5 % + ORB_table_phi cal_ST_Phi12_R 0.36894 126 0.0029 5.4 % + ORB_table_beta init_Table_Beta 0.15401 1 0.15 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15272 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.21037 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20866 66 0.0032 3.1 % + LOOP_ions opt_ions 5.4426 1 5.4 80 % + ESolver_KS_LCAO Run 4.8942 1 4.9 72 % + HSolverLCAO solve 2.5305 12 0.21 37 % + HamiltLCAO updateHk 1.2951 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.27 12 0.11 19 % + Gint_interface cal_gint 1.1736 25 0.047 17 % + Gint_Gamma distri_vl_value 0.45263 12 0.038 6.7 % + Gint_Gamma distri_vl 2.5471 6 0.42 37 % + LCAO_Deepks cal_projected_DM 5.1572 14 0.37 76 % + LCAO_gen_fixedH add_v_delta 2.418 6 0.4 36 % + LCAO_DESCRIPTOR add_v_delta 2.418 6 0.4 36 % + ElecStateLCAO psiToRho 1.2174 12 0.1 18 % + Charge mix_rho 0.82145 11 0.075 12 % + LOOP_ions force_stress 0.54827 1 0.55 8.1 % + Force_Stress_LCAO getForceStress 0.54824 1 0.55 8.1 % + Force_LCAO_gamma ftable_gamma 0.35005 1 0.35 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.2015 1 0.2 3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:43 2022 + FINISH Time : Wed Sep 28 11:03:50 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/264/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..123b490f0977fa1a6a90242fb843e97837d3a901 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.609741 0.101531 0.319092 +H 0.665166 0.0661267 0.305336 +H 0.565915 0.0555034 0.314162 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..10ed832c1c5dca579314292305fdadad529c6c64 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3964 2 + 2 -12.8344 2 + 3 -9.33919 2 + 4 -6.76787 2 + 5 1.24899 0 + 6 4.432 0 + 7 11.064 0 + 8 11.3295 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fa66e4d884bacf26607d6a10c93a94993598e8fd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:12 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.0727393524 2.84285776467 8.93457069754 0 0 0 0 + tauc_H1 18.6246488418 1.85154645953 8.54941446408 0 0 0 0 + tauc_H2 15.845631583 1.55409638694 8.79652849732 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874381706109 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.087835221911 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106199508362 (SEC) + + DONE : INIT CHARGE Time : 0.15462851218 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.430099 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013 + + Density error is 0.214282427197 + + Energy Rydberg eV + E_KohnSham -34.1878914798 -465.150126732 + E_Harris -34.379208643 -467.753130275 + E_Fermi -0.407136845567 -5.53938096546 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118705283978 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124506174505 + + Density error is 0.0978104385497 + + Energy Rydberg eV + E_KohnSham -34.2776610917 -466.37150496 + E_Harris -34.2845050519 -466.464621816 + E_Fermi -0.216950712439 -2.95176587433 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110627148623 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115503543949 + + Density error is 0.0628199851594 + + Energy Rydberg eV + E_KohnSham -34.2779928446 -466.376018689 + E_Harris -34.2824252179 -466.436324222 + E_Fermi -0.206126731595 -2.80449805981 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00097606949615 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100108092291 + + Density error is 0.00194482689249 + + Energy Rydberg eV + E_KohnSham -34.2779720121 -466.375735249 + E_Harris -34.2779725464 -466.375742518 + E_Fermi -0.170239928631 -2.31623305649 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000977349111526 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010012301489 + + Density error is 0.000916673895333 + + Energy Rydberg eV + E_KohnSham -34.277912448 -466.374924837 + E_Harris -34.2779136892 -466.374941726 + E_Fermi -0.169695611794 -2.30882724599 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000975548856551 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999200818098 + + Density error is 0.000112185169798 + + Energy Rydberg eV + E_KohnSham -34.2779494173 -466.375427831 + E_Harris -34.2779494341 -466.375428059 + E_Fermi -0.169611466061 -2.30768238456 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000975487155154 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999080607296 + + Density error is 4.03697660768e-05 + + Energy Rydberg eV + E_KohnSham -34.277937202 -466.375261633 + E_Harris -34.2779372108 -466.375261753 + E_Fermi -0.169509909896 -2.30630064206 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000975476773612 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999049068779 + + Density error is 1.43086886778e-05 + + Energy Rydberg eV + E_KohnSham -34.2779402772 -466.375303474 + E_Harris -34.277940278 -466.375303485 + E_Fermi -0.169550670831 -2.30685522302 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000975469166893 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999034859771 + + Density error is 2.88442769948e-06 + + Energy Rydberg eV + E_KohnSham -34.2779388962 -466.375284684 + E_Harris -34.2779388962 -466.375284684 + E_Fermi -0.169537254586 -2.30667268565 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000975464665658 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999032233979 + + Density error is 1.15132054443e-07 + + Energy Rydberg eV + E_KohnSham -34.2779390402 -466.375286644 + E_Harris -34.2779390402 -466.375286644 + E_Fermi -0.169534174571 -2.30663077989 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00097546498818 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999032591925 + + Density error is 4.66700085327e-08 + + Energy Rydberg eV + E_KohnSham -34.2779390998 -466.375287454 + E_Harris -34.2779390998 -466.375287454 + E_band -7.98751041544 -108.675654484 + E_one_elec -69.3315208317 -943.303734317 + E_Hartree +36.0510977865 +490.500349051 + E_xc -8.21165414028 -111.725286313 + E_Ewald +7.33836543511 +99.8435839237 + E_demet -7.97739372721e-77 -1.0853800988e-75 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194965600589 -2.652643082 + E_Fermi -0.169534177057 -2.30663081371 + + charge density convergence is achieved + final etot is -466.375287454 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3964 2.00000 + 2 -12.8344 2.00000 + 3 -9.33919 2.00000 + 4 -6.76787 2.00000 + 5 1.24899 0.00000 + 6 4.43200 0.00000 + 7 11.0640 0.00000 + 8 11.3295 0.00000 + + EFERMI = -2.306630813711582 eV + OUT.ABACUS/ final etot is -466.3752874542195 eV + correction force for each atom along direction 1 is -6.51870e-06 + correction force for each atom along direction 2 is -7.37465e-05 + correction force for each atom along direction 3 is 0.000127499 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +2.0174481 +0.36927350 -0.13945500 + H1 -0.47879292 +0.72167735 +0.20398130 + H2 -1.5386552 -1.0909508 -0.064526306 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3752874542195 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4154 11 0.58 1.0e+02% + Run_lcao lcao_line 6.4059 1 6.4 1.e+02% + Potential init_pot 0.28073 2 0.14 4.4% + PW_Basis recip2real 0.25831 16 0.016 4.0% + PW_Basis gathers_scatterp 0.11724 16 0.0073 1.8% + Potential v_of_rho 0.85658 13 0.066 13.% + XC_Functional v_xc 0.24918 14 0.018 3.9% + H_Hartree_pw v_hartree 0.57348 13 0.044 8.9% + PW_Basis real2recip 0.54779 38 0.014 8.5% + PW_Basis gatherp_scatters 0.21633 38 0.0057 3.4% + ORB_control set_orb_tables 1.1053 1 1.1 17.% + ORB_gen_tables gen_tables 1.1053 1 1.1 17.% + ORB_table_phi init_Table 0.48567 1 0.49 7.6% + ORB_table_phi cal_ST_Phi12_R 0.48079 126 0.0038 7.5% + ORB_table_beta init_Table_Beta 0.18578 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18431 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25316 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25127 66 0.0038 3.9% + LOOP_ions opt_ions 4.7880 1 4.8 75.% + ESolver_KS_LCAO Run 4.2273 1 4.2 66.% + HSolverLCAO solve 2.2721 11 0.21 35.% + HamiltLCAO updateHk 1.1834 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1551 11 0.11 18.% + Gint_interface cal_gint 0.94987 23 0.041 15.% + Gint_Gamma distri_vl_value 0.44166 11 0.040 6.9% + Gint_Gamma distri_vl 2.0334 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.4746 13 0.34 70.% + LCAO_gen_fixedH add_v_delta 1.9011 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9011 6 0.32 30.% + ElecStateLCAO psiToRho 1.0720 11 0.097 17.% + Charge mix_rho 0.65482 10 0.065 10.% + LOOP_ions force_stress 0.56048 1 0.56 8.7% + Force_Stress_LCAO getForceStress 0.56045 1 0.56 8.7% + Force_LCAO_gamma ftable_gamma 0.35093 1 0.35 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.19511 1 0.20 3.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:12 2022 + Finish Time : Wed Sep 28 11:03:19 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..689a11e1aca669355583d552645fffa7bac93e1f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123558 ima = 3.67177e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122866606366 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111702913188 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112296051833 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112555822901 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112503831192 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112533224321 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112528460382 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112531407335 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112530866743 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112530719713 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112530714546 + charge after normalized = 7.99999999999997 + charge before normalized = 7.99999999999997 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5ce9f713d116d49f48844d2973ec446fda7ec515 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.927260647614 30.842857764650 8.934570697556 0 0 0 +H +0.0 +2 +-9.375351158215 29.851546459525 8.549414464078 0 0 0 +-12.154368416996 29.554096386937 8.796528497339 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/conv new file mode 100644 index 0000000000000000000000000000000000000000..16a6062a9befa14513e6159108f5999e63df11df --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/conv @@ -0,0 +1 @@ +265 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c8daa642ef6160525d1feb93df418d03b8bb5c27 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752846489 0.01273606985 1.268032345 1.360593354 1.469755039 0.009221547956 0.01736825667 0.03914526774 +2.493039536e-19 0.0009585501544 0.002785765143 0.01290786614 0.04663269008 -3.26700486e-19 2.524310984e-06 6.923427406e-06 +0.001588639035 0.006071210378 + +H atom_index 1 n_descriptor 18 +1.21079398 0.03598499911 0.09682788036 0.132259048 0.3062813084 0.02094421939 0.02594503789 0.03924079596 +2.721262216e-17 4.555306462e-05 0.09251901423 0.1132587013 0.113556658 -7.700340977e-18 5.563939788e-06 0.0140343945 +0.02520018047 0.02881723474 + +H atom_index 2 n_descriptor 18 +1.286662452 0.03348475809 0.1235296936 0.1675604683 0.331322775 0.02462359187 0.03037395114 0.03696580877 +-3.746233308e-17 5.272817869e-05 0.1077476215 0.12048647 0.1437020208 -3.540481434e-18 1.524723968e-06 0.01348099706 +0.02800580935 0.03227937696 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..232d21f4158626ed78e42f39d0384b0d998349bc Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..363d38be34fd931357de179f7025295826d0a46b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..d8a1b0e478a2add832ec56ad7d5da7ceedd291e6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..c09e625a80d7591ab406dae325240f1084cddd40 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:12 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874607 SEC) : SETUP UNITCELL + DONE(0.0878634 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106218 SEC) : INIT PLANEWAVE + DONE(0.15476 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.430175 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651501e+02 0.000000e+00 2.143e-01 4.990e-01 + GE2 -4.663715e+02 -1.221378e+00 9.781e-02 4.254e-01 + GE3 -4.663760e+02 -4.513730e-03 6.282e-02 4.836e-01 + GE4 -4.663757e+02 2.834400e-04 1.945e-03 3.673e-01 + GE5 -4.663749e+02 8.104120e-04 9.167e-04 3.671e-01 + GE6 -4.663754e+02 -5.029934e-04 1.122e-04 3.599e-01 + GE7 -4.663753e+02 1.661979e-04 4.037e-05 3.484e-01 + GE8 -4.663753e+02 -4.184104e-05 1.431e-05 3.437e-01 + GE9 -4.663753e+02 1.879038e-05 2.884e-06 3.428e-01 + GE10 -4.663753e+02 -1.960381e-06 1.151e-07 3.431e-01 + GE11 -4.663753e+02 -8.102292e-07 4.667e-08 2.857e-01 +E_delta_band = -7.07382512e-02 Ry = -9.62443283e-01 eV +E_delta_NN= -1.94965601e-01 Ry = -2.65264308e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4154 11 0.58 1e+02 % + Run_lcao lcao_line 6.4059 1 6.4 1e+02 % + Potential init_pot 0.28073 2 0.14 4.4 % + PW_Basis recip2real 0.25831 16 0.016 4 % + PW_Basis gathers_scatterp 0.11724 16 0.0073 1.8 % + Potential v_of_rho 0.85658 13 0.066 13 % + XC_Functional v_xc 0.24918 14 0.018 3.9 % + H_Hartree_pw v_hartree 0.57348 13 0.044 8.9 % + PW_Basis real2recip 0.54779 38 0.014 8.5 % + PW_Basis gatherp_scatters 0.21633 38 0.0057 3.4 % + ORB_control set_orb_tables 1.1053 1 1.1 17 % + ORB_gen_tables gen_tables 1.1053 1 1.1 17 % + ORB_table_phi init_Table 0.48567 1 0.49 7.6 % + ORB_table_phi cal_ST_Phi12_R 0.48079 126 0.0038 7.5 % + ORB_table_beta init_Table_Beta 0.18578 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18431 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.25316 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25127 66 0.0038 3.9 % + LOOP_ions opt_ions 4.788 1 4.8 75 % + ESolver_KS_LCAO Run 4.2273 1 4.2 66 % + HSolverLCAO solve 2.2721 11 0.21 35 % + HamiltLCAO updateHk 1.1834 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1551 11 0.11 18 % + Gint_interface cal_gint 0.94987 23 0.041 15 % + Gint_Gamma distri_vl_value 0.44166 11 0.04 6.9 % + Gint_Gamma distri_vl 2.0334 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.4746 13 0.34 70 % + LCAO_gen_fixedH add_v_delta 1.9011 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9011 6 0.32 30 % + ElecStateLCAO psiToRho 1.072 11 0.097 17 % + Charge mix_rho 0.65482 10 0.065 10 % + LOOP_ions force_stress 0.56048 1 0.56 8.7 % + Force_Stress_LCAO getForceStress 0.56045 1 0.56 8.7 % + Force_LCAO_gamma ftable_gamma 0.35093 1 0.35 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.19511 1 0.2 3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:12 2022 + FINISH Time : Wed Sep 28 11:03:19 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/265/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e46af68172069777abd6d2850237128d9ce802a7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.610746 0.0930377 0.332678 +H 0.665754 0.127831 0.33519 +H 0.609966 0.0581043 0.389853 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..26e547c0a32ab8d0180e274b8f17d6ad3d89f4fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1805 2 + 2 -12.9955 2 + 3 -9.06747 2 + 4 -6.71992 2 + 5 1.21485 0 + 6 4.29092 0 + 7 11.0991 0 + 8 11.3463 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..05cdd44a2a0c496e0f3c66fac2f1efb4edf14882 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:13 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.1009005303 2.60505449026 9.31499703685 0 0 0 0 + tauc_H1 18.6411089826 3.57926414416 9.38533176583 0 0 0 0 + tauc_H2 17.0790521926 1.62692162547 10.9158794207 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.073991336332 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0742735781464 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0905931421366 (SEC) + + DONE : INIT CHARGE Time : 0.131926083309 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.373664 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000613 + + Density error is 0.213964194404 + + Energy Rydberg eV + E_KohnSham -34.1912480322 -465.195794969 + E_Harris -34.380947648 -467.776790653 + E_Fermi -0.399569527842 -5.43642232582 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120837375495 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856493790354 + + Density error is 0.098337054853 + + Energy Rydberg eV + E_KohnSham -34.2805110296 -466.410280354 + E_Harris -34.2873519344 -466.50335564 + E_Fermi -0.208660219209 -2.83896792717 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114775974127 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000828706278448 + + Density error is 0.063203840822 + + Energy Rydberg eV + E_KohnSham -34.2808368215 -466.41471298 + E_Harris -34.285253527 -466.474805342 + E_Fermi -0.198966116769 -2.70707289699 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105368344324 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802247885368 + + Density error is 0.0019934581251 + + Energy Rydberg eV + E_KohnSham -34.2807976056 -466.414179421 + E_Harris -34.2807994328 -466.414204282 + E_Fermi -0.163556282338 -2.2252973835 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105277982078 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802342775174 + + Density error is 0.000898348370838 + + Energy Rydberg eV + E_KohnSham -34.2807470305 -466.413491312 + E_Harris -34.2807477467 -466.413501056 + E_Fermi -0.163057559016 -2.2185119046 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105148846063 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000801918007838 + + Density error is 0.000173448991793 + + Energy Rydberg eV + E_KohnSham -34.280776037 -466.413885965 + E_Harris -34.2807760872 -466.413886649 + E_Fermi -0.162889005206 -2.21621861236 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010517000486 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802194624287 + + Density error is 3.5212443124e-05 + + Energy Rydberg eV + E_KohnSham -34.2807652042 -466.413738578 + E_Harris -34.28076521 -466.413738656 + E_Fermi -0.162796972838 -2.21496644774 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105161842974 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802113271475 + + Density error is 1.62007460721e-05 + + Energy Rydberg eV + E_KohnSham -34.2807693698 -466.413795253 + E_Harris -34.2807693708 -466.413795267 + E_Fermi -0.16283042795 -2.2154216279 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105161064687 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802119413152 + + Density error is 2.52128681735e-06 + + Energy Rydberg eV + E_KohnSham -34.2807680582 -466.413777409 + E_Harris -34.2807680583 -466.413777409 + E_Fermi -0.162814374752 -2.21520321294 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105161021821 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802121813862 + + Density error is 4.75506008459e-07 + + Energy Rydberg eV + E_KohnSham -34.2807682748 -466.413780354 + E_Harris -34.2807682748 -466.413780354 + E_Fermi -0.162811933835 -2.21517000256 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010516107758 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802122436288 + + Density error is 1.671471463e-07 + + Energy Rydberg eV + E_KohnSham -34.2807683037 -466.413780749 + E_Harris -34.2807683037 -466.413780749 + E_Fermi -0.162811734445 -2.21516728971 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105161084697 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802122653397 + + Density error is 1.04113110764e-08 + + Energy Rydberg eV + E_KohnSham -34.280768307 -466.413780793 + E_Harris -34.280768307 -466.413780793 + E_band -7.93247069016 -107.926800604 + E_one_elec -69.0901546718 -940.019779238 + E_Hartree +35.9466914423 +489.079827864 + E_xc -8.19460664042 -111.493343178 + E_Ewald +7.18205491384 +97.7168701771 + E_demet -1.11748343481e-71 -1.52041421341e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194428642064 -2.64533738647 + E_Fermi -0.162811573473 -2.21516509958 + + charge density convergence is achieved + final etot is -466.413780793 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1805 2.00000 + 2 -12.9955 2.00000 + 3 -9.06747 2.00000 + 4 -6.71992 2.00000 + 5 1.21485 0.00000 + 6 4.29092 0.00000 + 7 11.0991 0.00000 + 8 11.3463 0.00000 + + EFERMI = -2.215165099579139 eV + OUT.ABACUS/ final etot is -466.4137807926658 eV + correction force for each atom along direction 1 is -3.05354e-06 + correction force for each atom along direction 2 is 5.43881e-05 + correction force for each atom along direction 3 is 0.000149362 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.52978752 -0.71619589 +0.62093298 + H1 +0.46577518 +0.25891837 +0.074158360 + H2 +0.064012337 +0.45727752 -0.69509134 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4137807926658 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2483 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2411 1 7.2 1.e+02% + Potential init_pot 0.24025 2 0.12 3.3% + PW_Basis recip2real 0.23449 17 0.014 3.2% + PW_Basis gathers_scatterp 0.10866 17 0.0064 1.5% + Potential v_of_rho 0.94779 14 0.068 13.% + XC_Functional v_xc 0.31241 15 0.021 4.3% + H_Hartree_pw v_hartree 0.60404 14 0.043 8.3% + PW_Basis real2recip 0.65502 41 0.016 9.0% + PW_Basis gatherp_scatters 0.29721 41 0.0072 4.1% + ORB_control set_orb_tables 0.90054 1 0.90 12.% + ORB_gen_tables gen_tables 0.90054 1 0.90 12.% + ORB_table_phi init_Table 0.37580 1 0.38 5.2% + ORB_table_phi cal_ST_Phi12_R 0.37156 126 0.0029 5.1% + ORB_table_beta init_Table_Beta 0.15672 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15540 56 0.0028 2.1% + ORB_table_alpha init_Table_Alpha 0.21084 1 0.21 2.9% + ORB_table_alpha S_PhiAlpha_R 0.20916 66 0.0032 2.9% + LOOP_ions opt_ions 5.8974 1 5.9 81.% + ESolver_KS_LCAO Run 5.3532 1 5.4 74.% + HSolverLCAO solve 3.0382 12 0.25 42.% + HamiltLCAO updateHk 1.5196 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.4943 12 0.12 21.% + Gint_interface cal_gint 0.84461 25 0.034 12.% + Gint_Gamma distri_vl_value 0.78016 12 0.065 11.% + Gint_Gamma distri_vl 2.7797 6 0.46 38.% + LCAO_Deepks cal_projected_DM 5.5493 14 0.40 77.% + LCAO_gen_fixedH add_v_delta 2.6510 6 0.44 37.% + LCAO_DESCRIPTOR add_v_delta 2.6511 6 0.44 37.% + ElecStateLCAO psiToRho 1.4947 12 0.12 21.% + Charge mix_rho 0.80617 11 0.073 11.% + LOOP_ions force_stress 0.54407 1 0.54 7.5% + Force_Stress_LCAO getForceStress 0.54406 1 0.54 7.5% + Force_LCAO_gamma ftable_gamma 0.35676 1 0.36 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.16122 1 0.16 2.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:13 2022 + Finish Time : Wed Sep 28 11:11:20 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..25908661702fdf1fd8acdafeb55e31f2cd290871 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123589 ima = 3.69064e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123342548094 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112185010678 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112795064988 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011302115335 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112983571729 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113007047605 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112999510733 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113002155369 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113001496223 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113001410122 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113001393135 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001130013847 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d5eaa37f47d02287f70179df308275053b1b9dfd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.899099469671 30.605054490240 9.314997036872 0 0 0 +H +0.0 +2 +-9.358891017415 31.579264144136 9.385331765828 0 0 0 +-10.920947807357 29.626921625448 10.915879420728 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/conv new file mode 100644 index 0000000000000000000000000000000000000000..9eabc3c01b4fa89cc0d12001d4d5cfeec88831fd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/conv @@ -0,0 +1 @@ +266 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7c5e5036f7d9ff66a856271e743777f39d0725b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74874662 0.01259848756 1.264524034 1.357017811 1.468842066 0.008345742635 0.01858296808 0.03902165645 +-1.756474034e-18 0.00101729887 0.002506547903 0.01207523943 0.0437259286 6.811427435e-19 1.826726839e-06 5.479122266e-06 +0.001654425281 0.005893879392 + +H atom_index 1 n_descriptor 18 +1.252708061 0.03408645652 0.1088901471 0.1515198162 0.3224770109 0.02219989583 0.02850657473 0.03729302957 +3.248371321e-17 4.324387537e-05 0.101411095 0.1152182335 0.1300114244 -3.998813715e-18 3.952824705e-06 0.01310190509 +0.0261342559 0.0308986818 + +H atom_index 2 n_descriptor 18 +1.21121306 0.03550516429 0.09527024972 0.1331221169 0.308366468 0.02029070937 0.02608430825 0.03878394833 +-6.029586357e-18 3.959118868e-05 0.09065563599 0.1138483252 0.114005116 7.256553851e-18 5.859978608e-06 0.01376926276 +0.02452055022 0.02889864273 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c5d1c656f269655f954d2ca5ce792ccb92343b89 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:13 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0740066 SEC) : SETUP UNITCELL + DONE(0.0742817 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0906074 SEC) : INIT PLANEWAVE + DONE(0.132027 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.373712 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651958e+02 0.000000e+00 2.140e-01 5.277e-01 + GE2 -4.664103e+02 -1.214485e+00 9.834e-02 4.941e-01 + GE3 -4.664147e+02 -4.432626e-03 6.320e-02 5.581e-01 + GE4 -4.664142e+02 5.335589e-04 1.993e-03 4.342e-01 + GE5 -4.664135e+02 6.881098e-04 8.983e-04 4.313e-01 + GE6 -4.664139e+02 -3.946530e-04 1.734e-04 4.268e-01 + GE7 -4.664137e+02 1.473870e-04 3.521e-05 4.217e-01 + GE8 -4.664138e+02 -5.667532e-05 1.620e-05 4.140e-01 + GE9 -4.664138e+02 1.784444e-05 2.521e-06 4.143e-01 + GE10 -4.664138e+02 -2.945904e-06 4.755e-07 4.150e-01 + GE11 -4.664138e+02 -3.941057e-07 1.671e-07 4.161e-01 + GE12 -4.664138e+02 -4.412979e-08 1.041e-08 3.473e-01 +E_delta_band = -6.96752911e-02 Ry = -9.47980969e-01 eV +E_delta_NN= -1.94428642e-01 Ry = -2.64533739e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2483 11 0.66 1e+02 % + Run_lcao lcao_line 7.2411 1 7.2 1e+02 % + Potential init_pot 0.24025 2 0.12 3.3 % + PW_Basis recip2real 0.23449 17 0.014 3.2 % + PW_Basis gathers_scatterp 0.10866 17 0.0064 1.5 % + Potential v_of_rho 0.94779 14 0.068 13 % + XC_Functional v_xc 0.31241 15 0.021 4.3 % + H_Hartree_pw v_hartree 0.60404 14 0.043 8.3 % + PW_Basis real2recip 0.65502 41 0.016 9 % + PW_Basis gatherp_scatters 0.29721 41 0.0072 4.1 % + ORB_control set_orb_tables 0.90054 1 0.9 12 % + ORB_gen_tables gen_tables 0.90054 1 0.9 12 % + ORB_table_phi init_Table 0.3758 1 0.38 5.2 % + ORB_table_phi cal_ST_Phi12_R 0.37156 126 0.0029 5.1 % + ORB_table_beta init_Table_Beta 0.15672 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.1554 56 0.0028 2.1 % + ORB_table_alpha init_Table_Alpha 0.21084 1 0.21 2.9 % + ORB_table_alpha S_PhiAlpha_R 0.20916 66 0.0032 2.9 % + LOOP_ions opt_ions 5.8974 1 5.9 81 % + ESolver_KS_LCAO Run 5.3532 1 5.4 74 % + HSolverLCAO solve 3.0382 12 0.25 42 % + HamiltLCAO updateHk 1.5196 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.4943 12 0.12 21 % + Gint_interface cal_gint 0.84461 25 0.034 12 % + Gint_Gamma distri_vl_value 0.78016 12 0.065 11 % + Gint_Gamma distri_vl 2.7797 6 0.46 38 % + LCAO_Deepks cal_projected_DM 5.5493 14 0.4 77 % + LCAO_gen_fixedH add_v_delta 2.651 6 0.44 37 % + LCAO_DESCRIPTOR add_v_delta 2.6511 6 0.44 37 % + ElecStateLCAO psiToRho 1.4947 12 0.12 21 % + Charge mix_rho 0.80617 11 0.073 11 % + LOOP_ions force_stress 0.54407 1 0.54 7.5 % + Force_Stress_LCAO getForceStress 0.54406 1 0.54 7.5 % + Force_LCAO_gamma ftable_gamma 0.35676 1 0.36 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.16122 1 0.16 2.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:13 2022 + FINISH Time : Wed Sep 28 11:11:20 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/266/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3d08be5e8fd65ec252256a40a2674d49a779bed5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.61377 0.0918599 0.343569 +H 0.578427 0.135414 0.31478 +H 0.571671 0.071608 0.386398 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..829b226605850ee7b2654ca4271f8f3186a4a030 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.8109 2 + 2 -13.1102 2 + 3 -9.44177 2 + 4 -6.85688 2 + 5 1.57883 0 + 6 4.97284 0 + 7 10.9687 0 + 8 11.2436 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..dbdd43b634b6f98459199149cbc6edff83a34a1a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:36 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.1855552499 2.5720785532 9.61991898034 0 0 0 0 + tauc_H1 16.1959560782 3.79160181475 8.81384854651 0 0 0 0 + tauc_H2 16.0067940234 2.00502501024 10.8191555189 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0727821679751 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0730454377547 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0893239471119 (SEC) + + DONE : INIT CHARGE Time : 0.130534041553 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375536 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000834 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121 + + Density error is 0.21862149753 + + Energy Rydberg eV + E_KohnSham -34.1812447419 -465.059693222 + E_Harris -34.382033643 -467.791566373 + E_Fermi -0.432138122188 -5.87954078477 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119139601637 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117066338534 + + Density error is 0.0968609057114 + + Energy Rydberg eV + E_KohnSham -34.2731095091 -466.309577502 + E_Harris -34.2797925353 -466.400504739 + E_Fermi -0.238185930564 -3.2406858391 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113488929453 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109173889932 + + Density error is 0.0616334147361 + + Energy Rydberg eV + E_KohnSham -34.2733350868 -466.312646644 + E_Harris -34.2775714721 -466.370285622 + E_Fermi -0.222161659423 -3.02266444529 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105506247975 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972765026747 + + Density error is 0.00211934950426 + + Energy Rydberg eV + E_KohnSham -34.2734115414 -466.313686862 + E_Harris -34.27341522 -466.313736911 + E_Fermi -0.185996463159 -2.53061170681 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105972966862 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000974180317368 + + Density error is 0.000928496407052 + + Energy Rydberg eV + E_KohnSham -34.2733283003 -466.312554308 + E_Harris -34.2733314519 -466.312597189 + E_Fermi -0.184632355872 -2.51205207503 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105782098767 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972747856353 + + Density error is 0.000158758469014 + + Energy Rydberg eV + E_KohnSham -34.2733876771 -466.313362171 + E_Harris -34.2733877695 -466.313363428 + E_Fermi -0.185059949957 -2.51786979101 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105769254861 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972677400253 + + Density error is 4.53228686812e-05 + + Energy Rydberg eV + E_KohnSham -34.2733664974 -466.313074006 + E_Harris -34.2733665082 -466.313074154 + E_Fermi -0.184872225789 -2.51531567268 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105763195768 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972673581387 + + Density error is 2.60214161972e-05 + + Energy Rydberg eV + E_KohnSham -34.2733710054 -466.313135342 + E_Harris -34.273371008 -466.313135377 + E_Fermi -0.184936754496 -2.51619363078 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105762262634 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972651282134 + + Density error is 1.53710719365e-06 + + Energy Rydberg eV + E_KohnSham -34.2733692432 -466.313111365 + E_Harris -34.2733692432 -466.313111365 + E_Fermi -0.184906418221 -2.51578088457 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105762455485 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972649511618 + + Density error is 1.69547468017e-07 + + Energy Rydberg eV + E_KohnSham -34.2733696019 -466.313116245 + E_Harris -34.2733696019 -466.313116245 + E_Fermi -0.184905285557 -2.51576547389 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105762534989 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972650134809 + + Density error is 4.77067723485e-08 + + Energy Rydberg eV + E_KohnSham -34.2733696259 -466.313116573 + E_Harris -34.2733696259 -466.313116573 + E_band -8.11715793286 -110.439599453 + E_one_elec -70.1300608404 -954.168428516 + E_Hartree +36.4253646933 +495.592511556 + E_xc -8.27201111393 -112.546485069 + E_Ewald +7.82591497374 +106.477035706 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196442187038 -2.6727330713 + E_Fermi -0.184905346481 -2.51576630281 + + charge density convergence is achieved + final etot is -466.313116573 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.8109 2.00000 + 2 -13.1102 2.00000 + 3 -9.44177 2.00000 + 4 -6.85688 2.00000 + 5 1.57883 0.00000 + 6 4.97284 0.00000 + 7 10.9687 0.00000 + 8 11.2436 0.00000 + + EFERMI = -2.515766302809752 eV + OUT.ABACUS/ final etot is -466.3131165726861 eV + correction force for each atom along direction 1 is -0.000119910 + correction force for each atom along direction 2 is 0.000122839 + correction force for each atom along direction 3 is 2.90587e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +2.0345374 -0.78122896 -0.18301912 + H1 -0.96713341 +1.8579625 -1.5023823 + H2 -1.0674040 -1.0767336 +1.6854015 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3131165726861 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5432 11 0.59 1.0e+02% + Run_lcao lcao_line 6.5362 1 6.5 1.e+02% + Potential init_pot 0.24159 2 0.12 3.7% + PW_Basis recip2real 0.22639 16 0.014 3.5% + PW_Basis gathers_scatterp 0.10833 16 0.0068 1.7% + Potential v_of_rho 0.89916 13 0.069 14.% + XC_Functional v_xc 0.30426 14 0.022 4.7% + H_Hartree_pw v_hartree 0.56223 13 0.043 8.6% + PW_Basis real2recip 0.60268 38 0.016 9.2% + PW_Basis gatherp_scatters 0.27292 38 0.0072 4.2% + ORB_control set_orb_tables 0.89627 1 0.90 14.% + ORB_gen_tables gen_tables 0.89627 1 0.90 14.% + ORB_table_phi init_Table 0.37510 1 0.38 5.7% + ORB_table_phi cal_ST_Phi12_R 0.37087 126 0.0029 5.7% + ORB_table_beta init_Table_Beta 0.15596 1 0.16 2.4% + ORB_table_beta VNL_PhiBeta_R 0.15468 56 0.0028 2.4% + ORB_table_alpha init_Table_Alpha 0.20758 1 0.21 3.2% + ORB_table_alpha S_PhiAlpha_R 0.20597 66 0.0031 3.1% + LOOP_ions opt_ions 5.1950 1 5.2 79.% + ESolver_KS_LCAO Run 4.6493 1 4.6 71.% + HSolverLCAO solve 2.4846 11 0.23 38.% + HamiltLCAO updateHk 1.2671 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2438 11 0.11 19.% + Gint_interface cal_gint 0.73211 23 0.032 11.% + Gint_Gamma distri_vl_value 0.59480 11 0.054 9.1% + Gint_Gamma distri_vl 2.2311 6 0.37 34.% + LCAO_Deepks cal_projected_DM 4.8513 13 0.37 74.% + LCAO_gen_fixedH add_v_delta 2.1049 6 0.35 32.% + LCAO_DESCRIPTOR add_v_delta 2.1049 6 0.35 32.% + ElecStateLCAO psiToRho 1.2016 11 0.11 18.% + Charge mix_rho 0.74486 10 0.074 11.% + LOOP_ions force_stress 0.54554 1 0.55 8.3% + Force_Stress_LCAO getForceStress 0.54552 1 0.55 8.3% + Force_LCAO_gamma ftable_gamma 0.35631 1 0.36 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.15144 1 0.15 2.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:36 2022 + Finish Time : Wed Sep 28 11:11:42 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d231aa24a822d0611d27d84675babc20ec1e61b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012431 ima = 3.70689e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122328908062 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111484301194 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011186158562 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112188680486 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112102018276 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112150758597 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112143593876 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112146888276 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112145919158 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112145862391 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112145856991 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a9a65aeb5279e2ac64560136f4c3d8b276b9170b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.814444750088 30.572078553182 9.619918980354 0 0 0 +H +0.0 +2 +-11.804043921771 31.791601814734 8.813848546485 0 0 0 +-11.993205976626 30.005025010233 10.819155518898 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/conv new file mode 100644 index 0000000000000000000000000000000000000000..42d9eeb67b3d540c42ff880b768484d076e7df1b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/conv @@ -0,0 +1 @@ +267 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..40e9c03cb6b57b796912ec03c2a1318ab0392f89 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753516711 0.01296659598 1.303617097 1.381963685 1.471596422 0.009680253873 0.01785642707 0.03913918025 +8.191640438e-18 0.001109532447 0.003098839344 0.01432578739 0.05115436012 -1.919677084e-20 3.393368583e-06 8.32648374e-06 +0.001593900704 0.006125920112 + +H atom_index 1 n_descriptor 18 +1.301860528 0.03320195706 0.1316418153 0.1753652133 0.3345375905 0.02600226909 0.03121262386 0.03690731905 +-1.997569285e-17 6.300843506e-05 0.1089641834 0.1280665686 0.1505580284 1.954535838e-18 5.926261859e-07 0.01398000059 +0.02963060733 0.03287093063 + +H atom_index 2 n_descriptor 18 +1.294602876 0.0334051342 0.1286459955 0.1714942329 0.3325474943 0.02564495412 0.03080143044 0.03694182966 +5.015582978e-17 6.231010689e-05 0.1092673485 0.1256807854 0.1473107411 5.534261569e-18 8.750906801e-07 0.01378145344 +0.02941964714 0.03261990958 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3181a7caddc1d135e297af6c3218290125e0072a Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..2f45dbb102f55e84df27f13df26b4a7621048fc8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..b3e7c5a65f9f2ebef9f7ece3c60da4db62eeb5a6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..aef2bd6f78609b33b4720d05e7f4eb54643c834a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..38f73b40276df6d2b9418d7da02785a9a72a8e54 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:36 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0727975 SEC) : SETUP UNITCELL + DONE(0.0730534 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0893362 SEC) : INIT PLANEWAVE + DONE(0.130635 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.375586 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650597e+02 0.000000e+00 2.186e-01 4.971e-01 + GE2 -4.663096e+02 -1.249884e+00 9.686e-02 4.674e-01 + GE3 -4.663126e+02 -3.069142e-03 6.163e-02 5.288e-01 + GE4 -4.663137e+02 -1.040218e-03 2.119e-03 4.067e-01 + GE5 -4.663126e+02 1.132554e-03 9.285e-04 4.052e-01 + GE6 -4.663134e+02 -8.078628e-04 1.588e-04 4.012e-01 + GE7 -4.663131e+02 2.881648e-04 4.532e-05 4.004e-01 + GE8 -4.663131e+02 -6.133541e-05 2.602e-05 3.852e-01 + GE9 -4.663131e+02 2.397655e-05 1.537e-06 3.930e-01 + GE10 -4.663131e+02 -4.880153e-06 1.695e-07 3.889e-01 + GE11 -4.663131e+02 -3.272400e-07 4.771e-08 3.225e-01 +E_delta_band = -7.38648484e-02 Ry = -1.00498282e+00 eV +E_delta_NN= -1.96442187e-01 Ry = -2.67273307e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5432 11 0.59 1e+02 % + Run_lcao lcao_line 6.5362 1 6.5 1e+02 % + Potential init_pot 0.24159 2 0.12 3.7 % + PW_Basis recip2real 0.22639 16 0.014 3.5 % + PW_Basis gathers_scatterp 0.10833 16 0.0068 1.7 % + Potential v_of_rho 0.89916 13 0.069 14 % + XC_Functional v_xc 0.30426 14 0.022 4.7 % + H_Hartree_pw v_hartree 0.56223 13 0.043 8.6 % + PW_Basis real2recip 0.60268 38 0.016 9.2 % + PW_Basis gatherp_scatters 0.27292 38 0.0072 4.2 % + ORB_control set_orb_tables 0.89627 1 0.9 14 % + ORB_gen_tables gen_tables 0.89627 1 0.9 14 % + ORB_table_phi init_Table 0.3751 1 0.38 5.7 % + ORB_table_phi cal_ST_Phi12_R 0.37087 126 0.0029 5.7 % + ORB_table_beta init_Table_Beta 0.15596 1 0.16 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.15468 56 0.0028 2.4 % + ORB_table_alpha init_Table_Alpha 0.20758 1 0.21 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.20597 66 0.0031 3.1 % + LOOP_ions opt_ions 5.195 1 5.2 79 % + ESolver_KS_LCAO Run 4.6493 1 4.6 71 % + HSolverLCAO solve 2.4846 11 0.23 38 % + HamiltLCAO updateHk 1.2671 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2438 11 0.11 19 % + Gint_interface cal_gint 0.73211 23 0.032 11 % + Gint_Gamma distri_vl_value 0.5948 11 0.054 9.1 % + Gint_Gamma distri_vl 2.2311 6 0.37 34 % + LCAO_Deepks cal_projected_DM 4.8513 13 0.37 74 % + LCAO_gen_fixedH add_v_delta 2.1049 6 0.35 32 % + LCAO_DESCRIPTOR add_v_delta 2.1049 6 0.35 32 % + ElecStateLCAO psiToRho 1.2016 11 0.11 18 % + Charge mix_rho 0.74486 10 0.074 11 % + LOOP_ions force_stress 0.54554 1 0.55 8.3 % + Force_Stress_LCAO getForceStress 0.54552 1 0.55 8.3 % + Force_LCAO_gamma ftable_gamma 0.35631 1 0.36 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.15144 1 0.15 2.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:36 2022 + FINISH Time : Wed Sep 28 11:11:42 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/267/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..66e92be3cf72e03a20b286a45a9d573c46b14cd5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.622811 0.0768571 0.346847 +H 0.571569 0.0809743 0.301365 +H 0.607588 0.0230646 0.384976 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bd8701b967d44436e9e6811ffa5751f396d8a61d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.8459 2 + 2 -12.7015 2 + 3 -9.0234 2 + 4 -6.64564 2 + 5 0.916539 0 + 6 3.77877 0 + 7 11.1788 0 + 8 11.4226 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..5a39c363150a0c0454cd2ff75a28f4fb3601eb32 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:38 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.4387172825 2.15199855937 9.71171614584 0 0 0 0 + tauc_H1 16.0039204229 2.2672792915 8.43822668843 0 0 0 0 + tauc_H2 17.0124720063 0.645808835856 10.7793147879 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0869315264022 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0960453059375 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.114503735857 (SEC) + + DONE : INIT CHARGE Time : 0.163967559371 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447154 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00068 + + Density error is 0.210429066176 + + Energy Rydberg eV + E_KohnSham -34.1899075068 -465.177556185 + E_Harris -34.3718738028 -467.653334655 + E_Fermi -0.379254650245 -5.16002423632 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00129606037929 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000875326250174 + + Density error is 0.0991441844331 + + Energy Rydberg eV + E_KohnSham -34.2770977712 -466.363840592 + E_Harris -34.2843917433 -466.463080173 + E_Fermi -0.190694980026 -2.59453830835 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121531144763 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00084453520819 + + Density error is 0.0641291190142 + + Energy Rydberg eV + E_KohnSham -34.2775309975 -466.369734938 + E_Harris -34.2821554385 -466.432653685 + E_Fermi -0.185482338431 -2.52361668103 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106867552618 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000817080191286 + + Density error is 0.00202736182381 + + Energy Rydberg eV + E_KohnSham -34.2774067894 -466.368044999 + E_Harris -34.2774108277 -466.368099943 + E_Fermi -0.150569434716 -2.04860225678 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106708310147 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000816049393176 + + Density error is 0.000915370529889 + + Energy Rydberg eV + E_KohnSham -34.2773872454 -466.36777909 + E_Harris -34.277387555 -466.367783302 + E_Fermi -0.150616229542 -2.04923893305 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106498958768 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000815943728344 + + Density error is 0.000197440016932 + + Energy Rydberg eV + E_KohnSham -34.2773922329 -466.367846948 + E_Harris -34.2773922238 -466.367846825 + E_Fermi -0.150093088403 -2.04212123269 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106507598661 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000816134312245 + + Density error is 2.26816554613e-05 + + Energy Rydberg eV + E_KohnSham -34.277392211 -466.367846651 + E_Harris -34.2773922117 -466.367846661 + E_Fermi -0.150094044805 -2.04213424521 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010650120344 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000816085932686 + + Density error is 8.50339925555e-06 + + Energy Rydberg eV + E_KohnSham -34.2773936744 -466.367866562 + E_Harris -34.2773936748 -466.367866566 + E_Fermi -0.150098737638 -2.04219809448 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106500543257 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000816089974269 + + Density error is 1.81695972192e-06 + + Energy Rydberg eV + E_KohnSham -34.2773930241 -466.367857714 + E_Harris -34.2773930241 -466.367857714 + E_Fermi -0.150090734839 -2.04208921081 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106500240603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000816090813092 + + Density error is 4.30990344821e-07 + + Energy Rydberg eV + E_KohnSham -34.2773931644 -466.367859622 + E_Harris -34.2773931644 -466.367859622 + E_Fermi -0.150089464636 -2.04207192882 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106500234673 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000816091127431 + + Density error is 1.45503449562e-07 + + Energy Rydberg eV + E_KohnSham -34.2773931679 -466.36785967 + E_Harris -34.2773931679 -466.36785967 + E_Fermi -0.150089234262 -2.04206879442 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106500212482 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000816091193002 + + Density error is 1.12171174222e-08 + + Energy Rydberg eV + E_KohnSham -34.277393172 -466.367859725 + E_Harris -34.277393172 -466.367859726 + E_band -7.82267271964 -106.432922576 + E_one_elec -68.3901628437 -930.495901822 + E_Hartree +35.6167371246 +484.590569062 + E_xc -8.14176319855 -110.774371267 + E_Ewald +6.7639356709 +92.0280660297 + E_demet -5.15620038168e-54 -7.01537052206e-53 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193209736472 -2.6287533251 + E_Fermi -0.150089110127 -2.04206710548 + + charge density convergence is achieved + final etot is -466.367859725 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.8459 2.00000 + 2 -12.7015 2.00000 + 3 -9.02340 2.00000 + 4 -6.64564 2.00000 + 5 0.916539 0.00000 + 6 3.77877 0.00000 + 7 11.1788 0.00000 + 8 11.4226 0.00000 + + EFERMI = -2.042067105480830 eV + OUT.ABACUS/ final etot is -466.3678597254931 eV + correction force for each atom along direction 1 is -2.53059e-05 + correction force for each atom along direction 2 is 4.30621e-06 + correction force for each atom along direction 3 is -5.52983e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.4209355 -0.71782326 -0.48191525 + H1 +1.2662638 -0.21820021 +1.2341219 + H2 +0.15467169 +0.93602347 -0.75220666 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3678597254931 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5793 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5702 1 7.6 1.e+02% + Potential init_pot 0.28484 2 0.14 3.8% + PW_Basis recip2real 0.28073 17 0.017 3.7% + PW_Basis gathers_scatterp 0.13054 17 0.0077 1.7% + Potential v_of_rho 1.0523 14 0.075 14.% + XC_Functional v_xc 0.33754 15 0.023 4.5% + H_Hartree_pw v_hartree 0.67622 14 0.048 8.9% + PW_Basis real2recip 0.70386 41 0.017 9.3% + PW_Basis gatherp_scatters 0.31240 41 0.0076 4.1% + ORB_control set_orb_tables 1.0958 1 1.1 14.% + ORB_gen_tables gen_tables 1.0958 1 1.1 14.% + ORB_table_phi init_Table 0.47315 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46797 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18625 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18464 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24871 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24670 66 0.0037 3.3% + LOOP_ions opt_ions 5.9487 1 5.9 78.% + ESolver_KS_LCAO Run 5.3578 1 5.4 71.% + HSolverLCAO solve 2.9189 12 0.24 39.% + HamiltLCAO updateHk 1.4700 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4396 12 0.12 19.% + Gint_interface cal_gint 0.84570 25 0.034 11.% + Gint_Gamma distri_vl_value 0.70818 12 0.059 9.3% + Gint_Gamma distri_vl 2.7863 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.5782 14 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.6492 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6494 6 0.44 35.% + ElecStateLCAO psiToRho 1.4146 12 0.12 19.% + Charge mix_rho 0.80770 11 0.073 11.% + LOOP_ions force_stress 0.59068 1 0.59 7.8% + Force_Stress_LCAO getForceStress 0.59065 1 0.59 7.8% + Force_LCAO_gamma ftable_gamma 0.37880 1 0.38 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.17180 1 0.17 2.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:38 2022 + Finish Time : Wed Sep 28 11:13:45 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c799319b23f468f2d17140f3a8ac8a500b9fc5bb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123502 ima = 3.69515e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123796162088 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011233811127 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113164744179 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113332849453 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011333236678 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113334690529 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113332938791 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113334186922 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113333783955 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113333760479 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113333743064 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113333736506 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/STRU new file mode 100644 index 0000000000000000000000000000000000000000..73cd1ee317db6388bc272ae7310c9d86bd6245ee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.561282717530 30.151998559349 9.711716145836 0 0 0 +H +0.0 +2 +-11.996079577130 30.267279291476 8.438226688441 0 0 0 +-10.987527993678 28.645808835845 10.779314787920 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/conv new file mode 100644 index 0000000000000000000000000000000000000000..c33654a35ccc9fe3d92232009e2a0ab3d1ef7d2c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/conv @@ -0,0 +1 @@ +268 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..47ce10bf093c5289d0f00b67f650295e76305088 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749538856 0.01229695259 1.236683788 1.331613355 1.467483336 0.00823952015 0.01799481884 0.03909292141 +6.237159769e-19 0.00086162612 0.002294559667 0.01110582384 0.03999154163 -1.620358498e-20 1.419052691e-06 4.511706833e-06 +0.001614651475 0.005763916407 + +H atom_index 1 n_descriptor 18 +1.175770443 0.03665290061 0.08412602843 0.1191553971 0.2955984143 0.01840802337 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:38 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0869549 SEC) : SETUP UNITCELL + DONE(0.0960629 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.114524 SEC) : INIT PLANEWAVE + DONE(0.164102 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447232 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651776e+02 0.000000e+00 2.104e-01 5.557e-01 + GE2 -4.663638e+02 -1.186284e+00 9.914e-02 5.023e-01 + GE3 -4.663697e+02 -5.894346e-03 6.413e-02 5.691e-01 + GE4 -4.663680e+02 1.689939e-03 2.027e-03 4.292e-01 + GE5 -4.663678e+02 2.659090e-04 9.154e-04 4.302e-01 + GE6 -4.663678e+02 -6.785801e-05 1.974e-04 4.263e-01 + GE7 -4.663678e+02 2.976991e-07 2.268e-05 4.086e-01 + GE8 -4.663679e+02 -1.991110e-05 8.503e-06 4.089e-01 + GE9 -4.663679e+02 8.847977e-06 1.817e-06 4.077e-01 + GE10 -4.663679e+02 -1.908697e-06 4.310e-07 4.076e-01 + GE11 -4.663679e+02 -4.786828e-08 1.455e-07 4.093e-01 + GE12 -4.663679e+02 -5.529045e-08 1.122e-08 3.378e-01 +E_delta_band = -6.70698113e-02 Ry = -9.12531597e-01 eV +E_delta_NN= -1.93209736e-01 Ry = -2.62875333e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5793 11 0.69 1e+02 % + Run_lcao lcao_line 7.5702 1 7.6 1e+02 % + Potential init_pot 0.28484 2 0.14 3.8 % + PW_Basis recip2real 0.28073 17 0.017 3.7 % + PW_Basis gathers_scatterp 0.13054 17 0.0077 1.7 % + Potential v_of_rho 1.0523 14 0.075 14 % + XC_Functional v_xc 0.33754 15 0.023 4.5 % + H_Hartree_pw v_hartree 0.67622 14 0.048 8.9 % + PW_Basis real2recip 0.70386 41 0.017 9.3 % + PW_Basis gatherp_scatters 0.3124 41 0.0076 4.1 % + ORB_control set_orb_tables 1.0958 1 1.1 14 % + ORB_gen_tables gen_tables 1.0958 1 1.1 14 % + ORB_table_phi init_Table 0.47315 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.46797 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18625 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18464 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24871 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.2467 66 0.0037 3.3 % + LOOP_ions opt_ions 5.9487 1 5.9 78 % + ESolver_KS_LCAO Run 5.3578 1 5.4 71 % + HSolverLCAO solve 2.9189 12 0.24 39 % + HamiltLCAO updateHk 1.47 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.4396 12 0.12 19 % + Gint_interface cal_gint 0.8457 25 0.034 11 % + Gint_Gamma distri_vl_value 0.70818 12 0.059 9.3 % + Gint_Gamma distri_vl 2.7863 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.5782 14 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.6492 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6494 6 0.44 35 % + ElecStateLCAO psiToRho 1.4146 12 0.12 19 % + Charge mix_rho 0.8077 11 0.073 11 % + LOOP_ions force_stress 0.59068 1 0.59 7.8 % + Force_Stress_LCAO getForceStress 0.59065 1 0.59 7.8 % + Force_LCAO_gamma ftable_gamma 0.3788 1 0.38 5 % + Force_LCAO_gamma cal_fvl_dphi 0.1718 1 0.17 2.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:38 2022 + FINISH Time : Wed Sep 28 11:13:45 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/268/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..db2f5389e05b0170632d96e8ca03f0b729fb57ab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.622992 0.0727781 0.345806 +H 0.577514 0.0530063 0.306222 +H 0.663321 0.0220849 0.348215 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0b27347be13244eda170e707607917ff75c6ef11 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5507 2 + 2 -13.1877 2 + 3 -9.21042 2 + 4 -6.80227 2 + 5 1.48397 0 + 6 4.75333 0 + 7 11.0155 0 + 8 11.2695 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f8ea009b65c8353475bcc8c0327a7488be174254 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:52 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.4437663914 2.0377869687 9.68257909082 0 0 0 0 + tauc_H1 16.1703974621 1.48417586401 8.5742254473 0 0 0 0 + tauc_H2 18.5729971095 0.618378587322 9.75002186079 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0738220913855 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0741182152749 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0904571722233 (SEC) + + DONE : INIT CHARGE Time : 0.13198099478 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.376173 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119 + + Density error is 0.21731038235 + + Energy Rydberg eV + E_KohnSham -34.1873405058 -465.142630346 + E_Harris -34.3844487783 -467.824425974 + E_Fermi -0.419974717271 -5.71404917083 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00126188331181 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123538707653 + + Density error is 0.0973459847127 + + Energy Rydberg eV + E_KohnSham -34.2782116661 -466.378995909 + E_Harris -34.2848487321 -466.469297825 + E_Fermi -0.227497306908 -3.0952596536 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117162437975 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115854492602 + + Density error is 0.0621407070766 + + Energy Rydberg eV + E_KohnSham -34.2784709073 -466.382523067 + E_Harris -34.2827255377 -466.440410283 + E_Fermi -0.213374858761 -2.9031138891 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102581724583 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103381521222 + + Density error is 0.00203649263622 + + Energy Rydberg eV + E_KohnSham -34.2785129984 -466.383095745 + E_Harris -34.278514893 -466.383121523 + E_Fermi -0.177549749902 -2.41568827715 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102493964244 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103341473316 + + Density error is 0.000919293227099 + + Energy Rydberg eV + E_KohnSham -34.278435107 -466.382035978 + E_Harris -34.2784379964 -466.38207529 + E_Fermi -0.176337965271 -2.39920110142 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010236033273 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103195951808 + + Density error is 0.000112951748688 + + Energy Rydberg eV + E_KohnSham -34.2784900583 -466.382783629 + E_Harris -34.2784900856 -466.382784 + E_Fermi -0.176651423103 -2.40346591401 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102357048204 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103184127492 + + Density error is 4.7114319113e-05 + + Energy Rydberg eV + E_KohnSham -34.2784714223 -466.382530074 + E_Harris -34.2784714344 -466.382530238 + E_Fermi -0.176506067389 -2.40148824807 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102355970019 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103181377424 + + Density error is 1.42364704292e-05 + + Energy Rydberg eV + E_KohnSham -34.2784747683 -466.382575599 + E_Harris -34.2784747691 -466.382575609 + E_Fermi -0.176562596264 -2.40225736287 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010235385319 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103180033347 + + Density error is 2.60188310849e-06 + + Energy Rydberg eV + E_KohnSham -34.2784733357 -466.382556106 + E_Harris -34.2784733357 -466.382556107 + E_Fermi -0.176548477161 -2.40206526261 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010235353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103179995347 + + Density error is 1.382858821e-07 + + Energy Rydberg eV + E_KohnSham -34.278473482 -466.382558097 + E_Harris -34.278473482 -466.382558097 + E_Fermi -0.1765455286 -2.40202514539 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102353552151 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103180003246 + + Density error is 3.07157784385e-08 + + Energy Rydberg eV + E_KohnSham -34.2784735388 -466.382558869 + E_Harris -34.2784735388 -466.382558869 + E_band -8.04824995037 -109.502058253 + E_one_elec -69.7749385415 -949.336741764 + E_Hartree +36.2651741282 +493.413007106 + E_xc -8.24611315469 -112.194125257 + E_Ewald +7.60072669368 +103.413191975 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195735452411 -2.6631174534 + E_Fermi -0.176545631649 -2.40202654743 + + charge density convergence is achieved + final etot is -466.382558869 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5507 2.00000 + 2 -13.1877 2.00000 + 3 -9.21042 2.00000 + 4 -6.80227 2.00000 + 5 1.48397 0.00000 + 6 4.75333 0.00000 + 7 11.0155 0.00000 + 8 11.2695 0.00000 + + EFERMI = -2.402026547434831 eV + OUT.ABACUS/ final etot is -466.3825588694281 eV + correction force for each atom along direction 1 is 5.89053e-05 + correction force for each atom along direction 2 is -0.000186544 + correction force for each atom along direction 3 is -0.000167639 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.93139990 +1.0048224 +1.0923381 + H1 -1.5277475 -0.47039283 -1.2341422 + H2 +0.59634762 -0.53442955 +0.14180416 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3825588694281 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7869 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7794 1 6.8 1.e+02% + Potential init_pot 0.24176 2 0.12 3.6% + PW_Basis recip2real 0.22499 16 0.014 3.3% + PW_Basis gathers_scatterp 0.10630 16 0.0066 1.6% + Potential v_of_rho 0.88572 13 0.068 13.% + XC_Functional v_xc 0.29171 14 0.021 4.3% + H_Hartree_pw v_hartree 0.56241 13 0.043 8.3% + PW_Basis real2recip 0.60064 38 0.016 8.9% + PW_Basis gatherp_scatters 0.26952 38 0.0071 4.0% + ORB_control set_orb_tables 0.90017 1 0.90 13.% + ORB_gen_tables gen_tables 0.90017 1 0.90 13.% + ORB_table_phi init_Table 0.37986 1 0.38 5.6% + ORB_table_phi cal_ST_Phi12_R 0.37557 126 0.0030 5.5% + ORB_table_beta init_Table_Beta 0.15545 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15416 56 0.0028 2.3% + ORB_table_alpha init_Table_Alpha 0.20739 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20577 66 0.0031 3.0% + LOOP_ions opt_ions 5.4331 1 5.4 80.% + ESolver_KS_LCAO Run 4.8776 1 4.9 72.% + HSolverLCAO solve 2.7169 11 0.25 40.% + HamiltLCAO updateHk 1.3807 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3573 11 0.12 20.% + Gint_interface cal_gint 0.87768 23 0.038 13.% + Gint_Gamma distri_vl_value 0.64693 11 0.059 9.5% + Gint_Gamma distri_vl 2.3406 6 0.39 34.% + LCAO_Deepks cal_projected_DM 5.0963 13 0.39 75.% + LCAO_gen_fixedH add_v_delta 2.2117 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2115 6 0.37 33.% + ElecStateLCAO psiToRho 1.3193 11 0.12 19.% + Charge mix_rho 0.74419 10 0.074 11.% + LOOP_ions force_stress 0.55538 1 0.56 8.2% + Force_Stress_LCAO getForceStress 0.55535 1 0.56 8.2% + Force_LCAO_gamma ftable_gamma 0.36051 1 0.36 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.17239 1 0.17 2.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:52 2022 + Finish Time : Wed Sep 28 11:13:59 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b7d620da1e5a6482f1d5a6a3d2818b7a05474721 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124011 ima = 3.70516e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012276630088 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111879304448 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112307012108 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112593937373 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112517245387 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112561227037 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112556017954 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112559097432 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011255857275 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112558441431 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112558443068 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d70c85b6791b045db7e7a8bf51f11a597ec43674 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.556233608564 30.037786968689 9.682579090834 0 0 0 +H +0.0 +2 +-11.829602537904 29.484175864026 8.574225447297 0 0 0 +-9.427002890444 28.618378587338 9.750021860786 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/conv new file mode 100644 index 0000000000000000000000000000000000000000..fef520ea3a6d49163b4614ae2a5863713dd40a67 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/conv @@ -0,0 +1 @@ +269 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ddd4e7e8f81396370cea556985ff1a916f99122a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750186323 0.0128361888 1.29160298 1.376609934 1.470527141 0.008862598459 0.01868829087 0.03905026011 +-1.915726043e-18 0.001139219162 0.002797064094 0.01321051833 0.04801476036 -3.895407193e-19 2.488462619e-06 6.787091105e-06 +0.001637267422 0.006007783754 + +H atom_index 1 n_descriptor 18 +1.290935686 0.03299611446 0.1244321395 0.1698417754 0.3325827468 0.02452391147 0.0306327274 0.03656489445 +-2.847682024e-17 5.508993636e-05 0.108552249 0.1220014541 0.1458713511 3.900482556e-18 1.728763732e-06 0.01351097252 +0.02833144883 0.03245712733 + +H atom_index 2 n_descriptor 18 +1.260624693 0.03397796461 0.112995378 0.1547071435 0.3236498003 0.02310548201 0.02889170259 0.03712526345 +-1.385423601e-17 5.212226857e-05 0.1061109614 0.1157483552 0.1329901909 -1.688321743e-18 3.444278638e-06 0.01320996643 +0.02732289536 0.03125126525 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..6c2d997d07c8dc92a04c260e6b1590b1febf9e1c Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..642c952fb026b916fd4d3eb8768d3ab25f6eb855 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..57200d3a1f1270b1c37696976e9dbf22a37caea0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..8bb64e8133120eeef0d97af3d1cf30899714b8d3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:52 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0738378 SEC) : SETUP UNITCELL + DONE(0.0741273 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0904721 SEC) : INIT PLANEWAVE + DONE(0.13209 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.376217 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651426e+02 0.000000e+00 2.173e-01 5.185e-01 + GE2 -4.663790e+02 -1.236366e+00 9.735e-02 4.916e-01 + GE3 -4.663825e+02 -3.527158e-03 6.214e-02 5.514e-01 + GE4 -4.663831e+02 -5.726780e-04 2.036e-03 4.261e-01 + GE5 -4.663820e+02 1.059767e-03 9.193e-04 4.268e-01 + GE6 -4.663828e+02 -7.476508e-04 1.130e-04 4.162e-01 + GE7 -4.663825e+02 2.535552e-04 4.711e-05 4.153e-01 + GE8 -4.663826e+02 -4.552483e-05 1.424e-05 4.071e-01 + GE9 -4.663826e+02 1.949254e-05 2.602e-06 4.140e-01 + GE10 -4.663826e+02 -1.990901e-06 1.383e-07 4.141e-01 + GE11 -4.663826e+02 -7.723925e-07 3.072e-08 3.437e-01 +E_delta_band = -7.24127879e-02 Ry = -9.85226524e-01 eV +E_delta_NN= -1.95735452e-01 Ry = -2.66311745e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7869 11 0.62 1e+02 % + Run_lcao lcao_line 6.7794 1 6.8 1e+02 % + Potential init_pot 0.24176 2 0.12 3.6 % + PW_Basis recip2real 0.22499 16 0.014 3.3 % + PW_Basis gathers_scatterp 0.1063 16 0.0066 1.6 % + Potential v_of_rho 0.88572 13 0.068 13 % + XC_Functional v_xc 0.29171 14 0.021 4.3 % + H_Hartree_pw v_hartree 0.56241 13 0.043 8.3 % + PW_Basis real2recip 0.60064 38 0.016 8.9 % + PW_Basis gatherp_scatters 0.26952 38 0.0071 4 % + ORB_control set_orb_tables 0.90017 1 0.9 13 % + ORB_gen_tables gen_tables 0.90017 1 0.9 13 % + ORB_table_phi init_Table 0.37986 1 0.38 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.37557 126 0.003 5.5 % + ORB_table_beta init_Table_Beta 0.15545 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15416 56 0.0028 2.3 % + ORB_table_alpha init_Table_Alpha 0.20739 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20577 66 0.0031 3 % + LOOP_ions opt_ions 5.4331 1 5.4 80 % + ESolver_KS_LCAO Run 4.8776 1 4.9 72 % + HSolverLCAO solve 2.7169 11 0.25 40 % + HamiltLCAO updateHk 1.3807 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3573 11 0.12 20 % + Gint_interface cal_gint 0.87768 23 0.038 13 % + Gint_Gamma distri_vl_value 0.64693 11 0.059 9.5 % + Gint_Gamma distri_vl 2.3406 6 0.39 34 % + LCAO_Deepks cal_projected_DM 5.0963 13 0.39 75 % + LCAO_gen_fixedH add_v_delta 2.2117 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2115 6 0.37 33 % + ElecStateLCAO psiToRho 1.3193 11 0.12 19 % + Charge mix_rho 0.74419 10 0.074 11 % + LOOP_ions force_stress 0.55538 1 0.56 8.2 % + Force_Stress_LCAO getForceStress 0.55535 1 0.56 8.2 % + Force_LCAO_gamma ftable_gamma 0.36051 1 0.36 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.17239 1 0.17 2.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:52 2022 + FINISH Time : Wed Sep 28 11:13:59 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/269/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..75004c55135b3aab084a37c39f69274e234b7ea1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.513788 0.418042 0.431753 +H 0.573358 0.41682 0.404504 +H 0.505456 0.357863 0.455955 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..4b4a8a4bb53678b9096c3fe902bbf5e9ab2f9ea3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2833 2 + 2 -13.0755 2 + 3 -9.0924 2 + 4 -6.74353 2 + 5 1.31326 0 + 6 4.43214 0 + 7 11.0747 0 + 8 11.3244 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..dbf83dfdbd5ebb6c8ed13ac1ec67721fb007b19c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:00 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.3860741367 11.7051775851 12.0890767539 0 0 0 0 + tauc_H1 16.0540340392 11.6709636591 11.3261121561 0 0 0 0 + tauc_H2 14.1527610464 10.0201675268 12.7667435114 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.08723167523 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0965503890397 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115506420154 (SEC) + + DONE : INIT CHARGE Time : 0.163251429945 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.442518 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00152 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000657 + + Density error is 0.214771945711 + + Energy Rydberg eV + E_KohnSham -34.1919966673 -465.205980672 + E_Harris -34.3831697267 -467.807023585 + E_Fermi -0.405310577247 -5.51453331022 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013929440241 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000877481598546 + + Density error is 0.0979325391643 + + Energy Rydberg eV + E_KohnSham -34.2811867763 -466.41947436 + E_Harris -34.2879124083 -466.510981278 + E_Fermi -0.214335001338 -2.91617729903 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001283630203 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000846662323703 + + Density error is 0.0627853661973 + + Energy Rydberg eV + E_KohnSham -34.281447975 -466.423028151 + E_Harris -34.2857920203 -466.48213192 + E_Fermi -0.202977434076 -2.76164966886 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109169409643 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000809913926638 + + Density error is 0.00200271709534 + + Energy Rydberg eV + E_KohnSham -34.2814386417 -466.422901164 + E_Harris -34.2814403558 -466.422924486 + E_Fermi -0.167493655694 -2.27886809629 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108949637596 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000810073397971 + + Density error is 0.00087408237496 + + Energy Rydberg eV + E_KohnSham -34.2813819708 -466.422130117 + E_Harris -34.281382979 -466.422143835 + E_Fermi -0.166775262952 -2.2690938616 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108754221693 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000809516218898 + + Density error is 0.000155153467382 + + Energy Rydberg eV + E_KohnSham -34.2814172318 -466.422609868 + E_Harris -34.2814172582 -466.422610227 + E_Fermi -0.16675655635 -2.26883934522 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108742625711 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000809753757903 + + Density error is 3.74745448999e-05 + + Energy Rydberg eV + E_KohnSham -34.2814050123 -466.422443613 + E_Harris -34.2814050195 -466.422443712 + E_Fermi -0.166632719008 -2.26715445175 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108740770878 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000809677568024 + + Density error is 1.76258116547e-05 + + Energy Rydberg eV + E_KohnSham -34.28140884 -466.422495692 + E_Harris -34.2814088415 -466.422495712 + E_Fermi -0.166673704867 -2.26771209296 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108738173994 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000809682049503 + + Density error is 2.34648222325e-06 + + Energy Rydberg eV + E_KohnSham -34.2814073683 -466.422475668 + E_Harris -34.2814073683 -466.422475668 + E_Fermi -0.166656279004 -2.26747500193 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108737613792 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000809683442127 + + Density error is 3.80234731579e-07 + + Energy Rydberg eV + E_KohnSham -34.2814076461 -466.422479447 + E_Harris -34.2814076461 -466.422479447 + E_Fermi -0.166653944967 -2.26744324573 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108737608224 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000809683922834 + + Density error is 1.49029221907e-07 + + Energy Rydberg eV + E_KohnSham -34.2814076725 -466.422479806 + E_Harris -34.2814076725 -466.422479806 + E_Fermi -0.166653824296 -2.26744160392 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108737578816 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000809684117137 + + Density error is 1.06539617086e-08 + + Energy Rydberg eV + E_KohnSham -34.2814076747 -466.422479837 + E_Harris -34.2814076747 -466.422479837 + E_band -7.9664727124 -108.38942185 + E_one_elec -69.299916753 -942.873738766 + E_Hartree +36.0449690645 +490.416963511 + E_xc -8.21036850001 -111.70779428 + E_Ewald +7.30822473684 +99.4334986856 + E_demet -7.12119042281e-78 -9.68887662932e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194802329392 -2.65042166341 + E_Fermi -0.166653687528 -2.26743974309 + + charge density convergence is achieved + final etot is -466.422479837 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2833 2.00000 + 2 -13.0755 2.00000 + 3 -9.09240 2.00000 + 4 -6.74353 2.00000 + 5 1.31326 0.00000 + 6 4.43214 0.00000 + 7 11.0747 0.00000 + 8 11.3244 0.00000 + + EFERMI = -2.267439743090973 eV + OUT.ABACUS/ final etot is -466.4224798372031 eV + correction force for each atom along direction 1 is 0.000132865 + correction force for each atom along direction 2 is -0.000110792 + correction force for each atom along direction 3 is -0.000121079 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.18013288 +0.31992914 -0.029211217 + H1 +0.20433901 -0.022329373 -0.085008909 + H2 -0.024206138 -0.29759976 +0.11422013 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4224798372031 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1799 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1703 1 6.2 1.e+02% + Potential init_pot 0.28679 2 0.14 4.6% + PW_Basis recip2real 0.27848 17 0.016 4.5% + PW_Basis gathers_scatterp 0.12812 17 0.0075 2.1% + Potential v_of_rho 0.92304 14 0.066 15.% + XC_Functional v_xc 0.25954 15 0.017 4.2% + H_Hartree_pw v_hartree 0.62573 14 0.045 10.% + PW_Basis real2recip 0.60784 41 0.015 9.8% + PW_Basis gatherp_scatters 0.24785 41 0.0060 4.0% + ORB_control set_orb_tables 1.1095 1 1.1 18.% + ORB_gen_tables gen_tables 1.1095 1 1.1 18.% + ORB_table_phi init_Table 0.48682 1 0.49 7.9% + ORB_table_phi cal_ST_Phi12_R 0.48188 126 0.0038 7.8% + ORB_table_beta init_Table_Beta 0.18993 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18842 56 0.0034 3.0% + ORB_table_alpha init_Table_Alpha 0.25237 1 0.25 4.1% + ORB_table_alpha S_PhiAlpha_R 0.25051 66 0.0038 4.1% + LOOP_ions opt_ions 4.5419 1 4.5 73.% + ESolver_KS_LCAO Run 4.0444 1 4.0 65.% + HSolverLCAO solve 1.9157 12 0.16 31.% + HamiltLCAO updateHk 1.0229 12 0.085 17.% + LCAO_Hamilt cal_Hgamma 0.99251 12 0.083 16.% + Gint_interface cal_gint 0.11193 25 0.0045 1.8% + Gint_Gamma distri_vl_value 0.59176 12 0.049 9.6% + Gint_Gamma distri_vl 2.1101 6 0.35 34.% + LCAO_Deepks cal_projected_DM 4.2095 14 0.30 68.% + LCAO_gen_fixedH add_v_delta 1.9767 6 0.33 32.% + LCAO_DESCRIPTOR add_v_delta 1.9767 6 0.33 32.% + ElecStateLCAO psiToRho 0.87325 12 0.073 14.% + Charge mix_rho 0.71349 11 0.065 12.% + LOOP_ions force_stress 0.49739 1 0.50 8.0% + Force_Stress_LCAO getForceStress 0.49736 1 0.50 8.0% + Force_LCAO_gamma ftable_gamma 0.28778 1 0.29 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:59 2022 + Finish Time : Wed Sep 28 11:08:06 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ad2434c82ecf1ebdd6bba6ce2380d72f400e68cc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123792 ima = 3.65616e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123099140889 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112087406081 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112617644195 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112854265697 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011280646048 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112834024991 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112827641523 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112830561481 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112829757199 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112829681815 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112829668624 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112829661623 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ca7a07cbd5dfbee16959d3f1b9852c9ff0c66b4a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.613925863276 11.705177585088 12.089076753850 0 0 0 +H +0.0 +2 +-11.945965960835 11.670963659154 11.326112156039 0 0 0 +-13.847238953583 10.020167526832 12.766743511412 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/conv new file mode 100644 index 0000000000000000000000000000000000000000..67b96e55855ceadff49034dd726fc29ed51ae9b1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/conv @@ -0,0 +1 @@ +27 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..cfc4f1b7d9e088017c8a6b577058c7e244d2b7dc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74877006 0.01268626534 1.274301743 1.362556905 1.469289653 0.008418818 0.01870238075 0.039011009 +-3.649445518e-18 0.001062980776 0.002576611864 0.01241267131 0.04488114046 -3.706648396e-20 1.988083215e-06 5.80704863e-06 +0.001661182809 0.005935100381 + +H atom_index 1 n_descriptor 18 +1.244267191 0.03438346296 0.1062961103 0.1474797269 0.3194421288 0.02192942532 0.0279986556 0.03753009013 +7.965188387e-19 4.448466777e-05 0.1002379277 0.1147509414 0.1265944222 -2.730739916e-18 4.44035763e-06 0.01318983718 +0.02605978513 0.03051800574 + +H atom_index 2 n_descriptor 18 +1.246962845 0.03429053563 0.1072159981 0.148715829 0.3203196082 0.02205362685 0.0281552687 0.03744347184 +-8.007917211e-18 4.47296006e-05 0.1009090726 0.1148620278 0.1276633269 -7.902983811e-19 4.298838655e-06 0.01316437723 +0.02616109878 0.03064155583 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e15db741351b6c46a5c5bcc50e7e49ddf926bd99 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:59 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872599 SEC) : SETUP UNITCELL + DONE(0.0965677 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115529 SEC) : INIT PLANEWAVE + DONE(0.163387 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.442577 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652060e+02 0.000000e+00 2.148e-01 4.558e-01 + GE2 -4.664195e+02 -1.213494e+00 9.793e-02 3.810e-01 + GE3 -4.664230e+02 -3.553791e-03 6.279e-02 4.331e-01 + GE4 -4.664229e+02 1.269866e-04 2.003e-03 3.243e-01 + GE5 -4.664221e+02 7.710473e-04 8.741e-04 3.222e-01 + GE6 -4.664226e+02 -4.797514e-04 1.552e-04 3.184e-01 + GE7 -4.664224e+02 1.662558e-04 3.747e-05 3.110e-01 + GE8 -4.664225e+02 -5.207960e-05 1.763e-05 3.000e-01 + GE9 -4.664225e+02 2.002448e-05 2.346e-06 2.955e-01 + GE10 -4.664225e+02 -3.779498e-06 3.802e-07 3.014e-01 + GE11 -4.664225e+02 -3.591994e-07 1.490e-07 2.987e-01 + GE12 -4.664225e+02 -3.081841e-08 1.065e-08 2.422e-01 +E_delta_band = -7.04861063e-02 Ry = -9.59012676e-01 eV +E_delta_NN= -1.94802329e-01 Ry = -2.65042166e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1799 11 0.56 1e+02 % + Run_lcao lcao_line 6.1703 1 6.2 1e+02 % + Potential init_pot 0.28679 2 0.14 4.6 % + PW_Basis recip2real 0.27848 17 0.016 4.5 % + PW_Basis gathers_scatterp 0.12812 17 0.0075 2.1 % + Potential v_of_rho 0.92304 14 0.066 15 % + XC_Functional v_xc 0.25954 15 0.017 4.2 % + H_Hartree_pw v_hartree 0.62573 14 0.045 10 % + PW_Basis real2recip 0.60784 41 0.015 9.8 % + PW_Basis gatherp_scatters 0.24785 41 0.006 4 % + ORB_control set_orb_tables 1.1095 1 1.1 18 % + ORB_gen_tables gen_tables 1.1095 1 1.1 18 % + ORB_table_phi init_Table 0.48682 1 0.49 7.9 % + ORB_table_phi cal_ST_Phi12_R 0.48188 126 0.0038 7.8 % + ORB_table_beta init_Table_Beta 0.18993 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18842 56 0.0034 3 % + ORB_table_alpha init_Table_Alpha 0.25237 1 0.25 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.25051 66 0.0038 4.1 % + LOOP_ions opt_ions 4.5419 1 4.5 73 % + ESolver_KS_LCAO Run 4.0444 1 4 65 % + HSolverLCAO solve 1.9157 12 0.16 31 % + HamiltLCAO updateHk 1.0229 12 0.085 17 % + LCAO_Hamilt cal_Hgamma 0.99251 12 0.083 16 % + Gint_interface cal_gint 0.11193 25 0.0045 1.8 % + Gint_Gamma distri_vl_value 0.59176 12 0.049 9.6 % + Gint_Gamma distri_vl 2.1101 6 0.35 34 % + LCAO_Deepks cal_projected_DM 4.2095 14 0.3 68 % + LCAO_gen_fixedH add_v_delta 1.9767 6 0.33 32 % + LCAO_DESCRIPTOR add_v_delta 1.9767 6 0.33 32 % + ElecStateLCAO psiToRho 0.87325 12 0.073 14 % + Charge mix_rho 0.71349 11 0.065 12 % + LOOP_ions force_stress 0.49739 1 0.5 8 % + Force_Stress_LCAO getForceStress 0.49736 1 0.5 8 % + Force_LCAO_gamma ftable_gamma 0.28778 1 0.29 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:59 2022 + FINISH Time : Wed Sep 28 11:08:06 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/27/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..aafab35ca6de64026c874b3bdd265b506f125a15 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.635094 0.0836215 0.338151 +H 0.602769 0.0303723 0.312424 +H 0.698196 0.061377 0.348737 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3987e10572be92c16e387046726bd73b6b5b584c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9434 2 + 2 -12.7643 2 + 3 -9.05609 2 + 4 -6.668 2 + 5 1.00568 0 + 6 3.9146 0 + 7 11.1569 0 + 8 11.405 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d1e15209b269cb0b5e024b751f30759073c5ab75 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:41 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.7826257028 2.34140161587 9.46821736368 0 0 0 0 + tauc_H1 16.8775292246 0.850424463963 8.74787623405 0 0 0 0 + tauc_H2 19.5494814268 1.71855689961 9.76464354697 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0879738527278 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.103186473434 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.121385384553 (SEC) + + DONE : INIT CHARGE Time : 0.170978572394 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44958 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000608 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00166 + + Density error is 0.211274071575 + + Energy Rydberg eV + E_KohnSham -34.1913255318 -465.196849405 + E_Harris -34.3750481084 -467.696523298 + E_Fermi -0.384325631478 -5.22901847555 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000824112236698 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134837399073 + + Density error is 0.0988751908094 + + Energy Rydberg eV + E_KohnSham -34.2789674885 -466.3892794 + E_Harris -34.2861180893 -466.486568315 + E_Fermi -0.195626938593 -2.66164104716 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000790645851692 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124730179487 + + Density error is 0.063861804468 + + Energy Rydberg eV + E_KohnSham -34.2793846531 -466.394955216 + E_Harris -34.2839525416 -466.457104528 + E_Fermi -0.189200209451 -2.57420091132 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000755867923148 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104864044019 + + Density error is 0.00199800459533 + + Energy Rydberg eV + E_KohnSham -34.2792840118 -466.393585921 + E_Harris -34.2792872219 -466.393629597 + E_Fermi -0.154120366708 -2.09691516508 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756307637702 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010464741271 + + Density error is 0.000913830167496 + + Energy Rydberg eV + E_KohnSham -34.2792557184 -466.393200969 + E_Harris -34.279256061 -466.393205631 + E_Fermi -0.154048696347 -2.09594003979 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000755971280792 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104348366947 + + Density error is 0.00019050752412 + + Energy Rydberg eV + E_KohnSham -34.279266537 -466.393348164 + E_Harris -34.2792665313 -466.393348086 + E_Fermi -0.153609141309 -2.08995958668 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756122225565 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104341571521 + + Density error is 2.51285352459e-05 + + Energy Rydberg eV + E_KohnSham -34.2792639713 -466.393313256 + E_Harris -34.2792639729 -466.393313278 + E_Fermi -0.153581963011 -2.08958980697 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00075608968595 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104337188575 + + Density error is 1.11743292218e-05 + + Energy Rydberg eV + E_KohnSham -34.2792661785 -466.393343286 + E_Harris -34.2792661791 -466.393343294 + E_Fermi -0.153594268103 -2.08975722634 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756094858112 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010433558436 + + Density error is 2.08612983873e-06 + + Energy Rydberg eV + E_KohnSham -34.2792653135 -466.393331517 + E_Harris -34.2792653135 -466.393331517 + E_Fermi -0.15358385275 -2.0896155182 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756093087089 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104334913564 + + Density error is 4.84584829578e-07 + + Energy Rydberg eV + E_KohnSham -34.2792654952 -466.393333989 + E_Harris -34.2792654952 -466.393333989 + E_Fermi -0.153582168346 -2.08959260071 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756093720873 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104334917 + + Density error is 1.64120003696e-07 + + Energy Rydberg eV + E_KohnSham -34.2792655038 -466.393334106 + E_Harris -34.2792655038 -466.393334106 + E_Fermi -0.153581928132 -2.08958933243 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756093910315 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010433488955 + + Density error is 1.1003802006e-08 + + Energy Rydberg eV + E_KohnSham -34.279265508 -466.393334163 + E_Harris -34.2792655079 -466.393334163 + E_band -7.85432849519 -106.863621498 + E_one_elec -68.5847234337 -933.143034453 + E_Hartree +35.7077460856 +485.828809501 + E_xc -8.15625351406 -110.971522124 + E_Ewald +6.87972982043 +93.6035262584 + E_demet -7.24518510636e-59 -9.85758005112e-58 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193540696338 -2.63325626509 + E_Fermi -0.153581773962 -2.08958723483 + + charge density convergence is achieved + final etot is -466.393334163 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9434 2.00000 + 2 -12.7643 2.00000 + 3 -9.05609 2.00000 + 4 -6.66800 2.00000 + 5 1.00568 0.00000 + 6 3.91460 0.00000 + 7 11.1569 0.00000 + 8 11.4050 0.00000 + + EFERMI = -2.089587234826430 eV + OUT.ABACUS/ final etot is -466.3933341629954 eV + correction force for each atom along direction 1 is -3.75693e-07 + correction force for each atom along direction 2 is -5.45176e-05 + correction force for each atom along direction 3 is -0.000152114 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.61616564 -1.1028607 -0.18158784 + H1 +0.57285984 +0.77119207 +0.40505612 + H2 -1.1890255 +0.33166861 -0.22346828 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3933341629954 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0428 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0331 1 7.0 1.e+02% + Potential init_pot 0.28533 2 0.14 4.1% + PW_Basis recip2real 0.27437 17 0.016 3.9% + PW_Basis gathers_scatterp 0.12474 17 0.0073 1.8% + Potential v_of_rho 0.91832 14 0.066 13.% + XC_Functional v_xc 0.25536 15 0.017 3.6% + H_Hartree_pw v_hartree 0.62367 14 0.045 8.9% + PW_Basis real2recip 0.60748 41 0.015 8.6% + PW_Basis gatherp_scatters 0.24515 41 0.0060 3.5% + ORB_control set_orb_tables 1.1149 1 1.1 16.% + ORB_gen_tables gen_tables 1.1149 1 1.1 16.% + ORB_table_phi init_Table 0.48955 1 0.49 7.0% + ORB_table_phi cal_ST_Phi12_R 0.48459 126 0.0038 6.9% + ORB_table_beta init_Table_Beta 0.19405 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.19252 56 0.0034 2.7% + ORB_table_alpha init_Table_Alpha 0.24999 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24810 66 0.0038 3.5% + LOOP_ions opt_ions 5.3921 1 5.4 77.% + ESolver_KS_LCAO Run 4.8174 1 4.8 68.% + HSolverLCAO solve 2.6939 12 0.22 38.% + HamiltLCAO updateHk 1.3681 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.3375 12 0.11 19.% + Gint_interface cal_gint 0.88193 25 0.035 13.% + Gint_Gamma distri_vl_value 0.62846 12 0.052 8.9% + Gint_Gamma distri_vl 2.4964 6 0.42 35.% + LCAO_Deepks cal_projected_DM 5.0429 14 0.36 72.% + LCAO_gen_fixedH add_v_delta 2.3654 6 0.39 34.% + LCAO_DESCRIPTOR add_v_delta 2.3653 6 0.39 34.% + ElecStateLCAO psiToRho 1.3045 12 0.11 19.% + Charge mix_rho 0.71169 11 0.065 10.% + LOOP_ions force_stress 0.57456 1 0.57 8.2% + Force_Stress_LCAO getForceStress 0.57454 1 0.57 8.2% + Force_LCAO_gamma ftable_gamma 0.36207 1 0.36 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.17938 1 0.18 2.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:41 2022 + Finish Time : Wed Sep 28 11:06:48 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..35de8fb14ed32654d933d2a7d1fe737ab96b95cf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123553 ima = 3.68292e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123628536973 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112231702781 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112998644231 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113181891409 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113171435051 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113178775175 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113175526612 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113177201863 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113176672874 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113176633726 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113176614391 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113176606163 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b2f0766ab69b72fbe2e02f0838de8fe992d06220 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.217374297166 30.341401615890 9.468217363687 0 0 0 +H +0.0 +2 +-11.122470775465 28.850424463967 8.747876234035 0 0 0 +-8.450518573212 29.718556899604 9.764643546944 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/conv new file mode 100644 index 0000000000000000000000000000000000000000..e3b8e6039123e71f4e5c9f4c3bad80aa454e981f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/conv @@ -0,0 +1 @@ +270 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0dc6ea29b35d541d5a2cc96c509b1f51fb12c1c8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749572629 0.01240137669 1.244826272 1.337534363 1.467854251 0.008307249244 0.01802195491 0.03907641312 +2.904711679e-18 0.000897140601 0.002366462978 0.01141208223 0.04115206011 1.26282337e-19 1.566428997e-06 4.861979446e-06 +0.001622896012 0.005833523061 + +H atom_index 1 n_descriptor 18 +1.203354501 0.03584007369 0.09237751221 0.129961049 0.3058157158 0.01976840848 0.02563590786 0.0392519268 +3.076438644e-18 3.562293591e-05 0.08671109697 0.1110672697 0.1138984833 4.562250278e-18 5.800372449e-06 0.01398535587 +0.02373646249 0.02846832354 + +H atom_index 2 n_descriptor 18 +1.195752762 0.03607904327 0.09011148869 0.1268662442 0.3029746707 0.01941998352 0.02519128719 0.03956468955 +-3.105381376e-17 3.500784103e-05 0.08475337536 0.1083398937 0.1135826789 -4.881451058e-19 6.029222083e-06 0.01420458475 +0.02342108088 0.0280652774 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5b050e7f71315c0bbedfd354dbc48aa6c053dd97 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:41 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0879947 SEC) : SETUP UNITCELL + DONE(0.103204 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.121404 SEC) : INIT PLANEWAVE + DONE(0.171111 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449643 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651968e+02 0.000000e+00 2.113e-01 5.193e-01 + GE2 -4.663893e+02 -1.192430e+00 9.888e-02 4.413e-01 + GE3 -4.663950e+02 -5.675816e-03 6.386e-02 5.008e-01 + GE4 -4.663936e+02 1.369295e-03 1.998e-03 3.890e-01 + GE5 -4.663932e+02 3.849513e-04 9.138e-04 3.859e-01 + GE6 -4.663933e+02 -1.471945e-04 1.905e-04 3.852e-01 + GE7 -4.663933e+02 3.490786e-05 2.513e-05 3.636e-01 + GE8 -4.663933e+02 -3.003046e-05 1.117e-05 3.638e-01 + GE9 -4.663933e+02 1.176966e-05 2.086e-06 3.636e-01 + GE10 -4.663933e+02 -2.472437e-06 4.846e-07 3.669e-01 + GE11 -4.663933e+02 -1.170132e-07 1.641e-07 3.670e-01 + GE12 -4.663933e+02 -5.672335e-08 1.100e-08 3.104e-01 +E_delta_band = -6.77762302e-02 Ry = -9.22142919e-01 eV +E_delta_NN= -1.93540696e-01 Ry = -2.63325627e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0428 11 0.64 1e+02 % + Run_lcao lcao_line 7.0331 1 7 1e+02 % + Potential init_pot 0.28533 2 0.14 4.1 % + PW_Basis recip2real 0.27437 17 0.016 3.9 % + PW_Basis gathers_scatterp 0.12474 17 0.0073 1.8 % + Potential v_of_rho 0.91832 14 0.066 13 % + XC_Functional v_xc 0.25536 15 0.017 3.6 % + H_Hartree_pw v_hartree 0.62367 14 0.045 8.9 % + PW_Basis real2recip 0.60748 41 0.015 8.6 % + PW_Basis gatherp_scatters 0.24515 41 0.006 3.5 % + ORB_control set_orb_tables 1.1149 1 1.1 16 % + ORB_gen_tables gen_tables 1.1149 1 1.1 16 % + ORB_table_phi init_Table 0.48955 1 0.49 7 % + ORB_table_phi cal_ST_Phi12_R 0.48459 126 0.0038 6.9 % + ORB_table_beta init_Table_Beta 0.19405 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.19252 56 0.0034 2.7 % + ORB_table_alpha init_Table_Alpha 0.24999 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.2481 66 0.0038 3.5 % + LOOP_ions opt_ions 5.3921 1 5.4 77 % + ESolver_KS_LCAO Run 4.8174 1 4.8 68 % + HSolverLCAO solve 2.6939 12 0.22 38 % + HamiltLCAO updateHk 1.3681 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.3375 12 0.11 19 % + Gint_interface cal_gint 0.88193 25 0.035 13 % + Gint_Gamma distri_vl_value 0.62846 12 0.052 8.9 % + Gint_Gamma distri_vl 2.4964 6 0.42 35 % + LCAO_Deepks cal_projected_DM 5.0429 14 0.36 72 % + LCAO_gen_fixedH add_v_delta 2.3654 6 0.39 34 % + LCAO_DESCRIPTOR add_v_delta 2.3653 6 0.39 34 % + ElecStateLCAO psiToRho 1.3045 12 0.11 19 % + Charge mix_rho 0.71169 11 0.065 10 % + LOOP_ions force_stress 0.57456 1 0.57 8.2 % + Force_Stress_LCAO getForceStress 0.57454 1 0.57 8.2 % + Force_LCAO_gamma ftable_gamma 0.36207 1 0.36 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.17938 1 0.18 2.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:41 2022 + FINISH Time : Wed Sep 28 11:06:48 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/270/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d630af98a00823eda5bc187ddac1f9f50f1d84fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.650389 0.0852843 0.335567 +H 0.624633 0.0292687 0.31455 +H 0.714807 0.0785854 0.334434 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1161959941cf899e30b73207d3b1632514ab6644 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3132 2 + 2 -13.2798 2 + 3 -8.96596 2 + 4 -6.74909 2 + 5 1.39182 0 + 6 4.56987 0 + 7 11.059 0 + 8 11.2937 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0a6f5a60320910f8590cacb4e22cb743259de7c3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:08 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.2108985979 2.38796065225 9.39587152922 0 0 0 0 + tauc_H1 17.4897110185 0.819523045357 8.80741039356 0 0 0 0 + tauc_H2 20.0145908051 2.20039213711 9.36415711039 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0868148384847 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0895575844434 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107942042979 (SEC) + + DONE : INIT CHARGE Time : 0.158115593825 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438121 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000546 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00192 + + Density error is 0.21652058214 + + Energy Rydberg eV + E_KohnSham -34.1900000219 -465.178814918 + E_Harris -34.3847027161 -467.827880975 + E_Fermi -0.410031117376 -5.57875955362 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000840703779688 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00149784299564 + + Density error is 0.0978511071222 + + Energy Rydberg eV + E_KohnSham -34.2802906822 -466.407282375 + E_Harris -34.2869295873 -466.497609311 + E_Fermi -0.217715076822 -2.96216558528 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000811766524292 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013681991678 + + Density error is 0.06265889834 + + Energy Rydberg eV + E_KohnSham -34.28056521 -466.411017516 + E_Harris -34.2848338672 -466.469095577 + E_Fermi -0.205297184367 -2.79321149074 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000779661777393 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113729842565 + + Density error is 0.00206284862533 + + Energy Rydberg eV + E_KohnSham -34.2805777046 -466.411187514 + E_Harris -34.2805801812 -466.411221211 + E_Fermi -0.169856143209 -2.31101138794 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000781625576557 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011337617642 + + Density error is 0.000890608480187 + + Energy Rydberg eV + E_KohnSham -34.2805139225 -466.410319715 + E_Harris -34.280515233 -466.410337544 + E_Fermi -0.168927053959 -2.2983704802 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00078089228092 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113152590019 + + Density error is 0.000184074191942 + + Energy Rydberg eV + E_KohnSham -34.2805545628 -466.410872654 + E_Harris -34.2805546326 -466.410873604 + E_Fermi -0.169024965843 -2.29970263972 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000781115215804 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113116724628 + + Density error is 4.24652560063e-05 + + Energy Rydberg eV + E_KohnSham -34.2805392367 -466.410664132 + E_Harris -34.2805392465 -466.410664265 + E_Fermi -0.168861176582 -2.2974741725 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000781055173659 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113119180665 + + Density error is 1.87598207103e-05 + + Energy Rydberg eV + E_KohnSham -34.2805442515 -466.410732362 + E_Harris -34.2805442531 -466.410732383 + E_Fermi -0.168909915296 -2.29813729672 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000781065607102 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113115315003 + + Density error is 2.50820119817e-06 + + Energy Rydberg eV + E_KohnSham -34.280542672 -466.410710871 + E_Harris -34.280542672 -466.410710872 + E_Fermi -0.16889102738 -2.29788031344 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000781064705689 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113114392011 + + Density error is 4.18290820155e-07 + + Energy Rydberg eV + E_KohnSham -34.2805429435 -466.410714565 + E_Harris -34.2805429435 -466.410714565 + E_Fermi -0.168888492324 -2.29784582224 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000781065486398 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113114406853 + + Density error is 1.61923227761e-07 + + Energy Rydberg eV + E_KohnSham -34.2805429727 -466.410714963 + E_Harris -34.2805429727 -466.410714963 + E_Fermi -0.168888345621 -2.29784382624 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000781065723517 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113114370516 + + Density error is 1.0116099706e-08 + + Energy Rydberg eV + E_KohnSham -34.280542975 -466.410714994 + E_Harris -34.280542975 -466.410714994 + E_band -7.98313116549 -108.616071732 + E_one_elec -69.4611752902 -945.067773723 + E_Hartree +36.1258398362 +491.517266808 + E_xc -8.22335501001 -111.884484813 + E_Ewald +7.40215001075 +100.711417597 + E_demet -1.60648102196e-82 -2.18572956275e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195045491176 -2.65373004921 + E_Fermi -0.168888191902 -2.29784173479 + + charge density convergence is achieved + final etot is -466.410714994 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3132 2.00000 + 2 -13.2798 2.00000 + 3 -8.96596 2.00000 + 4 -6.74909 2.00000 + 5 1.39182 0.00000 + 6 4.56987 0.00000 + 7 11.0590 0.00000 + 8 11.2937 0.00000 + + EFERMI = -2.297841734790544 eV + OUT.ABACUS/ final etot is -466.4107149936992 eV + correction force for each atom along direction 1 is -1.05364e-06 + correction force for each atom along direction 2 is -2.45219e-05 + correction force for each atom along direction 3 is 3.08291e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.72615101 +0.72405409 +0.25193847 + H1 +0.015008023 -0.45550016 -0.16726432 + H2 +0.71114298 -0.26855393 -0.084674150 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4107149936992 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.0768 11 0.73 1.0e+02% + Run_lcao lcao_line 8.0676 1 8.1 1.e+02% + Potential init_pot 0.28253 2 0.14 3.5% + PW_Basis recip2real 0.28867 17 0.017 3.6% + PW_Basis gathers_scatterp 0.13916 17 0.0082 1.7% + Potential v_of_rho 1.1152 14 0.080 14.% + XC_Functional v_xc 0.37997 15 0.025 4.7% + H_Hartree_pw v_hartree 0.69434 14 0.050 8.6% + PW_Basis real2recip 0.71861 41 0.018 8.9% + PW_Basis gatherp_scatters 0.32143 41 0.0078 4.0% + ORB_control set_orb_tables 1.0909 1 1.1 14.% + ORB_gen_tables gen_tables 1.0909 1 1.1 14.% + ORB_table_phi init_Table 0.47479 1 0.47 5.9% + ORB_table_phi cal_ST_Phi12_R 0.46966 126 0.0037 5.8% + ORB_table_beta init_Table_Beta 0.18322 1 0.18 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18170 56 0.0032 2.2% + ORB_table_alpha init_Table_Alpha 0.24837 1 0.25 3.1% + ORB_table_alpha S_PhiAlpha_R 0.24644 66 0.0037 3.1% + LOOP_ions opt_ions 6.4607 1 6.5 80.% + ESolver_KS_LCAO Run 5.8520 1 5.9 72.% + HSolverLCAO solve 3.3425 12 0.28 41.% + HamiltLCAO updateHk 1.6660 12 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.6365 12 0.14 20.% + Gint_interface cal_gint 1.1477 25 0.046 14.% + Gint_Gamma distri_vl_value 0.78124 12 0.065 9.7% + Gint_Gamma distri_vl 3.0415 6 0.51 38.% + LCAO_Deepks cal_projected_DM 6.1015 14 0.44 76.% + LCAO_gen_fixedH add_v_delta 2.9076 6 0.48 36.% + LCAO_DESCRIPTOR add_v_delta 2.9077 6 0.48 36.% + ElecStateLCAO psiToRho 1.6414 12 0.14 20.% + Charge mix_rho 0.79031 11 0.072 9.8% + LOOP_ions force_stress 0.60858 1 0.61 7.5% + Force_Stress_LCAO getForceStress 0.60856 1 0.61 7.5% + Force_LCAO_gamma ftable_gamma 0.39007 1 0.39 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.20929 1 0.21 2.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:08 2022 + Finish Time : Wed Sep 28 11:04:16 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8d5bb0f07fb6e75ba5378ee1b00696f74aae0bf1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123583 ima = 3.68909e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123327356184 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112443929718 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112914609341 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113162843793 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113108377144 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113140863025 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113132002573 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113135178095 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113134388366 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113134305285 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113134291358 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113134283698 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5bcc6ad218cb60e54917dda2b99ef3a0d021d939 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.789101402145 30.387960652242 9.395871529229 0 0 0 +H +0.0 +2 +-10.510288981513 28.819523045382 8.807410393575 0 0 0 +-7.985409194877 30.200392137098 9.364157110403 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/conv new file mode 100644 index 0000000000000000000000000000000000000000..f5963d2dd142bb9a43734ef0838d860278e275c8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/conv @@ -0,0 +1 @@ +271 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9439bf6d7448b68699a2522d31d7bec36910047d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74635301 0.0126937625 1.282771443 1.372027839 1.469504865 0.00808485305 0.01967914257 0.0389418433 +-1.715440531e-18 0.001149057038 0.002513125075 0.01252437338 0.04459331935 9.184687444e-22 1.805170742e-06 5.444982489e-06 +0.001721339433 0.005803079632 + +H atom_index 1 n_descriptor 18 +1.250192383 0.03388515143 0.108380492 0.1507093922 0.3221048614 0.02203245687 0.02840985446 0.03705056498 +-2.32723082e-19 4.309932686e-05 0.1022814239 0.114852486 0.1294625677 -2.005583229e-18 4.255427019e-06 0.01302104153 +0.02629026031 0.03083799798 + +H atom_index 2 n_descriptor 18 +1.258276784 0.0336027962 0.1112026688 0.1545050513 0.3246079294 0.02239265471 0.0288763097 0.03682064244 +-5.213436315e-18 4.381583277e-05 0.1041147252 0.1153381176 0.132731005 2.376065967e-18 3.83522346e-06 0.01299172759 +0.02658365501 0.03119129088 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..854af3ed00d806bf3491e396432c36f615a89697 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:08 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.086837 SEC) : SETUP UNITCELL + DONE(0.0895771 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107964 SEC) : INIT PLANEWAVE + DONE(0.158261 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438192 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651788e+02 0.000000e+00 2.165e-01 5.900e-01 + GE2 -4.664073e+02 -1.228467e+00 9.785e-02 5.453e-01 + GE3 -4.664110e+02 -3.735142e-03 6.266e-02 6.084e-01 + GE4 -4.664112e+02 -1.699976e-04 2.063e-03 4.689e-01 + GE5 -4.664103e+02 8.677992e-04 8.906e-04 4.731e-01 + GE6 -4.664109e+02 -5.529390e-04 1.841e-04 4.647e-01 + GE7 -4.664107e+02 2.085216e-04 4.247e-05 4.571e-01 + GE8 -4.664107e+02 -6.822956e-05 1.876e-05 4.463e-01 + GE9 -4.664107e+02 2.149025e-05 2.508e-06 4.500e-01 + GE10 -4.664107e+02 -3.693508e-06 4.183e-07 4.544e-01 + GE11 -4.664107e+02 -3.975582e-07 1.619e-07 4.500e-01 + GE12 -4.664107e+02 -3.115126e-08 1.012e-08 3.768e-01 +E_delta_band = -7.10429694e-02 Ry = -9.66589187e-01 eV +E_delta_NN= -1.95045491e-01 Ry = -2.65373005e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.0768 11 0.73 1e+02 % + Run_lcao lcao_line 8.0676 1 8.1 1e+02 % + Potential init_pot 0.28253 2 0.14 3.5 % + PW_Basis recip2real 0.28867 17 0.017 3.6 % + PW_Basis gathers_scatterp 0.13916 17 0.0082 1.7 % + Potential v_of_rho 1.1152 14 0.08 14 % + XC_Functional v_xc 0.37997 15 0.025 4.7 % + H_Hartree_pw v_hartree 0.69434 14 0.05 8.6 % + PW_Basis real2recip 0.71861 41 0.018 8.9 % + PW_Basis gatherp_scatters 0.32143 41 0.0078 4 % + ORB_control set_orb_tables 1.0909 1 1.1 14 % + ORB_gen_tables gen_tables 1.0909 1 1.1 14 % + ORB_table_phi init_Table 0.47479 1 0.47 5.9 % + ORB_table_phi cal_ST_Phi12_R 0.46966 126 0.0037 5.8 % + ORB_table_beta init_Table_Beta 0.18322 1 0.18 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.1817 56 0.0032 2.2 % + ORB_table_alpha init_Table_Alpha 0.24837 1 0.25 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.24644 66 0.0037 3.1 % + LOOP_ions opt_ions 6.4607 1 6.5 80 % + ESolver_KS_LCAO Run 5.852 1 5.9 72 % + HSolverLCAO solve 3.3425 12 0.28 41 % + HamiltLCAO updateHk 1.666 12 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.6365 12 0.14 20 % + Gint_interface cal_gint 1.1477 25 0.046 14 % + Gint_Gamma distri_vl_value 0.78124 12 0.065 9.7 % + Gint_Gamma distri_vl 3.0415 6 0.51 38 % + LCAO_Deepks cal_projected_DM 6.1015 14 0.44 76 % + LCAO_gen_fixedH add_v_delta 2.9076 6 0.48 36 % + LCAO_DESCRIPTOR add_v_delta 2.9077 6 0.48 36 % + ElecStateLCAO psiToRho 1.6414 12 0.14 20 % + Charge mix_rho 0.79031 11 0.072 9.8 % + LOOP_ions force_stress 0.60858 1 0.61 7.5 % + Force_Stress_LCAO getForceStress 0.60856 1 0.61 7.5 % + Force_LCAO_gamma ftable_gamma 0.39007 1 0.39 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.20929 1 0.21 2.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:08 2022 + FINISH Time : Wed Sep 28 11:04:16 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/271/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..864d9f8ddae8869aab39266d08daa25118b50930 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.665011 0.0948028 0.335209 +H 0.61384 0.0560202 0.333817 +H 0.711782 0.0509542 0.328045 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2a3000aed966be43b90ead0c708d88f9e04301e3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5859 2 + 2 -12.9699 2 + 3 -9.3872 2 + 4 -6.81017 2 + 5 1.43164 0 + 6 4.68202 0 + 7 11.0201 0 + 8 11.2958 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7e9883665e3db4e4edec28788905edf7a4490a1c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/running_scf.log @@ -0,0 +1,780 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:57 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.6203089463 2.65447921649 9.38586233651 0 0 0 0 + tauc_H1 17.1875136555 1.56856499884 9.34688171206 0 0 0 0 + tauc_H2 19.9298925134 1.42671712323 9.18527278819 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0872270386687 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0909542510673 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.109026536866 (SEC) + + DONE : INIT CHARGE Time : 0.158304739948 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.436208 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132 + + Density error is 0.216127390725 + + Energy Rydberg eV + E_KohnSham -34.187621287 -465.146450569 + E_Harris -34.382604189 -467.799329049 + E_Fermi -0.418050549451 -5.68786952456 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109989287719 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124754962598 + + Density error is 0.0972758116217 + + Energy Rydberg eV + E_KohnSham -34.2779671194 -466.375668681 + E_Harris -34.2846799264 -466.467001105 + E_Fermi -0.226563620799 -3.08255620238 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102590269269 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115611054175 + + Density error is 0.0622049697451 + + Energy Rydberg eV + E_KohnSham -34.278243218 -466.379425195 + E_Harris -34.2825708757 -466.438305998 + E_Fermi -0.213172403139 -2.90035933904 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000912230644173 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100223209256 + + Density error is 0.00199378790641 + + Energy Rydberg eV + E_KohnSham -34.2782714203 -466.379808906 + E_Harris -34.2782729454 -466.379829657 + E_Fermi -0.177194626039 -2.41085656911 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000913183536049 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100200184555 + + Density error is 0.000935876867711 + + Energy Rydberg eV + E_KohnSham -34.2781951817 -466.378771628 + E_Harris -34.2781981189 -466.37881159 + E_Fermi -0.176153200711 -2.39668725061 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000911759413847 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100019415813 + + Density error is 9.88288064173e-05 + + Energy Rydberg eV + E_KohnSham -34.2782499129 -466.379516284 + E_Harris -34.2782499272 -466.379516478 + E_Fermi -0.176388350205 -2.3998866236 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000911675511076 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999829050443 + + Density error is 4.6886720205e-05 + + Energy Rydberg eV + E_KohnSham -34.2782324268 -466.379278373 + E_Harris -34.2782324387 -466.379278534 + E_Fermi -0.176265107986 -2.39820982719 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00091166884292 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999854772813 + + Density error is 1.63620630584e-05 + + Energy Rydberg eV + E_KohnSham -34.278234709 -466.379309424 + E_Harris -34.2782347102 -466.37930944 + E_Fermi -0.176324738164 -2.39902113739 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000911662800919 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999846387136 + + Density error is 2.54097305352e-06 + + Energy Rydberg eV + E_KohnSham -34.2782332032 -466.379288936 + E_Harris -34.2782332032 -466.379288937 + E_Fermi -0.176308738134 -2.39880344581 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000911661118241 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999844304267 + + Density error is 2.26947063977e-07 + + Energy Rydberg eV + E_KohnSham -34.2782334206 -466.379291895 + E_Harris -34.2782334206 -466.379291895 + E_Fermi -0.176306043348 -2.39876678136 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000911661336712 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999844854091 + + Density error is 4.68838676867e-08 + + Energy Rydberg eV + E_KohnSham -34.2782334659 -466.37929251 + E_Harris -34.2782334659 -466.37929251 + E_band -8.04855747826 -109.506242385 + E_one_elec -69.7113640135 -948.471765936 + E_Hartree +36.2293164826 +492.925138809 + E_xc -8.24018247004 -112.113434152 + E_Ewald +7.56742127651 +102.960048527 + E_demet -2.08887606019e-88 -2.84206168343e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195628597344 -2.66166361563 + E_Fermi -0.176305993581 -2.39876610425 + + charge density convergence is achieved + final etot is -466.37929251 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5859 2.00000 + 2 -12.9699 2.00000 + 3 -9.38720 2.00000 + 4 -6.81017 2.00000 + 5 1.43164 0.00000 + 6 4.68202 0.00000 + 7 11.0201 0.00000 + 8 11.2958 0.00000 + + EFERMI = -2.398766104249374 eV + OUT.ABACUS/ final etot is -466.3792925102395 eV + correction force for each atom along direction 1 is -4.55097e-05 + correction force for each atom along direction 2 is -0.000147555 + correction force for each atom along direction 3 is 9.40514e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.24161177 +0.95110521 +0.093662100 + H1 -1.4077983 -0.49029981 +0.020375498 + H2 +1.1661865 -0.46080540 -0.11403760 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3792925102395 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7808 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7705 1 6.8 1.e+02% + Potential init_pot 0.28422 2 0.14 4.2% + PW_Basis recip2real 0.25806 16 0.016 3.8% + PW_Basis gathers_scatterp 0.11626 16 0.0073 1.7% + Charge atomic_rho 0.10023 1 0.10 1.5% + Potential v_of_rho 0.86411 13 0.066 13.% + XC_Functional v_xc 0.24813 14 0.018 3.7% + H_Hartree_pw v_hartree 0.58142 13 0.045 8.6% + PW_Basis real2recip 0.56559 38 0.015 8.3% + PW_Basis gatherp_scatters 0.22693 38 0.0060 3.3% + ORB_control set_orb_tables 1.1124 1 1.1 16.% + ORB_gen_tables gen_tables 1.1124 1 1.1 16.% + ORB_table_phi init_Table 0.49000 1 0.49 7.2% + ORB_table_phi cal_ST_Phi12_R 0.48506 126 0.0038 7.2% + ORB_table_beta init_Table_Beta 0.19151 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18996 56 0.0034 2.8% + ORB_table_alpha init_Table_Alpha 0.25113 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.24925 66 0.0038 3.7% + LOOP_ions opt_ions 5.1467 1 5.1 76.% + ESolver_KS_LCAO Run 4.5654 1 4.6 67.% + HSolverLCAO solve 2.5870 11 0.24 38.% + HamiltLCAO updateHk 1.3095 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2811 11 0.12 19.% + Gint_interface cal_gint 0.85318 23 0.037 13.% + Gint_Gamma distri_vl_value 0.59266 11 0.054 8.7% + Gint_Gamma distri_vl 2.1835 6 0.36 32.% + LCAO_Deepks cal_projected_DM 4.7917 13 0.37 71.% + LCAO_gen_fixedH add_v_delta 2.0521 6 0.34 30.% + LCAO_DESCRIPTOR add_v_delta 2.0520 6 0.34 30.% + ElecStateLCAO psiToRho 1.2593 11 0.11 19.% + Charge mix_rho 0.65992 10 0.066 9.7% + LOOP_ions force_stress 0.58109 1 0.58 8.6% + Force_Stress_LCAO getForceStress 0.58106 1 0.58 8.6% + Force_LCAO_gamma ftable_gamma 0.36968 1 0.37 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.18323 1 0.18 2.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:57 2022 + Finish Time : Wed Sep 28 11:03:04 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..fcf80b879ceb41c3c8756e39774ac445324117e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123766 ima = 3.7036e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122528805868 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111550148989 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112026882385 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112316067994 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112237950194 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112281640796 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112279136667 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112282220855 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112281521651 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112281403537 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112281391361 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3d1878a6b7bb85bf898ebf226198ea49761b740b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.379691053722 30.654479216514 9.385862336485 0 0 0 +H +0.0 +2 +-10.812486344513 29.568564998853 9.346881712084 0 0 0 +-8.070107486631 29.426717123225 9.185272788202 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/conv new file mode 100644 index 0000000000000000000000000000000000000000..b5584d90300968bcc11fd9c9c9e4c09e3a29e934 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/conv @@ -0,0 +1 @@ +272 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..06afaeaaa00e4bd4095a361c78613c9560b9dd74 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752953148 0.01288705469 1.287647639 1.368524085 1.470553363 0.009382245898 0.01755926091 0.03912436067 +1.38897041e-18 0.00103231937 0.002928593767 0.01362093595 0.04874674134 1.471488135e-19 2.95096235e-06 7.629692691e-06 +0.001601999588 0.006139912364 + +H atom_index 1 n_descriptor 18 +1.276160662 0.03387636658 0.1203692642 0.1620938249 0.3277056443 0.02441368273 0.02975469068 0.03714436696 +-3.583770746e-17 5.586685261e-05 0.1083074457 0.1189726505 0.1391982033 1.575529472e-18 1.942500188e-06 0.01340033505 +0.02821847305 0.0318896944 + +H atom_index 2 n_descriptor 18 +1.269835421 0.03408129698 0.1179694533 0.158956094 0.3257863694 0.02410352941 0.02938881538 0.03727819702 +4.429963516e-17 5.525199239e-05 0.1078056908 0.1176507891 0.1365234795 8.031075942e-18 2.293222186e-06 0.01335639283 +0.02800521551 0.03163078211 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..1e44272b15f85439026d95e10fd2581a98f9ceb7 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..3be9461cee46794a7a39e171256be7430548d950 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:57 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872538 SEC) : SETUP UNITCELL + DONE(0.0909699 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.109043 SEC) : INIT PLANEWAVE + DONE(0.158434 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.43627 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651465e+02 0.000000e+00 2.161e-01 5.275e-01 + GE2 -4.663757e+02 -1.229218e+00 9.728e-02 4.520e-01 + GE3 -4.663794e+02 -3.756514e-03 6.220e-02 5.078e-01 + GE4 -4.663798e+02 -3.837113e-04 1.994e-03 4.039e-01 + GE5 -4.663788e+02 1.037278e-03 9.359e-04 3.957e-01 + GE6 -4.663795e+02 -7.446557e-04 9.883e-05 3.835e-01 + GE7 -4.663793e+02 2.379110e-04 4.689e-05 3.817e-01 + GE8 -4.663793e+02 -3.105129e-05 1.636e-05 3.795e-01 + GE9 -4.663793e+02 2.048760e-05 2.541e-06 3.762e-01 + GE10 -4.663793e+02 -2.958298e-06 2.269e-07 3.757e-01 + GE11 -4.663793e+02 -6.156133e-07 4.688e-08 3.207e-01 +E_delta_band = -7.22038559e-02 Ry = -9.82383858e-01 eV +E_delta_NN= -1.95628597e-01 Ry = -2.66166362e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7808 11 0.62 1e+02 % + Run_lcao lcao_line 6.7705 1 6.8 1e+02 % + Potential init_pot 0.28422 2 0.14 4.2 % + PW_Basis recip2real 0.25806 16 0.016 3.8 % + PW_Basis gathers_scatterp 0.11626 16 0.0073 1.7 % + Charge atomic_rho 0.10023 1 0.1 1.5 % + Potential v_of_rho 0.86411 13 0.066 13 % + XC_Functional v_xc 0.24813 14 0.018 3.7 % + H_Hartree_pw v_hartree 0.58142 13 0.045 8.6 % + PW_Basis real2recip 0.56559 38 0.015 8.3 % + PW_Basis gatherp_scatters 0.22693 38 0.006 3.3 % + ORB_control set_orb_tables 1.1124 1 1.1 16 % + ORB_gen_tables gen_tables 1.1124 1 1.1 16 % + ORB_table_phi init_Table 0.49 1 0.49 7.2 % + ORB_table_phi cal_ST_Phi12_R 0.48506 126 0.0038 7.2 % + ORB_table_beta init_Table_Beta 0.19151 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18996 56 0.0034 2.8 % + ORB_table_alpha init_Table_Alpha 0.25113 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.24925 66 0.0038 3.7 % + LOOP_ions opt_ions 5.1467 1 5.1 76 % + ESolver_KS_LCAO Run 4.5654 1 4.6 67 % + HSolverLCAO solve 2.587 11 0.24 38 % + HamiltLCAO updateHk 1.3095 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2811 11 0.12 19 % + Gint_interface cal_gint 0.85318 23 0.037 13 % + Gint_Gamma distri_vl_value 0.59266 11 0.054 8.7 % + Gint_Gamma distri_vl 2.1835 6 0.36 32 % + LCAO_Deepks cal_projected_DM 4.7917 13 0.37 71 % + LCAO_gen_fixedH add_v_delta 2.0521 6 0.34 30 % + LCAO_DESCRIPTOR add_v_delta 2.052 6 0.34 30 % + ElecStateLCAO psiToRho 1.2593 11 0.11 19 % + Charge mix_rho 0.65992 10 0.066 9.7 % + LOOP_ions force_stress 0.58109 1 0.58 8.6 % + Force_Stress_LCAO getForceStress 0.58106 1 0.58 8.6 % + Force_LCAO_gamma ftable_gamma 0.36968 1 0.37 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.18323 1 0.18 2.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:57 2022 + FINISH Time : Wed Sep 28 11:03:04 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/272/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b7fc2d4487a698e9441416c1f03bce9682cdbfbb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.67314 0.0924036 0.331656 +H 0.617048 0.119581 0.358711 +H 0.652848 0.0427388 0.285926 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c3adc1e03e86dd4933a3c24cd02687e6bc5b6cd5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.6381 2 + 2 -12.6868 2 + 3 -8.84682 2 + 4 -6.59249 2 + 5 0.731978 0 + 6 3.57165 0 + 7 11.2221 0 + 8 11.4458 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0c5fbb22628f3a4158a512cf4c5990db59a4272b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.8479081256 2.587300926 9.28635415377 0 0 0 0 + tauc_H1 17.2773470835 3.3482793497 10.0438994169 0 0 0 0 + tauc_H2 18.2797554357 1.19668775898 8.00592101733 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.102697145675 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.107639754032 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.125691502068 (SEC) + + DONE : INIT CHARGE Time : 0.168768577738 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.452875 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000555 + + Density error is 0.209839882115 + + Energy Rydberg eV + E_KohnSham -34.1841808497 -465.099641018 + E_Harris -34.3647203398 -467.556006797 + E_Fermi -0.370073980599 -5.03511481769 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117138471752 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000693192382814 + + Density error is 0.0999779271811 + + Energy Rydberg eV + E_KohnSham -34.2710509565 -466.281569457 + E_Harris -34.2786508044 -466.384970692 + E_Fermi -0.181310323886 -2.46685351107 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110928184268 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000670008570095 + + Density error is 0.0648051503444 + + Energy Rydberg eV + E_KohnSham -34.2715415526 -466.28824436 + E_Harris -34.27626044 -466.352448116 + E_Fermi -0.178252622994 -2.42525135617 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000997583220423 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000653650467257 + + Density error is 0.00216670804541 + + Energy Rydberg eV + E_KohnSham -34.2713802002 -466.286049048 + E_Harris -34.2713884605 -466.286161435 + E_Fermi -0.143728017885 -1.95552000548 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000994052426454 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000651650453312 + + Density error is 0.000932081832086 + + Energy Rydberg eV + E_KohnSham -34.2713772514 -466.286008926 + E_Harris -34.2713779287 -466.286018142 + E_Fermi -0.143919871236 -1.95813030424 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992355210799 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000651751102308 + + Density error is 0.000223413679235 + + Energy Rydberg eV + E_KohnSham -34.2713722062 -466.285940284 + E_Harris -34.2713722131 -466.285940377 + E_Fermi -0.143232508119 -1.94877824925 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992445313419 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000651836216023 + + Density error is 2.14327698274e-05 + + Energy Rydberg eV + E_KohnSham -34.2713767035 -466.286001472 + E_Harris -34.2713767036 -466.286001473 + E_Fermi -0.14329961057 -1.94969122493 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992391578363 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000651806386727 + + Density error is 6.61329599608e-06 + + Energy Rydberg eV + E_KohnSham -34.2713767881 -466.286002622 + E_Harris -34.2713767881 -466.286002624 + E_Fermi -0.143298550661 -1.94967680413 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992382161268 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000651808274654 + + Density error is 2.11224938868e-06 + + Energy Rydberg eV + E_KohnSham -34.2713764895 -466.285998561 + E_Harris -34.2713764895 -466.285998561 + E_Fermi -0.14329217444 -1.9495900512 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992379830935 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000651808406141 + + Density error is 4.15403559607e-07 + + Energy Rydberg eV + E_KohnSham -34.2713765836 -466.28599984 + E_Harris -34.2713765836 -466.28599984 + E_Fermi -0.143292014465 -1.94958787462 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992379491626 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000651808779043 + + Density error is 1.85866226166e-07 + + Energy Rydberg eV + E_KohnSham -34.2713765485 -466.285999363 + E_Harris -34.2713765485 -466.285999363 + E_Fermi -0.143291484883 -1.94958066929 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992379500297 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000651808641907 + + Density error is 1.11452524165e-08 + + Energy Rydberg eV + E_KohnSham -34.2713765637 -466.28599957 + E_Harris -34.2713765637 -466.28599957 + E_band -7.75619177148 -105.528402873 + E_one_elec -68.0354642288 -925.669979587 + E_Hartree +35.455737889 +482.400062085 + E_xc -8.1161436764 -110.425799786 + E_Ewald +6.55132295871 +89.1353216767 + E_demet -7.53666153417e-45 -1.02541540762e-43 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.192571592804 -2.62007093508 + E_Fermi -0.14329165287 -1.94958295487 + + charge density convergence is achieved + final etot is -466.28599957 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.6381 2.00000 + 2 -12.6868 2.00000 + 3 -8.84682 2.00000 + 4 -6.59249 2.00000 + 5 0.731978 0.00000 + 6 3.57165 0.00000 + 7 11.2221 0.00000 + 8 11.4458 0.00000 + + EFERMI = -1.949582954868453 eV + OUT.ABACUS/ final etot is -466.2859995698151 eV + correction force for each atom along direction 1 is -0.000146176 + correction force for each atom along direction 2 is 4.41765e-05 + correction force for each atom along direction 3 is -5.69258e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.3948963 -1.2167473 -1.0982762 + H1 +0.95179899 -0.80236584 -0.77473853 + H2 +0.44309730 +2.0191132 +1.8730148 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2859995698151 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5300 11 0.59 1.0e+02% + Run_lcao lcao_line 6.5200 1 6.5 1.e+02% + Potential init_pot 0.28629 2 0.14 4.4% + PW_Basis recip2real 0.27780 17 0.016 4.3% + PW_Basis gathers_scatterp 0.12649 17 0.0074 1.9% + Potential v_of_rho 0.87905 14 0.063 13.% + XC_Functional v_xc 0.23233 15 0.015 3.6% + H_Hartree_pw v_hartree 0.60261 14 0.043 9.2% + PW_Basis real2recip 0.69635 41 0.017 11.% + PW_Basis gatherp_scatters 0.27971 41 0.0068 4.3% + ORB_control set_orb_tables 1.0945 1 1.1 17.% + ORB_gen_tables gen_tables 1.0945 1 1.1 17.% + ORB_table_phi init_Table 0.47479 1 0.47 7.3% + ORB_table_phi cal_ST_Phi12_R 0.46961 126 0.0037 7.2% + ORB_table_beta init_Table_Beta 0.18246 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18097 56 0.0032 2.8% + ORB_table_alpha init_Table_Alpha 0.24805 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24605 66 0.0037 3.8% + LOOP_ions opt_ions 4.8905 1 4.9 75.% + ESolver_KS_LCAO Run 4.4110 1 4.4 68.% + HSolverLCAO solve 1.9592 12 0.16 30.% + HamiltLCAO updateHk 1.0692 12 0.089 16.% + LCAO_Hamilt cal_Hgamma 1.0395 12 0.087 16.% + Gint_interface cal_gint 0.75337 25 0.030 12.% + Gint_Gamma distri_vl_value 0.33708 12 0.028 5.2% + Gint_Gamma distri_vl 2.2991 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.6325 14 0.33 71.% + LCAO_gen_fixedH add_v_delta 2.1510 6 0.36 33.% + LCAO_DESCRIPTOR add_v_delta 2.1510 6 0.36 33.% + ElecStateLCAO psiToRho 0.87047 12 0.073 13.% + Charge mix_rho 0.97201 11 0.088 15.% + LOOP_ions force_stress 0.47936 1 0.48 7.3% + Force_Stress_LCAO getForceStress 0.47933 1 0.48 7.3% + Force_LCAO_gamma ftable_gamma 0.28236 1 0.28 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.16082 1 0.16 2.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:48 2022 + Finish Time : Wed Sep 28 11:03:54 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4eaf8c2431ee1e51854ca728faf5208590b98304 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123335 ima = 3.66583e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124345589346 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112751945223 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113679979109 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113818963599 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113836450937 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113830061395 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113831287192 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113831828703 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113831639868 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113831703995 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113831676231 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113831686402 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d96cb683bb257c9bf2c02985d14a72e07e5b83b1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.152091874440 30.587300926016 9.286354153756 0 0 0 +H +0.0 +2 +-10.722652916468 31.348279349671 10.043899416907 0 0 0 +-9.720244564306 29.196687758982 8.005921017337 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/conv new file mode 100644 index 0000000000000000000000000000000000000000..0fb5b9efe530598043ef85aa5a038233018aa7e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/conv @@ -0,0 +1 @@ +273 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8d019cf701078ed01adf4e3edfee1d4fd677c135 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74762211 0.01204326226 1.221334926 1.326284562 1.466664021 0.007829309549 0.01864835313 0.0390645469 +-8.123750864e-19 0.0008260354111 0.002097522041 0.0104558601 0.03714408978 -2.37280528e-19 1.03616198e-06 3.563656907e-06 +0.001639501283 0.005499373019 + +H atom_index 1 n_descriptor 18 +1.188254776 0.0361043215 0.08725560159 0.1248926823 0.3021715239 0.01869172686 0.02491035696 0.03974700485 +-5.725836869e-18 2.799476268e-05 0.08113973336 0.1064527531 0.1136833156 1.84895381e-18 5.558964906e-06 0.01424243543 +0.02252078283 0.02776140336 + +H atom_index 2 n_descriptor 18 +1.132456498 0.03751722895 0.07243897768 0.1042665064 0.2796578703 0.01624668948 0.02169654385 0.04194053431 +-1.526785534e-17 2.432193556e-05 0.06778730378 0.08810077935 0.1099064017 -2.270889228e-18 6.122318906e-06 0.01614475173 +0.02020770542 0.02462054575 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..cc633e0306a98b5e7a7bd216b97112cada0a8b64 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.102722 SEC) : SETUP UNITCELL + DONE(0.107656 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.125712 SEC) : INIT PLANEWAVE + DONE(0.168904 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.45294 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650996e+02 0.000000e+00 2.098e-01 4.756e-01 + GE2 -4.662816e+02 -1.181928e+00 9.998e-02 4.182e-01 + GE3 -4.662882e+02 -6.674903e-03 6.481e-02 4.894e-01 + GE4 -4.662860e+02 2.195312e-03 2.167e-03 3.472e-01 + GE5 -4.662860e+02 4.012159e-05 9.321e-04 3.461e-01 + GE6 -4.662859e+02 6.864244e-05 2.234e-04 3.444e-01 + GE7 -4.662860e+02 -6.118857e-05 2.143e-05 3.325e-01 + GE8 -4.662860e+02 -1.150290e-06 6.613e-06 3.300e-01 + GE9 -4.662860e+02 4.061961e-06 2.112e-06 3.292e-01 + GE10 -4.662860e+02 -1.279559e-06 4.154e-07 3.309e-01 + GE11 -4.662860e+02 4.772374e-07 1.859e-07 3.297e-01 + GE12 -4.662860e+02 -2.069611e-07 1.115e-08 2.745e-01 +E_delta_band = -6.57420866e-02 Ry = -8.94466976e-01 eV +E_delta_NN= -1.92571593e-01 Ry = -2.62007094e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.53 11 0.59 1e+02 % + Run_lcao lcao_line 6.52 1 6.5 1e+02 % + Potential init_pot 0.28629 2 0.14 4.4 % + PW_Basis recip2real 0.2778 17 0.016 4.3 % + PW_Basis gathers_scatterp 0.12649 17 0.0074 1.9 % + Potential v_of_rho 0.87905 14 0.063 13 % + XC_Functional v_xc 0.23233 15 0.015 3.6 % + H_Hartree_pw v_hartree 0.60261 14 0.043 9.2 % + PW_Basis real2recip 0.69635 41 0.017 11 % + PW_Basis gatherp_scatters 0.27971 41 0.0068 4.3 % + ORB_control set_orb_tables 1.0945 1 1.1 17 % + ORB_gen_tables gen_tables 1.0945 1 1.1 17 % + ORB_table_phi init_Table 0.47479 1 0.47 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.46961 126 0.0037 7.2 % + ORB_table_beta init_Table_Beta 0.18246 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18097 56 0.0032 2.8 % + ORB_table_alpha init_Table_Alpha 0.24805 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24605 66 0.0037 3.8 % + LOOP_ions opt_ions 4.8905 1 4.9 75 % + ESolver_KS_LCAO Run 4.411 1 4.4 68 % + HSolverLCAO solve 1.9592 12 0.16 30 % + HamiltLCAO updateHk 1.0692 12 0.089 16 % + LCAO_Hamilt cal_Hgamma 1.0395 12 0.087 16 % + Gint_interface cal_gint 0.75337 25 0.03 12 % + Gint_Gamma distri_vl_value 0.33708 12 0.028 5.2 % + Gint_Gamma distri_vl 2.2991 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.6325 14 0.33 71 % + LCAO_gen_fixedH add_v_delta 2.151 6 0.36 33 % + LCAO_DESCRIPTOR add_v_delta 2.151 6 0.36 33 % + ElecStateLCAO psiToRho 0.87047 12 0.073 13 % + Charge mix_rho 0.97201 11 0.088 15 % + LOOP_ions force_stress 0.47936 1 0.48 7.3 % + Force_Stress_LCAO getForceStress 0.47933 1 0.48 7.3 % + Force_LCAO_gamma ftable_gamma 0.28236 1 0.28 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.16082 1 0.16 2.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:48 2022 + FINISH Time : Wed Sep 28 11:03:54 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/273/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c43c6bcaef6dbe7b80c1ee1675fa889755539f89 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.666563 0.0812142 0.330228 +H 0.65359 0.143653 0.337724 +H 0.616606 0.0636851 0.29711 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..55886776133c6f0beae2d5dd1ce155493efb20bf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.7702 2 + 2 -13.1449 2 + 3 -9.3895 2 + 4 -6.84818 2 + 5 1.56431 0 + 6 4.9496 0 + 7 10.9747 0 + 8 11.2414 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..8bf964c54976cb13afdcc77c063b5254ba7ae3fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.6637551609 2.27399719228 9.24637357058 0 0 0 0 + tauc_H1 18.3005307047 4.0222959975 9.4562812726 0 0 0 0 + tauc_H2 17.2649802004 1.78318396251 8.31907886482 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105086762567 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105470321263 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123471707117 (SEC) + + DONE : INIT CHARGE Time : 0.16682509381 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449623 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000685 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0016 + + Density error is 0.218075800689 + + Energy Rydberg eV + E_KohnSham -34.1828039353 -465.080907137 + E_Harris -34.3821889105 -467.793678895 + E_Fermi -0.43028057845 -5.85426760566 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000972324378729 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00143755992967 + + Density error is 0.0968176987406 + + Energy Rydberg eV + E_KohnSham -34.2735682248 -466.315818648 + E_Harris -34.2802310513 -466.406471054 + E_Fermi -0.237413755622 -3.23017986003 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000924322999206 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132613411239 + + Density error is 0.0615360040623 + + Energy Rydberg eV + E_KohnSham -34.2737204523 -466.31788981 + E_Harris -34.2779301847 -466.375166158 + E_Fermi -0.221021929615 -3.00715762572 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000857061358646 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115157106298 + + Density error is 0.00210391434516 + + Energy Rydberg eV + E_KohnSham -34.2738016169 -466.318994112 + E_Harris -34.2738054562 -466.319046347 + E_Fermi -0.185011544969 -2.51721120736 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000861137630065 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115211633672 + + Density error is 0.000921735881453 + + Energy Rydberg eV + E_KohnSham -34.27372064 -466.317892365 + E_Harris -34.273724 -466.31793808 + E_Fermi -0.183558451371 -2.4974408547 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000859531151358 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115044079503 + + Density error is 0.000161138987383 + + Energy Rydberg eV + E_KohnSham -34.2737813104 -466.318717827 + E_Harris -34.2737814138 -466.318719234 + E_Fermi -0.184044419592 -2.50405279156 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000859405498025 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115013551654 + + Density error is 4.4639230508e-05 + + Energy Rydberg eV + E_KohnSham -34.2737592302 -466.318417411 + E_Harris -34.2737592397 -466.31841754 + E_Fermi -0.183851829752 -2.50143247235 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000859370753521 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115017480822 + + Density error is 1.96311893598e-05 + + Energy Rydberg eV + E_KohnSham -34.2737637395 -466.318478763 + E_Harris -34.2737637407 -466.318478779 + E_Fermi -0.183907539679 -2.5021904448 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000859358245157 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115012915303 + + Density error is 1.95289687197e-06 + + Energy Rydberg eV + E_KohnSham -34.2737623387 -466.318459704 + E_Harris -34.2737623387 -466.318459704 + E_Fermi -0.183885284119 -2.50188764237 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000859360909762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115012664164 + + Density error is 6.17405846491e-07 + + Energy Rydberg eV + E_KohnSham -34.2737625337 -466.318462358 + E_Harris -34.2737625337 -466.318462358 + E_Fermi -0.183884260835 -2.50187371988 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000859361909129 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115012664609 + + Density error is 1.77173701517e-07 + + Energy Rydberg eV + E_KohnSham -34.2737625495 -466.318462572 + E_Harris -34.2737625495 -466.318462572 + E_Fermi -0.18388389728 -2.50186877345 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000859362040022 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115012635267 + + Density error is 1.02814201883e-08 + + Energy Rydberg eV + E_KohnSham -34.273762555 -466.318462647 + E_Harris -34.273762555 -466.318462647 + E_band -8.10730084365 -110.305486874 + E_one_elec -70.0845777161 -953.549598863 + E_Hartree +36.4054944503 +495.322163031 + E_xc -8.26889027885 -112.504023929 + E_Ewald +7.7968890877 +106.082118267 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196364108329 -2.67167075597 + E_Fermi -0.183883696273 -2.50186603861 + + charge density convergence is achieved + final etot is -466.318462647 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.7702 2.00000 + 2 -13.1449 2.00000 + 3 -9.38950 2.00000 + 4 -6.84818 2.00000 + 5 1.56431 0.00000 + 6 4.94960 0.00000 + 7 10.9747 0.00000 + 8 11.2414 0.00000 + + EFERMI = -2.501866038611169 eV + OUT.ABACUS/ final etot is -466.3184626468592 eV + correction force for each atom along direction 1 is -0.000176437 + correction force for each atom along direction 2 is 4.09182e-05 + correction force for each atom along direction 3 is -0.000154952 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +2.1780058 -0.087995078 +1.2359809 + H1 +0.12451413 +1.4165093 +0.41397693 + H2 -2.3025200 -1.3285142 -1.6499578 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3184626468592 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6768 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6677 1 6.7 1.e+02% + Potential init_pot 0.28479 2 0.14 4.3% + PW_Basis recip2real 0.27204 17 0.016 4.1% + PW_Basis gathers_scatterp 0.12052 17 0.0071 1.8% + Potential v_of_rho 0.97484 14 0.070 15.% + XC_Functional v_xc 0.30165 15 0.020 4.5% + H_Hartree_pw v_hartree 0.62987 14 0.045 9.4% + PW_Basis real2recip 0.73334 41 0.018 11.% + PW_Basis gatherp_scatters 0.30408 41 0.0074 4.6% + ORB_control set_orb_tables 1.1000 1 1.1 16.% + ORB_gen_tables gen_tables 1.1000 1 1.1 16.% + ORB_table_phi init_Table 0.47520 1 0.48 7.1% + ORB_table_phi cal_ST_Phi12_R 0.46982 126 0.0037 7.0% + ORB_table_beta init_Table_Beta 0.18350 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18195 56 0.0032 2.7% + ORB_table_alpha init_Table_Alpha 0.25110 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24905 66 0.0038 3.7% + LOOP_ions opt_ions 5.0382 1 5.0 75.% + ESolver_KS_LCAO Run 4.5464 1 4.5 68.% + HSolverLCAO solve 1.9948 12 0.17 30.% + HamiltLCAO updateHk 1.0819 12 0.090 16.% + LCAO_Hamilt cal_Hgamma 1.0524 12 0.088 16.% + Gint_interface cal_gint 0.80497 25 0.032 12.% + Gint_Gamma distri_vl_value 0.33601 12 0.028 5.0% + Gint_Gamma distri_vl 2.3774 6 0.40 36.% + LCAO_Deepks cal_projected_DM 4.7788 14 0.34 72.% + LCAO_gen_fixedH add_v_delta 2.2315 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2316 6 0.37 33.% + ElecStateLCAO psiToRho 0.89172 12 0.074 13.% + Charge mix_rho 0.97531 11 0.089 15.% + LOOP_ions force_stress 0.49159 1 0.49 7.4% + Force_Stress_LCAO getForceStress 0.49155 1 0.49 7.4% + Force_LCAO_gamma ftable_gamma 0.28885 1 0.29 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.16728 1 0.17 2.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:47 2022 + Finish Time : Wed Sep 28 11:07:54 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0d7bcf8579501a25deccbfec99d10e79eabec4cf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124405 ima = 3.66539e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122328604032 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111605456419 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111952992832 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011226770076 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112180404213 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112230762844 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112222965827 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112225816785 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011222524955 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112225189567 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112225167969 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112225158992 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8573f5c622921ad82b62e3174cb378f97218fa41 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.336244839060 30.273997192260 9.246373570573 0 0 0 +H +0.0 +2 +-9.699469295317 32.022295997478 9.456281272582 0 0 0 +-10.735019799556 29.783183962513 8.319078864803 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/conv new file mode 100644 index 0000000000000000000000000000000000000000..46b56c134ae68c873177bc0c357d56b7b3701ee2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/conv @@ -0,0 +1 @@ +274 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..817c40e6080e0c1a12da224fbb541507832103a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752803813 0.01293289861 1.30106508 1.383083052 1.471464344 0.009508763281 0.01811125683 0.03912577614 +5.667373069e-19 0.001127686693 0.00303998204 0.01406214869 0.05066271252 -1.341673674e-19 3.175754654e-06 7.971163915e-06 +0.00159748311 0.006090920452 + +H atom_index 1 n_descriptor 18 +1.275860194 0.03384928667 0.120482863 0.1618702258 0.3273148561 0.02449708613 0.02973027568 0.03708602338 +-2.345863389e-17 5.940889788e-05 0.1092364156 0.1195463623 0.1391782548 1.075034636e-18 2.003028359e-06 0.0134306878 +0.02861138178 0.03190077948 + +H atom_index 2 n_descriptor 18 +1.314488073 0.03274897851 0.1362034421 0.182296271 0.3380041472 0.02637364046 0.03192127978 0.03684459995 +1.324715193e-17 6.318386646e-05 0.1081677184 0.1317021414 0.1563435269 -2.674387526e-18 3.250138665e-07 0.01440298586 +0.02975798791 0.03326150425 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9b72cfd22e11a4b842b5eeaa4aa7854735f60c0f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:47 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105112 SEC) : SETUP UNITCELL + DONE(0.105484 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123492 SEC) : INIT PLANEWAVE + DONE(0.166961 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449689 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650809e+02 0.000000e+00 2.181e-01 4.829e-01 + GE2 -4.663158e+02 -1.234912e+00 9.682e-02 4.288e-01 + GE3 -4.663179e+02 -2.071162e-03 6.154e-02 5.002e-01 + GE4 -4.663190e+02 -1.104302e-03 2.104e-03 3.594e-01 + GE5 -4.663179e+02 1.101747e-03 9.217e-04 3.585e-01 + GE6 -4.663187e+02 -8.254620e-04 1.611e-04 3.540e-01 + GE7 -4.663184e+02 3.004160e-04 4.464e-05 3.526e-01 + GE8 -4.663185e+02 -6.135236e-05 1.963e-05 3.414e-01 + GE9 -4.663185e+02 1.905907e-05 1.953e-06 3.414e-01 + GE10 -4.663185e+02 -2.653370e-06 6.174e-07 3.407e-01 + GE11 -4.663185e+02 -2.146085e-07 1.772e-07 3.431e-01 + GE12 -4.663185e+02 -7.466997e-08 1.028e-08 2.799e-01 +E_delta_band = -7.36860103e-02 Ry = -1.00254960e+00 eV +E_delta_NN= -1.96364108e-01 Ry = -2.67167076e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6768 11 0.61 1e+02 % + Run_lcao lcao_line 6.6677 1 6.7 1e+02 % + Potential init_pot 0.28479 2 0.14 4.3 % + PW_Basis recip2real 0.27204 17 0.016 4.1 % + PW_Basis gathers_scatterp 0.12052 17 0.0071 1.8 % + Potential v_of_rho 0.97484 14 0.07 15 % + XC_Functional v_xc 0.30165 15 0.02 4.5 % + H_Hartree_pw v_hartree 0.62987 14 0.045 9.4 % + PW_Basis real2recip 0.73334 41 0.018 11 % + PW_Basis gatherp_scatters 0.30408 41 0.0074 4.6 % + ORB_control set_orb_tables 1.1 1 1.1 16 % + ORB_gen_tables gen_tables 1.1 1 1.1 16 % + ORB_table_phi init_Table 0.4752 1 0.48 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.46982 126 0.0037 7 % + ORB_table_beta init_Table_Beta 0.1835 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18195 56 0.0032 2.7 % + ORB_table_alpha init_Table_Alpha 0.2511 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24905 66 0.0038 3.7 % + LOOP_ions opt_ions 5.0382 1 5 75 % + ESolver_KS_LCAO Run 4.5464 1 4.5 68 % + HSolverLCAO solve 1.9948 12 0.17 30 % + HamiltLCAO updateHk 1.0819 12 0.09 16 % + LCAO_Hamilt cal_Hgamma 1.0524 12 0.088 16 % + Gint_interface cal_gint 0.80497 25 0.032 12 % + Gint_Gamma distri_vl_value 0.33601 12 0.028 5 % + Gint_Gamma distri_vl 2.3774 6 0.4 36 % + LCAO_Deepks cal_projected_DM 4.7788 14 0.34 72 % + LCAO_gen_fixedH add_v_delta 2.2315 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2316 6 0.37 33 % + ElecStateLCAO psiToRho 0.89172 12 0.074 13 % + Charge mix_rho 0.97531 11 0.089 15 % + LOOP_ions force_stress 0.49159 1 0.49 7.4 % + Force_Stress_LCAO getForceStress 0.49155 1 0.49 7.4 % + Force_LCAO_gamma ftable_gamma 0.28885 1 0.29 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.16728 1 0.17 2.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:47 2022 + FINISH Time : Wed Sep 28 11:07:54 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/274/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9f4eec1f0c553cca907715da78ef3749a5a5e345 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.657961 0.0830377 0.320481 +H 0.641495 0.145768 0.306489 +H 0.59842 0.0563319 0.337109 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..61bff515ba48862038ba9e735c70b06ab0b9c7e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1058 2 + 2 -12.753 2 + 3 -9.19397 2 + 4 -6.70631 2 + 5 1.10187 0 + 6 4.07652 0 + 7 11.1246 0 + 8 11.3854 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3a9f8e63f7ff45502ed3a36b21f872976c723318 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:09 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.4229208571 2.32505507179 8.9734740176 0 0 0 0 + tauc_H1 17.9618501153 4.08150844986 8.58168296458 0 0 0 0 + tauc_H2 16.7557549291 1.57729336245 9.43904355104 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874430711627 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0934618419516 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.1114825514 (SEC) + + DONE : INIT CHARGE Time : 0.159591223374 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437807 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000722 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00151 + + Density error is 0.21145708217 + + Energy Rydberg eV + E_KohnSham -34.1929431005 -465.218857557 + E_Harris -34.3775398966 -467.730425816 + E_Fermi -0.392110774214 -5.3349407765 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00092412482381 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124271626012 + + Density error is 0.0983728206013 + + Energy Rydberg eV + E_KohnSham -34.2803035472 -466.407457412 + E_Harris -34.2872778813 -466.502348095 + E_Fermi -0.203188966981 -2.76452772168 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000879626745495 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114926190944 + + Density error is 0.0633066074559 + + Energy Rydberg eV + E_KohnSham -34.2805983394 -466.411468265 + E_Harris -34.2850996302 -466.472711469 + E_Fermi -0.194869049271 -2.65132943393 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000814442727347 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000982753008419 + + Density error is 0.00194430978259 + + Energy Rydberg eV + E_KohnSham -34.2805280161 -466.410511468 + E_Harris -34.2805288437 -466.410522728 + E_Fermi -0.159535810306 -2.17059605522 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813852633689 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000982495730293 + + Density error is 0.000857272447426 + + Energy Rydberg eV + E_KohnSham -34.280492953 -466.410034409 + E_Harris -34.2804934466 -466.410041126 + E_Fermi -0.159331960447 -2.16782253559 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0008130207128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980304541784 + + Density error is 0.000149365287508 + + Energy Rydberg eV + E_KohnSham -34.2805106206 -466.410274789 + E_Harris -34.280510461 -466.410272618 + E_Fermi -0.159006592302 -2.16339567487 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813094994534 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980241846873 + + Density error is 2.67553552306e-05 + + Energy Rydberg eV + E_KohnSham -34.2805057922 -466.410209096 + E_Harris -34.2805057946 -466.410209129 + E_Fermi -0.15895134662 -2.16264401881 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813043040511 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980222700441 + + Density error is 1.31746716394e-05 + + Energy Rydberg eV + E_KohnSham -34.2805080947 -466.410240424 + E_Harris -34.2805080956 -466.410240435 + E_Fermi -0.158970742901 -2.16290791874 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813044542715 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980212386444 + + Density error is 1.90965547347e-06 + + Energy Rydberg eV + E_KohnSham -34.280507058 -466.410226319 + E_Harris -34.280507058 -466.410226319 + E_Fermi -0.158958140975 -2.16273646074 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813043920075 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980206303376 + + Density error is 4.32845784944e-07 + + Energy Rydberg eV + E_KohnSham -34.2805072854 -466.410229412 + E_Harris -34.2805072854 -466.410229412 + E_Fermi -0.158956573829 -2.16271513864 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813044578973 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980206497 + + Density error is 1.43617735529e-07 + + Energy Rydberg eV + E_KohnSham -34.2805072975 -466.410229577 + E_Harris -34.2805072975 -466.410229577 + E_Fermi -0.158956375278 -2.16271243721 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813044748637 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980206292311 + + Density error is 1.11746946512e-08 + + Energy Rydberg eV + E_KohnSham -34.2805073017 -466.410229634 + E_Harris -34.2805073017 -466.410229634 + E_band -7.90242559171 -107.518016068 + E_one_elec -68.8392102595 -936.60550535 + E_Hartree +35.8231767353 +487.399324061 + E_xc -8.1748068791 -111.223953605 + E_Ewald +7.03557570655 +95.7239183195 + E_demet -3.50155143126e-65 -4.76410513052e-64 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194021740458 -2.63980120611 + E_Fermi -0.158956243097 -2.1627106388 + + charge density convergence is achieved + final etot is -466.410229634 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1058 2.00000 + 2 -12.7530 2.00000 + 3 -9.19397 2.00000 + 4 -6.70631 2.00000 + 5 1.10187 0.00000 + 6 4.07652 0.00000 + 7 11.1246 0.00000 + 8 11.3854 0.00000 + + EFERMI = -2.162710638795527 eV + OUT.ABACUS/ final etot is -466.4102296339032 eV + correction force for each atom along direction 1 is -0.000165943 + correction force for each atom along direction 2 is 0.000108002 + correction force for each atom along direction 3 is -1.93747e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0882054 -0.022718580 +0.17960694 + H1 +0.18833826 -0.25118580 +0.036880981 + H2 +0.89986710 +0.27390439 -0.21648792 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4102296339032 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0195 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0092 1 7.0 1.e+02% + Potential init_pot 0.28375 2 0.14 4.0% + PW_Basis recip2real 0.27385 17 0.016 3.9% + PW_Basis gathers_scatterp 0.12367 17 0.0073 1.8% + Potential v_of_rho 0.91713 14 0.066 13.% + XC_Functional v_xc 0.25618 15 0.017 3.6% + H_Hartree_pw v_hartree 0.62340 14 0.045 8.9% + PW_Basis real2recip 0.60803 41 0.015 8.7% + PW_Basis gatherp_scatters 0.24874 41 0.0061 3.5% + ORB_control set_orb_tables 1.1137 1 1.1 16.% + ORB_gen_tables gen_tables 1.1137 1 1.1 16.% + ORB_table_phi init_Table 0.48695 1 0.49 6.9% + ORB_table_phi cal_ST_Phi12_R 0.48203 126 0.0038 6.9% + ORB_table_beta init_Table_Beta 0.19078 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18927 56 0.0034 2.7% + ORB_table_alpha init_Table_Alpha 0.25598 1 0.26 3.6% + ORB_table_alpha S_PhiAlpha_R 0.25412 66 0.0039 3.6% + LOOP_ions opt_ions 5.3461 1 5.3 76.% + ESolver_KS_LCAO Run 4.7752 1 4.8 68.% + HSolverLCAO solve 2.6440 12 0.22 38.% + HamiltLCAO updateHk 1.3416 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.3109 12 0.11 19.% + Gint_interface cal_gint 1.0093 25 0.040 14.% + Gint_Gamma distri_vl_value 0.56115 12 0.047 8.0% + Gint_Gamma distri_vl 2.4688 6 0.41 35.% + LCAO_Deepks cal_projected_DM 5.0181 14 0.36 71.% + LCAO_gen_fixedH add_v_delta 2.3391 6 0.39 33.% + LCAO_DESCRIPTOR add_v_delta 2.3391 6 0.39 33.% + ElecStateLCAO psiToRho 1.2816 12 0.11 18.% + Charge mix_rho 0.71534 11 0.065 10.% + LOOP_ions force_stress 0.57077 1 0.57 8.1% + Force_Stress_LCAO getForceStress 0.57074 1 0.57 8.1% + Force_LCAO_gamma ftable_gamma 0.35735 1 0.36 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.19501 1 0.20 2.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:09 2022 + Finish Time : Wed Sep 28 11:12:16 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6d88120fb719622fdedf1ae8c4a3ebf31443db39 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123433 ima = 3.66687e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123173443034 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111999233727 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112681471056 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011288507578 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112863763594 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112876108215 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112872533813 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112874514511 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112873871568 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112873827145 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112873809089 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112873802085 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/STRU new file mode 100644 index 0000000000000000000000000000000000000000..81de834692ddb147bb529c3d7d5df0e3ea91c2ed --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.577079142900 30.325055071818 8.973474017606 0 0 0 +H +0.0 +2 +-10.038149884733 32.081508449854 8.581682964587 0 0 0 +-11.244245070863 29.577293362443 9.439043551056 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/conv new file mode 100644 index 0000000000000000000000000000000000000000..26929dd59e85f6c0baa2f61a6cd69e959fa9687e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/conv @@ -0,0 +1 @@ +275 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..09ed2f9940e48874564f387ead43a16cc55d02c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751255523 0.01255425482 1.253880357 1.342687535 1.468531757 0.00870542154 0.01753401123 0.03911532676 +-9.010800738e-19 0.0009071204217 0.002531230957 0.01197688464 0.04326111268 -1.839039704e-19 1.942720558e-06 5.70550798e-06 +0.001602136238 0.00597621552 + +H atom_index 1 n_descriptor 18 +1.228236136 0.035211418 0.1010084643 0.1400650093 0.3136757872 0.02127215048 0.02702232347 0.038422144 +-3.39881053e-17 4.161884453e-05 0.09442736222 0.11457905 0.1199715822 -3.786039697e-18 4.852456499e-06 0.0135190001 +0.02515682136 0.02970227168 + +H atom_index 2 n_descriptor 18 +1.206313896 0.0359316482 0.09407391484 0.1307165146 0.3057767082 0.020239841 0.02573556207 0.03928147279 +3.966386473e-18 3.96930263e-05 0.08870905578 0.1117858269 0.1137934443 -6.488957999e-18 5.775525388e-06 0.01402837544 +0.02427092966 0.0285850459 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4d7ea246ad2f9a0e82d2399a14a182a17b8dcc4c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:09 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874663 SEC) : SETUP UNITCELL + DONE(0.0934832 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.111504 SEC) : INIT PLANEWAVE + DONE(0.159726 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.437874 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652189e+02 0.000000e+00 2.115e-01 5.146e-01 + GE2 -4.664075e+02 -1.188600e+00 9.837e-02 4.414e-01 + GE3 -4.664115e+02 -4.010853e-03 6.331e-02 4.915e-01 + GE4 -4.664105e+02 9.567968e-04 1.944e-03 3.859e-01 + GE5 -4.664100e+02 4.770584e-04 8.573e-04 3.829e-01 + GE6 -4.664103e+02 -2.403800e-04 1.494e-04 3.808e-01 + GE7 -4.664102e+02 6.569356e-05 2.676e-05 3.631e-01 + GE8 -4.664102e+02 -3.132787e-05 1.317e-05 3.632e-01 + GE9 -4.664102e+02 1.410510e-05 1.910e-06 3.609e-01 + GE10 -4.664102e+02 -3.093391e-06 4.328e-07 3.628e-01 + GE11 -4.664102e+02 -1.650862e-07 1.436e-07 3.619e-01 + GE12 -4.664102e+02 -5.686875e-08 1.117e-08 3.051e-01 +E_delta_band = -6.87791356e-02 Ry = -9.35788147e-01 eV +E_delta_NN= -1.94021740e-01 Ry = -2.63980121e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0195 11 0.64 1e+02 % + Run_lcao lcao_line 7.0092 1 7 1e+02 % + Potential init_pot 0.28375 2 0.14 4 % + PW_Basis recip2real 0.27385 17 0.016 3.9 % + PW_Basis gathers_scatterp 0.12367 17 0.0073 1.8 % + Potential v_of_rho 0.91713 14 0.066 13 % + XC_Functional v_xc 0.25618 15 0.017 3.6 % + H_Hartree_pw v_hartree 0.6234 14 0.045 8.9 % + PW_Basis real2recip 0.60803 41 0.015 8.7 % + PW_Basis gatherp_scatters 0.24874 41 0.0061 3.5 % + ORB_control set_orb_tables 1.1137 1 1.1 16 % + ORB_gen_tables gen_tables 1.1137 1 1.1 16 % + ORB_table_phi init_Table 0.48695 1 0.49 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.48203 126 0.0038 6.9 % + ORB_table_beta init_Table_Beta 0.19078 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18927 56 0.0034 2.7 % + ORB_table_alpha init_Table_Alpha 0.25598 1 0.26 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.25412 66 0.0039 3.6 % + LOOP_ions opt_ions 5.3461 1 5.3 76 % + ESolver_KS_LCAO Run 4.7752 1 4.8 68 % + HSolverLCAO solve 2.644 12 0.22 38 % + HamiltLCAO updateHk 1.3416 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.3109 12 0.11 19 % + Gint_interface cal_gint 1.0093 25 0.04 14 % + Gint_Gamma distri_vl_value 0.56115 12 0.047 8 % + Gint_Gamma distri_vl 2.4688 6 0.41 35 % + LCAO_Deepks cal_projected_DM 5.0181 14 0.36 71 % + LCAO_gen_fixedH add_v_delta 2.3391 6 0.39 33 % + LCAO_DESCRIPTOR add_v_delta 2.3391 6 0.39 33 % + ElecStateLCAO psiToRho 1.2816 12 0.11 18 % + Charge mix_rho 0.71534 11 0.065 10 % + LOOP_ions force_stress 0.57077 1 0.57 8.1 % + Force_Stress_LCAO getForceStress 0.57074 1 0.57 8.1 % + Force_LCAO_gamma ftable_gamma 0.35735 1 0.36 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.19501 1 0.2 2.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:09 2022 + FINISH Time : Wed Sep 28 11:12:16 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/275/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..bc83887be5c2dd51d80e698ea63452cb179f8775 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.657301 0.0803928 0.321776 +H 0.612389 0.126007 0.310492 +H 0.695455 0.105949 0.367429 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..a1e9ce7e435ba4e97c1ebcfe6f4270e24a8fdc3e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3834 2 + 2 -13.1596 2 + 3 -9.108 2 + 4 -6.76575 2 + 5 1.39512 0 + 6 4.57418 0 + 7 11.0504 0 + 8 11.2995 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c80a483a6d67df9c37ba8f96e28bd8d784680b5a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:57 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.4044353328 2.25099969342 9.00972835399 0 0 0 0 + tauc_H1 17.1468976931 3.52818817895 8.69378340691 0 0 0 0 + tauc_H2 19.4727322504 2.96657488958 10.2880143673 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0736639491914 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0866575872035 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103322402862 (SEC) + + DONE : INIT CHARGE Time : 0.14494950149 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.393258 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119 + + Density error is 0.216120661457 + + Energy Rydberg eV + E_KohnSham -34.1903386442 -465.183422111 + E_Harris -34.3844807601 -467.824861108 + E_Fermi -0.41128900324 -5.59587396881 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000954247952971 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123844285665 + + Density error is 0.0977534542957 + + Energy Rydberg eV + E_KohnSham -34.2805127952 -466.410304376 + E_Harris -34.2871828197 -466.501054716 + E_Fermi -0.219535348513 -2.98693165219 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000911527564932 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116443113188 + + Density error is 0.0625717227878 + + Energy Rydberg eV + E_KohnSham -34.2807989972 -466.414198355 + E_Harris -34.2850963147 -466.472666359 + E_Fermi -0.207082465836 -2.81750149126 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000856341593072 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104367261849 + + Density error is 0.0020142845131 + + Energy Rydberg eV + E_KohnSham -34.2808107934 -466.41435885 + E_Harris -34.2808127066 -466.414384881 + E_Fermi -0.171475025826 -2.33303741594 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0008583857193 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104342757918 + + Density error is 0.000901270986914 + + Energy Rydberg eV + E_KohnSham -34.2807432072 -466.413439293 + E_Harris -34.2807449599 -466.413463139 + E_Fermi -0.170536082533 -2.32026243705 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000857323461214 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010419147367 + + Density error is 0.000150586788208 + + Energy Rydberg eV + E_KohnSham -34.2807884211 -466.414054459 + E_Harris -34.2807884714 -466.414055144 + E_Fermi -0.170673229579 -2.32212841834 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000857479667281 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104190991581 + + Density error is 4.18204478396e-05 + + Energy Rydberg eV + E_KohnSham -34.2807719211 -466.413829966 + E_Harris -34.2807719306 -466.413830094 + E_Fermi -0.170526405726 -2.32013077733 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000857429923381 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001041869149 + + Density error is 1.5440974345e-05 + + Energy Rydberg eV + E_KohnSham -34.2807761812 -466.413887927 + E_Harris -34.2807761821 -466.41388794 + E_Fermi -0.17057406218 -2.32077917665 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00085743217048 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104185337155 + + Density error is 1.95925478937e-06 + + Energy Rydberg eV + E_KohnSham -34.2807747658 -466.41386867 + E_Harris -34.2807747658 -466.41386867 + E_Fermi -0.170557977261 -2.3205603301 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000857431697628 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104185223278 + + Density error is 2.00394040524e-07 + + Energy Rydberg eV + E_KohnSham -34.2807749608 -466.413871323 + E_Harris -34.2807749608 -466.413871323 + E_Fermi -0.170556005981 -2.32053350946 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000857432182212 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104185284785 + + Density error is 6.99433231919e-08 + + Energy Rydberg eV + E_KohnSham -34.2807749933 -466.413871764 + E_Harris -34.2807749933 -466.413871764 + E_band -7.99911702212 -108.83357047 + E_one_elec -69.5026360268 -945.631875984 + E_Hartree +36.1401689848 +491.712224876 + E_xc -8.22577197127 -111.917369258 + E_Ewald +7.43135657297 +101.108793262 + E_demet -1.19477171433e-83 -1.62557031241e-82 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19518244428 -2.65559339177 + E_Fermi -0.170555986937 -2.32053325036 + + charge density convergence is achieved + final etot is -466.413871764 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3834 2.00000 + 2 -13.1596 2.00000 + 3 -9.10800 2.00000 + 4 -6.76575 2.00000 + 5 1.39512 0.00000 + 6 4.57418 0.00000 + 7 11.0504 0.00000 + 8 11.2995 0.00000 + + EFERMI = -2.320533250361687 eV + OUT.ABACUS/ final etot is -466.4138717643226 eV + correction force for each atom along direction 1 is -5.74287e-05 + correction force for each atom along direction 2 is 3.20865e-05 + correction force for each atom along direction 3 is -4.37479e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.059940979 -0.75289335 -0.47210529 + H1 -0.43136733 +0.43282006 -0.11123012 + H2 +0.49130831 +0.32007329 +0.58333541 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4138717643226 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0284 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0206 1 7.0 1.e+02% + Potential init_pot 0.24869 2 0.12 3.5% + PW_Basis recip2real 0.23011 16 0.014 3.3% + PW_Basis gathers_scatterp 0.10920 16 0.0068 1.6% + Potential v_of_rho 0.92012 13 0.071 13.% + XC_Functional v_xc 0.32278 14 0.023 4.6% + H_Hartree_pw v_hartree 0.56831 13 0.044 8.1% + PW_Basis real2recip 0.60914 38 0.016 8.7% + PW_Basis gatherp_scatters 0.27552 38 0.0073 3.9% + ORB_control set_orb_tables 0.90861 1 0.91 13.% + ORB_gen_tables gen_tables 0.90860 1 0.91 13.% + ORB_table_phi init_Table 0.38306 1 0.38 5.5% + ORB_table_phi cal_ST_Phi12_R 0.37878 126 0.0030 5.4% + ORB_table_beta init_Table_Beta 0.15664 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15533 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.21087 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20923 66 0.0032 3.0% + LOOP_ions opt_ions 5.6465 1 5.6 80.% + ESolver_KS_LCAO Run 5.0942 1 5.1 72.% + HSolverLCAO solve 2.9473 11 0.27 42.% + HamiltLCAO updateHk 1.4666 11 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.4430 11 0.13 21.% + Gint_interface cal_gint 1.0320 23 0.045 15.% + Gint_Gamma distri_vl_value 0.67750 11 0.062 9.6% + Gint_Gamma distri_vl 2.4325 6 0.41 35.% + LCAO_Deepks cal_projected_DM 5.3253 13 0.41 76.% + LCAO_gen_fixedH add_v_delta 2.3066 6 0.38 33.% + LCAO_DESCRIPTOR add_v_delta 2.3066 6 0.38 33.% + ElecStateLCAO psiToRho 1.4619 11 0.13 21.% + Charge mix_rho 0.71531 10 0.072 10.% + LOOP_ions force_stress 0.55216 1 0.55 7.9% + Force_Stress_LCAO getForceStress 0.55214 1 0.55 7.9% + Force_LCAO_gamma ftable_gamma 0.35885 1 0.36 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.19393 1 0.19 2.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:57 2022 + Finish Time : Wed Sep 28 11:11:04 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..f0a650abcc2a836e61ce7d9529e589855a87b9fb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123749 ima = 3.66557e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123053079116 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112106762873 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011259276595 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112852127192 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112791172294 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112827688175 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112820175845 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112823146677 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112822555767 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112822472279 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112822464391 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/STRU new file mode 100644 index 0000000000000000000000000000000000000000..00d2073f97c8c780451b8a8ab0a2f7f754228c02 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.595564667216 30.250999693409 9.009728353969 0 0 0 +H +0.0 +2 +-10.853102306910 31.528188178954 8.693783406889 0 0 0 +-8.527267749597 30.966574889555 10.288014367314 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/conv new file mode 100644 index 0000000000000000000000000000000000000000..2d2fcdeb02af513a6fdf3f68d0d94d0e5620cea2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/conv @@ -0,0 +1 @@ +276 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b01be39cf4db7fc9156918777423d8c2e9a1ad61 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748760602 0.01274858363 1.282532828 1.369278575 1.469761494 0.008495403107 0.01888857945 0.0390076206 +-4.537454323e-18 0.001110535258 0.002640254072 0.01270139757 0.04596065777 -6.025183582e-20 2.117942438e-06 6.07559141e-06 +0.001664700808 0.005945612414 + +H atom_index 1 n_descriptor 18 +1.255641335 0.03398060759 0.1104943152 0.1526747376 0.3228551137 0.02254734492 0.0286480637 0.03714416247 +1.410173358e-18 4.733528582e-05 0.1037915501 0.1152431344 0.131154919 -1.208780265e-17 3.869746707e-06 0.01312609313 +0.02669829873 0.03103725151 + +H atom_index 2 n_descriptor 18 +1.261113175 0.03379314872 0.1124420384 0.1552785156 0.3245656159 0.02279962669 0.02896519264 0.03699506394 +5.466840519e-18 4.785079388e-05 0.1049276875 0.1156861213 0.1333926142 2.338428748e-18 3.562833873e-06 0.01311578374 +0.02689469384 0.03127501003 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/dm_eig.npy new file mode 100644 index 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..df4f1f1aa594377e9187bf01a734a689fee73442 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:57 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0736813 SEC) : SETUP UNITCELL + DONE(0.0866722 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103336 SEC) : INIT PLANEWAVE + DONE(0.145054 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.393302 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651834e+02 0.000000e+00 2.161e-01 5.322e-01 + GE2 -4.664103e+02 -1.226882e+00 9.775e-02 5.092e-01 + GE3 -4.664142e+02 -3.893978e-03 6.257e-02 5.698e-01 + GE4 -4.664144e+02 -1.604954e-04 2.014e-03 4.501e-01 + GE5 -4.664134e+02 9.195566e-04 9.013e-04 4.480e-01 + GE6 -4.664141e+02 -6.151658e-04 1.506e-04 4.412e-01 + GE7 -4.664138e+02 2.244936e-04 4.182e-05 4.370e-01 + GE8 -4.664139e+02 -5.796107e-05 1.544e-05 4.291e-01 + GE9 -4.664139e+02 1.925681e-05 1.959e-06 4.319e-01 + GE10 -4.664139e+02 -2.652669e-06 2.004e-07 4.298e-01 + GE11 -4.664139e+02 -4.418100e-07 6.994e-08 3.607e-01 +E_delta_band = -7.12898913e-02 Ry = -9.69948731e-01 eV +E_delta_NN= -1.95182444e-01 Ry = -2.65559339e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0284 11 0.64 1e+02 % + Run_lcao lcao_line 7.0206 1 7 1e+02 % + Potential init_pot 0.24869 2 0.12 3.5 % + PW_Basis recip2real 0.23011 16 0.014 3.3 % + PW_Basis gathers_scatterp 0.1092 16 0.0068 1.6 % + Potential v_of_rho 0.92012 13 0.071 13 % + XC_Functional v_xc 0.32278 14 0.023 4.6 % + H_Hartree_pw v_hartree 0.56831 13 0.044 8.1 % + PW_Basis real2recip 0.60914 38 0.016 8.7 % + PW_Basis gatherp_scatters 0.27552 38 0.0073 3.9 % + ORB_control set_orb_tables 0.90861 1 0.91 13 % + ORB_gen_tables gen_tables 0.9086 1 0.91 13 % + ORB_table_phi init_Table 0.38306 1 0.38 5.5 % + ORB_table_phi cal_ST_Phi12_R 0.37878 126 0.003 5.4 % + ORB_table_beta init_Table_Beta 0.15664 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15533 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.21087 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20923 66 0.0032 3 % + LOOP_ions opt_ions 5.6465 1 5.6 80 % + ESolver_KS_LCAO Run 5.0942 1 5.1 72 % + HSolverLCAO solve 2.9473 11 0.27 42 % + HamiltLCAO updateHk 1.4666 11 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.443 11 0.13 21 % + Gint_interface cal_gint 1.032 23 0.045 15 % + Gint_Gamma distri_vl_value 0.6775 11 0.062 9.6 % + Gint_Gamma distri_vl 2.4325 6 0.41 35 % + LCAO_Deepks cal_projected_DM 5.3253 13 0.41 76 % + LCAO_gen_fixedH add_v_delta 2.3066 6 0.38 33 % + LCAO_DESCRIPTOR add_v_delta 2.3066 6 0.38 33 % + ElecStateLCAO psiToRho 1.4619 11 0.13 21 % + Charge mix_rho 0.71531 10 0.072 10 % + LOOP_ions force_stress 0.55216 1 0.55 7.9 % + Force_Stress_LCAO getForceStress 0.55214 1 0.55 7.9 % + Force_LCAO_gamma ftable_gamma 0.35885 1 0.36 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.19393 1 0.19 2.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:57 2022 + FINISH Time : Wed Sep 28 11:11:04 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/276/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..1668feb9ef23d39810e29b6e6cf76ed8be02610c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.671988 0.0780059 0.329981 +H 0.611879 0.105457 0.32646 +H 0.710402 0.12895 0.32713 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..4e55e99163339128901776d5194aefa8c547414f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4137 2 + 2 -13.023 2 + 3 -9.22351 2 + 4 -6.77192 2 + 5 1.34735 0 + 6 4.5387 0 + 7 11.0514 0 + 8 11.3086 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4998fa672578467a4570c934abac20a644f8b8fd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:53 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.8156520494 2.18416655007 9.23945553097 0 0 0 0 + tauc_H1 17.132617189 2.95279572435 9.14087020263 0 0 0 0 + tauc_H2 19.8912533428 3.61059960126 9.15963967342 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0729287132555 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0875169025692 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103844762431 (SEC) + + DONE : INIT CHARGE Time : 0.14595805473 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388313 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112 + + Density error is 0.215542533228 + + Energy Rydberg eV + E_KohnSham -34.1892117966 -465.168090563 + E_Harris -34.3825141851 -467.798104483 + E_Fermi -0.410745231314 -5.5884755722 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00123712732215 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113299560446 + + Density error is 0.0977362014794 + + Energy Rydberg eV + E_KohnSham -34.2793086113 -466.393920614 + E_Harris -34.2860423693 -466.485538091 + E_Fermi -0.219575792472 -2.98748192049 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114667690533 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105732582092 + + Density error is 0.0626110406416 + + Energy Rydberg eV + E_KohnSham -34.2796071758 -466.397982793 + E_Harris -34.2839578738 -466.457177076 + E_Fermi -0.207580028907 -2.82427118414 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000997498221012 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000931289333179 + + Density error is 0.00198333360223 + + Energy Rydberg eV + E_KohnSham -34.2796098308 -466.398018916 + E_Harris -34.2796110548 -466.398035569 + E_Fermi -0.171809583121 -2.33758930145 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000997443495804 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000930956028334 + + Density error is 0.000910245704691 + + Energy Rydberg eV + E_KohnSham -34.2795440908 -466.397124477 + E_Harris -34.2795456293 -466.39714541 + E_Fermi -0.171014643301 -2.32677359033 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000995747772513 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000929433347842 + + Density error is 0.000117983741368 + + Energy Rydberg eV + E_KohnSham -34.2795863952 -466.397700057 + E_Harris -34.2795864145 -466.39770032 + E_Fermi -0.171065370832 -2.3274637738 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00099566404416 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000929353876831 + + Density error is 4.32057961973e-05 + + Energy Rydberg eV + E_KohnSham -34.2795722657 -466.397507816 + E_Harris -34.2795722763 -466.39750796 + E_Fermi -0.170940677086 -2.32576722835 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000995661950603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092932384234 + + Density error is 1.31874643173e-05 + + Energy Rydberg eV + E_KohnSham -34.2795756302 -466.397553592 + E_Harris -34.2795756309 -466.397553602 + E_Fermi -0.170988254278 -2.32641454926 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000995647016927 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000929309386135 + + Density error is 1.66008945046e-06 + + Energy Rydberg eV + E_KohnSham -34.2795742059 -466.397534214 + E_Harris -34.2795742059 -466.397534214 + E_Fermi -0.170974288726 -2.32622453817 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00099564384409 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009293094817 + + Density error is 1.83230354744e-07 + + Energy Rydberg eV + E_KohnSham -34.2795743854 -466.397536656 + E_Harris -34.2795743854 -466.397536656 + E_Fermi -0.17097284353 -2.32620487527 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000995644108148 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000929310006837 + + Density error is 5.21500091147e-08 + + Energy Rydberg eV + E_KohnSham -34.2795744145 -466.397537053 + E_Harris -34.2795744145 -466.397537053 + E_band -8.00137316376 -108.864266851 + E_one_elec -69.4689451093 -945.173487535 + E_Hartree +36.120161273 +491.440005992 + E_xc -8.22269129193 -111.875454465 + E_Ewald +7.41585536156 +100.897888461 + E_demet -7.97146392028e-82 -1.08457330717e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195173328582 -2.65546936634 + E_Fermi -0.170972825119 -2.32620462477 + + charge density convergence is achieved + final etot is -466.397537053 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4137 2.00000 + 2 -13.0230 2.00000 + 3 -9.22351 2.00000 + 4 -6.77192 2.00000 + 5 1.34735 0.00000 + 6 4.53870 0.00000 + 7 11.0514 0.00000 + 8 11.3086 0.00000 + + EFERMI = -2.326204624772461 eV + OUT.ABACUS/ final etot is -466.3975370527519 eV + correction force for each atom along direction 1 is -2.46655e-05 + correction force for each atom along direction 2 is 8.12170e-05 + correction force for each atom along direction 3 is -0.000189607 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.2621110 -0.96288710 +0.031546567 + H1 +0.11213819 -0.25050239 +0.025979985 + H2 +1.1499728 +1.2133895 -0.057526552 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3975370527519 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1041 11 0.65 1.0e+02% + Run_lcao lcao_line 7.0965 1 7.1 1.e+02% + Potential init_pot 0.24103 2 0.12 3.4% + PW_Basis recip2real 0.22525 16 0.014 3.2% + PW_Basis gathers_scatterp 0.10685 16 0.0067 1.5% + Potential v_of_rho 0.91726 13 0.071 13.% + XC_Functional v_xc 0.32448 14 0.023 4.6% + H_Hartree_pw v_hartree 0.56342 13 0.043 7.9% + PW_Basis real2recip 0.60510 38 0.016 8.5% + PW_Basis gatherp_scatters 0.27290 38 0.0072 3.8% + ORB_control set_orb_tables 0.90114 1 0.90 13.% + ORB_gen_tables gen_tables 0.90114 1 0.90 13.% + ORB_table_phi init_Table 0.37812 1 0.38 5.3% + ORB_table_phi cal_ST_Phi12_R 0.37392 126 0.0030 5.3% + ORB_table_beta init_Table_Beta 0.15480 1 0.15 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15351 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.21033 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20870 66 0.0032 2.9% + LOOP_ions opt_ions 5.7356 1 5.7 81.% + ESolver_KS_LCAO Run 5.1733 1 5.2 73.% + HSolverLCAO solve 3.0003 11 0.27 42.% + HamiltLCAO updateHk 1.5065 11 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.4830 11 0.13 21.% + Gint_interface cal_gint 1.0838 23 0.047 15.% + Gint_Gamma distri_vl_value 0.69344 11 0.063 9.8% + Gint_Gamma distri_vl 2.4735 6 0.41 35.% + LCAO_Deepks cal_projected_DM 5.4090 13 0.42 76.% + LCAO_gen_fixedH add_v_delta 2.3469 6 0.39 33.% + LCAO_DESCRIPTOR add_v_delta 2.3469 6 0.39 33.% + ElecStateLCAO psiToRho 1.4726 11 0.13 21.% + Charge mix_rho 0.72219 10 0.072 10.% + LOOP_ions force_stress 0.56211 1 0.56 7.9% + Force_Stress_LCAO getForceStress 0.56209 1 0.56 7.9% + Force_LCAO_gamma ftable_gamma 0.36490 1 0.36 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.19797 1 0.20 2.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:53 2022 + Finish Time : Wed Sep 28 11:08:01 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..f45be52e3dff212a404d20124f2e69e00b515e76 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123608 ima = 3.67312e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122924220844 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111897162884 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011242010133 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112685176106 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112626100016 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112659413349 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112654062856 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112657117117 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112656579492 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112656504481 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112656497083 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9f06617a886331f2f36dfca98ed5cc055229f2fa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.184347950567 30.184166550050 9.239455530974 0 0 0 +H +0.0 +2 +-10.867382810953 30.952795724373 9.140870202612 0 0 0 +-8.108746657174 31.610599601253 9.159639673396 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/conv new file mode 100644 index 0000000000000000000000000000000000000000..467e7597bb788b3abaa03848e18b8db1b1d9c957 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/conv @@ -0,0 +1 @@ +277 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..37268bfd1a91d11edf3135bac5123a9272c8e101 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750763635 0.01275793896 1.277516832 1.366664028 1.469861788 0.008854004924 0.0181912155 0.03907242361 +2.019944198e-19 0.00105076852 0.002728881648 0.01282171702 0.04663704852 2.811015094e-20 2.349567666e-06 6.543735524e-06 +0.001622358576 0.006022620672 + +H atom_index 1 n_descriptor 18 +1.231440422 0.03505528358 0.1027171993 0.1413157735 0.3142194894 0.02166438906 0.02719085888 0.03817936053 +6.441430519e-18 4.704622218e-05 0.09798560674 0.1142171402 0.1212746515 9.364251639e-18 4.960565702e-06 0.01348589279 +0.02593635384 0.02988680681 + +H atom_index 2 n_descriptor 18 +1.282412327 0.03334285934 0.1209036878 0.1655026176 0.3303937434 0.02407465843 0.03015145005 0.0367765519 +6.264386523e-18 5.192116631e-05 0.1077286049 0.1192242785 0.1420662783 -7.378044028e-18 2.114374363e-06 0.01334718784 +0.02777212264 0.03212479736 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e0b62d9672056016bd0c695fd7a0decbae1d6f83 Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..b4e8548eb63718cd516da4c38488ec7f2323c0de --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:53 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0729433 SEC) : SETUP UNITCELL + DONE(0.0875299 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103857 SEC) : INIT PLANEWAVE + DONE(0.146064 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.388367 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651681e+02 0.000000e+00 2.155e-01 5.415e-01 + GE2 -4.663939e+02 -1.225830e+00 9.774e-02 5.155e-01 + GE3 -4.663980e+02 -4.062179e-03 6.261e-02 5.780e-01 + GE4 -4.663980e+02 -3.612332e-05 1.983e-03 4.574e-01 + GE5 -4.663971e+02 8.944388e-04 9.102e-04 4.566e-01 + GE6 -4.663977e+02 -5.755799e-04 1.180e-04 4.495e-01 + GE7 -4.663975e+02 1.922412e-04 4.321e-05 4.409e-01 + GE8 -4.663976e+02 -4.577614e-05 1.319e-05 4.367e-01 + GE9 -4.663975e+02 1.937862e-05 1.660e-06 4.360e-01 + GE10 -4.663975e+02 -2.442133e-06 1.832e-07 4.372e-01 + GE11 -4.663975e+02 -3.969087e-07 5.215e-08 3.679e-01 +E_delta_band = -7.12186806e-02 Ry = -9.68979861e-01 eV +E_delta_NN= -1.95173329e-01 Ry = -2.65546937e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1041 11 0.65 1e+02 % + Run_lcao lcao_line 7.0965 1 7.1 1e+02 % + Potential init_pot 0.24103 2 0.12 3.4 % + PW_Basis recip2real 0.22525 16 0.014 3.2 % + PW_Basis gathers_scatterp 0.10685 16 0.0067 1.5 % + Potential v_of_rho 0.91726 13 0.071 13 % + XC_Functional v_xc 0.32448 14 0.023 4.6 % + H_Hartree_pw v_hartree 0.56342 13 0.043 7.9 % + PW_Basis real2recip 0.6051 38 0.016 8.5 % + PW_Basis gatherp_scatters 0.2729 38 0.0072 3.8 % + ORB_control set_orb_tables 0.90114 1 0.9 13 % + ORB_gen_tables gen_tables 0.90114 1 0.9 13 % + ORB_table_phi init_Table 0.37812 1 0.38 5.3 % + ORB_table_phi cal_ST_Phi12_R 0.37392 126 0.003 5.3 % + ORB_table_beta init_Table_Beta 0.1548 1 0.15 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15351 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.21033 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.2087 66 0.0032 2.9 % + LOOP_ions opt_ions 5.7356 1 5.7 81 % + ESolver_KS_LCAO Run 5.1733 1 5.2 73 % + HSolverLCAO solve 3.0003 11 0.27 42 % + HamiltLCAO updateHk 1.5065 11 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.483 11 0.13 21 % + Gint_interface cal_gint 1.0838 23 0.047 15 % + Gint_Gamma distri_vl_value 0.69344 11 0.063 9.8 % + Gint_Gamma distri_vl 2.4735 6 0.41 35 % + LCAO_Deepks cal_projected_DM 5.409 13 0.42 76 % + LCAO_gen_fixedH add_v_delta 2.3469 6 0.39 33 % + LCAO_DESCRIPTOR add_v_delta 2.3469 6 0.39 33 % + ElecStateLCAO psiToRho 1.4726 11 0.13 21 % + Charge mix_rho 0.72219 10 0.072 10 % + LOOP_ions force_stress 0.56211 1 0.56 7.9 % + Force_Stress_LCAO getForceStress 0.56209 1 0.56 7.9 % + Force_LCAO_gamma ftable_gamma 0.3649 1 0.36 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.19797 1 0.2 2.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:53 2022 + FINISH Time : Wed Sep 28 11:08:01 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/277/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..007aac9d03166e106888812fcf0f5f01642c1be1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.683932 0.0717728 0.331616 +H 0.633619 0.0777707 0.372619 +H 0.72608 0.125645 0.342264 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..55fb620635fc12d7027e271b8daed89dbebec323 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9584 2 + 2 -12.9613 2 + 3 -8.89712 2 + 4 -6.66453 2 + 5 1.00938 0 + 6 4.07138 0 + 7 11.1462 0 + 8 11.3739 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3e986d1fcf120d7847191e0438a7d45dc4d54f53 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:34 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.1500852135 2.00963920309 9.28523606496 0 0 0 0 + tauc_H1 17.7413441898 2.17757832395 10.4333423359 0 0 0 0 + tauc_H2 20.3302349286 3.51805170353 9.58340260757 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0729986345123 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.073287191807 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0889606358254 (SEC) + + DONE : INIT CHARGE Time : 0.130317714359 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375238 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103 + + Density error is 0.213097245292 + + Energy Rydberg eV + E_KohnSham -34.187301189 -465.142095412 + E_Harris -34.3748377197 -467.693660814 + E_Fermi -0.38865035735 -5.2878593897 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118319912821 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105676255996 + + Density error is 0.0990235897933 + + Energy Rydberg eV + E_KohnSham -34.2761147621 -466.350466066 + E_Harris -34.2831734347 -466.446504234 + E_Fermi -0.198516197107 -2.70095142595 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111162758596 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100105515938 + + Density error is 0.0638598993793 + + Energy Rydberg eV + E_KohnSham -34.2764954323 -466.355645351 + E_Harris -34.2810048871 -466.416999631 + E_Fermi -0.191178639689 -2.60111883566 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000987717144663 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904405668442 + + Density error is 0.00207876116522 + + Energy Rydberg eV + E_KohnSham -34.2764141799 -466.354539854 + E_Harris -34.2764185901 -466.354599858 + E_Fermi -0.156092383208 -2.12374582603 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000985495524224 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00090106603967 + + Density error is 0.000898134801405 + + Energy Rydberg eV + E_KohnSham -34.2763826968 -466.354111505 + E_Harris -34.2763828812 -466.354114014 + E_Fermi -0.15584151993 -2.12033265603 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983892257453 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000899705822185 + + Density error is 0.000199994773731 + + Energy Rydberg eV + E_KohnSham -34.2763965913 -466.354300549 + E_Harris -34.2763965937 -466.354300582 + E_Fermi -0.155459657142 -2.11513714625 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983997808311 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000899743865897 + + Density error is 2.84855169465e-05 + + Energy Rydberg eV + E_KohnSham -34.2763925244 -466.354245216 + E_Harris -34.276392526 -466.354245239 + E_Fermi -0.155422333653 -2.11462933414 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983931593306 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000899686914674 + + Density error is 1.22793952205e-05 + + Energy Rydberg eV + E_KohnSham -34.2763951789 -466.354281332 + E_Harris -34.2763951795 -466.354281342 + E_Fermi -0.155437386821 -2.11483414299 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983929302089 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000899684086724 + + Density error is 2.64905978311e-06 + + Energy Rydberg eV + E_KohnSham -34.2763942804 -466.354269108 + E_Harris -34.2763942804 -466.354269108 + E_Fermi -0.155426009374 -2.11467934489 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00098392486066 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000899679680798 + + Density error is 5.97481224548e-07 + + Energy Rydberg eV + E_KohnSham -34.2763945101 -466.354272233 + E_Harris -34.2763945101 -466.354272233 + E_Fermi -0.155424198059 -2.11465470068 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983924771351 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000899680040617 + + Density error is 2.07921200845e-07 + + Energy Rydberg eV + E_KohnSham -34.2763944968 -466.354272053 + E_Harris -34.2763944968 -466.354272053 + E_Fermi -0.155423902566 -2.11465068029 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983924632071 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000899680059931 + + Density error is 1.05208594716e-08 + + Energy Rydberg eV + E_KohnSham -34.2763945007 -466.354272105 + E_Harris -34.2763945007 -466.354272105 + E_band -7.8616132851 -106.96273615 + E_one_elec -68.7043928822 -934.771220829 + E_Hartree +35.770675973 +486.685014544 + E_xc -8.16645676258 -111.110344442 + E_Ewald +6.94931024689 +94.5502165275 + E_demet -6.46649962647e-60 -8.79812410348e-59 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19372321196 -2.63573951751 + E_Fermi -0.155423696911 -2.11464788222 + + charge density convergence is achieved + final etot is -466.354272105 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9584 2.00000 + 2 -12.9613 2.00000 + 3 -8.89712 2.00000 + 4 -6.66453 2.00000 + 5 1.00938 0.00000 + 6 4.07138 0.00000 + 7 11.1462 0.00000 + 8 11.3739 0.00000 + + EFERMI = -2.114647882217124 eV + OUT.ABACUS/ final etot is -466.3542721047835 eV + correction force for each atom along direction 1 is -7.78115e-06 + correction force for each atom along direction 2 is 1.07130e-05 + correction force for each atom along direction 3 is 7.47796e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.7489643 +1.2892694 -0.27820600 + H1 -0.23041943 +0.31201187 +0.40400500 + H2 -1.5185448 -1.6012812 -0.12579900 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3542721047835 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6708 11 0.70 1.0e+02% + Run_lcao lcao_line 7.6636 1 7.7 1.e+02% + Potential init_pot 0.24288 2 0.12 3.2% + PW_Basis recip2real 0.23738 17 0.014 3.1% + PW_Basis gathers_scatterp 0.11158 17 0.0066 1.5% + Potential v_of_rho 0.99851 14 0.071 13.% + XC_Functional v_xc 0.36327 15 0.024 4.7% + H_Hartree_pw v_hartree 0.60490 14 0.043 7.9% + PW_Basis real2recip 0.65387 41 0.016 8.5% + PW_Basis gatherp_scatters 0.29500 41 0.0072 3.8% + ORB_control set_orb_tables 0.90465 1 0.90 12.% + ORB_gen_tables gen_tables 0.90465 1 0.90 12.% + ORB_table_phi init_Table 0.37669 1 0.38 4.9% + ORB_table_phi cal_ST_Phi12_R 0.37237 126 0.0030 4.9% + ORB_table_beta init_Table_Beta 0.15704 1 0.16 2.0% + ORB_table_beta VNL_PhiBeta_R 0.15571 56 0.0028 2.0% + ORB_table_alpha init_Table_Alpha 0.21267 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.21104 66 0.0032 2.8% + LOOP_ions opt_ions 6.3144 1 6.3 82.% + ESolver_KS_LCAO Run 5.7467 1 5.7 75.% + HSolverLCAO solve 3.3819 12 0.28 44.% + HamiltLCAO updateHk 1.6663 12 0.14 22.% + LCAO_Hamilt cal_Hgamma 1.6412 12 0.14 21.% + Gint_interface cal_gint 0.96611 25 0.039 13.% + Gint_Gamma distri_vl_value 0.88610 12 0.074 12.% + Gint_Gamma distri_vl 2.9790 6 0.50 39.% + LCAO_Deepks cal_projected_DM 5.9560 14 0.43 78.% + LCAO_gen_fixedH add_v_delta 2.8539 6 0.48 37.% + LCAO_DESCRIPTOR add_v_delta 2.8541 6 0.48 37.% + ElecStateLCAO psiToRho 1.6962 12 0.14 22.% + Charge mix_rho 0.76494 11 0.070 10.% + LOOP_ions force_stress 0.56757 1 0.57 7.4% + Force_Stress_LCAO getForceStress 0.56755 1 0.57 7.4% + Force_LCAO_gamma ftable_gamma 0.37244 1 0.37 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.17554 1 0.18 2.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:34 2022 + Finish Time : Wed Sep 28 11:05:42 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..7bc506a063fca2d83ca2abc103d3912831c78d51 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123761 ima = 3.68047e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123884826282 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112603354297 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011331525457 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113506018751 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113491267564 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113501317959 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113497086154 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113498756593 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113498162533 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113498177604 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011349815656 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113498145606 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/STRU new file mode 100644 index 0000000000000000000000000000000000000000..2367402eb08aaa93b24beaea0a823a4dcff6b3f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.849914786500 30.009639203077 9.285236064980 0 0 0 +H +0.0 +2 +-10.258655810144 30.177578323973 10.433342335928 0 0 0 +-7.669765071409 31.518051703518 9.583402607575 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/conv new file mode 100644 index 0000000000000000000000000000000000000000..257c3f8ceed42ba4f4622d36808ff1fbe23448eb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/conv @@ -0,0 +1 @@ +278 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b7821e7e5e55da21d52d6baa04a8784e799ffbf3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.7467775 0.01235823804 1.246126294 1.352357808 1.467921415 0.007919605654 0.01913656219 0.03899037468 +-4.972521215e-18 0.0009708173171 0.002295383079 0.0113183913 0.04074241021 -2.766054124e-20 1.345353943e-06 4.451941265e-06 +0.001681072116 0.005654134872 + +H atom_index 1 n_descriptor 18 +1.249419737 0.03396951773 0.1070965236 0.1508247349 0.3228280683 0.0216445432 0.02842626217 0.03724763029 +6.319581229e-19 3.679424447e-05 0.09920334107 0.115126252 0.1292934996 2.231205685e-18 4.026957977e-06 0.01298090737 +0.02549160767 0.03079867176 + +H atom_index 2 n_descriptor 18 +1.159693069 0.03683572395 0.08000053441 0.1137019423 0.2904075544 0.01764810254 0.02321604416 0.04075437812 +-2.518034906e-17 2.993437113e-05 0.07607780522 0.09670196427 0.1116833949 -3.148722969e-18 6.614255408e-06 0.01521396585 +0.02184639529 0.02618655427 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..25ab480d41c310e3205db02c1ab0b8629c0b265a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:34 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0730134 SEC) : SETUP UNITCELL + DONE(0.0732959 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0889731 SEC) : INIT PLANEWAVE + DONE(0.130442 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.375284 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651421e+02 0.000000e+00 2.131e-01 5.521e-01 + GE2 -4.663505e+02 -1.208371e+00 9.902e-02 5.270e-01 + GE3 -4.663556e+02 -5.179284e-03 6.386e-02 5.914e-01 + GE4 -4.663545e+02 1.105496e-03 2.079e-03 4.672e-01 + GE5 -4.663541e+02 4.283494e-04 8.981e-04 4.678e-01 + GE6 -4.663543e+02 -1.890443e-04 2.000e-04 4.644e-01 + GE7 -4.663542e+02 5.533286e-05 2.849e-05 4.482e-01 + GE8 -4.663543e+02 -3.611604e-05 1.228e-05 4.516e-01 + GE9 -4.663543e+02 1.222472e-05 2.649e-06 4.493e-01 + GE10 -4.663543e+02 -3.125370e-06 5.975e-07 4.466e-01 + GE11 -4.663543e+02 1.803088e-07 2.079e-07 4.485e-01 + GE12 -4.663543e+02 -5.206694e-08 1.052e-08 3.763e-01 +E_delta_band = -6.81921363e-02 Ry = -9.27801612e-01 eV +E_delta_NN= -1.93723212e-01 Ry = -2.63573952e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6708 11 0.7 1e+02 % + Run_lcao lcao_line 7.6636 1 7.7 1e+02 % + Potential init_pot 0.24288 2 0.12 3.2 % + PW_Basis recip2real 0.23738 17 0.014 3.1 % + PW_Basis gathers_scatterp 0.11158 17 0.0066 1.5 % + Potential v_of_rho 0.99851 14 0.071 13 % + XC_Functional v_xc 0.36327 15 0.024 4.7 % + H_Hartree_pw v_hartree 0.6049 14 0.043 7.9 % + PW_Basis real2recip 0.65387 41 0.016 8.5 % + PW_Basis gatherp_scatters 0.295 41 0.0072 3.8 % + ORB_control set_orb_tables 0.90465 1 0.9 12 % + ORB_gen_tables gen_tables 0.90465 1 0.9 12 % + ORB_table_phi init_Table 0.37669 1 0.38 4.9 % + ORB_table_phi cal_ST_Phi12_R 0.37237 126 0.003 4.9 % + ORB_table_beta init_Table_Beta 0.15704 1 0.16 2 % + ORB_table_beta VNL_PhiBeta_R 0.15571 56 0.0028 2 % + ORB_table_alpha init_Table_Alpha 0.21267 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.21104 66 0.0032 2.8 % + LOOP_ions opt_ions 6.3144 1 6.3 82 % + ESolver_KS_LCAO Run 5.7467 1 5.7 75 % + HSolverLCAO solve 3.3819 12 0.28 44 % + HamiltLCAO updateHk 1.6663 12 0.14 22 % + LCAO_Hamilt cal_Hgamma 1.6412 12 0.14 21 % + Gint_interface cal_gint 0.96611 25 0.039 13 % + Gint_Gamma distri_vl_value 0.8861 12 0.074 12 % + Gint_Gamma distri_vl 2.979 6 0.5 39 % + LCAO_Deepks cal_projected_DM 5.956 14 0.43 78 % + LCAO_gen_fixedH add_v_delta 2.8539 6 0.48 37 % + LCAO_DESCRIPTOR add_v_delta 2.8541 6 0.48 37 % + ElecStateLCAO psiToRho 1.6962 12 0.14 22 % + Charge mix_rho 0.76494 11 0.07 10 % + LOOP_ions force_stress 0.56757 1 0.57 7.4 % + Force_Stress_LCAO getForceStress 0.56755 1 0.57 7.4 % + Force_LCAO_gamma ftable_gamma 0.37244 1 0.37 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.17554 1 0.18 2.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:34 2022 + FINISH Time : Wed Sep 28 11:05:42 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/278/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..29c4343637af1a760d2fee7f899612dcd1a34dac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.712205 0.0622205 0.340061 +H 0.703028 0.0598392 0.403823 +H 0.694177 0.118546 0.325209 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..326432ac9a6f3193790e69e69ee6dbe75aff1c69 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.8155 2 + 2 -13.422 2 + 3 -9.22702 2 + 4 -6.85741 2 + 5 1.64881 0 + 6 5.11697 0 + 7 10.9501 0 + 8 11.1864 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9a51ff2c07896ab16df1c62521924c62ad73a7af --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:22 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.9417412292 1.74217483105 9.52171439022 0 0 0 0 + tauc_H1 19.6847927981 1.67549780783 11.3070416226 0 0 0 0 + tauc_H2 19.4369543864 3.31928255544 9.10584436097 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101882180567 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.102235401956 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.120357941423 (SEC) + + DONE : INIT CHARGE Time : 0.16351467308 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445879 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00174 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112 + + Density error is 0.220606688751 + + Energy Rydberg eV + E_KohnSham -34.1768863072 -465.000393676 + E_Harris -34.3815488109 -467.784969893 + E_Fermi -0.436839493036 -5.94350621672 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00158878409022 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00141645181315 + + Density error is 0.0969854204236 + + Energy Rydberg eV + E_KohnSham -34.2691807811 -466.256124416 + E_Harris -34.2758077441 -466.346288872 + E_Fermi -0.242816072241 -3.30368214846 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00144962638497 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013513773333 + + Density error is 0.0615031986288 + + Energy Rydberg eV + E_KohnSham -34.269344381 -466.258350306 + E_Harris -34.2734633075 -466.314391176 + E_Fermi -0.224903171414 -3.05996462951 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122765343804 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125707127017 + + Density error is 0.00217530927692 + + Energy Rydberg eV + E_KohnSham -34.269454516 -466.25984877 + E_Harris -34.269458788 -466.259906893 + E_Fermi -0.188968423732 -2.57104730484 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122474972578 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126188373995 + + Density error is 0.000973774515702 + + Energy Rydberg eV + E_KohnSham -34.2693646243 -466.258625731 + E_Harris -34.2693685507 -466.258679151 + E_Fermi -0.187211910824 -2.54714872068 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122353850736 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126023014096 + + Density error is 0.000140499181691 + + Energy Rydberg eV + E_KohnSham -34.2694294379 -466.259507564 + E_Harris -34.2694295154 -466.259508619 + E_Fermi -0.187809159933 -2.55527471169 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122308276934 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126008792633 + + Density error is 5.72736235445e-05 + + Energy Rydberg eV + E_KohnSham -34.2694073027 -466.2592064 + E_Harris -34.2694073198 -466.259206633 + E_Fermi -0.187609359894 -2.55255629269 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122316339317 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126003617363 + + Density error is 1.6709437491e-05 + + Energy Rydberg eV + E_KohnSham -34.2694117256 -466.259266576 + E_Harris -34.2694117265 -466.259266588 + E_Fermi -0.187679112223 -2.55350532182 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122311709976 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126003101552 + + Density error is 1.8991358522e-06 + + Energy Rydberg eV + E_KohnSham -34.2694101144 -466.259244654 + E_Harris -34.2694101144 -466.259244654 + E_Fermi -0.187660487643 -2.5532519214 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122311249699 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126003063559 + + Density error is 2.41937240155e-07 + + Energy Rydberg eV + E_KohnSham -34.2694102781 -466.259246881 + E_Harris -34.2694102781 -466.259246881 + E_Fermi -0.187658872358 -2.55322994433 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122311252519 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126003111971 + + Density error is 1.35621952089e-07 + + Energy Rydberg eV + E_KohnSham -34.2694103141 -466.259247372 + E_Harris -34.2694103141 -466.259247372 + E_Fermi -0.187658900606 -2.55323032865 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012231122248 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126003122379 + + Density error is 1.13985589606e-08 + + Energy Rydberg eV + E_KohnSham -34.2694103115 -466.259247336 + E_Harris -34.2694103115 -466.259247336 + E_band -8.13216978703 -110.643846207 + E_one_elec -70.296453884 -956.432322017 + E_Hartree +36.5105697619 +496.751785988 + E_xc -8.28641624292 -112.742476904 + E_Ewald +7.92517469391 +107.827533483 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196800867175 -2.67761316491 + E_Fermi -0.187658749376 -2.55322827106 + + charge density convergence is achieved + final etot is -466.259247336 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.8155 2.00000 + 2 -13.4220 2.00000 + 3 -9.22702 2.00000 + 4 -6.85741 2.00000 + 5 1.64881 0.00000 + 6 5.11697 0.00000 + 7 10.9501 0.00000 + 8 11.1864 0.00000 + + EFERMI = -2.553228271061859 eV + OUT.ABACUS/ final etot is -466.2592473360214 eV + correction force for each atom along direction 1 is -0.000155092 + correction force for each atom along direction 2 is 6.94924e-05 + correction force for each atom along direction 3 is 0.000104012 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.3981938 -4.0111873 +0.29493635 + H1 -0.076731928 -0.23688226 +1.0500078 + H2 -1.3214619 +4.2480695 -1.3449441 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2592473360214 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8648 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8553 1 6.9 1.e+02% + Potential init_pot 0.28528 2 0.14 4.2% + PW_Basis recip2real 0.27622 17 0.016 4.0% + PW_Basis gathers_scatterp 0.12572 17 0.0074 1.8% + Potential v_of_rho 0.84669 14 0.060 12.% + XC_Functional v_xc 0.19797 15 0.013 2.9% + H_Hartree_pw v_hartree 0.60890 14 0.043 8.9% + PW_Basis real2recip 0.71048 41 0.017 10.% + PW_Basis gatherp_scatters 0.29339 41 0.0072 4.3% + ORB_control set_orb_tables 1.0889 1 1.1 16.% + ORB_gen_tables gen_tables 1.0889 1 1.1 16.% + ORB_table_phi init_Table 0.47194 1 0.47 6.9% + ORB_table_phi cal_ST_Phi12_R 0.46672 126 0.0037 6.8% + ORB_table_beta init_Table_Beta 0.18070 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.17919 56 0.0032 2.6% + ORB_table_alpha init_Table_Alpha 0.24826 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24622 66 0.0037 3.6% + LOOP_ions opt_ions 5.2444 1 5.2 76.% + ESolver_KS_LCAO Run 4.7151 1 4.7 69.% + HSolverLCAO solve 2.2957 12 0.19 33.% + HamiltLCAO updateHk 1.2143 12 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1848 12 0.099 17.% + Gint_interface cal_gint 0.64155 25 0.026 9.3% + Gint_Gamma distri_vl_value 0.52142 12 0.043 7.6% + Gint_Gamma distri_vl 2.4587 6 0.41 36.% + LCAO_Deepks cal_projected_DM 4.9171 14 0.35 72.% + LCAO_gen_fixedH add_v_delta 2.3132 6 0.39 34.% + LCAO_DESCRIPTOR add_v_delta 2.3133 6 0.39 34.% + ElecStateLCAO psiToRho 1.0610 12 0.088 15.% + Charge mix_rho 0.95775 11 0.087 14.% + LOOP_ions force_stress 0.52920 1 0.53 7.7% + Force_Stress_LCAO getForceStress 0.52918 1 0.53 7.7% + Force_LCAO_gamma ftable_gamma 0.33561 1 0.34 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.15074 1 0.15 2.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:22 2022 + Finish Time : Wed Sep 28 11:13:29 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a1edeadcd54b75f6ad7f18b145df311114f5d5df --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124281 ima = 3.69569e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122685045474 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011206254545 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112337802343 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011266790582 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112573880934 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112625240915 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112618182374 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112621633554 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112621115731 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112621031833 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112621032291 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112621025786 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/STRU new file mode 100644 index 0000000000000000000000000000000000000000..884138809dd46ee539d716cfe0eb4f2a59c72983 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.058258770793 29.742174831069 9.521714390232 0 0 0 +H +0.0 +2 +-8.315207201856 29.675497807811 11.307041622593 0 0 0 +-8.563045613627 31.319282555434 9.105844360952 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/conv new file mode 100644 index 0000000000000000000000000000000000000000..037ae66f2e625584aec6356f49f5ae4db5caee28 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/conv @@ -0,0 +1 @@ +279 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9b48744932599d4af94aefaee2bfb85e3a150d62 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750358699 0.01286519044 1.308250995 1.397912051 1.471966469 0.009139543982 0.01945538411 0.03909392902 +-6.752129428e-19 0.001272788319 0.002951787918 0.0138202799 0.05062735043 3.098949447e-20 2.722719273e-06 7.203689749e-06 +0.001620992854 0.005892471606 + +H atom_index 1 n_descriptor 18 +1.267934743 0.03367809885 0.1161451794 0.1581094951 0.3254456942 0.02362815218 0.02929796175 0.0368422327 +1.939002338e-17 5.758893979e-05 0.1088163938 0.1172325413 0.1361496501 -8.98575708e-18 3.049761503e-06 0.01326981483 +0.02812684175 0.03159417884 + +H atom_index 2 n_descriptor 18 +1.344289033 0.03176175077 0.1479422831 0.1997698766 0.3450582956 0.0271228716 0.0335359873 0.03725859494 +-1.588747231e-17 6.498259512e-05 0.1055956621 0.1423295359 0.1708543743 -4.721456827e-18 1.85135737e-08 0.01608579131 +0.03022115387 0.03398567692 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d5a8dcb82daf9a48d34b264d893ae3c8f6d5a0dc Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:22 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101907 SEC) : SETUP UNITCELL + DONE(0.102251 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.12038 SEC) : INIT PLANEWAVE + DONE(0.163647 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445938 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650004e+02 0.000000e+00 2.206e-01 4.968e-01 + GE2 -4.662561e+02 -1.255731e+00 9.699e-02 4.424e-01 + GE3 -4.662584e+02 -2.225890e-03 6.150e-02 5.114e-01 + GE4 -4.662598e+02 -1.498464e-03 2.175e-03 3.717e-01 + GE5 -4.662586e+02 1.223039e-03 9.738e-04 3.724e-01 + GE6 -4.662595e+02 -8.818338e-04 1.405e-04 3.640e-01 + GE7 -4.662592e+02 3.011649e-04 5.727e-05 3.656e-01 + GE8 -4.662593e+02 -6.017620e-05 1.671e-05 3.559e-01 + GE9 -4.662592e+02 2.192174e-05 1.899e-06 3.573e-01 + GE10 -4.662592e+02 -2.227419e-06 2.419e-07 3.603e-01 + GE11 -4.662592e+02 -4.901810e-07 1.356e-07 3.555e-01 + GE12 -4.662592e+02 3.557208e-08 1.140e-08 3.015e-01 +E_delta_band = -7.45162268e-02 Ry = -1.01384528e+00 eV +E_delta_NN= -1.96800867e-01 Ry = -2.67761316e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8648 11 0.62 1e+02 % + Run_lcao lcao_line 6.8553 1 6.9 1e+02 % + Potential init_pot 0.28528 2 0.14 4.2 % + PW_Basis recip2real 0.27622 17 0.016 4 % + PW_Basis gathers_scatterp 0.12572 17 0.0074 1.8 % + Potential v_of_rho 0.84669 14 0.06 12 % + XC_Functional v_xc 0.19797 15 0.013 2.9 % + H_Hartree_pw v_hartree 0.6089 14 0.043 8.9 % + PW_Basis real2recip 0.71048 41 0.017 10 % + PW_Basis gatherp_scatters 0.29339 41 0.0072 4.3 % + ORB_control set_orb_tables 1.0889 1 1.1 16 % + ORB_gen_tables gen_tables 1.0889 1 1.1 16 % + ORB_table_phi init_Table 0.47194 1 0.47 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.46672 126 0.0037 6.8 % + ORB_table_beta init_Table_Beta 0.1807 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.17919 56 0.0032 2.6 % + ORB_table_alpha init_Table_Alpha 0.24826 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24622 66 0.0037 3.6 % + LOOP_ions opt_ions 5.2444 1 5.2 76 % + ESolver_KS_LCAO Run 4.7151 1 4.7 69 % + HSolverLCAO solve 2.2957 12 0.19 33 % + HamiltLCAO updateHk 1.2143 12 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1848 12 0.099 17 % + Gint_interface cal_gint 0.64155 25 0.026 9.3 % + Gint_Gamma distri_vl_value 0.52142 12 0.043 7.6 % + Gint_Gamma distri_vl 2.4587 6 0.41 36 % + LCAO_Deepks cal_projected_DM 4.9171 14 0.35 72 % + LCAO_gen_fixedH add_v_delta 2.3132 6 0.39 34 % + LCAO_DESCRIPTOR add_v_delta 2.3133 6 0.39 34 % + ElecStateLCAO psiToRho 1.061 12 0.088 15 % + Charge mix_rho 0.95775 11 0.087 14 % + LOOP_ions force_stress 0.5292 1 0.53 7.7 % + Force_Stress_LCAO getForceStress 0.52918 1 0.53 7.7 % + Force_LCAO_gamma ftable_gamma 0.33561 1 0.34 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.15074 1 0.15 2.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:22 2022 + FINISH Time : Wed Sep 28 11:13:29 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/279/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a327ed2e0a50139be06c7d31141aea3fa47b25f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.508603 0.428619 0.423911 +H 0.565503 0.443639 0.44778 +H 0.477417 0.390903 0.468104 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b305949cec7b57ee776000b3f3b16a644d49cc52 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3504 2 + 2 -13.3384 2 + 3 -8.94637 2 + 4 -6.75601 2 + 5 1.40925 0 + 6 4.63989 0 + 7 11.0486 0 + 8 11.277 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fb4a062eed97e491fc54946a59442d50f19e09ca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:36 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.2408762648 12.0013331609 11.8695105803 0 0 0 0 + tauc_H1 15.83407531 12.4218927003 12.5378351543 0 0 0 0 + tauc_H2 13.3676861317 10.9452704411 13.1069004564 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.100874404891 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101266615799 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.1193761835 (SEC) + + DONE : INIT CHARGE Time : 0.164527736652 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445591 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906 + + Density error is 0.217507485423 + + Energy Rydberg eV + E_KohnSham -34.1868920392 -465.136528644 + E_Harris -34.3841559543 -467.820441899 + E_Fermi -0.413222016282 -5.62217396049 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00131518146381 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100921105453 + + Density error is 0.0979807951745 + + Energy Rydberg eV + E_KohnSham -34.2784299406 -466.381965686 + E_Harris -34.2850652334 -466.472243476 + E_Fermi -0.219786573805 -2.99034974765 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00124769676999 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957682353058 + + Density error is 0.0627366101375 + + Energy Rydberg eV + E_KohnSham -34.278749525 -466.386313854 + E_Harris -34.2830098202 -466.444278144 + E_Fermi -0.207211755719 -2.81926057036 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114121411168 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000875350036448 + + Density error is 0.00207792111637 + + Energy Rydberg eV + E_KohnSham -34.2787660725 -466.386538996 + E_Harris -34.2787688538 -466.386576837 + E_Fermi -0.171673820256 -2.33574215291 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114054453249 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000873976828429 + + Density error is 0.00091655875578 + + Energy Rydberg eV + E_KohnSham -34.2786978565 -466.385610869 + E_Harris -34.2786992446 -466.385629755 + E_Fermi -0.170716793748 -2.32272113926 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113917219698 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000872893989541 + + Density error is 0.00019176531227 + + Energy Rydberg eV + E_KohnSham -34.278739848 -466.386182192 + E_Harris -34.2787399509 -466.386183592 + E_Fermi -0.170826442541 -2.32421298763 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113938832388 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000873008752562 + + Density error is 4.44622140318e-05 + + Energy Rydberg eV + E_KohnSham -34.2787235766 -466.385960809 + E_Harris -34.2787235875 -466.385960957 + E_Fermi -0.170651790847 -2.32183672942 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113930336333 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000872950427566 + + Density error is 1.94956864787e-05 + + Energy Rydberg eV + E_KohnSham -34.2787290923 -466.386035853 + E_Harris -34.2787290937 -466.386035873 + E_Fermi -0.170703808507 -2.32254446599 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113928928406 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000872940369865 + + Density error is 3.13470398606e-06 + + Energy Rydberg eV + E_KohnSham -34.2787274978 -466.386014159 + E_Harris -34.2787274978 -466.386014159 + E_Fermi -0.170684570719 -2.32228272246 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113928846347 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000872939797034 + + Density error is 4.06838643574e-07 + + Energy Rydberg eV + E_KohnSham -34.2787277267 -466.386017273 + E_Harris -34.2787277267 -466.386017273 + E_Fermi -0.17068121339 -2.32223704366 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113928887177 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000872940340176 + + Density error is 1.71929215186e-07 + + Energy Rydberg eV + E_KohnSham -34.2787277733 -466.386017908 + E_Harris -34.2787277733 -466.386017908 + E_Fermi -0.170681099885 -2.32223549934 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113928892022 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00087294046089 + + Density error is 9.90973921747e-09 + + Energy Rydberg eV + E_KohnSham -34.2787277743 -466.386017922 + E_Harris -34.2787277743 -466.386017922 + E_band -7.99535647987 -108.782405667 + E_one_elec -69.5456822517 -946.217549921 + E_Hartree +36.1663795138 +492.068837418 + E_xc -8.23001911278 -111.975154583 + E_Ewald +7.45443513802 +101.422793248 + E_demet -2.42952370428e-84 -3.30553658043e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195217436281 -2.65606948237 + E_Fermi -0.170680936377 -2.32223327471 + + charge density convergence is achieved + final etot is -466.386017922 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3504 2.00000 + 2 -13.3384 2.00000 + 3 -8.94637 2.00000 + 4 -6.75601 2.00000 + 5 1.40925 0.00000 + 6 4.63989 0.00000 + 7 11.0486 0.00000 + 8 11.2770 0.00000 + + EFERMI = -2.322233274708854 eV + OUT.ABACUS/ final etot is -466.3860179215146 eV + correction force for each atom along direction 1 is -6.97481e-06 + correction force for each atom along direction 2 is 6.22504e-05 + correction force for each atom along direction 3 is 1.23517e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.8806425 -0.43673941 -0.89805843 + H1 +1.6043993 +0.30962569 +0.89097861 + H2 +0.27624326 +0.12711372 +0.0070798239 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3860179215146 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4241 11 0.67 1.0e+02% + Run_lcao lcao_line 7.4142 1 7.4 1.e+02% + Potential init_pot 0.28274 2 0.14 3.8% + PW_Basis recip2real 0.26536 17 0.016 3.6% + PW_Basis gathers_scatterp 0.11626 17 0.0068 1.6% + Potential v_of_rho 0.83032 14 0.059 11.% + XC_Functional v_xc 0.19676 15 0.013 2.7% + H_Hartree_pw v_hartree 0.59398 14 0.042 8.0% + PW_Basis real2recip 0.69764 41 0.017 9.4% + PW_Basis gatherp_scatters 0.27084 41 0.0066 3.6% + ORB_control set_orb_tables 1.0963 1 1.1 15.% + ORB_gen_tables gen_tables 1.0963 1 1.1 15.% + ORB_table_phi init_Table 0.47604 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47076 126 0.0037 6.3% + ORB_table_beta init_Table_Beta 0.18391 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18234 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24725 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24528 66 0.0037 3.3% + LOOP_ions opt_ions 5.7971 1 5.8 78.% + ESolver_KS_LCAO Run 5.2322 1 5.2 70.% + HSolverLCAO solve 3.0214 12 0.25 41.% + HamiltLCAO updateHk 1.5109 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4812 12 0.12 20.% + Gint_interface cal_gint 0.10007 25 0.0040 1.3% + Gint_Gamma distri_vl_value 1.0144 12 0.085 14.% + Gint_Gamma distri_vl 2.7168 6 0.45 37.% + LCAO_Deepks cal_projected_DM 5.3587 14 0.38 72.% + LCAO_gen_fixedH add_v_delta 2.5861 6 0.43 35.% + LCAO_DESCRIPTOR add_v_delta 2.5862 6 0.43 35.% + ElecStateLCAO psiToRho 1.4884 12 0.12 20.% + Charge mix_rho 0.78614 11 0.071 11.% + LOOP_ions force_stress 0.56482 1 0.56 7.6% + Force_Stress_LCAO getForceStress 0.56480 1 0.56 7.6% + Force_LCAO_gamma ftable_gamma 0.36663 1 0.37 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:36 2022 + Finish Time : Wed Sep 28 11:02:44 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d73a99d0e34693c292c2b767156a0cbac79dc2fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123643 ima = 3.67086e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123449986579 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112503617091 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112974644226 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113235988318 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113179046723 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113213196453 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113203159414 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113206417105 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113205690986 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113205568114 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113205557004 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113205548859 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/STRU new file mode 100644 index 0000000000000000000000000000000000000000..82ede621145ae654264581e55f28a60cc117c34d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.759123735207 12.001333160887 11.869510580359 0 0 0 +H +0.0 +2 +-12.165924689968 12.421892700315 12.537835154249 0 0 0 +-14.632313868238 10.945270441126 13.106900456355 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/conv new file mode 100644 index 0000000000000000000000000000000000000000..513fc20133af6fa2ac79545232b5744d7bf44b7c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/conv @@ -0,0 +1 @@ +28 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..abcacc3a3390783e7d7ca514b9a2456c628b4cc3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745990443 0.0126900895 1.2845213 1.377451356 1.469712525 0.008076233043 0.01994139521 0.0389367851 +-5.246419004e-19 0.001176368629 0.002519541194 0.01258791257 0.04483534739 -1.178672816e-18 1.781287621e-06 5.425066191e-06 +0.001728130278 0.005753532183 + +H atom_index 1 n_descriptor 18 +1.285989934 0.03261178058 0.1215121876 0.1682860052 0.3327237965 0.02359076364 0.03046981898 0.0362296188 +7.015807027e-19 4.625119502e-05 0.1078687683 0.1196961381 0.1445097425 2.198997472e-18 2.396234153e-06 0.01321012352 +0.02756760471 0.03230475012 + +H atom_index 2 n_descriptor 18 +1.231717385 0.03447391485 0.102261778 0.1424295903 0.3162457681 0.02119625749 0.02735078166 0.03760181695 +-6.743102161e-18 4.147097308e-05 0.09785602359 0.1141606122 0.1223170449 -5.159872784e-18 5.179045265e-06 0.01320209522 +0.02563974815 0.02999870207 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..11ff2a6a2a8e1eb4ede82eca25af2ae4f60c1883 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:36 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.100898 SEC) : SETUP UNITCELL + DONE(0.101282 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119397 SEC) : INIT PLANEWAVE + DONE(0.16466 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445656 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651365e+02 0.000000e+00 2.175e-01 5.344e-01 + GE2 -4.663820e+02 -1.245437e+00 9.798e-02 4.899e-01 + GE3 -4.663863e+02 -4.348169e-03 6.274e-02 5.428e-01 + GE4 -4.663865e+02 -2.251412e-04 2.078e-03 4.170e-01 + GE5 -4.663856e+02 9.281269e-04 9.166e-04 4.156e-01 + GE6 -4.663862e+02 -5.713237e-04 1.918e-04 4.109e-01 + GE7 -4.663860e+02 2.213831e-04 4.446e-05 4.087e-01 + GE8 -4.663860e+02 -7.504368e-05 1.950e-05 4.020e-01 + GE9 -4.663860e+02 2.169427e-05 3.135e-06 4.006e-01 + GE10 -4.663860e+02 -3.114530e-06 4.068e-07 4.001e-01 + GE11 -4.663860e+02 -6.348799e-07 1.719e-07 3.998e-01 + GE12 -4.663860e+02 -1.334666e-08 9.910e-09 3.491e-01 +E_delta_band = -7.13763747e-02 Ry = -9.71125398e-01 eV +E_delta_NN= -1.95217436e-01 Ry = -2.65606948e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4241 11 0.67 1e+02 % + Run_lcao lcao_line 7.4142 1 7.4 1e+02 % + Potential init_pot 0.28274 2 0.14 3.8 % + PW_Basis recip2real 0.26536 17 0.016 3.6 % + PW_Basis gathers_scatterp 0.11626 17 0.0068 1.6 % + Potential v_of_rho 0.83032 14 0.059 11 % + XC_Functional v_xc 0.19676 15 0.013 2.7 % + H_Hartree_pw v_hartree 0.59398 14 0.042 8 % + PW_Basis real2recip 0.69764 41 0.017 9.4 % + PW_Basis gatherp_scatters 0.27084 41 0.0066 3.6 % + ORB_control set_orb_tables 1.0963 1 1.1 15 % + ORB_gen_tables gen_tables 1.0963 1 1.1 15 % + ORB_table_phi init_Table 0.47604 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47076 126 0.0037 6.3 % + ORB_table_beta init_Table_Beta 0.18391 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18234 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24725 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24528 66 0.0037 3.3 % + LOOP_ions opt_ions 5.7971 1 5.8 78 % + ESolver_KS_LCAO Run 5.2322 1 5.2 70 % + HSolverLCAO solve 3.0214 12 0.25 41 % + HamiltLCAO updateHk 1.5109 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4812 12 0.12 20 % + Gint_interface cal_gint 0.10007 25 0.004 1.3 % + Gint_Gamma distri_vl_value 1.0144 12 0.085 14 % + Gint_Gamma distri_vl 2.7168 6 0.45 37 % + LCAO_Deepks cal_projected_DM 5.3587 14 0.38 72 % + LCAO_gen_fixedH add_v_delta 2.5861 6 0.43 35 % + LCAO_DESCRIPTOR add_v_delta 2.5862 6 0.43 35 % + ElecStateLCAO psiToRho 1.4884 12 0.12 20 % + Charge mix_rho 0.78614 11 0.071 11 % + LOOP_ions force_stress 0.56482 1 0.56 7.6 % + Force_Stress_LCAO getForceStress 0.5648 1 0.56 7.6 % + Force_LCAO_gamma ftable_gamma 0.36663 1 0.37 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:36 2022 + FINISH Time : Wed Sep 28 11:02:44 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/28/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..0ec9e08c153b1f8ae54b49b2b8a00105f5903de1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.730119 0.0516306 0.3558 +H 0.753651 0.0344404 0.414963 +H 0.669249 0.0823272 0.368769 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c72456f2eb2092121e7725ae172d8ae2ab2ca16e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9249 2 + 2 -12.7868 2 + 3 -9.01139 2 + 4 -6.66086 2 + 5 0.953418 0 + 6 3.92792 0 + 7 11.1598 0 + 8 11.3984 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..71ab53c4c381e3986f0708a5a2554cc0ec4c7dc9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:23 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 20.4433431405 1.44565634582 9.96240879614 0 0 0 0 + tauc_H1 21.1022337848 0.964331064184 11.6189688742 0 0 0 0 + tauc_H2 18.7389614506 2.30516120889 10.3255435042 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0867581571245 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0981420447051 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116562530314 (SEC) + + DONE : INIT CHARGE Time : 0.167233848875 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44993 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000877 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0015 + + Density error is 0.212187790009 + + Energy Rydberg eV + E_KohnSham -34.187407065 -465.14353593 + E_Harris -34.3731974377 -467.671343632 + E_Fermi -0.384587320229 -5.23257893367 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116764447972 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012856246133 + + Density error is 0.0992210328489 + + Energy Rydberg eV + E_KohnSham -34.2765090138 -466.355830136 + E_Harris -34.2837697988 -466.454618184 + E_Fermi -0.194690526437 -2.64890050616 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011168417497 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119898180939 + + Density error is 0.0641628709649 + + Energy Rydberg eV + E_KohnSham -34.2770104642 -466.362652718 + E_Harris -34.2816172427 -466.425331156 + E_Fermi -0.189012137075 -2.57164205538 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104969363626 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103250537376 + + Density error is 0.00201650425571 + + Energy Rydberg eV + E_KohnSham -34.2769010988 -466.361164727 + E_Harris -34.2769043555 -466.361209035 + E_Fermi -0.153914530381 -2.09411461817 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104839011866 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103042746156 + + Density error is 0.000980105438497 + + Energy Rydberg eV + E_KohnSham -34.2768664853 -466.360693785 + E_Harris -34.2768669315 -466.360699856 + E_Fermi -0.15385936896 -2.09336410854 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104742171968 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102768420406 + + Density error is 0.000199917004889 + + Energy Rydberg eV + E_KohnSham -34.2768794748 -466.360870517 + E_Harris -34.2768794905 -466.36087073 + E_Fermi -0.153384572609 -2.08690417277 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104765985942 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102781163316 + + Density error is 3.11340778479e-05 + + Energy Rydberg eV + E_KohnSham -34.2768756468 -466.360818433 + E_Harris -34.2768756494 -466.360818469 + E_Fermi -0.153376726017 -2.08679741441 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001047565089 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102774771754 + + Density error is 1.20561098568e-05 + + Energy Rydberg eV + E_KohnSham -34.2768783797 -466.360855617 + E_Harris -34.2768783803 -466.360855625 + E_Fermi -0.15338994325 -2.08697724409 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104756452876 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102772939005 + + Density error is 1.86710694383e-06 + + Energy Rydberg eV + E_KohnSham -34.2768774176 -466.360842527 + E_Harris -34.2768774176 -466.360842527 + E_Fermi -0.15337775506 -2.08681141527 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104756450906 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102772597364 + + Density error is 5.96986681511e-07 + + Energy Rydberg eV + E_KohnSham -34.2768776043 -466.360845067 + E_Harris -34.2768776043 -466.360845067 + E_Fermi -0.153376559892 -2.08679515417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104756516729 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102772586495 + + Density error is 1.98596545027e-07 + + Energy Rydberg eV + E_KohnSham -34.2768776031 -466.36084505 + E_Harris -34.2768776031 -466.36084505 + E_Fermi -0.153376251532 -2.08679095871 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104756529809 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102772559199 + + Density error is 1.13118973081e-08 + + Energy Rydberg eV + E_KohnSham -34.2768776076 -466.360845112 + E_Harris -34.2768776076 -466.360845112 + E_band -7.84729437638 -106.767917402 + E_one_elec -68.5555306026 -932.745845608 + E_Hartree +35.6955279841 +485.662573702 + E_xc -8.15451934959 -110.947927606 + E_Ewald +6.86345458631 +93.382090338 + E_demet -6.93876097498e-57 -9.44066863198e-56 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193516203584 -2.63292302407 + E_Fermi -0.153376058541 -2.08678833294 + + charge density convergence is achieved + final etot is -466.360845112 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9249 2.00000 + 2 -12.7868 2.00000 + 3 -9.01139 2.00000 + 4 -6.66086 2.00000 + 5 0.953418 0.00000 + 6 3.92792 0.00000 + 7 11.1598 0.00000 + 8 11.3984 0.00000 + + EFERMI = -2.086788332942678 eV + OUT.ABACUS/ final etot is -466.3608451120894 eV + correction force for each atom along direction 1 is -7.95882e-05 + correction force for each atom along direction 2 is 9.79106e-05 + correction force for each atom along direction 3 is 0.000146119 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.8075180 +0.92543237 +0.25836931 + H1 -0.14869254 +0.074922610 +0.010060947 + H2 +1.9562106 -1.0003550 -0.26843026 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3608451120894 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.3639 11 0.76 1.0e+02% + Run_lcao lcao_line 8.3548 1 8.4 1.e+02% + Potential init_pot 0.28713 2 0.14 3.4% + PW_Basis recip2real 0.28746 17 0.017 3.4% + PW_Basis gathers_scatterp 0.13644 17 0.0080 1.6% + Potential v_of_rho 1.1195 14 0.080 13.% + XC_Functional v_xc 0.38426 15 0.026 4.6% + H_Hartree_pw v_hartree 0.69500 14 0.050 8.3% + PW_Basis real2recip 0.70915 41 0.017 8.5% + PW_Basis gatherp_scatters 0.31200 41 0.0076 3.7% + ORB_control set_orb_tables 1.0982 1 1.1 13.% + ORB_gen_tables gen_tables 1.0982 1 1.1 13.% + ORB_table_phi init_Table 0.47852 1 0.48 5.7% + ORB_table_phi cal_ST_Phi12_R 0.47327 126 0.0038 5.7% + ORB_table_beta init_Table_Beta 0.18695 1 0.19 2.2% + ORB_table_beta VNL_PhiBeta_R 0.18541 56 0.0033 2.2% + ORB_table_alpha init_Table_Alpha 0.24676 1 0.25 3.0% + ORB_table_alpha S_PhiAlpha_R 0.24476 66 0.0037 2.9% + LOOP_ions opt_ions 6.7271 1 6.7 80.% + ESolver_KS_LCAO Run 6.1059 1 6.1 73.% + HSolverLCAO solve 3.6038 12 0.30 43.% + HamiltLCAO updateHk 1.7784 12 0.15 21.% + LCAO_Hamilt cal_Hgamma 1.7487 12 0.15 21.% + Gint_interface cal_gint 0.61895 25 0.025 7.4% + Gint_Gamma distri_vl_value 1.0869 12 0.091 13.% + Gint_Gamma distri_vl 3.1670 6 0.53 38.% + LCAO_Deepks cal_projected_DM 6.2920 14 0.45 75.% + LCAO_gen_fixedH add_v_delta 3.0378 6 0.51 36.% + LCAO_DESCRIPTOR add_v_delta 3.0379 6 0.51 36.% + ElecStateLCAO psiToRho 1.7828 12 0.15 21.% + Charge mix_rho 0.78761 11 0.072 9.4% + LOOP_ions force_stress 0.62098 1 0.62 7.4% + Force_Stress_LCAO getForceStress 0.62094 1 0.62 7.4% + Force_LCAO_gamma ftable_gamma 0.40248 1 0.40 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.14961 1 0.15 1.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:23 2022 + Finish Time : Wed Sep 28 11:06:31 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a7b38754f131abb809143be028dd0880713b15a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123818 ima = 3.67017e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123845495189 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112256388328 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113072085757 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113268911167 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113254915079 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011326489886 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113260412232 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113262339998 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113261819387 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113261803208 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113261780718 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113261770181 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/STRU new file mode 100644 index 0000000000000000000000000000000000000000..671b0633b3a9e227907bff471fee35c46f2971a2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-7.556656859519 29.445656345839 9.962408796166 0 0 0 +H +0.0 +2 +-6.897766215129 28.964331064168 11.618968874171 0 0 0 +-9.261038549411 30.305161208887 10.325543504227 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/conv new file mode 100644 index 0000000000000000000000000000000000000000..6c2f9a5b28e4e2114deb7d1d37b732e3f66d7d0c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/conv @@ -0,0 +1 @@ +280 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..543414e18a1b02661d96e2245d95a669de3b67e5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749063371 0.01234313767 1.239980192 1.341784186 1.467816489 0.008231614591 0.01828097893 0.03907288393 +1.96309316e-18 0.0009025972339 0.002335625006 0.01123299095 0.04083152244 4.273280908e-19 1.454289438e-06 4.675459131e-06 +0.001624355205 0.005756127433 + +H atom_index 1 n_descriptor 18 +1.234644982 0.03472368382 0.1020204814 0.1435695447 0.317277735 0.0211020363 0.0274948601 0.03797806294 +1.84781616e-18 3.712318786e-05 0.09469224024 0.1148950688 0.1229651948 6.868238307e-20 4.616597709e-06 0.01325594516 +0.02489086776 0.03006175138 + +H atom_index 2 n_descriptor 18 +1.158655613 0.0370522584 0.07954683271 0.1127884498 0.2888089897 0.01765670648 0.02306589298 0.04101580385 +1.751244539e-17 3.114055481e-05 0.07531667159 0.09584983569 0.1115081762 -5.217117239e-18 6.72256833e-06 0.01539912297 +0.02175111213 0.02603845732 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..02d1f32cbfa055d6c2483d9d4289e7c1aead565b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:23 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0867813 SEC) : SETUP UNITCELL + DONE(0.0981633 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116586 SEC) : INIT PLANEWAVE + DONE(0.167367 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449988 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651435e+02 0.000000e+00 2.122e-01 6.048e-01 + GE2 -4.663558e+02 -1.212294e+00 9.922e-02 5.646e-01 + GE3 -4.663627e+02 -6.822582e-03 6.416e-02 6.371e-01 + GE4 -4.663612e+02 1.487992e-03 2.017e-03 4.961e-01 + GE5 -4.663607e+02 4.709412e-04 9.801e-04 4.931e-01 + GE6 -4.663609e+02 -1.767319e-04 1.999e-04 4.901e-01 + GE7 -4.663608e+02 5.208372e-05 3.113e-05 4.709e-01 + GE8 -4.663609e+02 -3.718354e-05 1.206e-05 4.696e-01 + GE9 -4.663608e+02 1.309035e-05 1.867e-06 4.708e-01 + GE10 -4.663608e+02 -2.540199e-06 5.970e-07 4.724e-01 + GE11 -4.663608e+02 1.672523e-08 1.986e-07 4.729e-01 + GE12 -4.663608e+02 -6.193845e-08 1.131e-08 3.970e-01 +E_delta_band = -6.77059777e-02 Ry = -9.21187086e-01 eV +E_delta_NN= -1.93516204e-01 Ry = -2.63292302e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.3639 11 0.76 1e+02 % + Run_lcao lcao_line 8.3548 1 8.4 1e+02 % + Potential init_pot 0.28713 2 0.14 3.4 % + PW_Basis recip2real 0.28746 17 0.017 3.4 % + PW_Basis gathers_scatterp 0.13644 17 0.008 1.6 % + Potential v_of_rho 1.1195 14 0.08 13 % + XC_Functional v_xc 0.38426 15 0.026 4.6 % + H_Hartree_pw v_hartree 0.695 14 0.05 8.3 % + PW_Basis real2recip 0.70915 41 0.017 8.5 % + PW_Basis gatherp_scatters 0.312 41 0.0076 3.7 % + ORB_control set_orb_tables 1.0982 1 1.1 13 % + ORB_gen_tables gen_tables 1.0982 1 1.1 13 % + ORB_table_phi init_Table 0.47852 1 0.48 5.7 % + ORB_table_phi cal_ST_Phi12_R 0.47327 126 0.0038 5.7 % + ORB_table_beta init_Table_Beta 0.18695 1 0.19 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.18541 56 0.0033 2.2 % + ORB_table_alpha init_Table_Alpha 0.24676 1 0.25 3 % + ORB_table_alpha S_PhiAlpha_R 0.24476 66 0.0037 2.9 % + LOOP_ions opt_ions 6.7271 1 6.7 80 % + ESolver_KS_LCAO Run 6.1059 1 6.1 73 % + HSolverLCAO solve 3.6038 12 0.3 43 % + HamiltLCAO updateHk 1.7784 12 0.15 21 % + LCAO_Hamilt cal_Hgamma 1.7487 12 0.15 21 % + Gint_interface cal_gint 0.61895 25 0.025 7.4 % + Gint_Gamma distri_vl_value 1.0869 12 0.091 13 % + Gint_Gamma distri_vl 3.167 6 0.53 38 % + LCAO_Deepks cal_projected_DM 6.292 14 0.45 75 % + LCAO_gen_fixedH add_v_delta 3.0378 6 0.51 36 % + LCAO_DESCRIPTOR add_v_delta 3.0379 6 0.51 36 % + ElecStateLCAO psiToRho 1.7828 12 0.15 21 % + Charge mix_rho 0.78761 11 0.072 9.4 % + LOOP_ions force_stress 0.62098 1 0.62 7.4 % + Force_Stress_LCAO getForceStress 0.62094 1 0.62 7.4 % + Force_LCAO_gamma ftable_gamma 0.40248 1 0.4 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.14961 1 0.15 1.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:23 2022 + FINISH Time : Wed Sep 28 11:06:31 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/280/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..57c01b30c6da3a4c131c6e5ab4c1fd54dd0e480d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.745854 0.0444985 0.364741 +H 0.77274 0.0288754 0.423034 +H 0.694284 0.079679 0.382392 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..23fc509a3e3ae543f43e366a9da5e96fa6aa9154 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3326 2 + 2 -12.9549 2 + 3 -9.21625 2 + 4 -6.7552 2 + 5 1.29619 0 + 6 4.41884 0 + 7 11.0706 0 + 8 11.3316 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..bb1818ef90fff9fb83c4e9b438e184c97d2bf692 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:26 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 20.8839055596 1.24595711764 10.212759853 0 0 0 0 + tauc_H1 21.6367189553 0.808511141666 11.8449579208 0 0 0 0 + tauc_H2 19.4399496868 2.23101334201 10.7069705548 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0735052516548 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.073834853048 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0901914128899 (SEC) + + DONE : INIT CHARGE Time : 0.131087956304 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.373993 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00154 + + Density error is 0.214758432661 + + Energy Rydberg eV + E_KohnSham -34.1904027589 -465.184294436 + E_Harris -34.3821816515 -467.793580132 + E_Fermi -0.406070538353 -5.52487311152 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00136214589249 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00141782618248 + + Density error is 0.0979405142245 + + Energy Rydberg eV + E_KohnSham -34.280599084 -466.411478395 + E_Harris -34.2874067598 -466.504101576 + E_Fermi -0.214731428789 -2.92157097122 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012886199904 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131620679818 + + Density error is 0.0629206439759 + + Energy Rydberg eV + E_KohnSham -34.2809542541 -466.416310732 + E_Harris -34.2853605378 -466.476261298 + E_Fermi -0.204122835549 -2.77723365538 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117501308032 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114092299687 + + Density error is 0.00196675731584 + + Energy Rydberg eV + E_KohnSham -34.2809333644 -466.416026515 + E_Harris -34.2809342887 -466.41603909 + E_Fermi -0.168440775244 -2.29175431885 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117671435456 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114051915941 + + Density error is 0.000953342049748 + + Energy Rydberg eV + E_KohnSham -34.2808693507 -466.415155562 + E_Harris -34.2808707734 -466.41517492 + E_Fermi -0.167810555054 -2.28317973328 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011748972517 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113825329454 + + Density error is 0.000126473913606 + + Energy Rydberg eV + E_KohnSham -34.2809088861 -466.415693469 + E_Harris -34.2809089059 -466.41569374 + E_Fermi -0.167766390193 -2.28257883951 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117491673488 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113813851827 + + Density error is 3.8260851675e-05 + + Energy Rydberg eV + E_KohnSham -34.2808954833 -466.415511116 + E_Harris -34.2808954913 -466.415511224 + E_Fermi -0.167654954811 -2.28106268337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117485916766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113811825523 + + Density error is 1.44312096773e-05 + + Energy Rydberg eV + E_KohnSham -34.2808987939 -466.415556159 + E_Harris -34.2808987948 -466.41555617 + E_Fermi -0.167696814834 -2.2816322182 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117484979063 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011380939404 + + Density error is 1.78743719158e-06 + + Energy Rydberg eV + E_KohnSham -34.2808974469 -466.415537832 + E_Harris -34.2808974469 -466.415537832 + E_Fermi -0.167681547118 -2.28142449026 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117484851501 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113809104007 + + Density error is 2.02106702053e-07 + + Energy Rydberg eV + E_KohnSham -34.2808976393 -466.415540449 + E_Harris -34.2808976393 -466.415540449 + E_Fermi -0.167679914366 -2.28140227552 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117484922538 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113809162033 + + Density error is 6.84510116477e-08 + + Energy Rydberg eV + E_KohnSham -34.2808976699 -466.415540865 + E_Harris -34.2808976699 -466.415540865 + E_band -7.9759162541 -108.517907827 + E_one_elec -69.3086763673 -942.992919433 + E_Hartree +36.0446280611 +490.412323922 + E_xc -8.21037308091 -111.707856606 + E_Ewald +7.31780364395 +99.5638264028 + E_demet -9.61624782803e-78 -1.30835763841e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194861154449 -2.65122201936 + E_Fermi -0.167679899359 -2.28140207135 + + charge density convergence is achieved + final etot is -466.415540865 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3326 2.00000 + 2 -12.9549 2.00000 + 3 -9.21625 2.00000 + 4 -6.75520 2.00000 + 5 1.29619 0.00000 + 6 4.41884 0.00000 + 7 11.0706 0.00000 + 8 11.3316 0.00000 + + EFERMI = -2.281402071346718 eV + OUT.ABACUS/ final etot is -466.4155408651955 eV + correction force for each atom along direction 1 is -6.51185e-05 + correction force for each atom along direction 2 is 0.000134807 + correction force for each atom along direction 3 is 0.000173810 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.60565059 -0.39516905 +0.13378554 + H1 +0.073279209 -0.058665117 -0.18635583 + H2 -0.67892980 +0.45383417 +0.052570293 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4155408651955 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3672 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3601 1 7.4 1.e+02% + Potential init_pot 0.24197 2 0.12 3.3% + PW_Basis recip2real 0.21748 16 0.014 3.0% + PW_Basis gathers_scatterp 0.10296 16 0.0064 1.4% + Potential v_of_rho 0.95625 13 0.074 13.% + XC_Functional v_xc 0.37444 14 0.027 5.1% + H_Hartree_pw v_hartree 0.55209 13 0.042 7.5% + PW_Basis real2recip 0.59815 38 0.016 8.1% + PW_Basis gatherp_scatters 0.26863 38 0.0071 3.6% + ORB_control set_orb_tables 0.89985 1 0.90 12.% + ORB_gen_tables gen_tables 0.89984 1 0.90 12.% + ORB_table_phi init_Table 0.37746 1 0.38 5.1% + ORB_table_phi cal_ST_Phi12_R 0.37317 126 0.0030 5.1% + ORB_table_beta init_Table_Beta 0.15527 1 0.16 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15401 56 0.0028 2.1% + ORB_table_alpha init_Table_Alpha 0.20984 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20815 66 0.0032 2.8% + LOOP_ions opt_ions 6.0156 1 6.0 82.% + ESolver_KS_LCAO Run 5.4547 1 5.5 74.% + HSolverLCAO solve 3.3104 11 0.30 45.% + HamiltLCAO updateHk 1.5996 11 0.15 22.% + LCAO_Hamilt cal_Hgamma 1.5762 11 0.14 21.% + Gint_interface cal_gint 0.46098 23 0.020 6.3% + Gint_Gamma distri_vl_value 1.0142 11 0.092 14.% + Gint_Gamma distri_vl 2.5980 6 0.43 35.% + LCAO_Deepks cal_projected_DM 5.5957 13 0.43 76.% + LCAO_gen_fixedH add_v_delta 2.4823 6 0.41 34.% + LCAO_DESCRIPTOR add_v_delta 2.4825 6 0.41 34.% + ElecStateLCAO psiToRho 1.6817 11 0.15 23.% + Charge mix_rho 0.66220 10 0.066 9.0% + LOOP_ions force_stress 0.56085 1 0.56 7.6% + Force_Stress_LCAO getForceStress 0.56083 1 0.56 7.6% + Force_LCAO_gamma ftable_gamma 0.36954 1 0.37 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.11884 1 0.12 1.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:26 2022 + Finish Time : Wed Sep 28 11:04:34 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d92f6519e09ba090fd05371f115e12a76c1cbb5f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012387 ima = 3.65011e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123022582134 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111804856175 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112393735363 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112649420331 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112594706104 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112626263688 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001126207935 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112623618935 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112623036703 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112622957766 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112622949787 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/STRU new file mode 100644 index 0000000000000000000000000000000000000000..24ab0e870fe68a8af7dd56255a39a635eae97aef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-7.116094440373 29.245957117643 10.212759852988 0 0 0 +H +0.0 +2 +-6.363281044635 28.808511141657 11.844957920812 0 0 0 +-8.560050313249 30.231013341991 10.706970554816 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/conv new file mode 100644 index 0000000000000000000000000000000000000000..d2300ef7ff717388a26b86a6984ab59087c75651 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/conv @@ -0,0 +1 @@ +281 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8a15494719400aa3bfe8948bc6de7d440809930b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750807085 0.01272399645 1.272660528 1.359590782 1.469471899 0.008792091581 0.01799903771 0.03907175505 +6.870294707e-18 0.001013723423 0.002677216836 0.01262944622 0.0457677594 -1.596657106e-19 2.258268857e-06 6.351426643e-06 +0.001622236202 0.006031048759 + +H atom_index 1 n_descriptor 18 +1.233950076 0.03498236351 0.103405017 0.1424675826 0.3152214061 0.02172707885 0.02734277042 0.03811763248 +2.588158503e-17 4.595295019e-05 0.09795065635 0.114425484 0.1222175615 -7.048271432e-18 4.769844197e-06 0.01343682773 +0.02587149215 0.03000019491 + +H atom_index 2 n_descriptor 18 +1.260361313 0.03408045252 0.1125426086 0.1546595744 0.3238921533 0.02297787019 0.02888435161 0.03727469043 +1.204973503e-17 4.844145032e-05 0.1042398792 0.1158145199 0.1327554695 1.461490682e-18 3.324664074e-06 0.01319852378 +0.02685808235 0.03121394046 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a526cd519c269f3ef9073a709bea4809fa608fdd Binary files /dev/null and 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new file mode 100644 index 0000000000000000000000000000000000000000..2cba45abeb289e7623b52754c701b41b8d968204 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:26 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0735213 SEC) : SETUP UNITCELL + DONE(0.0738446 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.090203 SEC) : INIT PLANEWAVE + DONE(0.131195 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374041 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651843e+02 0.000000e+00 2.148e-01 5.637e-01 + GE2 -4.664115e+02 -1.227184e+00 9.794e-02 5.440e-01 + GE3 -4.664163e+02 -4.832337e-03 6.292e-02 6.032e-01 + GE4 -4.664160e+02 2.842176e-04 1.967e-03 4.833e-01 + GE5 -4.664152e+02 8.709523e-04 9.533e-04 4.780e-01 + GE6 -4.664157e+02 -5.379070e-04 1.265e-04 4.737e-01 + GE7 -4.664155e+02 1.823538e-04 3.826e-05 4.691e-01 + GE8 -4.664156e+02 -4.504291e-05 1.443e-05 4.609e-01 + GE9 -4.664155e+02 1.832683e-05 1.787e-06 4.653e-01 + GE10 -4.664155e+02 -2.617749e-06 2.021e-07 4.640e-01 + GE11 -4.664155e+02 -4.157490e-07 6.845e-08 3.897e-01 +E_delta_band = -7.05812277e-02 Ry = -9.60306868e-01 eV +E_delta_NN= -1.94861154e-01 Ry = -2.65122202e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3672 11 0.67 1e+02 % + Run_lcao lcao_line 7.3601 1 7.4 1e+02 % + Potential init_pot 0.24197 2 0.12 3.3 % + PW_Basis recip2real 0.21748 16 0.014 3 % + PW_Basis gathers_scatterp 0.10296 16 0.0064 1.4 % + Potential v_of_rho 0.95625 13 0.074 13 % + XC_Functional v_xc 0.37444 14 0.027 5.1 % + H_Hartree_pw v_hartree 0.55209 13 0.042 7.5 % + PW_Basis real2recip 0.59815 38 0.016 8.1 % + PW_Basis gatherp_scatters 0.26863 38 0.0071 3.6 % + ORB_control set_orb_tables 0.89985 1 0.9 12 % + ORB_gen_tables gen_tables 0.89984 1 0.9 12 % + ORB_table_phi init_Table 0.37746 1 0.38 5.1 % + ORB_table_phi cal_ST_Phi12_R 0.37317 126 0.003 5.1 % + ORB_table_beta init_Table_Beta 0.15527 1 0.16 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15401 56 0.0028 2.1 % + ORB_table_alpha init_Table_Alpha 0.20984 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20815 66 0.0032 2.8 % + LOOP_ions opt_ions 6.0156 1 6 82 % + ESolver_KS_LCAO Run 5.4547 1 5.5 74 % + HSolverLCAO solve 3.3104 11 0.3 45 % + HamiltLCAO updateHk 1.5996 11 0.15 22 % + LCAO_Hamilt cal_Hgamma 1.5762 11 0.14 21 % + Gint_interface cal_gint 0.46098 23 0.02 6.3 % + Gint_Gamma distri_vl_value 1.0142 11 0.092 14 % + Gint_Gamma distri_vl 2.598 6 0.43 35 % + LCAO_Deepks cal_projected_DM 5.5957 13 0.43 76 % + LCAO_gen_fixedH add_v_delta 2.4823 6 0.41 34 % + LCAO_DESCRIPTOR add_v_delta 2.4825 6 0.41 34 % + ElecStateLCAO psiToRho 1.6817 11 0.15 23 % + Charge mix_rho 0.6622 10 0.066 9 % + LOOP_ions force_stress 0.56085 1 0.56 7.6 % + Force_Stress_LCAO getForceStress 0.56083 1 0.56 7.6 % + Force_LCAO_gamma ftable_gamma 0.36954 1 0.37 5 % + Force_LCAO_gamma cal_fvl_dphi 0.11884 1 0.12 1.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:26 2022 + FINISH Time : Wed Sep 28 11:04:34 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/281/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d2272838a5b26bc668fe98236f9d996bffa72d25 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.756199 0.0425801 0.375564 +H 0.813965 0.0140774 0.378532 +H 0.765143 0.102381 0.399263 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..359984fccc7ee05e204b6ad360ff0149f3f7faba --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3942 2 + 2 -13.2249 2 + 3 -9.06934 2 + 4 -6.76796 2 + 5 1.42098 0 + 6 4.6188 0 + 7 11.0451 0 + 8 11.2888 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fe0598a98158b825d9fe2af0ab7ec7409da855ef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/running_scf.log @@ -0,0 +1,802 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:15 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 21.1735770824 1.19224283779 10.515804881 0 0 0 0 + tauc_H1 22.7910183137 0.394167203391 10.5988994612 0 0 0 0 + tauc_H2 21.4239929944 2.86667078731 11.1793506121 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.113106532677 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.113699316077 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.144439155076 (SEC) + + DONE : INIT CHARGE Time : 0.196397088423 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.496935 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00158 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000596 + + Density error is 0.216085070204 + + Energy Rydberg eV + E_KohnSham -34.19067834 -465.188043909 + E_Harris -34.3848494882 -467.829877911 + E_Fermi -0.413169378017 -5.62145778015 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00146072758767 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000800951170503 + + Density error is 0.0976429312891 + + Energy Rydberg eV + E_KohnSham -34.2802636898 -466.406915124 + E_Harris -34.2868855953 -466.497010771 + E_Fermi -0.221180448215 -3.00931438192 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013412568479 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000775746676415 + + Density error is 0.0624241953815 + + Energy Rydberg eV + E_KohnSham -34.2804562347 -466.409534831 + E_Harris -34.284710395 -466.467415651 + E_Fermi -0.207851744239 -2.82796806089 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113281817394 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00074891109992 + + Density error is 0.00203375296661 + + Energy Rydberg eV + E_KohnSham -34.2804825281 -466.409892571 + E_Harris -34.2804840561 -466.409913361 + E_Fermi -0.172324656894 -2.34459723965 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112924616618 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000750018582062 + + Density error is 0.000869670999486 + + Energy Rydberg eV + E_KohnSham -34.2804156836 -466.408983105 + E_Harris -34.2804176699 -466.409010131 + E_Fermi -0.171262252713 -2.33014248921 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112757678239 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000749377417627 + + Density error is 0.000152807106861 + + Energy Rydberg eV + E_KohnSham -34.2804620814 -466.409614381 + E_Harris -34.280462135 -466.409615109 + E_Fermi -0.171469749945 -2.33296563389 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112734338997 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000749647676878 + + Density error is 4.22588119438e-05 + + Energy Rydberg eV + E_KohnSham -34.2804451933 -466.409384605 + E_Harris -34.2804452034 -466.409384742 + E_Fermi -0.171311882639 -2.330817739 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112735815232 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000749572000204 + + Density error is 1.75944790668e-05 + + Energy Rydberg eV + E_KohnSham -34.2804495894 -466.409444417 + E_Harris -34.2804495907 -466.409444435 + E_Fermi -0.171363388114 -2.33151850693 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112732035684 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000749576836551 + + Density error is 2.48410634546e-06 + + Energy Rydberg eV + E_KohnSham -34.2804480447 -466.409423401 + E_Harris -34.2804480447 -466.409423401 + E_Fermi -0.17134548781 -2.3312749608 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112731417224 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000749579109849 + + Density error is 3.25085795175e-07 + + Energy Rydberg eV + E_KohnSham -34.2804482884 -466.409426716 + E_Harris -34.2804482884 -466.409426716 + E_Fermi -0.171342892491 -2.33123964967 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112731437435 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000749579438081 + + Density error is 1.28292803928e-07 + + Energy Rydberg eV + E_KohnSham -34.2804483247 -466.40942721 + E_Harris -34.2804483247 -466.40942721 + E_Fermi -0.171342798475 -2.33123837052 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112731416509 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0007495795995 + + Density error is 1.00800263453e-08 + + Energy Rydberg eV + E_KohnSham -34.2804483268 -466.409427239 + E_Harris -34.2804483268 -466.409427239 + E_band -8.00493158609 -108.912681671 + E_one_elec -69.555946533 -946.357202632 + E_Hartree +36.1667551314 +492.073947958 + E_xc -8.23007113002 -111.975862314 + E_Ewald +7.46260289664 +101.533921306 + E_demet -2.9913584539e-85 -4.06995197335e-84 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195268945991 -2.65677030793 + E_Fermi -0.171342687038 -2.33123685435 + + charge density convergence is achieved + final etot is -466.409427239 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3942 2.00000 + 2 -13.2249 2.00000 + 3 -9.06934 2.00000 + 4 -6.76796 2.00000 + 5 1.42098 0.00000 + 6 4.61880 0.00000 + 7 11.0451 0.00000 + 8 11.2888 0.00000 + + EFERMI = -2.331236854348529 eV + OUT.ABACUS/ final etot is -466.4094272385676 eV + correction force for each atom along direction 1 is 0.000156239 + correction force for each atom along direction 2 is 3.66635e-05 + correction force for each atom along direction 3 is -4.45938e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0709962 -0.16790485 -0.31161487 + H1 +0.93651086 -0.41135605 +0.068773654 + H2 +0.13448533 +0.57926090 +0.24284122 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4094272385676 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6643 11 0.70 1.0e+02% + Run_lcao lcao_line 7.6562 1 7.7 1.e+02% + Potential init_pot 0.30072 2 0.15 3.9% + PW_Basis recip2real 0.26837 17 0.016 3.5% + PW_Basis gathers_scatterp 0.11854 17 0.0070 1.5% + Charge atomic_rho 0.10601 1 0.11 1.4% + Potential v_of_rho 0.83236 14 0.059 11.% + XC_Functional v_xc 0.19982 15 0.013 2.6% + H_Hartree_pw v_hartree 0.59257 14 0.042 7.7% + PW_Basis real2recip 0.70382 41 0.017 9.2% + PW_Basis gatherp_scatters 0.28558 41 0.0070 3.7% + ORB_control set_orb_tables 1.0919 1 1.1 14.% + ORB_gen_tables gen_tables 1.0919 1 1.1 14.% + ORB_table_phi init_Table 0.47282 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46762 126 0.0037 6.1% + ORB_table_beta init_Table_Beta 0.18083 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.17926 56 0.0032 2.3% + ORB_table_alpha init_Table_Alpha 0.24856 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24662 66 0.0037 3.2% + LOOP_ions opt_ions 5.9883 1 6.0 78.% + ESolver_KS_LCAO Run 5.4047 1 5.4 71.% + HSolverLCAO solve 3.1227 12 0.26 41.% + HamiltLCAO updateHk 1.5742 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.5445 12 0.13 20.% + Gint_interface cal_gint 0.49424 25 0.020 6.4% + Gint_Gamma distri_vl_value 0.92352 12 0.077 12.% + Gint_Gamma distri_vl 2.8030 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.5685 14 0.40 73.% + LCAO_gen_fixedH add_v_delta 2.6694 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6696 6 0.44 35.% + ElecStateLCAO psiToRho 1.5251 12 0.13 20.% + Charge mix_rho 0.84165 11 0.077 11.% + LOOP_ions force_stress 0.58349 1 0.58 7.6% + Force_Stress_LCAO getForceStress 0.58347 1 0.58 7.6% + Force_LCAO_gamma ftable_gamma 0.39013 1 0.39 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.13120 1 0.13 1.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:15 2022 + Finish Time : Wed Sep 28 11:07:23 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0ba0fc55ef09784227ccc1b38bf03362991d85ad --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123813 ima = 3.65487e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123010873417 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112212653419 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011264998226 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112905245513 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112842548609 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112879787605 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011287218947 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112875315537 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112874588729 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112874492478 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112874481115 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112874475477 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/STRU new file mode 100644 index 0000000000000000000000000000000000000000..86467e38858904a6513996175b05cdd4abd44261 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-6.826422917608 29.192242837788 10.515804880988 0 0 0 +H +0.0 +2 +-5.208981686320 28.394167203416 10.598899461201 0 0 0 +-6.576007005574 30.866670787283 11.179350612085 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/conv new file mode 100644 index 0000000000000000000000000000000000000000..88640a16832ab40a03d7b62c709d5a04180e410b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/conv @@ -0,0 +1 @@ +282 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..38d69494d5817422de99746cbc102ac60d61bf0f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748036223 0.01275026441 1.285219227 1.372337833 1.469850653 0.008392539084 0.01919765345 0.03898981475 +-4.285079062e-18 0.001139803996 0.002621185591 0.01272468111 0.045905848 -2.403035071e-19 2.054443705e-06 5.957241486e-06 +0.001681228519 0.005905332852 + +H atom_index 1 n_descriptor 18 +1.266391881 0.03351883366 0.1142932164 0.1579481236 0.3263534839 0.02297230032 0.02928588007 0.03677390769 +3.102235412e-17 4.782097822e-05 0.1060173982 0.116203093 0.135711275 -1.27066416e-18 3.334991875e-06 0.01309315187 +0.02707539527 0.03150931935 + +H atom_index 2 n_descriptor 18 +1.256157442 0.0338698584 0.110626651 0.1530423212 0.3232138439 0.02250599904 0.0286946144 0.03703802139 +1.862045541e-17 4.686702098e-05 0.1040549785 0.1152273514 0.1315014234 -1.931857771e-18 3.906472741e-06 0.01309076491 +0.02671291539 0.03107251873 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..04a71c18895f8c639e24e2095eff10c47f2dbe87 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/log.scf @@ -0,0 +1,104 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:15 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.113145 SEC) : SETUP UNITCELL + DONE(0.11372 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.144467 SEC) : INIT PLANEWAVE + DONE(0.196549 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.497009 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651880e+02 0.000000e+00 2.161e-01 5.436e-01 + GE2 -4.664069e+02 -1.218871e+00 9.764e-02 5.001e-01 + GE3 -4.664095e+02 -2.619707e-03 6.242e-02 5.640e-01 + GE4 -4.664099e+02 -3.577399e-04 2.034e-03 4.346e-01 + GE5 -4.664090e+02 9.094660e-04 8.697e-04 4.317e-01 + GE6 -4.664096e+02 -6.312753e-04 1.528e-04 4.250e-01 + GE7 -4.664094e+02 2.297751e-04 4.226e-05 4.210e-01 + GE8 -4.664094e+02 -5.981201e-05 1.759e-05 4.153e-01 + GE9 -4.664094e+02 2.101666e-05 2.484e-06 4.156e-01 + GE10 -4.664094e+02 -3.315228e-06 3.251e-07 4.146e-01 + GE11 -4.664094e+02 -4.943991e-07 1.283e-07 4.145e-01 + GE12 -4.664094e+02 -2.815939e-08 1.008e-08 3.642e-01 +E_delta_band = -7.14802541e-02 Ry = -9.72538751e-01 eV +E_delta_NN= -1.95268946e-01 Ry = -2.65677031e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6643 11 0.7 1e+02 % + Run_lcao lcao_line 7.6562 1 7.7 1e+02 % + Potential init_pot 0.30072 2 0.15 3.9 % + PW_Basis recip2real 0.26837 17 0.016 3.5 % + PW_Basis gathers_scatterp 0.11854 17 0.007 1.5 % + Charge atomic_rho 0.10601 1 0.11 1.4 % + Potential v_of_rho 0.83236 14 0.059 11 % + XC_Functional v_xc 0.19982 15 0.013 2.6 % + H_Hartree_pw v_hartree 0.59257 14 0.042 7.7 % + PW_Basis real2recip 0.70382 41 0.017 9.2 % + PW_Basis gatherp_scatters 0.28558 41 0.007 3.7 % + ORB_control set_orb_tables 1.0919 1 1.1 14 % + ORB_gen_tables gen_tables 1.0919 1 1.1 14 % + ORB_table_phi init_Table 0.47282 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.46762 126 0.0037 6.1 % + ORB_table_beta init_Table_Beta 0.18083 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.17926 56 0.0032 2.3 % + ORB_table_alpha init_Table_Alpha 0.24856 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24662 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9883 1 6 78 % + ESolver_KS_LCAO Run 5.4047 1 5.4 71 % + HSolverLCAO solve 3.1227 12 0.26 41 % + HamiltLCAO updateHk 1.5742 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.5445 12 0.13 20 % + Gint_interface cal_gint 0.49424 25 0.02 6.4 % + Gint_Gamma distri_vl_value 0.92352 12 0.077 12 % + Gint_Gamma distri_vl 2.803 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.5685 14 0.4 73 % + LCAO_gen_fixedH add_v_delta 2.6694 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6696 6 0.44 35 % + ElecStateLCAO psiToRho 1.5251 12 0.13 20 % + Charge mix_rho 0.84165 11 0.077 11 % + LOOP_ions force_stress 0.58349 1 0.58 7.6 % + Force_Stress_LCAO getForceStress 0.58347 1 0.58 7.6 % + Force_LCAO_gamma ftable_gamma 0.39013 1 0.39 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.1312 1 0.13 1.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:15 2022 + FINISH Time : Wed Sep 28 11:07:23 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/282/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..45a0d93b01c97c8bfda8937c3f82a896e24f5cce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.774985 0.0379935 0.38138 +H 0.780816 0.0352373 0.31527 +H 0.761987 0.104483 0.388989 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..a50eaaad01b1c3fc4e1d54077d8efd9f87da525c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0801 2 + 2 -12.5802 2 + 3 -9.30272 2 + 4 -6.70243 2 + 5 1.0191 0 + 6 3.95531 0 + 7 11.1371 0 + 8 11.4057 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d6e5845bd774cd8c2e12746cf308f3a5650778d6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:11 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 21.6995819712 1.06381707172 10.6786466605 0 0 0 0 + tauc_H1 21.8628521395 0.986644036922 8.82756893951 0 0 0 0 + tauc_H2 21.3356378065 2.9255229819 10.8916787308 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0741878516054 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0891497831701 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105604965055 (SEC) + + DONE : INIT CHARGE Time : 0.147824383783 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.393547 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00153 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000868 + + Density error is 0.21004980934 + + Energy Rydberg eV + E_KohnSham -34.1922658295 -465.209642812 + E_Harris -34.3741434753 -467.684215134 + E_Fermi -0.387520186681 -5.27248262889 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00135794565152 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120089455695 + + Density error is 0.0982874496466 + + Energy Rydberg eV + E_KohnSham -34.2786346997 -466.384751576 + E_Harris -34.2857124153 -466.481048837 + E_Fermi -0.200534596013 -2.72841315191 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125078264828 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115711016641 + + Density error is 0.0632950737326 + + Energy Rydberg eV + E_KohnSham -34.2789493521 -466.389032642 + E_Harris -34.2835025556 -466.450982153 + E_Fermi -0.19310127905 -2.62727768617 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104571807542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111396936284 + + Density error is 0.00191157708699 + + Energy Rydberg eV + E_KohnSham -34.2788565424 -466.387769901 + E_Harris -34.2788576073 -466.387784389 + E_Fermi -0.157793002438 -2.14688393768 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104383810685 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111302781451 + + Density error is 0.000815164979261 + + Energy Rydberg eV + E_KohnSham -34.2788329156 -466.387448442 + E_Harris -34.2788333379 -466.387454188 + E_Fermi -0.157771599575 -2.14659273679 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104128405004 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111283175706 + + Density error is 0.000149853780971 + + Energy Rydberg eV + E_KohnSham -34.2788428561 -466.387583689 + E_Harris -34.2788428508 -466.387583617 + E_Fermi -0.15734795279 -2.14082872658 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104127380853 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111307166164 + + Density error is 2.41012270006e-05 + + Energy Rydberg eV + E_KohnSham -34.2788411489 -466.387560461 + E_Harris -34.2788411496 -466.387560472 + E_Fermi -0.157322737575 -2.14048565598 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010412224038 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111298016911 + + Density error is 8.80532676249e-06 + + Energy Rydberg eV + E_KohnSham -34.2788425424 -466.387579421 + E_Harris -34.2788425428 -466.387579426 + E_Fermi -0.157329859224 -2.14058255098 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104121461038 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111298882635 + + Density error is 2.29503150923e-06 + + Energy Rydberg eV + E_KohnSham -34.2788418583 -466.387570114 + E_Harris -34.2788418583 -466.387570114 + E_Fermi -0.157322334497 -2.14048017182 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010412076185 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111298854428 + + Density error is 4.73939974729e-07 + + Energy Rydberg eV + E_KohnSham -34.278842014 -466.387572232 + E_Harris -34.278842014 -466.387572232 + E_Fermi -0.157320592782 -2.14045647457 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104120728525 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111298911459 + + Density error is 1.76711095317e-07 + + Energy Rydberg eV + E_KohnSham -34.2788420168 -466.387572271 + E_Harris -34.2788420168 -466.387572271 + E_Fermi -0.157320374871 -2.14045350974 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104120689977 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111298936939 + + Density error is 1.12293804613e-08 + + Energy Rydberg eV + E_KohnSham -34.27884202 -466.387572314 + E_Harris -34.27884202 -466.387572314 + E_band -7.88867229981 -107.330892932 + E_one_elec -68.7002097448 -934.714306325 + E_Hartree +35.7531923385 +486.447137493 + E_xc -8.16365140203 -111.072175553 + E_Ewald +6.95732415513 +94.6592513427 + E_demet -3.1746771845e-61 -4.31936990198e-60 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193816654745 -2.63701087183 + E_Fermi -0.157320215271 -2.14045133827 + + charge density convergence is achieved + final etot is -466.387572314 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0801 2.00000 + 2 -12.5802 2.00000 + 3 -9.30272 2.00000 + 4 -6.70243 2.00000 + 5 1.01910 0.00000 + 6 3.95531 0.00000 + 7 11.1371 0.00000 + 8 11.4057 0.00000 + + EFERMI = -2.140451338271157 eV + OUT.ABACUS/ final etot is -466.3875723138674 eV + correction force for each atom along direction 1 is -0.000163885 + correction force for each atom along direction 2 is 0.000111888 + correction force for each atom along direction 3 is -1.80470e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.28400737 +1.6585190 -0.40035516 + H1 +0.029757736 -0.26415180 +0.28739798 + H2 +0.25424964 -1.3943672 +0.11295719 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3875723138674 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8006 11 0.71 1.0e+02% + Run_lcao lcao_line 7.7935 1 7.8 1.e+02% + Potential init_pot 0.24441 2 0.12 3.1% + PW_Basis recip2real 0.23666 17 0.014 3.0% + PW_Basis gathers_scatterp 0.11348 17 0.0067 1.5% + Potential v_of_rho 0.99809 14 0.071 13.% + XC_Functional v_xc 0.37034 15 0.025 4.7% + H_Hartree_pw v_hartree 0.59791 14 0.043 7.7% + PW_Basis real2recip 0.66349 41 0.016 8.5% + PW_Basis gatherp_scatters 0.30750 41 0.0075 3.9% + ORB_control set_orb_tables 0.89779 1 0.90 12.% + ORB_gen_tables gen_tables 0.89779 1 0.90 12.% + ORB_table_phi init_Table 0.37541 1 0.38 4.8% + ORB_table_phi cal_ST_Phi12_R 0.37116 126 0.0029 4.8% + ORB_table_beta init_Table_Beta 0.15437 1 0.15 2.0% + ORB_table_beta VNL_PhiBeta_R 0.15305 56 0.0027 2.0% + ORB_table_alpha init_Table_Alpha 0.20993 1 0.21 2.7% + ORB_table_alpha S_PhiAlpha_R 0.20829 66 0.0032 2.7% + LOOP_ions opt_ions 6.4322 1 6.4 82.% + ESolver_KS_LCAO Run 5.8750 1 5.9 75.% + HSolverLCAO solve 3.5380 12 0.29 45.% + HamiltLCAO updateHk 1.7409 12 0.15 22.% + LCAO_Hamilt cal_Hgamma 1.7157 12 0.14 22.% + Gint_interface cal_gint 0.78009 25 0.031 10.% + Gint_Gamma distri_vl_value 1.0209 12 0.085 13.% + Gint_Gamma distri_vl 3.0431 6 0.51 39.% + LCAO_Deepks cal_projected_DM 6.0439 14 0.43 77.% + LCAO_gen_fixedH add_v_delta 2.9227 6 0.49 37.% + LCAO_DESCRIPTOR add_v_delta 2.9228 6 0.49 37.% + ElecStateLCAO psiToRho 1.7696 12 0.15 23.% + Charge mix_rho 0.74815 11 0.068 9.6% + LOOP_ions force_stress 0.55703 1 0.56 7.1% + Force_Stress_LCAO getForceStress 0.55701 1 0.56 7.1% + Force_LCAO_gamma ftable_gamma 0.36551 1 0.37 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.14742 1 0.15 1.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:11 2022 + Finish Time : Wed Sep 28 11:03:19 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1728d0d2929084f10341ec0c0d2e7ac8f8c08beb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012345 ima = 3.66297e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123026204242 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111801037832 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112538160117 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112728725819 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112719345566 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112724948331 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112723033499 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112724316508 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112723879444 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112723860355 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112723843141 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112723834418 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/STRU new file mode 100644 index 0000000000000000000000000000000000000000..f4fb2b6b059ecf55bdca1c2091ef35c586423844 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-6.300418028780 29.063817071716 10.678646660493 0 0 0 +H +0.0 +2 +-6.137147860456 28.986644036942 8.827568939484 0 0 0 +-6.664362193468 30.925522981892 10.891678730797 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/conv new file mode 100644 index 0000000000000000000000000000000000000000..1a6bbc0264c9a3b6f205802e78f4e7e0a6101848 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/conv @@ -0,0 +1 @@ +283 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..789ca9dee0c3a3da0cac74b7189a2b128597925f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75326937 0.0125284415 1.246718519 1.334361908 1.468451736 0.009061695182 0.0167669292 0.03919198333 +-3.888036923e-18 0.0008289803868 0.002568484743 0.01205378605 0.0430848624 -8.636717223e-19 2.058885863e-06 5.980060268e-06 +0.001570621047 0.006008536866 + +H atom_index 1 n_descriptor 18 +1.228191018 0.03543043346 0.1017716293 0.1398673202 0.3131616294 0.02152846192 0.0269851502 0.03864772399 +2.921096225e-18 4.19063111e-05 0.09423298454 0.1147295353 0.1197153979 8.040739596e-19 4.474122497e-06 0.01360711167 +0.02522323973 0.02967375984 + +H atom_index 2 n_descriptor 18 +1.189793306 0.03663747768 0.08979251229 0.1238112739 0.2988466344 0.01968907713 0.02472536259 0.04017282967 +-2.510441545e-17 3.856077498e-05 0.08438037081 0.1056194041 0.1130443605 -1.21329973e-18 6.008798034e-06 0.01461688093 +0.02364354939 0.02766295838 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..719fa57ce5a68da73cb13f1883194670e71e093d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:11 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0742314 SEC) : SETUP UNITCELL + DONE(0.0891618 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105619 SEC) : INIT PLANEWAVE + DONE(0.147925 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.393591 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652096e+02 0.000000e+00 2.100e-01 5.584e-01 + GE2 -4.663848e+02 -1.175109e+00 9.829e-02 5.379e-01 + GE3 -4.663890e+02 -4.281066e-03 6.330e-02 6.000e-01 + GE4 -4.663878e+02 1.262741e-03 1.912e-03 4.805e-01 + GE5 -4.663874e+02 3.214592e-04 8.152e-04 4.740e-01 + GE6 -4.663876e+02 -1.352477e-04 1.499e-04 4.738e-01 + GE7 -4.663876e+02 2.322785e-05 2.410e-05 4.629e-01 + GE8 -4.663876e+02 -1.895998e-05 8.805e-06 4.593e-01 + GE9 -4.663876e+02 9.307521e-06 2.295e-06 4.668e-01 + GE10 -4.663876e+02 -2.118114e-06 4.739e-07 4.568e-01 + GE11 -4.663876e+02 -3.866218e-08 1.767e-07 4.605e-01 + GE12 -4.663876e+02 -4.315260e-08 1.123e-08 3.832e-01 +E_delta_band = -6.83192880e-02 Ry = -9.29531600e-01 eV +E_delta_NN= -1.93816655e-01 Ry = -2.63701087e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8006 11 0.71 1e+02 % + Run_lcao lcao_line 7.7935 1 7.8 1e+02 % + Potential init_pot 0.24441 2 0.12 3.1 % + PW_Basis recip2real 0.23666 17 0.014 3 % + PW_Basis gathers_scatterp 0.11348 17 0.0067 1.5 % + Potential v_of_rho 0.99809 14 0.071 13 % + XC_Functional v_xc 0.37034 15 0.025 4.7 % + H_Hartree_pw v_hartree 0.59791 14 0.043 7.7 % + PW_Basis real2recip 0.66349 41 0.016 8.5 % + PW_Basis gatherp_scatters 0.3075 41 0.0075 3.9 % + ORB_control set_orb_tables 0.89779 1 0.9 12 % + ORB_gen_tables gen_tables 0.89779 1 0.9 12 % + ORB_table_phi init_Table 0.37541 1 0.38 4.8 % + ORB_table_phi cal_ST_Phi12_R 0.37116 126 0.0029 4.8 % + ORB_table_beta init_Table_Beta 0.15437 1 0.15 2 % + ORB_table_beta VNL_PhiBeta_R 0.15305 56 0.0027 2 % + ORB_table_alpha init_Table_Alpha 0.20993 1 0.21 2.7 % + ORB_table_alpha S_PhiAlpha_R 0.20829 66 0.0032 2.7 % + LOOP_ions opt_ions 6.4322 1 6.4 82 % + ESolver_KS_LCAO Run 5.875 1 5.9 75 % + HSolverLCAO solve 3.538 12 0.29 45 % + HamiltLCAO updateHk 1.7409 12 0.15 22 % + LCAO_Hamilt cal_Hgamma 1.7157 12 0.14 22 % + Gint_interface cal_gint 0.78009 25 0.031 10 % + Gint_Gamma distri_vl_value 1.0209 12 0.085 13 % + Gint_Gamma distri_vl 3.0431 6 0.51 39 % + LCAO_Deepks cal_projected_DM 6.0439 14 0.43 77 % + LCAO_gen_fixedH add_v_delta 2.9227 6 0.49 37 % + LCAO_DESCRIPTOR add_v_delta 2.9228 6 0.49 37 % + ElecStateLCAO psiToRho 1.7696 12 0.15 23 % + Charge mix_rho 0.74815 11 0.068 9.6 % + LOOP_ions force_stress 0.55703 1 0.56 7.1 % + Force_Stress_LCAO getForceStress 0.55701 1 0.56 7.1 % + Force_LCAO_gamma ftable_gamma 0.36551 1 0.37 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.14742 1 0.15 1.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:11 2022 + FINISH Time : Wed Sep 28 11:03:19 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/283/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..749c2037f7938aeb4d4f898d5d11c9a6f8ebc6e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.781874 0.0319966 0.378976 +H 0.751909 0.0462942 0.32218 +H 0.741374 0.0521036 0.423681 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0af9c0a35835d020f57125617188924cb10e4482 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4278 2 + 2 -13.1742 2 + 3 -9.12644 2 + 4 -6.77473 2 + 5 1.40605 0 + 6 4.62903 0 + 7 11.0409 0 + 8 11.2873 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4faec82f2c121debd4d2907cb7e4746d29e08527 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:42 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 21.8924665412 0.895905331796 10.6113354083 0 0 0 0 + tauc_H1 21.053441905 1.29623759881 9.02102974391 0 0 0 0 + tauc_H2 20.758474835 1.45890168247 11.8630755191 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0859864301235 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.086437435386 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104710433968 (SEC) + + DONE : INIT CHARGE Time : 0.155085318579 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.434587 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000938 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012 + + Density error is 0.217012117115 + + Energy Rydberg eV + E_KohnSham -34.1874139219 -465.143629222 + E_Harris -34.3839341051 -467.817423485 + E_Fermi -0.41493785501 -5.64551914404 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00130593715053 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118132239407 + + Density error is 0.097808148437 + + Energy Rydberg eV + E_KohnSham -34.2790392763 -466.390256124 + E_Harris -34.2857322233 -466.481318339 + E_Fermi -0.221353358976 -3.01166695351 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00124872914786 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110944428057 + + Density error is 0.0626330180075 + + Energy Rydberg eV + E_KohnSham -34.2793767244 -466.39484734 + E_Harris -34.2836930256 -466.453573631 + E_Fermi -0.209017074112 -2.84382318722 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117044179297 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999702364604 + + Density error is 0.00202722658698 + + Energy Rydberg eV + E_KohnSham -34.2793889369 -466.3950135 + E_Harris -34.2793906245 -466.39503646 + E_Fermi -0.173255341627 -2.35725985506 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117394099654 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100123753116 + + Density error is 0.00094876380098 + + Energy Rydberg eV + E_KohnSham -34.2793160151 -466.394021349 + E_Harris -34.2793177656 -466.394045165 + E_Fermi -0.172344117833 -2.34486201931 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117241191114 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999701946199 + + Density error is 0.000135677580952 + + Energy Rydberg eV + E_KohnSham -34.2793613661 -466.39463838 + E_Harris -34.2793614025 -466.394638876 + E_Fermi -0.172448548853 -2.34628287623 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117247960268 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999669702896 + + Density error is 4.38892035948e-05 + + Energy Rydberg eV + E_KohnSham -34.2793457534 -466.394425958 + E_Harris -34.2793457643 -466.394426107 + E_Fermi -0.172306433726 -2.34434930073 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117241519815 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999656077958 + + Density error is 1.67916859461e-05 + + Energy Rydberg eV + E_KohnSham -34.2793497223 -466.394479958 + E_Harris -34.2793497234 -466.394479973 + E_Fermi -0.17235894401 -2.34506373979 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117241658107 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009996483708 + + Density error is 2.45858603665e-06 + + Energy Rydberg eV + E_KohnSham -34.2793482133 -466.394459427 + E_Harris -34.2793482134 -466.394459428 + E_Fermi -0.172341784441 -2.34483027188 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117241487401 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999644548809 + + Density error is 1.71656996236e-07 + + Energy Rydberg eV + E_KohnSham -34.2793484067 -466.394462059 + E_Harris -34.2793484068 -466.394462059 + E_Fermi -0.172339103046 -2.34479378964 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117241554569 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00099964497594 + + Density error is 9.14977439007e-08 + + Energy Rydberg eV + E_KohnSham -34.279348454 -466.394462702 + E_Harris -34.279348454 -466.394462702 + E_band -8.01181656936 -109.006356674 + E_one_elec -69.5751267228 -946.618162502 + E_Hartree +36.1737439378 +492.169035547 + E_xc -8.23134715031 -111.99322346 + E_Ewald +7.47713207058 +101.731600858 + E_demet -3.43637525667e-85 -4.67542839569e-84 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195344108484 -2.65779294612 + E_Fermi -0.172339164526 -2.34479462611 + + charge density convergence is achieved + final etot is -466.394462702 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4278 2.00000 + 2 -13.1742 2.00000 + 3 -9.12644 2.00000 + 4 -6.77473 2.00000 + 5 1.40605 0.00000 + 6 4.62903 0.00000 + 7 11.0409 0.00000 + 8 11.2873 0.00000 + + EFERMI = -2.344794626114492 eV + OUT.ABACUS/ final etot is -466.3944627024660 eV + correction force for each atom along direction 1 is -0.000112365 + correction force for each atom along direction 2 is -5.83810e-05 + correction force for each atom along direction 3 is -1.71582e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.1354903 -0.56981709 -1.3087055 + H1 +0.024836969 -0.0094638045 -0.025793194 + H2 -1.1603273 +0.57928089 +1.3344987 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3944627024660 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7829 11 0.71 1.0e+02% + Run_lcao lcao_line 7.7742 1 7.8 1.e+02% + Potential init_pot 0.28277 2 0.14 3.6% + PW_Basis recip2real 0.26109 16 0.016 3.4% + PW_Basis gathers_scatterp 0.12059 16 0.0075 1.5% + Potential v_of_rho 1.0241 13 0.079 13.% + XC_Functional v_xc 0.35810 14 0.026 4.6% + H_Hartree_pw v_hartree 0.62989 13 0.048 8.1% + PW_Basis real2recip 0.65414 38 0.017 8.4% + PW_Basis gatherp_scatters 0.28712 38 0.0076 3.7% + ORB_control set_orb_tables 1.0933 1 1.1 14.% + ORB_gen_tables gen_tables 1.0933 1 1.1 14.% + ORB_table_phi init_Table 0.47457 1 0.47 6.1% + ORB_table_phi cal_ST_Phi12_R 0.46948 126 0.0037 6.0% + ORB_table_beta init_Table_Beta 0.18333 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18181 56 0.0032 2.3% + ORB_table_alpha init_Table_Alpha 0.24880 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24688 66 0.0037 3.2% + LOOP_ions opt_ions 6.1670 1 6.2 79.% + ESolver_KS_LCAO Run 5.5656 1 5.6 72.% + HSolverLCAO solve 3.3085 11 0.30 43.% + HamiltLCAO updateHk 1.6413 11 0.15 21.% + LCAO_Hamilt cal_Hgamma 1.6141 11 0.15 21.% + Gint_interface cal_gint 0.64051 23 0.028 8.2% + Gint_Gamma distri_vl_value 0.95325 11 0.087 12.% + Gint_Gamma distri_vl 2.6674 6 0.44 34.% + LCAO_Deepks cal_projected_DM 5.7463 13 0.44 74.% + LCAO_gen_fixedH add_v_delta 2.5381 6 0.42 33.% + LCAO_DESCRIPTOR add_v_delta 2.5383 6 0.42 33.% + ElecStateLCAO psiToRho 1.6324 11 0.15 21.% + Charge mix_rho 0.71419 10 0.071 9.2% + LOOP_ions force_stress 0.60122 1 0.60 7.7% + Force_Stress_LCAO getForceStress 0.60120 1 0.60 7.7% + Force_LCAO_gamma ftable_gamma 0.38989 1 0.39 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.15195 1 0.15 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:42 2022 + Finish Time : Wed Sep 28 11:11:50 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..43c9a5ef28bf20760ee27d0e099067eb6f954a62 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123813 ima = 3.68545e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123131936377 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112080222174 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112584459995 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112861171166 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112797514201 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011283344842 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112826873823 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112830021765 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112829401807 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112829288287 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112829285411 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8bb206a02d101ad34619c69b00a339b88ae0980f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-6.107533458746 28.895905331818 10.611335408298 0 0 0 +H +0.0 +2 +-6.946558094989 29.296237598833 9.021029743894 0 0 0 +-7.241525164959 29.458901682478 11.863075519042 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/conv new file mode 100644 index 0000000000000000000000000000000000000000..cb0dec190efd8325af406de16f8c2ccbea4e0a30 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/conv @@ -0,0 +1 @@ +284 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..473aa5ce894a6f29e60e0c0efb799b49014c82e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749048973 0.01275547742 1.283335541 1.373082881 1.469997632 0.008581476197 0.01890846675 0.03902482198 +-5.767931912e-19 0.001121434467 0.002676389934 0.01278426934 0.04647751278 -2.160065804e-19 2.175045256e-06 6.208434035e-06 +0.001655698381 0.005940698267 + +H atom_index 1 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:42 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0860085 SEC) : SETUP UNITCELL + DONE(0.0864552 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.10473 SEC) : INIT PLANEWAVE + DONE(0.15523 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.434651 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651436e+02 0.000000e+00 2.170e-01 6.010e-01 + GE2 -4.663903e+02 -1.246627e+00 9.781e-02 5.555e-01 + GE3 -4.663948e+02 -4.591216e-03 6.263e-02 6.223e-01 + GE4 -4.663950e+02 -1.661598e-04 2.027e-03 4.874e-01 + GE5 -4.663940e+02 9.921516e-04 9.488e-04 4.889e-01 + GE6 -4.663946e+02 -6.170316e-04 1.357e-04 4.781e-01 + GE7 -4.663944e+02 2.124223e-04 4.389e-05 4.730e-01 + GE8 -4.663945e+02 -5.400036e-05 1.679e-05 4.662e-01 + GE9 -4.663945e+02 2.053078e-05 2.459e-06 4.668e-01 + GE10 -4.663945e+02 -2.631652e-06 1.717e-07 4.671e-01 + GE11 -4.663945e+02 -6.434511e-07 9.150e-08 3.925e-01 +E_delta_band = -7.15935191e-02 Ry = -9.74079800e-01 eV +E_delta_NN= -1.95344108e-01 Ry = -2.65779295e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7829 11 0.71 1e+02 % + Run_lcao lcao_line 7.7742 1 7.8 1e+02 % + Potential init_pot 0.28277 2 0.14 3.6 % + PW_Basis recip2real 0.26109 16 0.016 3.4 % + PW_Basis gathers_scatterp 0.12059 16 0.0075 1.5 % + Potential v_of_rho 1.0241 13 0.079 13 % + XC_Functional v_xc 0.3581 14 0.026 4.6 % + H_Hartree_pw v_hartree 0.62989 13 0.048 8.1 % + PW_Basis real2recip 0.65414 38 0.017 8.4 % + PW_Basis gatherp_scatters 0.28712 38 0.0076 3.7 % + ORB_control set_orb_tables 1.0933 1 1.1 14 % + ORB_gen_tables gen_tables 1.0933 1 1.1 14 % + ORB_table_phi init_Table 0.47457 1 0.47 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.46948 126 0.0037 6 % + ORB_table_beta init_Table_Beta 0.18333 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18181 56 0.0032 2.3 % + ORB_table_alpha init_Table_Alpha 0.2488 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24688 66 0.0037 3.2 % + LOOP_ions opt_ions 6.167 1 6.2 79 % + ESolver_KS_LCAO Run 5.5656 1 5.6 72 % + HSolverLCAO solve 3.3085 11 0.3 43 % + HamiltLCAO updateHk 1.6413 11 0.15 21 % + LCAO_Hamilt cal_Hgamma 1.6141 11 0.15 21 % + Gint_interface cal_gint 0.64051 23 0.028 8.2 % + Gint_Gamma distri_vl_value 0.95325 11 0.087 12 % + Gint_Gamma distri_vl 2.6674 6 0.44 34 % + LCAO_Deepks cal_projected_DM 5.7463 13 0.44 74 % + LCAO_gen_fixedH add_v_delta 2.5381 6 0.42 33 % + LCAO_DESCRIPTOR add_v_delta 2.5383 6 0.42 33 % + ElecStateLCAO psiToRho 1.6324 11 0.15 21 % + Charge mix_rho 0.71419 10 0.071 9.2 % + LOOP_ions force_stress 0.60122 1 0.6 7.7 % + Force_Stress_LCAO getForceStress 0.6012 1 0.6 7.7 % + Force_LCAO_gamma ftable_gamma 0.38989 1 0.39 5 % + Force_LCAO_gamma cal_fvl_dphi 0.15195 1 0.15 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:42 2022 + FINISH Time : Wed Sep 28 11:11:50 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/284/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..41e0ba6c8641d2e5107f63e649ac4fdcb1b34706 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.791394 0.030859 0.371728 +H 0.75959 0.985252 0.338593 +H 0.762516 0.0265797 0.431645 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..685589de332bf62b4c08cc509684a4a54d494acd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3098 2 + 2 -12.8964 2 + 3 -9.23953 2 + 4 -6.75019 2 + 5 1.25559 0 + 6 4.36726 0 + 7 11.0778 0 + 8 11.3404 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..de8ee80dbf8f64067ac66d22a6045b140949c774 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:01 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 22.1590277202 0.864050628064 10.4083825058 0 0 0 0 + tauc_H1 21.2685183013 27.5870679855 9.48059177487 0 0 0 0 + tauc_H2 21.3504495051 0.744230536424 12.0860531078 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.114413499012 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.114992567507 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.136353399527 (SEC) + + DONE : INIT CHARGE Time : 0.179480737123 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.462648 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000615 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000915 + + Density error is 0.214099988727 + + Energy Rydberg eV + E_KohnSham -34.1907354099 -465.188820385 + E_Harris -34.3809919812 -467.777393836 + E_Fermi -0.404136675323 -5.49856155517 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983898398901 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108932649773 + + Density error is 0.0979699118231 + + Energy Rydberg eV + E_KohnSham -34.2801741132 -466.405696371 + E_Harris -34.2870042761 -466.498625506 + E_Fermi -0.213422302724 -2.90375939733 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000949377637999 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103819117158 + + Density error is 0.0628800830499 + + Energy Rydberg eV + E_KohnSham -34.2804982818 -466.410106911 + E_Harris -34.284915333 -466.470203977 + E_Fermi -0.203027375221 -2.76232915299 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914651960831 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972143175454 + + Density error is 0.00195502405498 + + Energy Rydberg eV + E_KohnSham -34.2804701633 -466.40972434 + E_Harris -34.2804711607 -466.409737911 + E_Fermi -0.167374744064 -2.27725022056 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000916618686497 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973832755676 + + Density error is 0.000907917674241 + + Energy Rydberg eV + E_KohnSham -34.2804126837 -466.40894229 + E_Harris -34.2804137958 -466.408957421 + E_Fermi -0.1668178118 -2.26967276837 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000915792393124 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009727022731 + + Density error is 0.000124027132126 + + Energy Rydberg eV + E_KohnSham -34.2804478914 -466.409421315 + E_Harris -34.2804479068 -466.409421525 + E_Fermi -0.166727038371 -2.26843773251 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000915957163915 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972832197518 + + Density error is 3.62157460111e-05 + + Energy Rydberg eV + E_KohnSham -34.2804362012 -466.409262261 + E_Harris -34.2804362081 -466.409262355 + E_Fermi -0.166625725829 -2.26705930466 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00091587336435 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00097276180769 + + Density error is 1.34557824808e-05 + + Energy Rydberg eV + E_KohnSham -34.280439277 -466.40930411 + E_Harris -34.2804392777 -466.40930412 + E_Fermi -0.166663308772 -2.26757064683 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000915877415843 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972760071304 + + Density error is 1.42429563907e-06 + + Energy Rydberg eV + E_KohnSham -34.2804380016 -466.409286758 + E_Harris -34.2804380016 -466.409286758 + E_Fermi -0.166648463205 -2.26736866254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000915880512497 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972762043 + + Density error is 1.58958622342e-07 + + Energy Rydberg eV + E_KohnSham -34.2804381919 -466.409289347 + E_Harris -34.2804381919 -466.409289347 + E_Fermi -0.16664743878 -2.26735472451 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000915880896999 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972762364514 + + Density error is 5.23280215665e-08 + + Energy Rydberg eV + E_KohnSham -34.280438217 -466.409289689 + E_Harris -34.280438217 -466.409289689 + E_band -7.96665367112 -108.39188392 + E_one_elec -69.2384420885 -942.037333046 + E_Hartree +36.0105638646 +489.948856751 + E_xc -8.20494968216 -111.634067481 + E_Ewald +7.27681278469 +99.0061171511 + E_demet -1.81392739946e-75 -2.46797483909e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194748010442 -2.64968261618 + E_Fermi -0.166647468075 -2.2673551231 + + charge density convergence is achieved + final etot is -466.409289689 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3098 2.00000 + 2 -12.8964 2.00000 + 3 -9.23953 2.00000 + 4 -6.75019 2.00000 + 5 1.25559 0.00000 + 6 4.36726 0.00000 + 7 11.0778 0.00000 + 8 11.3404 0.00000 + + EFERMI = -2.267355123095779 eV + OUT.ABACUS/ final etot is -466.4092896887381 eV + correction force for each atom along direction 1 is -0.000199417 + correction force for each atom along direction 2 is -1.20255e-05 + correction force for each atom along direction 3 is 7.41931e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.0074567309 +0.44614176 +1.0443763 + H1 -0.34964284 -0.62369948 -0.65128163 + H2 +0.34218611 +0.17755772 -0.39309470 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4092896887381 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1278 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1186 1 7.1 1.e+02% + Potential init_pot 0.28500 2 0.14 4.0% + PW_Basis recip2real 0.25132 16 0.016 3.5% + PW_Basis gathers_scatterp 0.11257 16 0.0070 1.6% + Potential v_of_rho 0.78407 13 0.060 11.% + XC_Functional v_xc 0.19209 14 0.014 2.7% + H_Hartree_pw v_hartree 0.55502 13 0.043 7.8% + PW_Basis real2recip 0.64339 38 0.017 9.0% + PW_Basis gatherp_scatters 0.25895 38 0.0068 3.6% + ORB_control set_orb_tables 1.1001 1 1.1 15.% + ORB_gen_tables gen_tables 1.1001 1 1.1 15.% + ORB_table_phi init_Table 0.47519 1 0.48 6.7% + ORB_table_phi cal_ST_Phi12_R 0.47000 126 0.0037 6.6% + ORB_table_beta init_Table_Beta 0.18562 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18403 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.24995 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24791 66 0.0038 3.5% + LOOP_ions opt_ions 5.4789 1 5.5 77.% + ESolver_KS_LCAO Run 4.9054 1 4.9 69.% + HSolverLCAO solve 2.7853 11 0.25 39.% + HamiltLCAO updateHk 1.4269 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3997 11 0.13 20.% + Gint_interface cal_gint 0.55450 23 0.024 7.8% + Gint_Gamma distri_vl_value 0.76824 11 0.070 11.% + Gint_Gamma distri_vl 2.3523 6 0.39 33.% + LCAO_Deepks cal_projected_DM 5.0823 13 0.39 71.% + LCAO_gen_fixedH add_v_delta 2.2141 6 0.37 31.% + LCAO_DESCRIPTOR add_v_delta 2.2142 6 0.37 31.% + ElecStateLCAO psiToRho 1.3355 11 0.12 19.% + Charge mix_rho 0.79247 10 0.079 11.% + LOOP_ions force_stress 0.57333 1 0.57 8.0% + Force_Stress_LCAO getForceStress 0.57331 1 0.57 8.0% + Force_LCAO_gamma ftable_gamma 0.38189 1 0.38 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.14300 1 0.14 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:01 2022 + Finish Time : Wed Sep 28 11:03:08 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..409634219999c781bff05c26c531436f8191fa50 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123755 ima = 3.65758e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122972411657 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111811554691 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112408933426 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112654492083 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112606262761 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112633926026 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112628872703 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112631537 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112630981773 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112630919569 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112630914937 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ad72fd462c18e9efc36ac4ba92c8f3d9eb9d2812 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-5.840972279827 28.864050628040 10.408382505785 0 0 0 +H +0.0 +2 +-6.731481698743 27.587067985448 9.480591774876 0 0 0 +-6.649550494970 28.744230536412 12.086053107769 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/conv new file mode 100644 index 0000000000000000000000000000000000000000..7b4c0ad305926f43d5eaf00540000605a37febb7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/conv @@ -0,0 +1 @@ +285 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..bd2d9ec3f280e5b6070037424989835292446e5a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751313328 0.01270284983 1.268617688 1.357152921 1.469376503 0.008866339398 0.01778184705 0.03909356242 +-1.194968572e-18 0.0009849946173 0.002677418116 0.01257578464 0.04556988488 3.524679202e-19 2.262800833e-06 6.372215071e-06 +0.001611349404 0.006036531774 + +H atom_index 1 n_descriptor 18 +1.264053386 0.03401597236 0.1139846571 0.1564095423 0.3250026897 0.02319699642 0.02909350635 0.03724159864 +-4.415055146e-17 4.858935883e-05 0.1047226379 0.1162214645 0.1342219701 1.442809519e-18 3.032467114e-06 0.01321304515 +0.02695879496 0.03136766008 + +H atom_index 2 n_descriptor 18 +1.221546588 0.0354559433 0.09942694413 0.1369900577 0.3107881224 0.0211732786 0.0266072715 0.03864684984 +-2.332590838e-17 4.460567101e-05 0.09447544397 0.1140523992 0.1174085609 1.952947058e-18 5.29539139e-06 0.01369178492 +0.02534999195 0.02937867848 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..71228911be4fdad655bb5123179ebb74417bbab7 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..ae07af592281ba62b4ebfc3cae5e547491339562 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..7287ea2b72c3b16e7cef60ba247e994a5664c75c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..9a29badd5faadaaa0dc5f9b8cbfb38bf3fc8c9bf Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..3ca1d722bcae4a80778ebb8177ba8207390db8e5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:01 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.114452 SEC) : SETUP UNITCELL + DONE(0.115013 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.136376 SEC) : INIT PLANEWAVE + DONE(0.179629 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.462717 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651888e+02 0.000000e+00 2.141e-01 5.442e-01 + GE2 -4.664057e+02 -1.216876e+00 9.797e-02 4.950e-01 + GE3 -4.664101e+02 -4.410540e-03 6.288e-02 5.546e-01 + GE4 -4.664097e+02 3.825716e-04 1.955e-03 4.244e-01 + GE5 -4.664089e+02 7.820495e-04 9.079e-04 4.225e-01 + GE6 -4.664094e+02 -4.790251e-04 1.240e-04 4.167e-01 + GE7 -4.664093e+02 1.590541e-04 3.622e-05 4.121e-01 + GE8 -4.664093e+02 -4.184845e-05 1.346e-05 4.086e-01 + GE9 -4.664093e+02 1.735213e-05 1.424e-06 4.072e-01 + GE10 -4.664093e+02 -2.589304e-06 1.590e-07 4.062e-01 + GE11 -4.664093e+02 -3.418866e-07 5.233e-08 3.531e-01 +E_delta_band = -7.03249147e-02 Ry = -9.56819552e-01 eV +E_delta_NN= -1.94748010e-01 Ry = -2.64968262e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1278 11 0.65 1e+02 % + Run_lcao lcao_line 7.1186 1 7.1 1e+02 % + Potential init_pot 0.285 2 0.14 4 % + PW_Basis recip2real 0.25132 16 0.016 3.5 % + PW_Basis gathers_scatterp 0.11257 16 0.007 1.6 % + Potential v_of_rho 0.78407 13 0.06 11 % + XC_Functional v_xc 0.19209 14 0.014 2.7 % + H_Hartree_pw v_hartree 0.55502 13 0.043 7.8 % + PW_Basis real2recip 0.64339 38 0.017 9 % + PW_Basis gatherp_scatters 0.25895 38 0.0068 3.6 % + ORB_control set_orb_tables 1.1001 1 1.1 15 % + ORB_gen_tables gen_tables 1.1001 1 1.1 15 % + ORB_table_phi init_Table 0.47519 1 0.48 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.47 126 0.0037 6.6 % + ORB_table_beta init_Table_Beta 0.18562 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18403 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.24995 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24791 66 0.0038 3.5 % + LOOP_ions opt_ions 5.4789 1 5.5 77 % + ESolver_KS_LCAO Run 4.9054 1 4.9 69 % + HSolverLCAO solve 2.7853 11 0.25 39 % + HamiltLCAO updateHk 1.4269 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3997 11 0.13 20 % + Gint_interface cal_gint 0.5545 23 0.024 7.8 % + Gint_Gamma distri_vl_value 0.76824 11 0.07 11 % + Gint_Gamma distri_vl 2.3523 6 0.39 33 % + LCAO_Deepks cal_projected_DM 5.0823 13 0.39 71 % + LCAO_gen_fixedH add_v_delta 2.2141 6 0.37 31 % + LCAO_DESCRIPTOR add_v_delta 2.2142 6 0.37 31 % + ElecStateLCAO psiToRho 1.3355 11 0.12 19 % + Charge mix_rho 0.79247 10 0.079 11 % + LOOP_ions force_stress 0.57333 1 0.57 8 % + Force_Stress_LCAO getForceStress 0.57331 1 0.57 8 % + Force_LCAO_gamma ftable_gamma 0.38189 1 0.38 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.143 1 0.14 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:01 2022 + FINISH Time : Wed Sep 28 11:03:08 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/285/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9a728db2fffe29ba01485bbe34f8107df076417c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.791564 0.0251291 0.367691 +H 0.746021 0.984343 0.387022 +H 0.812633 0.0507879 0.421561 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d4609b318cd7c56b2fe1437550fcdd3f996532fc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6125 2 + 2 -13.2897 2 + 3 -9.18554 2 + 4 -6.81595 2 + 5 1.55152 0 + 6 4.86151 0 + 7 10.9978 0 + 8 11.2467 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..2c964ef070168f47cf5ba80738d53891ca7fa129 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:36 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 22.163799817 0.703614575912 10.2953605529 0 0 0 0 + tauc_H1 20.8885938211 27.5615929483 10.8366145506 0 0 0 0 + tauc_H2 22.7537150576 1.42206030838 11.8037073691 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870555542801 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.102178706958 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.120306216467 (SEC) + + DONE : INIT CHARGE Time : 0.168497248613 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449922 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000943 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000946 + + Density error is 0.218335542473 + + Energy Rydberg eV + E_KohnSham -34.185610901 -465.119097864 + E_Harris -34.3851005663 -467.833294004 + E_Fermi -0.42469552428 -5.7782790453 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00124430255794 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117164853143 + + Density error is 0.0972943380721 + + Energy Rydberg eV + E_KohnSham -34.277136842 -466.364372177 + E_Harris -34.2837391309 -466.454200926 + E_Fermi -0.231346027796 -3.14762418769 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118120996349 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111584930366 + + Density error is 0.0620075149703 + + Energy Rydberg eV + E_KohnSham -34.2773838433 -466.367732802 + E_Harris -34.281589582 -466.424954812 + E_Fermi -0.216226682495 -2.94191494157 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010864620329 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103484317174 + + Density error is 0.00206824732355 + + Energy Rydberg eV + E_KohnSham -34.2774436411 -466.368546393 + E_Harris -34.2774463277 -466.368582946 + E_Fermi -0.180382162058 -2.45422522155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108910758245 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103776105406 + + Density error is 0.000936929799178 + + Energy Rydberg eV + E_KohnSham -34.2773600166 -466.367408623 + E_Harris -34.2773632684 -466.367452866 + E_Fermi -0.178978049975 -2.43512129659 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108748301018 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103620234149 + + Density error is 0.000102288282261 + + Energy Rydberg eV + E_KohnSham -34.2774194746 -466.368217591 + E_Harris -34.2774194914 -466.36821782 + E_Fermi -0.17939274243 -2.4407634769 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108727413048 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103602607496 + + Density error is 5.3226633111e-05 + + Energy Rydberg eV + E_KohnSham -34.2774001351 -466.367954464 + E_Harris -34.2774001489 -466.367954651 + E_Fermi -0.179240883057 -2.43869732413 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108726054244 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103600454736 + + Density error is 8.48851165372e-06 + + Energy Rydberg eV + E_KohnSham -34.2774029219 -466.36799238 + E_Harris -34.2774029221 -466.367992383 + E_Fermi -0.179303309238 -2.43954667589 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108727008092 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103601541055 + + Density error is 1.92614578426e-06 + + Energy Rydberg eV + E_KohnSham -34.2774016666 -466.3679753 + E_Harris -34.2774016666 -466.367975301 + E_Fermi -0.179296172817 -2.43944957991 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108727003549 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103601589303 + + Density error is 1.24843691637e-07 + + Energy Rydberg eV + E_KohnSham -34.2774017528 -466.367976473 + E_Harris -34.2774017528 -466.367976473 + E_Fermi -0.1792940217 -2.43942031246 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108727011624 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103601593806 + + Density error is 5.45200330744e-08 + + Energy Rydberg eV + E_KohnSham -34.2774017945 -466.367977041 + E_Harris -34.2774017945 -466.367977041 + E_band -8.07068124857 -109.807251722 + E_one_elec -69.9272224248 -951.408670291 + E_Hartree +36.3378976374 +494.40246121 + E_xc -8.25792808701 -112.354875658 + E_Ewald +7.69286536097 +104.666802856 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196020367432 -2.66699392112 + E_Fermi -0.179294146537 -2.43942201095 + + charge density convergence is achieved + final etot is -466.367977041 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6125 2.00000 + 2 -13.2897 2.00000 + 3 -9.18554 2.00000 + 4 -6.81595 2.00000 + 5 1.55152 0.00000 + 6 4.86151 0.00000 + 7 10.9978 0.00000 + 8 11.2467 0.00000 + + EFERMI = -2.439422010945689 eV + OUT.ABACUS/ final etot is -466.3679770405891 eV + correction force for each atom along direction 1 is -0.000127971 + correction force for each atom along direction 2 is -0.000109013 + correction force for each atom along direction 3 is 4.88847e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.18447933 -0.046665016 -2.0403723 + H1 -0.99330145 -0.90463842 +0.28251863 + H2 +0.80882212 +0.95130344 +1.7578537 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3679770405891 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9282 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9187 1 6.9 1.e+02% + Potential init_pot 0.28623 2 0.14 4.1% + PW_Basis recip2real 0.26414 16 0.017 3.8% + PW_Basis gathers_scatterp 0.12371 16 0.0077 1.8% + Potential v_of_rho 0.85839 13 0.066 12.% + XC_Functional v_xc 0.24891 14 0.018 3.6% + H_Hartree_pw v_hartree 0.57509 13 0.044 8.3% + PW_Basis real2recip 0.56225 38 0.015 8.1% + PW_Basis gatherp_scatters 0.23290 38 0.0061 3.4% + ORB_control set_orb_tables 1.1083 1 1.1 16.% + ORB_gen_tables gen_tables 1.1083 1 1.1 16.% + ORB_table_phi init_Table 0.48528 1 0.49 7.0% + ORB_table_phi cal_ST_Phi12_R 0.48033 126 0.0038 6.9% + ORB_table_beta init_Table_Beta 0.18854 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18706 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25581 1 0.26 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25391 66 0.0038 3.7% + LOOP_ions opt_ions 5.2834 1 5.3 76.% + ESolver_KS_LCAO Run 4.6956 1 4.7 68.% + HSolverLCAO solve 2.7492 11 0.25 40.% + HamiltLCAO updateHk 1.3923 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3639 11 0.12 20.% + Gint_interface cal_gint 0.36578 23 0.016 5.3% + Gint_Gamma distri_vl_value 0.84403 11 0.077 12.% + Gint_Gamma distri_vl 2.2425 6 0.37 32.% + LCAO_Deepks cal_projected_DM 4.8543 13 0.37 70.% + LCAO_gen_fixedH add_v_delta 2.1146 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.1147 6 0.35 31.% + ElecStateLCAO psiToRho 1.3356 11 0.12 19.% + Charge mix_rho 0.63788 10 0.064 9.2% + LOOP_ions force_stress 0.58773 1 0.59 8.5% + Force_Stress_LCAO getForceStress 0.58771 1 0.59 8.5% + Force_LCAO_gamma ftable_gamma 0.37450 1 0.37 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.12169 1 0.12 1.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:36 2022 + Finish Time : Wed Sep 28 11:08:43 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e9e273e48c22db96acb6eeeca633b50ee8993ee6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123986 ima = 3.65487e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122783196112 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111979235207 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112363535035 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112663011267 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112579203051 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011262591858 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112621904644 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112624732598 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112624418702 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011262432591 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112624329622 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/STRU new file mode 100644 index 0000000000000000000000000000000000000000..f8ef9cfb20679023dc82b612559d9b6a34cede8a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-5.836200182980 28.703614575905 10.295360552901 0 0 0 +H +0.0 +2 +-7.111406178958 27.561592948312 10.836614550597 0 0 0 +-5.246284942380 29.422060308364 11.803707369107 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/conv new file mode 100644 index 0000000000000000000000000000000000000000..d9e3cf62a19173ce669f93303e57676d0c596f72 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/conv @@ -0,0 +1 @@ +286 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..1fd6bb12180569b2377a3173096b8018db51f1a1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749645957 0.01285978327 1.298718909 1.382115019 1.470866972 0.008826798546 0.01905912317 0.03903709521 +5.431013769e-18 0.001192903212 0.002813617284 0.01336672461 0.04854495702 3.860861222e-19 2.499455482e-06 6.803481823e-06 +0.001648265986 0.005972737321 + +H atom_index 1 n_descriptor 18 +1.275573624 0.03339439177 0.1185097402 0.1620325847 0.3281737977 0.02378467588 0.02975862548 0.03668887877 +-1.547754807e-17 5.434366126e-05 0.1083519589 0.1183106241 0.1393315962 2.458730061e-18 2.649635551e-06 0.01326505879 +0.02794722809 0.03188352502 + +H atom_index 2 n_descriptor 18 +1.294132597 0.0328145458 0.1257042301 0.1715392777 0.3334324897 0.02464240701 0.03081669225 0.03645106676 +1.379164267e-17 5.616569647e-05 0.1086930343 0.1232827131 0.1473785067 -2.553359275e-18 1.631328054e-06 0.01358061067 +0.0285369057 0.03257995679 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ff63d8133ebf02a7bea5c8654132023447d69eb6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:36 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870765 SEC) : SETUP UNITCELL + DONE(0.102197 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.120326 SEC) : INIT PLANEWAVE + DONE(0.168625 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449987 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651191e+02 0.000000e+00 2.183e-01 5.404e-01 + GE2 -4.663644e+02 -1.245274e+00 9.729e-02 4.692e-01 + GE3 -4.663677e+02 -3.360626e-03 6.201e-02 5.217e-01 + GE4 -4.663685e+02 -8.135906e-04 2.068e-03 4.156e-01 + GE5 -4.663674e+02 1.137770e-03 9.369e-04 4.108e-01 + GE6 -4.663682e+02 -8.089679e-04 1.023e-04 3.881e-01 + GE7 -4.663680e+02 2.631268e-04 5.323e-05 3.894e-01 + GE8 -4.663680e+02 -3.791561e-05 8.489e-06 3.915e-01 + GE9 -4.663680e+02 1.707917e-05 1.926e-06 3.900e-01 + GE10 -4.663680e+02 -1.172963e-06 1.248e-07 3.875e-01 + GE11 -4.663680e+02 -5.672351e-07 5.452e-08 3.287e-01 +E_delta_band = -7.30060864e-02 Ry = -9.93298763e-01 eV +E_delta_NN= -1.96020367e-01 Ry = -2.66699392e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9282 11 0.63 1e+02 % + Run_lcao lcao_line 6.9187 1 6.9 1e+02 % + Potential init_pot 0.28623 2 0.14 4.1 % + PW_Basis recip2real 0.26414 16 0.017 3.8 % + PW_Basis gathers_scatterp 0.12371 16 0.0077 1.8 % + Potential v_of_rho 0.85839 13 0.066 12 % + XC_Functional v_xc 0.24891 14 0.018 3.6 % + H_Hartree_pw v_hartree 0.57509 13 0.044 8.3 % + PW_Basis real2recip 0.56225 38 0.015 8.1 % + PW_Basis gatherp_scatters 0.2329 38 0.0061 3.4 % + ORB_control set_orb_tables 1.1083 1 1.1 16 % + ORB_gen_tables gen_tables 1.1083 1 1.1 16 % + ORB_table_phi init_Table 0.48528 1 0.49 7 % + ORB_table_phi cal_ST_Phi12_R 0.48033 126 0.0038 6.9 % + ORB_table_beta init_Table_Beta 0.18854 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18706 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.25581 1 0.26 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25391 66 0.0038 3.7 % + LOOP_ions opt_ions 5.2834 1 5.3 76 % + ESolver_KS_LCAO Run 4.6956 1 4.7 68 % + HSolverLCAO solve 2.7492 11 0.25 40 % + HamiltLCAO updateHk 1.3923 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3639 11 0.12 20 % + Gint_interface cal_gint 0.36578 23 0.016 5.3 % + Gint_Gamma distri_vl_value 0.84403 11 0.077 12 % + Gint_Gamma distri_vl 2.2425 6 0.37 32 % + LCAO_Deepks cal_projected_DM 4.8543 13 0.37 70 % + LCAO_gen_fixedH add_v_delta 2.1146 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.1147 6 0.35 31 % + ElecStateLCAO psiToRho 1.3356 11 0.12 19 % + Charge mix_rho 0.63788 10 0.064 9.2 % + LOOP_ions force_stress 0.58773 1 0.59 8.5 % + Force_Stress_LCAO getForceStress 0.58771 1 0.59 8.5 % + Force_LCAO_gamma ftable_gamma 0.3745 1 0.37 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.12169 1 0.12 1.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:36 2022 + FINISH Time : Wed Sep 28 11:08:43 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/286/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..dc2a4410dddeb643a75e2dc8d041ecf71765fb32 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.799942 0.00899401 0.355135 +H 0.740138 0.00174186 0.38408 +H 0.835842 0.0431381 0.400269 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..84cf3c5546414e9b237131d84d03116bb638cc1f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0503 2 + 2 -12.8409 2 + 3 -9.08406 2 + 4 -6.69224 2 + 5 1.09939 0 + 6 4.06815 0 + 7 11.1321 0 + 8 11.3837 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7797f63dfbeaf3c79b63263fc11dd3866c6f8160 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:46 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 22.398388648 0.251832372 9.94377279336 0 0 0 0 + tauc_H1 20.7238561224 0.0487719960656 10.7542374572 0 0 0 0 + tauc_H2 23.4035813827 1.20786793562 11.2075269108 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101741034249 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.112817157599 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.130946268425 (SEC) + + DONE : INIT CHARGE Time : 0.17404777642 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.455797 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000971 + + Density error is 0.21279263808 + + Energy Rydberg eV + E_KohnSham -34.19097555 -465.192087658 + E_Harris -34.3780677735 -467.737607949 + E_Fermi -0.390953790599 -5.31919920684 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127072834365 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101924490139 + + Density error is 0.0987244994527 + + Energy Rydberg eV + E_KohnSham -34.2802720922 -466.407029445 + E_Harris -34.2873421499 -466.503222514 + E_Fermi -0.200623876271 -2.72962787213 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120935416327 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000962885086173 + + Density error is 0.0637433117806 + + Energy Rydberg eV + E_KohnSham -34.2807317283 -466.413283114 + E_Harris -34.2852651783 -466.474963866 + E_Fermi -0.193380130275 -2.63107165172 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111956985507 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000868087166171 + + Density error is 0.00197776804643 + + Energy Rydberg eV + E_KohnSham -34.2806514055 -466.412190266 + E_Harris -34.2806536476 -466.412220772 + E_Fermi -0.158112769153 -2.15123458704 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111935076907 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000866581781727 + + Density error is 0.000975448519091 + + Energy Rydberg eV + E_KohnSham -34.2806063762 -466.411577612 + E_Harris -34.2806068546 -466.411584121 + E_Fermi -0.157899504502 -2.1483329726 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111803017996 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865185335286 + + Density error is 0.000181470969586 + + Energy Rydberg eV + E_KohnSham -34.2806274627 -466.411864507 + E_Harris -34.2806274818 -466.411864768 + E_Fermi -0.157557246867 -2.14367631858 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111828044893 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00086530383069 + + Density error is 3.18980968003e-05 + + Energy Rydberg eV + E_KohnSham -34.2806203763 -466.411768093 + E_Harris -34.2806203803 -466.411768147 + E_Fermi -0.157498908851 -2.14288258915 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111818884906 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865247321907 + + Density error is 1.45733555066e-05 + + Energy Rydberg eV + E_KohnSham -34.2806237534 -466.41181404 + E_Harris -34.2806237543 -466.411814052 + E_Fermi -0.157523504056 -2.14321722409 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111818545306 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865237888036 + + Density error is 2.15310794205e-06 + + Energy Rydberg eV + E_KohnSham -34.2806225831 -466.411798117 + E_Harris -34.2806225831 -466.411798117 + E_Fermi -0.157509159631 -2.14302205817 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111818500358 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865237163827 + + Density error is 4.75485579352e-07 + + Energy Rydberg eV + E_KohnSham -34.2806227925 -466.411800967 + E_Harris -34.2806227925 -466.411800967 + E_Fermi -0.157507224844 -2.14299573405 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111818547943 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865237693045 + + Density error is 1.18935219722e-07 + + Energy Rydberg eV + E_KohnSham -34.2806228114 -466.411801223 + E_Harris -34.2806228114 -466.411801223 + E_Fermi -0.157506950786 -2.1429920053 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111818544761 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865237726996 + + Density error is 1.09526533385e-08 + + Energy Rydberg eV + E_KohnSham -34.2806228179 -466.411801313 + E_Harris -34.2806228179 -466.411801313 + E_band -7.88896315077 -107.334850163 + E_one_elec -68.7998537779 -936.070032946 + E_Hartree +35.8086366726 +487.201496359 + E_xc -8.17238761631 -111.191037846 + E_Ewald +7.00832451632 +95.353146855 + E_demet -2.46324029623e-64 -3.35141035719e-63 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193914770036 -2.63834579885 + E_Fermi -0.157506847806 -2.14299060418 + + charge density convergence is achieved + final etot is -466.411801313 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0503 2.00000 + 2 -12.8409 2.00000 + 3 -9.08406 2.00000 + 4 -6.69224 2.00000 + 5 1.09939 0.00000 + 6 4.06815 0.00000 + 7 11.1321 0.00000 + 8 11.3837 0.00000 + + EFERMI = -2.142990604179440 eV + OUT.ABACUS/ final etot is -466.4118013125099 eV + correction force for each atom along direction 1 is -7.45908e-05 + correction force for each atom along direction 2 is -6.47001e-05 + correction force for each atom along direction 3 is 0.000119262 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.16042455 +0.30787242 +0.77421979 + H1 +0.62308203 +0.097628467 -0.26006592 + H2 -0.46265748 -0.40550088 -0.51415387 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4118013125099 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7002 11 0.70 1.0e+02% + Run_lcao lcao_line 7.6911 1 7.7 1.e+02% + Potential init_pot 0.28234 2 0.14 3.7% + PW_Basis recip2real 0.26360 17 0.016 3.4% + PW_Basis gathers_scatterp 0.11775 17 0.0069 1.5% + Potential v_of_rho 0.83106 14 0.059 11.% + XC_Functional v_xc 0.19934 15 0.013 2.6% + H_Hartree_pw v_hartree 0.59302 14 0.042 7.7% + PW_Basis real2recip 0.70010 41 0.017 9.1% + PW_Basis gatherp_scatters 0.28440 41 0.0069 3.7% + ORB_control set_orb_tables 1.0990 1 1.1 14.% + ORB_gen_tables gen_tables 1.0990 1 1.1 14.% + ORB_table_phi init_Table 0.47529 1 0.48 6.2% + ORB_table_phi cal_ST_Phi12_R 0.47005 126 0.0037 6.1% + ORB_table_beta init_Table_Beta 0.18524 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18367 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24911 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24710 66 0.0037 3.2% + LOOP_ions opt_ions 6.0595 1 6.1 79.% + ESolver_KS_LCAO Run 5.4858 1 5.5 71.% + HSolverLCAO solve 3.2208 12 0.27 42.% + HamiltLCAO updateHk 1.6183 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.5887 12 0.13 21.% + Gint_interface cal_gint 0.57882 25 0.023 7.5% + Gint_Gamma distri_vl_value 0.93591 12 0.078 12.% + Gint_Gamma distri_vl 2.8401 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.6565 14 0.40 73.% + LCAO_gen_fixedH add_v_delta 2.7071 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.7072 6 0.45 35.% + ElecStateLCAO psiToRho 1.5802 12 0.13 21.% + Charge mix_rho 0.82169 11 0.075 11.% + LOOP_ions force_stress 0.57353 1 0.57 7.4% + Force_Stress_LCAO getForceStress 0.57351 1 0.57 7.4% + Force_LCAO_gamma ftable_gamma 0.38312 1 0.38 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.14277 1 0.14 1.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:46 2022 + Finish Time : Wed Sep 28 11:11:54 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3c50e1fcdee3720ac221696e5a179d729e598b2d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123662 ima = 3.66975e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123564352568 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112098932916 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112834650161 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011304852544 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113021450943 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113038013242 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113032269394 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113034621656 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113033991005 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113033923568 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113033901049 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113033895647 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3008c462ecf3e52b70849a9e68adca62da7e8a20 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-5.601611351983 28.251832372011 9.943772793337 0 0 0 +H +0.0 +2 +-7.276143877598 28.048771996049 10.754237457252 0 0 0 +-4.596418617255 29.207867935637 11.207526910860 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/conv new file mode 100644 index 0000000000000000000000000000000000000000..ddda5e4e66e98e097631b64fab442b5a1027847c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/conv @@ -0,0 +1 @@ +287 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..390d0918f2e6e958a553f45d6e8d02edd3d14853 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749543867 0.01250394298 1.253561163 1.344591267 1.46828271 0.008374542968 0.01811202069 0.03906004107 +7.697329915e-19 0.0009395159082 0.002441966523 0.01173765631 0.04239524689 -1.05266343e-18 1.722764888e-06 5.222282736e-06 +0.001631690188 0.0058916937 + +H atom_index 1 n_descriptor 18 +1.215825635 0.03543931421 0.09649085364 0.1350405313 0.3100360021 0.02045169074 0.02634750367 0.03872431296 +6.030254024e-18 3.846916987e-05 0.09079809543 0.1141949448 0.1155898926 2.909950739e-18 5.498272343e-06 0.0136840114 +0.02446943741 0.02911210884 + +H atom_index 2 n_descriptor 18 +1.211741586 0.03557448201 0.09522194645 0.1333173604 0.3085702317 0.02026339723 0.0261085842 0.03888753645 +-8.389282104e-18 3.812400306e-05 0.08972778344 0.1140588812 0.1140793648 2.706159945e-19 5.653136475e-06 0.01378313743 +0.02430388155 0.02890325237 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d79927845ad87d765a29db724080a027bd70a332 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:46 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101766 SEC) : SETUP UNITCELL + DONE(0.112836 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.130969 SEC) : INIT PLANEWAVE + DONE(0.174188 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.455865 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651921e+02 0.000000e+00 2.128e-01 5.547e-01 + GE2 -4.664070e+02 -1.214942e+00 9.872e-02 5.103e-01 + GE3 -4.664133e+02 -6.253669e-03 6.374e-02 5.651e-01 + GE4 -4.664122e+02 1.092847e-03 1.978e-03 4.402e-01 + GE5 -4.664116e+02 6.126548e-04 9.754e-04 4.379e-01 + GE6 -4.664119e+02 -2.868958e-04 1.815e-04 4.357e-01 + GE7 -4.664118e+02 9.641467e-05 3.190e-05 4.249e-01 + GE8 -4.664118e+02 -4.594713e-05 1.457e-05 4.214e-01 + GE9 -4.664118e+02 1.592266e-05 2.153e-06 4.207e-01 + GE10 -4.664118e+02 -2.849918e-06 4.755e-07 4.221e-01 + GE11 -4.664118e+02 -2.560702e-07 1.189e-07 4.224e-01 + GE12 -4.664118e+02 -8.930124e-08 1.095e-08 3.695e-01 +E_delta_band = -6.85721574e-02 Ry = -9.32972065e-01 eV +E_delta_NN= -1.93914770e-01 Ry = -2.63834580e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7002 11 0.7 1e+02 % + Run_lcao lcao_line 7.6911 1 7.7 1e+02 % + Potential init_pot 0.28234 2 0.14 3.7 % + PW_Basis recip2real 0.2636 17 0.016 3.4 % + PW_Basis gathers_scatterp 0.11775 17 0.0069 1.5 % + Potential v_of_rho 0.83106 14 0.059 11 % + XC_Functional v_xc 0.19934 15 0.013 2.6 % + H_Hartree_pw v_hartree 0.59302 14 0.042 7.7 % + PW_Basis real2recip 0.7001 41 0.017 9.1 % + PW_Basis gatherp_scatters 0.2844 41 0.0069 3.7 % + ORB_control set_orb_tables 1.099 1 1.1 14 % + ORB_gen_tables gen_tables 1.099 1 1.1 14 % + ORB_table_phi init_Table 0.47529 1 0.48 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.47005 126 0.0037 6.1 % + ORB_table_beta init_Table_Beta 0.18524 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18367 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24911 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.2471 66 0.0037 3.2 % + LOOP_ions opt_ions 6.0595 1 6.1 79 % + ESolver_KS_LCAO Run 5.4858 1 5.5 71 % + HSolverLCAO solve 3.2208 12 0.27 42 % + HamiltLCAO updateHk 1.6183 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.5887 12 0.13 21 % + Gint_interface cal_gint 0.57882 25 0.023 7.5 % + Gint_Gamma distri_vl_value 0.93591 12 0.078 12 % + Gint_Gamma distri_vl 2.8401 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.6565 14 0.4 73 % + LCAO_gen_fixedH add_v_delta 2.7071 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.7072 6 0.45 35 % + ElecStateLCAO psiToRho 1.5802 12 0.13 21 % + Charge mix_rho 0.82169 11 0.075 11 % + LOOP_ions force_stress 0.57353 1 0.57 7.4 % + Force_Stress_LCAO getForceStress 0.57351 1 0.57 7.4 % + Force_LCAO_gamma ftable_gamma 0.38312 1 0.38 5 % + Force_LCAO_gamma cal_fvl_dphi 0.14277 1 0.14 1.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:46 2022 + FINISH Time : Wed Sep 28 11:11:54 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/287/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4e7fcbf561aa1da87df87fb4b50c28db7470df9c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.799173 0.994004 0.341918 +H 0.751654 0.992825 0.386133 +H 0.852716 0.0142028 0.372538 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b22116b52a37acafc842ad6ab57cc3b83e0c243a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3336 2 + 2 -13.2569 2 + 3 -8.99925 2 + 4 -6.75381 2 + 5 1.39716 0 + 6 4.57658 0 + 7 11.0561 0 + 8 11.2938 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ecebb61a73a3ec82da9842f581399ff4e2c52cb1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/running_scf.log @@ -0,0 +1,780 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:40 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 22.3768373993 27.8321224121 9.57369279982 0 0 0 0 + tauc_H1 21.0463038132 27.7990983308 10.811729894 0 0 0 0 + tauc_H2 23.8760486165 0.397677500827 10.431068793 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0875757411771 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0882727848839 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107292198714 (SEC) + + DONE : INIT CHARGE Time : 0.155918407903 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437954 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000921 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00153 + + Density error is 0.21723098016 + + Energy Rydberg eV + E_KohnSham -34.1883899201 -465.15690836 + E_Harris -34.3848607704 -467.830031414 + E_Fermi -0.41111703385 -5.59353420522 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00130280250563 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132495971788 + + Density error is 0.0980549945993 + + Energy Rydberg eV + E_KohnSham -34.2802848935 -466.407203615 + E_Harris -34.2869749453 -466.498226439 + E_Fermi -0.217622911265 -2.96091160855 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012490840994 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122320561253 + + Density error is 0.062848222725 + + Energy Rydberg eV + E_KohnSham -34.2806704304 -466.412449113 + E_Harris -34.2849840204 -466.471138517 + E_Fermi -0.205956939654 -2.80218792194 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117590616806 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104117543073 + + Density error is 0.00205082683714 + + Energy Rydberg eV + E_KohnSham -34.2806732784 -466.412487862 + E_Harris -34.2806757274 -466.412521183 + E_Fermi -0.170369626693 -2.31799768916 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117792982766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103855314365 + + Density error is 0.000969792715126 + + Energy Rydberg eV + E_KohnSham -34.2806018161 -466.411515568 + E_Harris -34.2806033088 -466.411535877 + E_Fermi -0.169513706919 -2.3063523032 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117659285414 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103649625123 + + Density error is 0.000172339536159 + + Energy Rydberg eV + E_KohnSham -34.2806443829 -466.412094719 + E_Harris -34.2806444435 -466.412095543 + E_Fermi -0.169568921024 -2.30710352964 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117686243764 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103632083487 + + Density error is 4.37077311652e-05 + + Energy Rydberg eV + E_KohnSham -34.2806288281 -466.411883086 + E_Harris -34.2806288388 -466.41188323 + E_Fermi -0.169414519437 -2.30500278828 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117676432644 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103631564628 + + Density error is 1.826116675e-05 + + Energy Rydberg eV + E_KohnSham -34.2806336456 -466.411948631 + E_Harris -34.2806336471 -466.411948651 + E_Fermi -0.169465196946 -2.30569229116 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011767608441 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103627973104 + + Density error is 1.61505516527e-06 + + Energy Rydberg eV + E_KohnSham -34.2806320617 -466.41192708 + E_Harris -34.2806320617 -466.41192708 + E_Fermi -0.169445493392 -2.30542421055 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117676186479 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103627761578 + + Density error is 1.84783416927e-07 + + Energy Rydberg eV + E_KohnSham -34.2806323252 -466.411930666 + E_Harris -34.2806323252 -466.411930666 + E_Fermi -0.16944401557 -2.30540410376 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117676262797 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103627816703 + + Density error is 3.36889271778e-08 + + Energy Rydberg eV + E_KohnSham -34.2806323495 -466.411930996 + E_Harris -34.2806323495 -466.411930996 + E_band -7.98835180453 -108.68710217 + E_one_elec -69.479779211 -945.320893052 + E_Hartree +36.1333455337 +491.619387061 + E_xc -8.2245888892 -111.901272601 + E_Ewald +7.41434795045 +100.877379081 + E_demet -4.43093011269e-83 -6.02858969724e-82 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195096189001 -2.6544198285 + E_Fermi -0.16944397495 -2.30540355109 + + charge density convergence is achieved + final etot is -466.411930996 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3336 2.00000 + 2 -13.2569 2.00000 + 3 -8.99925 2.00000 + 4 -6.75381 2.00000 + 5 1.39716 0.00000 + 6 4.57658 0.00000 + 7 11.0561 0.00000 + 8 11.2938 0.00000 + + EFERMI = -2.305403551091779 eV + OUT.ABACUS/ final etot is -466.4119309962218 eV + correction force for each atom along direction 1 is -3.99553e-05 + correction force for each atom along direction 2 is -0.000126185 + correction force for each atom along direction 3 is 0.000184132 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.090974081 -0.25782846 -0.97049068 + H1 -0.36077020 +0.041975253 +0.53621593 + H2 +0.45174428 +0.21585321 +0.43427475 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4119309962218 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8964 11 0.63 1.0e+02% + Run_lcao lcao_line 6.8872 1 6.9 1.e+02% + Potential init_pot 0.28764 2 0.14 4.2% + PW_Basis recip2real 0.25735 16 0.016 3.7% + PW_Basis gathers_scatterp 0.11626 16 0.0073 1.7% + Charge atomic_rho 0.10017 1 0.10 1.5% + Potential v_of_rho 0.86592 13 0.067 13.% + XC_Functional v_xc 0.25720 14 0.018 3.7% + H_Hartree_pw v_hartree 0.57572 13 0.044 8.3% + PW_Basis real2recip 0.56596 38 0.015 8.2% + PW_Basis gatherp_scatters 0.23718 38 0.0062 3.4% + ORB_control set_orb_tables 1.1104 1 1.1 16.% + ORB_gen_tables gen_tables 1.1104 1 1.1 16.% + ORB_table_phi init_Table 0.49072 1 0.49 7.1% + ORB_table_phi cal_ST_Phi12_R 0.48569 126 0.0039 7.0% + ORB_table_beta init_Table_Beta 0.18838 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18682 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25289 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25098 66 0.0038 3.6% + LOOP_ions opt_ions 5.2614 1 5.3 76.% + ESolver_KS_LCAO Run 4.6743 1 4.7 68.% + HSolverLCAO solve 2.7024 11 0.25 39.% + HamiltLCAO updateHk 1.3857 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3569 11 0.12 20.% + Gint_interface cal_gint 0.56658 23 0.025 8.2% + Gint_Gamma distri_vl_value 0.76171 11 0.069 11.% + Gint_Gamma distri_vl 2.2419 6 0.37 33.% + LCAO_Deepks cal_projected_DM 4.8613 13 0.37 70.% + LCAO_gen_fixedH add_v_delta 2.1092 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.1092 6 0.35 31.% + ElecStateLCAO psiToRho 1.2992 11 0.12 19.% + Charge mix_rho 0.65480 10 0.065 9.5% + LOOP_ions force_stress 0.58699 1 0.59 8.5% + Force_Stress_LCAO getForceStress 0.58697 1 0.59 8.5% + Force_LCAO_gamma ftable_gamma 0.37576 1 0.38 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.15010 1 0.15 2.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:40 2022 + Finish Time : Wed Sep 28 11:04:47 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..f7653c7860d761d1bdccf77e65c01bab1ba655bd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123728 ima = 3.68618e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123411722559 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298430106 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112818829465 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113084249284 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011302561258 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113059639506 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001130512053 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113054435602 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113053686359 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113053621345 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113053610668 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/STRU new file mode 100644 index 0000000000000000000000000000000000000000..eb31617ebf27c67d2e742eca27a3ff2ebbddcca8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-5.623162600723 27.832122412064 9.573692799794 0 0 0 +H +0.0 +2 +-6.953696186770 27.799098330831 10.811729893948 0 0 0 +-4.123951383519 28.397677500840 10.431068793011 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/conv new file mode 100644 index 0000000000000000000000000000000000000000..1ba4690f0303481c86dcccc523544189ae1d3e5f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/conv @@ -0,0 +1 @@ +288 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c91e203227c02c9f6066e86eb2b68c42206a9172 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746915617 0.01270952115 1.283116993 1.371661387 1.46957741 0.008179411297 0.01950753258 0.03895491682 +1.903276415e-19 0.001143811743 0.00254478194 0.01256718962 0.0449688158 -2.923510161e-19 1.877008851e-06 5.596769826e-06 +0.001707471822 0.005838719015 + +H atom_index 1 n_descriptor 18 +1.25564166 0.03375842256 0.1102835575 0.1531013011 0.3235568128 0.02233271788 0.02870410572 0.03694664107 +7.924764212e-17 4.455797672e-05 0.1036057372 0.1151667866 0.131526503 2.014599986e-18 3.9687219e-06 0.0130277936 +0.02653844631 0.0310666005 + +H atom_index 2 n_descriptor 18 +1.255979985 0.03374704865 0.1104038521 0.1532623689 0.3236660439 0.02234805173 0.02872377665 0.03693766157 +5.901781705e-17 4.458944423e-05 0.1036812535 0.1151921861 0.1316648202 -1.643884545e-18 3.950648083e-06 0.01302685578 +0.02655087175 0.03108144297 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3b7dc49ec6332faea4489e4a4b36e9196e87cdec Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..0eb96da2f19ee88b5cdf5fb75685029f237e6f8e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..76d60cfa3478564e9f45914ba369cc5320510b2c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..a6a47d5b043231c2a0ee94fda1f4f38b5720b386 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:40 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0875973 SEC) : SETUP UNITCELL + DONE(0.0882894 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107313 SEC) : INIT PLANEWAVE + DONE(0.156056 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438021 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651569e+02 0.000000e+00 2.172e-01 5.385e-01 + GE2 -4.664072e+02 -1.250295e+00 9.805e-02 4.640e-01 + GE3 -4.664124e+02 -5.245498e-03 6.285e-02 5.248e-01 + GE4 -4.664125e+02 -3.874880e-05 2.051e-03 4.044e-01 + GE5 -4.664115e+02 9.722944e-04 9.698e-04 4.079e-01 + GE6 -4.664121e+02 -5.791512e-04 1.723e-04 4.014e-01 + GE7 -4.664119e+02 2.116332e-04 4.371e-05 3.911e-01 + GE8 -4.664119e+02 -6.554538e-05 1.826e-05 3.820e-01 + GE9 -4.664119e+02 2.155123e-05 1.615e-06 3.846e-01 + GE10 -4.664119e+02 -3.586064e-06 1.848e-07 3.864e-01 + GE11 -4.664119e+02 -3.302038e-07 3.369e-08 3.286e-01 +E_delta_band = -7.11384556e-02 Ry = -9.67888343e-01 eV +E_delta_NN= -1.95096189e-01 Ry = -2.65441983e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8964 11 0.63 1e+02 % + Run_lcao lcao_line 6.8872 1 6.9 1e+02 % + Potential init_pot 0.28764 2 0.14 4.2 % + PW_Basis recip2real 0.25735 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.11626 16 0.0073 1.7 % + Charge atomic_rho 0.10017 1 0.1 1.5 % + Potential v_of_rho 0.86592 13 0.067 13 % + XC_Functional v_xc 0.2572 14 0.018 3.7 % + H_Hartree_pw v_hartree 0.57572 13 0.044 8.3 % + PW_Basis real2recip 0.56596 38 0.015 8.2 % + PW_Basis gatherp_scatters 0.23718 38 0.0062 3.4 % + ORB_control set_orb_tables 1.1104 1 1.1 16 % + ORB_gen_tables gen_tables 1.1104 1 1.1 16 % + ORB_table_phi init_Table 0.49072 1 0.49 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.48569 126 0.0039 7 % + ORB_table_beta init_Table_Beta 0.18838 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18682 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.25289 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25098 66 0.0038 3.6 % + LOOP_ions opt_ions 5.2614 1 5.3 76 % + ESolver_KS_LCAO Run 4.6743 1 4.7 68 % + HSolverLCAO solve 2.7024 11 0.25 39 % + HamiltLCAO updateHk 1.3857 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3569 11 0.12 20 % + Gint_interface cal_gint 0.56658 23 0.025 8.2 % + Gint_Gamma distri_vl_value 0.76171 11 0.069 11 % + Gint_Gamma distri_vl 2.2419 6 0.37 33 % + LCAO_Deepks cal_projected_DM 4.8613 13 0.37 70 % + LCAO_gen_fixedH add_v_delta 2.1092 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.1092 6 0.35 31 % + ElecStateLCAO psiToRho 1.2992 11 0.12 19 % + Charge mix_rho 0.6548 10 0.065 9.5 % + LOOP_ions force_stress 0.58699 1 0.59 8.5 % + Force_Stress_LCAO getForceStress 0.58697 1 0.59 8.5 % + Force_LCAO_gamma ftable_gamma 0.37576 1 0.38 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.1501 1 0.15 2.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:40 2022 + FINISH Time : Wed Sep 28 11:04:47 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/288/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fa67b748647019e8ce486204591ee2f83736fb6e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.798208 0.986568 0.350708 +H 0.782166 0.995815 0.413745 +H 0.862308 0.967105 0.35363 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2f21db818145233a7c2789dbd0c232dd462c4b58 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1549 2 + 2 -12.888 2 + 3 -9.12983 2 + 4 -6.71537 2 + 5 1.17183 0 + 6 4.2034 0 + 7 11.1093 0 + 8 11.3632 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..020cdd32c99416d475ebd83b567cecca88834ec8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:58 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 22.3498292831 27.6238986121 9.81983395103 0 0 0 0 + tauc_H1 21.900653517 27.8828144724 11.5848463581 0 0 0 0 + tauc_H2 24.1446328351 27.0789501449 9.90164942969 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0878275326438 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0882409787584 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106800283381 (SEC) + + DONE : INIT CHARGE Time : 0.15779280636 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437883 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000853 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00174 + + Density error is 0.213824623831 + + Energy Rydberg eV + E_KohnSham -34.1904085835 -465.184373684 + E_Harris -34.37988082 -467.762275713 + E_Fermi -0.397001724785 -5.4014855729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00124019522415 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00140373861982 + + Density error is 0.0986077884595 + + Energy Rydberg eV + E_KohnSham -34.2806009663 -466.411504006 + E_Harris -34.2875821134 -466.506487385 + E_Fermi -0.205684561144 -2.79848202219 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118943742822 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129411515422 + + Density error is 0.0634977576811 + + Energy Rydberg eV + E_KohnSham -34.2810572007 -466.417711394 + E_Harris -34.2855540088 -466.478893607 + E_Fermi -0.197438100049 -2.68628316296 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112788355258 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108779482112 + + Density error is 0.00196938393012 + + Energy Rydberg eV + E_KohnSham -34.280996337 -466.416883301 + E_Harris -34.2809979847 -466.416905718 + E_Fermi -0.16198641875 -2.20393829362 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112914540916 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108634272216 + + Density error is 0.000999387549645 + + Energy Rydberg eV + E_KohnSham -34.2809413758 -466.416135514 + E_Harris -34.2809421368 -466.416145869 + E_Fermi -0.161655753098 -2.19943935661 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112806803148 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108333630702 + + Density error is 0.000164924154726 + + Energy Rydberg eV + E_KohnSham -34.2809693948 -466.416516732 + E_Harris -34.2809694218 -466.4165171 + E_Fermi -0.161402195658 -2.19598953066 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112834067097 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108328015086 + + Density error is 3.57842781183e-05 + + Energy Rydberg eV + E_KohnSham -34.2809597388 -466.416385357 + E_Harris -34.2809597448 -466.416385437 + E_Fermi -0.161318448387 -2.19485009058 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112823715939 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108325682163 + + Density error is 1.54648263295e-05 + + Energy Rydberg eV + E_KohnSham -34.280963453 -466.416435891 + E_Harris -34.280963454 -466.416435904 + E_Fermi -0.161350628641 -2.1952879254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112823682759 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108322295531 + + Density error is 1.57405054963e-06 + + Energy Rydberg eV + E_KohnSham -34.2809621409 -466.416418038 + E_Harris -34.2809621409 -466.416418038 + E_Fermi -0.161334044589 -2.1950622878 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112823903991 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108322017475 + + Density error is 2.84854168327e-07 + + Energy Rydberg eV + E_KohnSham -34.2809623664 -466.416421106 + E_Harris -34.2809623664 -466.416421106 + E_Fermi -0.161332907418 -2.19504681579 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112823975752 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108322039165 + + Density error is 4.87354365912e-08 + + Energy Rydberg eV + E_KohnSham -34.2809623854 -466.416421366 + E_Harris -34.2809623854 -466.416421366 + E_band -7.92140053646 -107.776183436 + E_one_elec -68.991328819 -938.67518453 + E_Hartree +35.897607503 +488.412006608 + E_xc -8.18671749148 -111.3860058 + E_Ewald +7.12442246299 +96.9327404559 + E_demet -3.67706348395e-69 -5.00290152894e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194270000791 -2.64317896123 + E_Fermi -0.161332776131 -2.19504502954 + + charge density convergence is achieved + final etot is -466.416421366 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1549 2.00000 + 2 -12.8880 2.00000 + 3 -9.12983 2.00000 + 4 -6.71537 2.00000 + 5 1.17183 0.00000 + 6 4.20340 0.00000 + 7 11.1093 0.00000 + 8 11.3632 0.00000 + + EFERMI = -2.195045029540376 eV + OUT.ABACUS/ final etot is -466.4164213657587 eV + correction force for each atom along direction 1 is 6.06560e-06 + correction force for each atom along direction 2 is -0.000170878 + correction force for each atom along direction 3 is 0.000111682 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.83898064 -0.27023079 -0.058335212 + H1 -0.058247237 +0.030804461 +0.12255877 + H2 -0.78073340 +0.23942633 -0.064223561 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4164213657587 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7705 11 0.71 1.0e+02% + Run_lcao lcao_line 7.7609 1 7.8 1.e+02% + Potential init_pot 0.28692 2 0.14 3.7% + PW_Basis recip2real 0.26486 16 0.017 3.4% + PW_Basis gathers_scatterp 0.12318 16 0.0077 1.6% + Potential v_of_rho 1.0426 13 0.080 13.% + XC_Functional v_xc 0.36905 14 0.026 4.7% + H_Hartree_pw v_hartree 0.63623 13 0.049 8.2% + PW_Basis real2recip 0.65504 38 0.017 8.4% + PW_Basis gatherp_scatters 0.28382 38 0.0075 3.7% + ORB_control set_orb_tables 1.1100 1 1.1 14.% + ORB_gen_tables gen_tables 1.1100 1 1.1 14.% + ORB_table_phi init_Table 0.47870 1 0.48 6.2% + ORB_table_phi cal_ST_Phi12_R 0.47364 126 0.0038 6.1% + ORB_table_beta init_Table_Beta 0.19041 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18886 56 0.0034 2.4% + ORB_table_alpha init_Table_Alpha 0.25475 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.25281 66 0.0038 3.3% + LOOP_ions opt_ions 6.1357 1 6.1 79.% + ESolver_KS_LCAO Run 5.5128 1 5.5 71.% + HSolverLCAO solve 3.2178 11 0.29 41.% + HamiltLCAO updateHk 1.5991 11 0.15 21.% + LCAO_Hamilt cal_Hgamma 1.5717 11 0.14 20.% + Gint_interface cal_gint 0.63061 23 0.027 8.1% + Gint_Gamma distri_vl_value 0.91617 11 0.083 12.% + Gint_Gamma distri_vl 2.6381 6 0.44 34.% + LCAO_Deepks cal_projected_DM 5.7134 13 0.44 74.% + LCAO_gen_fixedH add_v_delta 2.5063 6 0.42 32.% + LCAO_DESCRIPTOR add_v_delta 2.5065 6 0.42 32.% + ElecStateLCAO psiToRho 1.5823 11 0.14 20.% + Charge mix_rho 0.71719 10 0.072 9.2% + LOOP_ions force_stress 0.62274 1 0.62 8.0% + Force_Stress_LCAO getForceStress 0.62271 1 0.62 8.0% + Force_LCAO_gamma ftable_gamma 0.40299 1 0.40 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.16016 1 0.16 2.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:58 2022 + Finish Time : Wed Sep 28 11:07:06 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e03a2d66617f770e5275d93fd99684a4f796af62 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123487 ima = 3.68057e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123414586408 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111989540787 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112683795823 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112919626556 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112881391394 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112903702984 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112897295703 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112899969273 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112899313596 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112899255495 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112899240075 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4d55c80cbe6413ddb489c98a36c5926eff9ab097 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-5.650170716917 27.623898612123 9.819833951023 0 0 0 +H +0.0 +2 +-6.099346482984 27.882814472392 11.584846358070 0 0 0 +-3.855367164911 27.078950144862 9.901649429669 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/conv new file mode 100644 index 0000000000000000000000000000000000000000..332ce2886b062b4b2dc5bf30056a45a1b195f9e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/conv @@ -0,0 +1 @@ +289 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c7cac15886651422f07f368082e5133e7a11629b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749935162 0.01258803069 1.260374752 1.350832935 1.468714706 0.008516267833 0.01809144906 0.03906003774 +-4.650278215e-19 0.0009695147664 0.002526482934 0.01204707039 0.04365075354 -8.682087709e-20 1.900992657e-06 5.624158994e-06 +0.001628908135 0.005944658156 + +H atom_index 1 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:58 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0878506 SEC) : SETUP UNITCELL + DONE(0.0882628 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106823 SEC) : INIT PLANEWAVE + DONE(0.157926 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.437948 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651844e+02 0.000000e+00 2.138e-01 5.979e-01 + GE2 -4.664115e+02 -1.227130e+00 9.861e-02 5.532e-01 + GE3 -4.664177e+02 -6.207387e-03 6.350e-02 6.209e-01 + GE4 -4.664169e+02 8.280929e-04 1.969e-03 4.827e-01 + GE5 -4.664161e+02 7.477865e-04 9.994e-04 4.800e-01 + GE6 -4.664165e+02 -3.812180e-04 1.649e-04 4.750e-01 + GE7 -4.664164e+02 1.313755e-04 3.578e-05 4.637e-01 + GE8 -4.664164e+02 -5.053385e-05 1.546e-05 4.578e-01 + GE9 -4.664164e+02 1.785231e-05 1.574e-06 4.610e-01 + GE10 -4.664164e+02 -3.068131e-06 2.849e-07 4.626e-01 + GE11 -4.664164e+02 -2.592918e-07 4.874e-08 3.915e-01 +E_delta_band = -6.93239599e-02 Ry = -9.43200862e-01 eV +E_delta_NN= -1.94270001e-01 Ry = -2.64317896e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7705 11 0.71 1e+02 % + Run_lcao lcao_line 7.7609 1 7.8 1e+02 % + Potential init_pot 0.28692 2 0.14 3.7 % + PW_Basis recip2real 0.26486 16 0.017 3.4 % + PW_Basis gathers_scatterp 0.12318 16 0.0077 1.6 % + Potential v_of_rho 1.0426 13 0.08 13 % + XC_Functional v_xc 0.36905 14 0.026 4.7 % + H_Hartree_pw v_hartree 0.63623 13 0.049 8.2 % + PW_Basis real2recip 0.65504 38 0.017 8.4 % + PW_Basis gatherp_scatters 0.28382 38 0.0075 3.7 % + ORB_control set_orb_tables 1.11 1 1.1 14 % + ORB_gen_tables gen_tables 1.11 1 1.1 14 % + ORB_table_phi init_Table 0.4787 1 0.48 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.47364 126 0.0038 6.1 % + ORB_table_beta init_Table_Beta 0.19041 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18886 56 0.0034 2.4 % + ORB_table_alpha init_Table_Alpha 0.25475 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.25281 66 0.0038 3.3 % + LOOP_ions opt_ions 6.1357 1 6.1 79 % + ESolver_KS_LCAO Run 5.5128 1 5.5 71 % + HSolverLCAO solve 3.2178 11 0.29 41 % + HamiltLCAO updateHk 1.5991 11 0.15 21 % + LCAO_Hamilt cal_Hgamma 1.5717 11 0.14 20 % + Gint_interface cal_gint 0.63061 23 0.027 8.1 % + Gint_Gamma distri_vl_value 0.91617 11 0.083 12 % + Gint_Gamma distri_vl 2.6381 6 0.44 34 % + LCAO_Deepks cal_projected_DM 5.7134 13 0.44 74 % + LCAO_gen_fixedH add_v_delta 2.5063 6 0.42 32 % + LCAO_DESCRIPTOR add_v_delta 2.5065 6 0.42 32 % + ElecStateLCAO psiToRho 1.5823 11 0.14 20 % + Charge mix_rho 0.71719 10 0.072 9.2 % + LOOP_ions force_stress 0.62274 1 0.62 8 % + Force_Stress_LCAO getForceStress 0.62271 1 0.62 8 % + Force_LCAO_gamma ftable_gamma 0.40299 1 0.4 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.16016 1 0.16 2.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:58 2022 + FINISH Time : Wed Sep 28 11:07:06 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/289/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a8d4de11fd33d1ca6a73d5a8ed70a8e781bd986c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.502151 0.443523 0.427151 +H 0.552651 0.474592 0.39717 +H 0.518195 0.447892 0.490208 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d7d677f3df1465dc6f5aad9f54e1a8f3b2fda436 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2641 2 + 2 -12.9234 2 + 3 -9.18773 2 + 4 -6.74015 2 + 5 1.24762 0 + 6 4.33257 0 + 7 11.0857 0 + 8 11.3449 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..5f234d23cff6cfffb58d1b14fa72681c041d58eb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:23 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.0602169755 12.4186490255 11.9602157504 0 0 0 0 + tauc_H1 15.4742353287 13.2885777943 11.1207535443 0 0 0 0 + tauc_H2 14.5094569097 12.5409653365 13.7258280708 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0896427682219 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0900090441179 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.108460591797 (SEC) + + DONE : INIT CHARGE Time : 0.158032914118 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441634 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 +receiver_size is 324 ; receiver_size of each process is: +81 81 81 81 +sender_size is 369 ; sender_size of each process is: +81 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000759 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00098 + + Density error is 0.214296569564 + + Energy Rydberg eV + E_KohnSham -34.1907265051 -465.188699229 + E_Harris -34.3813934671 -467.782856333 + E_Fermi -0.40276402447 -5.4798856822 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00117057919846 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00126867634819 + + Density error is 0.0982082033318 + + Energy Rydberg eV + E_KohnSham -34.2807942713 -466.414134056 + E_Harris -34.287660128 -466.507548828 + E_Fermi -0.211210948784 -2.87367238345 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112638888408 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0012085997964 + + Density error is 0.0631275216872 + + Energy Rydberg eV + E_KohnSham -34.2811787763 -466.419365514 + E_Harris -34.2856162127 -466.479739934 + E_Fermi -0.201489087202 -2.74139967076 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107646496753 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00112370067069 + + Density error is 0.00196107793599 + + Energy Rydberg eV + E_KohnSham -34.2811423356 -466.418869714 + E_Harris -34.2811431671 -466.418881026 + E_Fermi -0.165896527453 -2.25713805178 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107902465217 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00112497417142 + + Density error is 0.000959345492361 + + Energy Rydberg eV + E_KohnSham -34.2810826814 -466.418058076 + E_Harris -34.2810839453 -466.418075272 + E_Fermi -0.165390910743 -2.25025878352 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107795498031 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00112357481172 + + Density error is 0.000141709196951 + + Energy Rydberg eV + E_KohnSham -34.2811172465 -466.418528359 + E_Harris -34.2811172719 -466.418528704 + E_Fermi -0.165260721426 -2.24848746698 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107815525597 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00112376254786 + + Density error is 3.6491011248e-05 + + Energy Rydberg eV + E_KohnSham -34.2811053298 -466.418366223 + E_Harris -34.2811053366 -466.418366315 + E_Fermi -0.165159850474 -2.24711504727 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0010780728861 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00112367659946 + + Density error is 1.50485873916e-05 + + Energy Rydberg eV + E_KohnSham -34.2811088528 -466.418414156 + E_Harris -34.2811088537 -466.418414168 + E_Fermi -0.165197182143 -2.24762297069 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107807594138 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00112366969475 + + Density error is 1.72667005239e-06 + + Energy Rydberg eV + E_KohnSham -34.2811075376 -466.418396262 + E_Harris -34.2811075376 -466.418396263 + E_Fermi -0.16518113271 -2.24740460695 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107807611004 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0011236712514 + + Density error is 2.44529864309e-07 + + Energy Rydberg eV + E_KohnSham -34.2811077411 -466.41839903 + E_Harris -34.2811077411 -466.41839903 + E_Fermi -0.165179641484 -2.24738431778 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107807689937 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00112367173077 + + Density error is 9.04051037291e-08 + + Energy Rydberg eV + E_KohnSham -34.2811077683 -466.4183994 + E_Harris -34.2811077683 -466.4183994 + E_band -7.9547992704 -108.230596524 + E_one_elec -69.1835791498 -941.290884471 + E_Hartree +35.9864592439 +489.620896562 + E_xc -8.20100681877 -111.580422072 + E_Ewald +7.2415615852 +98.5264999767 + E_demet -2.56280644546e-74 -3.48687705294e-73 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194627811893 -2.64804723101 + E_Fermi -0.165179611253 -2.24738390647 + + charge density convergence is achieved + final etot is -466.4183994 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2641 2.00000 + 2 -12.9234 2.00000 + 3 -9.18773 2.00000 + 4 -6.74015 2.00000 + 5 1.24762 0.00000 + 6 4.33257 0.00000 + 7 11.0857 0.00000 + 8 11.3449 0.00000 + + EFERMI = -2.247383906467184 eV + OUT.ABACUS/ final etot is -466.4183994004055 eV + correction force for each atom along direction 1 is 2.03805e-05 + correction force for each atom along direction 2 is 0.000171181 + correction force for each atom along direction 3 is 9.87151e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.31651954 +0.23482909 -0.60488260 + H1 -0.34556452 -0.20649218 +0.068327046 + H2 +0.029044984 -0.028336916 +0.53655556 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4183994004055 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3092 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2986 1 6.3 1.e+02% + Potential init_pot 0.28695 2 0.14 4.5% + PW_Basis recip2real 0.27895 16 0.017 4.4% + PW_Basis gathers_scatterp 0.13325 16 0.0083 2.1% + Potential v_of_rho 1.0016 13 0.077 16.% + XC_Functional v_xc 0.31538 14 0.023 5.0% + H_Hartree_pw v_hartree 0.64660 13 0.050 10.% + PW_Basis real2recip 0.66160 38 0.017 10.% + PW_Basis gatherp_scatters 0.29404 38 0.0077 4.7% + ORB_control set_orb_tables 1.1117 1 1.1 18.% + ORB_gen_tables gen_tables 1.1117 1 1.1 18.% + ORB_table_phi init_Table 0.48369 1 0.48 7.7% + ORB_table_phi cal_ST_Phi12_R 0.47845 126 0.0038 7.6% + ORB_table_beta init_Table_Beta 0.18999 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18838 56 0.0034 3.0% + ORB_table_alpha init_Table_Alpha 0.25312 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25111 66 0.0038 4.0% + LOOP_ions opt_ions 4.6670 1 4.7 74.% + ESolver_KS_LCAO Run 4.1595 1 4.2 66.% + HSolverLCAO solve 1.8605 11 0.17 29.% + HamiltLCAO updateHk 1.0072 11 0.092 16.% + LCAO_Hamilt cal_Hgamma 0.97984 11 0.089 16.% + Gint_interface cal_gint 0.11829 23 0.0051 1.9% + Gint_Gamma distri_vl_value 0.53940 11 0.049 8.5% + Gint_Gamma distri_vl 2.0259 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.3334 13 0.33 69.% + LCAO_gen_fixedH add_v_delta 1.8825 6 0.31 30.% + LCAO_DESCRIPTOR add_v_delta 1.8827 6 0.31 30.% + ElecStateLCAO psiToRho 0.82784 11 0.075 13.% + Charge mix_rho 0.76431 10 0.076 12.% + LOOP_ions force_stress 0.50727 1 0.51 8.0% + Force_Stress_LCAO getForceStress 0.50724 1 0.51 8.0% + Force_LCAO_gamma ftable_gamma 0.28932 1 0.29 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:23 2022 + Finish Time : Wed Sep 28 11:07:29 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..aedaf78332446f63ee028f9ae469f2cae4f6c185 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123719 ima = 3.68928e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123152903097 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111902182849 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112529495116 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112778815218 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112731585638 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112759158302 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753145626 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011275585571 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755252247 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755181093 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755172647 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/STRU new file mode 100644 index 0000000000000000000000000000000000000000..bba8c9121ffa696d406f25ce234a1867dd24d64d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.939783024434 12.418649025484 11.960215750404 0 0 0 +H +0.0 +2 +-12.525764671302 13.288577794336 11.120753544297 0 0 0 +-13.490543090260 12.540965336475 13.725828070850 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/conv new file mode 100644 index 0000000000000000000000000000000000000000..df12c43894b0c8446b2a7dca09df1fa7cde387f1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/conv @@ -0,0 +1 @@ +29 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ba8851bfd29d0ff7bd45795796efa044d6f97159 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750542239 0.01267517033 1.267810455 1.355924859 1.469182352 0.008695780226 0.01799864166 0.0390704492 +2.626856872e-18 0.0009942872596 0.002621402758 0.01240755147 0.04496925284 3.030235787e-19 2.125503329e-06 6.086308789e-06 +0.001623766618 0.00600475708 + +H atom_index 1 n_descriptor 18 +1.225501556 0.03523434134 0.1003552919 0.1388336445 0.3125443807 0.02122326663 0.02686028905 0.03841379097 +2.147977409e-17 4.375360546e-05 0.0951053762 0.1142323661 0.1190147798 -3.716630434e-18 5.185613607e-06 0.01356341234 +0.02536514011 0.02958580065 + +H atom_index 2 n_descriptor 18 +1.252672902 0.03430631204 0.1095179624 0.15110946 0.3216897363 0.02250346929 0.02844925685 0.03747778782 +1.170651735e-17 4.625818933e-05 0.1019782673 0.1152937179 0.1296639797 4.987692299e-20 3.78223182e-06 0.01320233536 +0.02640518757 0.03087303272 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3817b6f83c97243fe641fe85e635a9f9bb1ca815 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:23 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0896679 SEC) : SETUP UNITCELL + DONE(0.0900248 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.108485 SEC) : INIT PLANEWAVE + DONE(0.158165 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.441695 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651887e+02 0.000000e+00 2.143e-01 4.929e-01 + GE2 -4.664141e+02 -1.225435e+00 9.821e-02 4.279e-01 + GE3 -4.664194e+02 -5.231458e-03 6.313e-02 4.975e-01 + GE4 -4.664189e+02 4.958002e-04 1.961e-03 3.581e-01 + GE5 -4.664181e+02 8.116382e-04 9.593e-04 3.565e-01 + GE6 -4.664185e+02 -4.702829e-04 1.417e-04 3.487e-01 + GE7 -4.664184e+02 1.621352e-04 3.649e-05 3.420e-01 + GE8 -4.664184e+02 -4.793242e-05 1.505e-05 3.324e-01 + GE9 -4.664184e+02 1.789336e-05 1.727e-06 3.379e-01 + GE10 -4.664184e+02 -2.767807e-06 2.445e-07 3.361e-01 + GE11 -4.664184e+02 -3.701708e-07 9.041e-08 2.689e-01 +E_delta_band = -7.00851831e-02 Ry = -9.53557836e-01 eV +E_delta_NN= -1.94627812e-01 Ry = -2.64804723e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3092 11 0.57 1e+02 % + Run_lcao lcao_line 6.2986 1 6.3 1e+02 % + Potential init_pot 0.28695 2 0.14 4.5 % + PW_Basis recip2real 0.27895 16 0.017 4.4 % + PW_Basis gathers_scatterp 0.13325 16 0.0083 2.1 % + Potential v_of_rho 1.0016 13 0.077 16 % + XC_Functional v_xc 0.31538 14 0.023 5 % + H_Hartree_pw v_hartree 0.6466 13 0.05 10 % + PW_Basis real2recip 0.6616 38 0.017 10 % + PW_Basis gatherp_scatters 0.29404 38 0.0077 4.7 % + ORB_control set_orb_tables 1.1117 1 1.1 18 % + ORB_gen_tables gen_tables 1.1117 1 1.1 18 % + ORB_table_phi init_Table 0.48369 1 0.48 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.47845 126 0.0038 7.6 % + ORB_table_beta init_Table_Beta 0.18999 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18838 56 0.0034 3 % + ORB_table_alpha init_Table_Alpha 0.25312 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.25111 66 0.0038 4 % + LOOP_ions opt_ions 4.667 1 4.7 74 % + ESolver_KS_LCAO Run 4.1595 1 4.2 66 % + HSolverLCAO solve 1.8605 11 0.17 29 % + HamiltLCAO updateHk 1.0072 11 0.092 16 % + LCAO_Hamilt cal_Hgamma 0.97984 11 0.089 16 % + Gint_interface cal_gint 0.11829 23 0.0051 1.9 % + Gint_Gamma distri_vl_value 0.5394 11 0.049 8.5 % + Gint_Gamma distri_vl 2.0259 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.3334 13 0.33 69 % + LCAO_gen_fixedH add_v_delta 1.8825 6 0.31 30 % + LCAO_DESCRIPTOR add_v_delta 1.8827 6 0.31 30 % + ElecStateLCAO psiToRho 0.82784 11 0.075 13 % + Charge mix_rho 0.76431 10 0.076 12 % + LOOP_ions force_stress 0.50727 1 0.51 8 % + Force_Stress_LCAO getForceStress 0.50724 1 0.51 8 % + Force_LCAO_gamma ftable_gamma 0.28932 1 0.29 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:23 2022 + FINISH Time : Wed Sep 28 11:07:29 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/29/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..45e07b5cdc269b25fd530127576d70e4eafbd63a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.806504 0.981977 0.36953 +H 0.829454 0.945654 0.420044 +H 0.848413 0.971554 0.32209 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..44616a787cb54a4ba5d97698d607e122071a68f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3327 2 + 2 -13.095 2 + 3 -9.11128 2 + 4 -6.75362 2 + 5 1.32946 0 + 6 4.49487 0 + 7 11.064 0 + 8 11.312 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3fee407320fbea31175acb62f50c2ea83df3af53 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:27 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 22.5821145674 27.4953694916 10.3468278456 0 0 0 0 + tauc_H1 23.2247079471 26.478308701 11.7612314434 0 0 0 0 + tauc_H2 23.7555502889 27.2035154907 9.01851121575 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0866982287087 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0992763667485 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117358432415 (SEC) + + DONE : INIT CHARGE Time : 0.16558682492 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443577 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000758 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126 + + Density error is 0.215722301685 + + Energy Rydberg eV + E_KohnSham -34.1894288184 -465.171043295 + E_Harris -34.3829375246 -467.803864312 + E_Fermi -0.408744277655 -5.56125120101 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113250401499 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123928377375 + + Density error is 0.0980194635771 + + Energy Rydberg eV + E_KohnSham -34.2799287925 -466.402358612 + E_Harris -34.2866694311 -466.494069706 + E_Fermi -0.216412148263 -2.9444383328 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010882844831 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116354831112 + + Density error is 0.0628372140934 + + Energy Rydberg eV + E_KohnSham -34.2802540684 -466.406784219 + E_Harris -34.2846058001 -466.465992565 + E_Fermi -0.20505612547 -2.78993171619 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103442427064 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010464350422 + + Density error is 0.00200658633459 + + Energy Rydberg eV + E_KohnSham -34.2802467913 -466.406685208 + E_Harris -34.2802483187 -466.406705989 + E_Fermi -0.169434350885 -2.30527260897 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103760002826 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010479559622 + + Density error is 0.000919276466056 + + Energy Rydberg eV + E_KohnSham -34.2801831232 -466.405818959 + E_Harris -34.2801844128 -466.405836505 + E_Fermi -0.168684911017 -2.29507595645 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103643019715 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104627031432 + + Density error is 0.000154967544318 + + Energy Rydberg eV + E_KohnSham -34.2802222473 -466.40635127 + E_Harris -34.2802222937 -466.406351901 + E_Fermi -0.168691809133 -2.29516981014 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103659961403 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104628188139 + + Density error is 3.91536002666e-05 + + Energy Rydberg eV + E_KohnSham -34.2802081451 -466.406159399 + E_Harris -34.280208153 -466.406159507 + E_Fermi -0.168563011325 -2.29341742606 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103653620516 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104626110227 + + Density error is 1.73810747257e-05 + + Energy Rydberg eV + E_KohnSham -34.2802123293 -466.406216329 + E_Harris -34.2802123305 -466.406216345 + E_Fermi -0.168606569543 -2.29401006602 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103654286048 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104625301401 + + Density error is 2.81276331566e-06 + + Energy Rydberg eV + E_KohnSham -34.2802109006 -466.40619689 + E_Harris -34.2802109006 -466.40619689 + E_Fermi -0.168589390331 -2.29377633085 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103654107627 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104624768537 + + Density error is 2.90438644341e-07 + + Energy Rydberg eV + E_KohnSham -34.2802111102 -466.406199742 + E_Harris -34.2802111102 -466.406199742 + E_Fermi -0.168586327496 -2.29373465883 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103654182877 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104624815013 + + Density error is 1.46733763253e-07 + + Energy Rydberg eV + E_KohnSham -34.2802111563 -466.406200369 + E_Harris -34.2802111563 -466.406200369 + E_Fermi -0.168586317614 -2.29373452439 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103654206314 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104624813145 + + Density error is 1.02629746067e-08 + + Energy Rydberg eV + E_KohnSham -34.2802111558 -466.406200363 + E_Harris -34.2802111558 -466.406200363 + E_band -7.98087194356 -108.585333441 + E_one_elec -69.3828002915 -944.001427161 + E_Hartree +36.0833766212 +490.939525128 + E_xc -8.21668121696 -111.7936832 + E_Ewald +7.36003982864 +100.138479176 + E_demet -1.13978121357e-79 -1.5507518978e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194980059726 -2.65283980865 + E_Fermi -0.168586184212 -2.29373270936 + + charge density convergence is achieved + final etot is -466.406200363 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3327 2.00000 + 2 -13.0950 2.00000 + 3 -9.11128 2.00000 + 4 -6.75362 2.00000 + 5 1.32946 0.00000 + 6 4.49487 0.00000 + 7 11.0640 0.00000 + 8 11.3120 0.00000 + + EFERMI = -2.293732709361517 eV + OUT.ABACUS/ final etot is -466.4062003625586 eV + correction force for each atom along direction 1 is 5.97193e-06 + correction force for each atom along direction 2 is 2.61584e-05 + correction force for each atom along direction 3 is -4.25072e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.75044315 +0.016049040 +1.2777520 + H1 -0.13157288 +0.20018309 -0.27101948 + H2 +0.88201602 -0.21623213 -1.0067325 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4062003625586 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1927 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1841 1 7.2 1.e+02% + Potential init_pot 0.28324 2 0.14 3.9% + PW_Basis recip2real 0.27131 17 0.016 3.8% + PW_Basis gathers_scatterp 0.12194 17 0.0072 1.7% + Potential v_of_rho 0.92324 14 0.066 13.% + XC_Functional v_xc 0.26457 15 0.018 3.7% + H_Hartree_pw v_hartree 0.62188 14 0.044 8.6% + PW_Basis real2recip 0.60393 41 0.015 8.4% + PW_Basis gatherp_scatters 0.24985 41 0.0061 3.5% + ORB_control set_orb_tables 1.1146 1 1.1 15.% + ORB_gen_tables gen_tables 1.1146 1 1.1 15.% + ORB_table_phi init_Table 0.48468 1 0.48 6.7% + ORB_table_phi cal_ST_Phi12_R 0.47970 126 0.0038 6.7% + ORB_table_beta init_Table_Beta 0.19299 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.19149 56 0.0034 2.7% + ORB_table_alpha init_Table_Alpha 0.25699 1 0.26 3.6% + ORB_table_alpha S_PhiAlpha_R 0.25509 66 0.0039 3.5% + LOOP_ions opt_ions 5.5488 1 5.5 77.% + ESolver_KS_LCAO Run 4.9703 1 5.0 69.% + HSolverLCAO solve 2.8303 12 0.24 39.% + HamiltLCAO updateHk 1.4361 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.4057 12 0.12 20.% + Gint_interface cal_gint 0.58811 25 0.024 8.2% + Gint_Gamma distri_vl_value 0.79966 12 0.067 11.% + Gint_Gamma distri_vl 2.5817 6 0.43 36.% + LCAO_Deepks cal_projected_DM 5.1517 14 0.37 72.% + LCAO_gen_fixedH add_v_delta 2.4517 6 0.41 34.% + LCAO_DESCRIPTOR add_v_delta 2.4517 6 0.41 34.% + ElecStateLCAO psiToRho 1.3736 12 0.11 19.% + Charge mix_rho 0.71629 11 0.065 10.% + LOOP_ions force_stress 0.57841 1 0.58 8.0% + Force_Stress_LCAO getForceStress 0.57838 1 0.58 8.0% + Force_LCAO_gamma ftable_gamma 0.36895 1 0.37 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.14103 1 0.14 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:27 2022 + Finish Time : Wed Sep 28 11:13:34 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..09fc9a5891259f003b85aadad64686077db372a1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123862 ima = 3.67126e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012317298088 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112107609461 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112649731324 + charge after normalized = 7.99999999999996 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112906353411 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112852982884 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112884423662 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112877127568 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112880033827 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112879363098 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112879247505 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112879241403 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011287923454 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a4ebdb56fd8fdc53f393e79b3ae34930e4fb75b8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-5.417885432586 27.495369491638 10.346827845592 0 0 0 +H +0.0 +2 +-4.775292052934 26.478308701049 11.761231443394 0 0 0 +-4.244449711081 27.203515490723 9.018511215747 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/conv new file mode 100644 index 0000000000000000000000000000000000000000..90ceface7784052439cb1484030bb48499893363 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/conv @@ -0,0 +1 @@ +290 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b0a489445a51e301c2d30cd1778037c1a58b989a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749044645 0.0127005372 1.275674505 1.366629349 1.469528563 0.008505963236 0.01872255129 0.03902250646 +1.25252649e-18 0.001076409761 0.002615438352 0.01251197487 0.04545349414 -3.654843476e-19 2.052200699e-06 5.960619143e-06 +0.001653578994 0.00593507494 + +H atom_index 1 n_descriptor 18 +1.226706261 0.03500981012 0.1005685041 0.1395589977 0.3133683168 0.02116957276 0.02696315359 0.03816428246 +-1.484657213e-17 4.382243931e-05 0.09600886481 0.1141273145 0.1197368558 -6.731407228e-18 5.33526163e-06 0.01346565661 +0.0254757554 0.0296793117 + +H atom_index 2 n_descriptor 18 +1.274700564 0.03336811273 0.1172588492 0.1619302913 0.3287416204 0.02338579366 0.02974978539 0.03673331931 +-2.605817102e-18 4.825981372e-05 0.106668744 0.1173448526 0.1390296875 6.771256472e-18 2.776485167e-06 0.01317363196 +0.02724075867 0.03183145466 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3a588f404778158e87941fc9811de602138f9e66 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:27 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0867189 SEC) : SETUP UNITCELL + DONE(0.0992952 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11738 SEC) : INIT PLANEWAVE + DONE(0.165718 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443639 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651710e+02 0.000000e+00 2.157e-01 5.331e-01 + GE2 -4.664024e+02 -1.231315e+00 9.802e-02 4.554e-01 + GE3 -4.664068e+02 -4.425607e-03 6.284e-02 5.106e-01 + GE4 -4.664067e+02 9.901097e-05 2.007e-03 4.035e-01 + GE5 -4.664058e+02 8.662490e-04 9.193e-04 4.028e-01 + GE6 -4.664064e+02 -5.323113e-04 1.550e-04 3.950e-01 + GE7 -4.664062e+02 1.918706e-04 3.915e-05 3.891e-01 + GE8 -4.664062e+02 -5.692941e-05 1.738e-05 3.746e-01 + GE9 -4.664062e+02 1.943904e-05 2.813e-06 3.801e-01 + GE10 -4.664062e+02 -2.852549e-06 2.904e-07 3.754e-01 + GE11 -4.664062e+02 -6.272274e-07 1.467e-07 3.723e-01 + GE12 -4.664062e+02 6.845217e-09 1.026e-08 3.176e-01 +E_delta_band = -7.08339625e-02 Ry = -9.63745502e-01 eV +E_delta_NN= -1.94980060e-01 Ry = -2.65283981e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1927 11 0.65 1e+02 % + Run_lcao lcao_line 7.1841 1 7.2 1e+02 % + Potential init_pot 0.28324 2 0.14 3.9 % + PW_Basis recip2real 0.27131 17 0.016 3.8 % + PW_Basis gathers_scatterp 0.12194 17 0.0072 1.7 % + Potential v_of_rho 0.92324 14 0.066 13 % + XC_Functional v_xc 0.26457 15 0.018 3.7 % + H_Hartree_pw v_hartree 0.62188 14 0.044 8.6 % + PW_Basis real2recip 0.60393 41 0.015 8.4 % + PW_Basis gatherp_scatters 0.24985 41 0.0061 3.5 % + ORB_control set_orb_tables 1.1146 1 1.1 15 % + ORB_gen_tables gen_tables 1.1146 1 1.1 15 % + ORB_table_phi init_Table 0.48468 1 0.48 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.4797 126 0.0038 6.7 % + ORB_table_beta init_Table_Beta 0.19299 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.19149 56 0.0034 2.7 % + ORB_table_alpha init_Table_Alpha 0.25699 1 0.26 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.25509 66 0.0039 3.5 % + LOOP_ions opt_ions 5.5488 1 5.5 77 % + ESolver_KS_LCAO Run 4.9703 1 5 69 % + HSolverLCAO solve 2.8303 12 0.24 39 % + HamiltLCAO updateHk 1.4361 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.4057 12 0.12 20 % + Gint_interface cal_gint 0.58811 25 0.024 8.2 % + Gint_Gamma distri_vl_value 0.79966 12 0.067 11 % + Gint_Gamma distri_vl 2.5817 6 0.43 36 % + LCAO_Deepks cal_projected_DM 5.1517 14 0.37 72 % + LCAO_gen_fixedH add_v_delta 2.4517 6 0.41 34 % + LCAO_DESCRIPTOR add_v_delta 2.4517 6 0.41 34 % + ElecStateLCAO psiToRho 1.3736 12 0.11 19 % + Charge mix_rho 0.71629 11 0.065 10 % + LOOP_ions force_stress 0.57841 1 0.58 8 % + Force_Stress_LCAO getForceStress 0.57838 1 0.58 8 % + Force_LCAO_gamma ftable_gamma 0.36895 1 0.37 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.14103 1 0.14 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:27 2022 + FINISH Time : Wed Sep 28 11:13:34 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/290/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..94131b9c78cf3e787932e9a765b540f7f0bc3686 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.829343 0.970325 0.386208 +H 0.858186 0.913691 0.398255 +H 0.798114 0.960225 0.326676 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2bffad0b216db5bffbf1d44724f443929caf75b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1662 2 + 2 -12.909 2 + 3 -9.11397 2 + 4 -6.7162 2 + 5 1.15118 0 + 6 4.23776 0 + 7 11.1058 0 + 8 11.3534 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..107dfe31912e01dc9dfa226b1b90dec7ac032311 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:07 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 23.2216033816 27.1690946982 10.813828305 0 0 0 0 + tauc_H1 24.0291988144 25.5833567843 11.1511280999 0 0 0 0 + tauc_H2 22.3471959401 26.8862957414 9.14693331499 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0880566502571 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.09891773318 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117120206616 (SEC) + + DONE : INIT CHARGE Time : 0.16622137063 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447483 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000492 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001 + + Density error is 0.213266290338 + + Energy Rydberg eV + E_KohnSham -34.1904524769 -465.184970884 + E_Harris -34.3786825024 -467.745971766 + E_Fermi -0.397012914152 -5.40163781205 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000771531986032 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118859898812 + + Density error is 0.0982425133294 + + Energy Rydberg eV + E_KohnSham -34.2790264491 -466.3900816 + E_Harris -34.2859174612 -466.48383863 + E_Fermi -0.207599470772 -2.82453570429 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00074602818797 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011337031115 + + Density error is 0.0631998394001 + + Energy Rydberg eV + E_KohnSham -34.27933284 -466.394250263 + E_Harris -34.283776461 -466.454708827 + E_Fermi -0.198221286449 -2.6969389606 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000724972061273 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105550991549 + + Density error is 0.00197921667837 + + Energy Rydberg eV + E_KohnSham -34.2792843583 -466.393590635 + E_Harris -34.2792857416 -466.393609457 + E_Fermi -0.162782003797 -2.21476278349 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000725397221576 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105516989573 + + Density error is 0.000862957343797 + + Energy Rydberg eV + E_KohnSham -34.2792411838 -466.393003216 + E_Harris -34.2792417907 -466.393011473 + E_Fermi -0.162391036335 -2.20944339828 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000725102913344 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105408816135 + + Density error is 0.000161401469103 + + Energy Rydberg eV + E_KohnSham -34.2792644712 -466.393320058 + E_Harris -34.2792644914 -466.393320332 + E_Fermi -0.162156682442 -2.20625484999 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000725321777883 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105426676638 + + Density error is 3.42830691064e-05 + + Energy Rydberg eV + E_KohnSham -34.2792565733 -466.393212601 + E_Harris -34.2792565785 -466.393212671 + E_Fermi -0.162080847809 -2.20522306687 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000725250676667 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105417459566 + + Density error is 1.42802742382e-05 + + Energy Rydberg eV + E_KohnSham -34.2792600274 -466.393259596 + E_Harris -34.2792600283 -466.393259608 + E_Fermi -0.162108044549 -2.2055930975 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000725257899826 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105417105544 + + Density error is 1.8698596473e-06 + + Energy Rydberg eV + E_KohnSham -34.279258784 -466.393242679 + E_Harris -34.279258784 -466.393242679 + E_Fermi -0.162093354641 -2.20539323105 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000725261028888 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105417353995 + + Density error is 4.16905903335e-07 + + Energy Rydberg eV + E_KohnSham -34.2792589892 -466.393245471 + E_Harris -34.2792589892 -466.393245471 + E_Fermi -0.16209201085 -2.20537494784 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000725261586543 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105417417673 + + Density error is 1.27331156376e-07 + + Energy Rydberg eV + E_KohnSham -34.2792590142 -466.393245811 + E_Harris -34.2792590142 -466.393245811 + E_Fermi -0.162091835358 -2.20537256015 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000725261709339 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105417423085 + + Density error is 1.15734478718e-08 + + Energy Rydberg eV + E_KohnSham -34.2792590178 -466.39324586 + E_Harris -34.2792590178 -466.39324586 + E_band -7.92393888048 -107.810719378 + E_one_elec -69.0118195359 -938.953975036 + E_Hartree +35.9078017002 +488.550705777 + E_xc -8.18855981921 -111.411071955 + E_Ewald +7.13821303447 +97.1203708066 + E_demet -9.38746405022e-69 -1.27723000853e-67 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194336300458 -2.64408101446 + E_Fermi -0.162091713747 -2.20537090555 + + charge density convergence is achieved + final etot is -466.39324586 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1662 2.00000 + 2 -12.9090 2.00000 + 3 -9.11397 2.00000 + 4 -6.71620 2.00000 + 5 1.15118 0.00000 + 6 4.23776 0.00000 + 7 11.1058 0.00000 + 8 11.3534 0.00000 + + EFERMI = -2.205370905548512 eV + OUT.ABACUS/ final etot is -466.3932458598335 eV + correction force for each atom along direction 1 is -8.86706e-05 + correction force for each atom along direction 2 is -0.000155463 + correction force for each atom along direction 3 is -0.000119474 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0693610 +0.59891874 -1.4167206 + H1 +0.42030780 -0.81446868 +0.17932435 + H2 +0.64905325 +0.21554994 +1.2373962 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3932458598335 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1890 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1797 1 7.2 1.e+02% + Potential init_pot 0.28560 2 0.14 4.0% + PW_Basis recip2real 0.28083 17 0.017 3.9% + PW_Basis gathers_scatterp 0.13019 17 0.0077 1.8% + Potential v_of_rho 0.92286 14 0.066 13.% + XC_Functional v_xc 0.26003 15 0.017 3.6% + H_Hartree_pw v_hartree 0.62492 14 0.045 8.7% + PW_Basis real2recip 0.61553 41 0.015 8.6% + PW_Basis gatherp_scatters 0.26031 41 0.0063 3.6% + ORB_control set_orb_tables 1.1219 1 1.1 16.% + ORB_gen_tables gen_tables 1.1219 1 1.1 16.% + ORB_table_phi init_Table 0.48612 1 0.49 6.8% + ORB_table_phi cal_ST_Phi12_R 0.48117 126 0.0038 6.7% + ORB_table_beta init_Table_Beta 0.19534 1 0.20 2.7% + ORB_table_beta VNL_PhiBeta_R 0.19383 56 0.0035 2.7% + ORB_table_alpha init_Table_Alpha 0.25980 1 0.26 3.6% + ORB_table_alpha S_PhiAlpha_R 0.25792 66 0.0039 3.6% + LOOP_ions opt_ions 5.5336 1 5.5 77.% + ESolver_KS_LCAO Run 4.9531 1 5.0 69.% + HSolverLCAO solve 2.8183 12 0.23 39.% + HamiltLCAO updateHk 1.4249 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3944 12 0.12 19.% + Gint_interface cal_gint 0.57887 25 0.023 8.1% + Gint_Gamma distri_vl_value 0.79306 12 0.066 11.% + Gint_Gamma distri_vl 2.5636 6 0.43 36.% + LCAO_Deepks cal_projected_DM 5.1332 14 0.37 71.% + LCAO_gen_fixedH add_v_delta 2.4344 6 0.41 34.% + LCAO_DESCRIPTOR add_v_delta 2.4345 6 0.41 34.% + ElecStateLCAO psiToRho 1.3728 12 0.11 19.% + Charge mix_rho 0.71518 11 0.065 9.9% + LOOP_ions force_stress 0.58038 1 0.58 8.1% + Force_Stress_LCAO getForceStress 0.58036 1 0.58 8.1% + Force_LCAO_gamma ftable_gamma 0.36878 1 0.37 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.13755 1 0.14 1.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:07 2022 + Finish Time : Wed Sep 28 11:06:14 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ae5b4f3aafa6244b756bda9adf211ef5c238e703 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123596 ima = 3.67955e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123280293783 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112150428379 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112780343159 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112997347376 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112967645745 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112985496241 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112979645011 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112982170369 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112981552606 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112981478063 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112981462614 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112981456173 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/STRU new file mode 100644 index 0000000000000000000000000000000000000000..17dbbfd01636b25aea78d56504716f699102d212 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-4.778396618410 27.169094698172 10.813828304986 0 0 0 +H +0.0 +2 +-3.970801185574 25.583356784324 11.151128099868 0 0 0 +-5.652804059909 26.886295741392 9.146933314994 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/conv new file mode 100644 index 0000000000000000000000000000000000000000..414e830178e05957ba247dc7fa0df20dd3b8da58 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/conv @@ -0,0 +1 @@ +291 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..bf3b757b492c115ad15cf60c141358b0d9764447 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749773626 0.01256364115 1.258049905 1.355198037 1.468807473 0.008510848889 0.01823974507 0.03906600188 +4.315570592e-18 0.0009788405739 0.002525675848 0.01198147684 0.04372856486 6.75332586e-19 1.852520275e-06 5.569877139e-06 +0.00162612251 0.005903482462 + +H atom_index 1 n_descriptor 18 +1.263523234 0.03382262918 0.1127522664 0.1565277112 0.325671363 0.02276118764 0.02911385256 0.03710502844 +1.385893251e-17 4.454745668e-05 0.1034953087 0.1159695332 0.1342790356 -5.512604956e-18 3.291758175e-06 0.01311392028 +0.02649186522 0.03135598271 + +H atom_index 2 n_descriptor 18 +1.190654963 0.0362490796 0.08909718791 0.124583429 0.300406855 0.01938530259 0.02485779341 0.0397362672 +-3.428271215e-17 3.813033769e-05 0.08501693879 0.1064499786 0.1130395225 -3.976557812e-18 6.497252153e-06 0.01440383822 +0.02363099584 0.02778997402 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..324741423ba5cb762efc91e34e1561824e94801a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:07 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0880819 SEC) : SETUP UNITCELL + DONE(0.0989357 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11714 SEC) : INIT PLANEWAVE + DONE(0.166345 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447546 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651850e+02 0.000000e+00 2.133e-01 5.275e-01 + GE2 -4.663901e+02 -1.205111e+00 9.824e-02 4.545e-01 + GE3 -4.663943e+02 -4.168662e-03 6.320e-02 5.105e-01 + GE4 -4.663936e+02 6.596272e-04 1.979e-03 4.007e-01 + GE5 -4.663930e+02 5.874190e-04 8.630e-04 4.008e-01 + GE6 -4.663933e+02 -3.168412e-04 1.614e-04 3.948e-01 + GE7 -4.663932e+02 1.074567e-04 3.428e-05 3.785e-01 + GE8 -4.663933e+02 -4.699544e-05 1.428e-05 3.782e-01 + GE9 -4.663932e+02 1.691762e-05 1.870e-06 3.786e-01 + GE10 -4.663932e+02 -2.792081e-06 4.169e-07 3.750e-01 + GE11 -4.663932e+02 -3.405225e-07 1.273e-07 3.775e-01 + GE12 -4.663932e+02 -4.848574e-08 1.157e-08 3.159e-01 +E_delta_band = -6.94419031e-02 Ry = -9.44805562e-01 eV +E_delta_NN= -1.94336300e-01 Ry = -2.64408101e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.189 11 0.65 1e+02 % + Run_lcao lcao_line 7.1797 1 7.2 1e+02 % + Potential init_pot 0.2856 2 0.14 4 % + PW_Basis recip2real 0.28083 17 0.017 3.9 % + PW_Basis gathers_scatterp 0.13019 17 0.0077 1.8 % + Potential v_of_rho 0.92286 14 0.066 13 % + XC_Functional v_xc 0.26003 15 0.017 3.6 % + H_Hartree_pw v_hartree 0.62492 14 0.045 8.7 % + PW_Basis real2recip 0.61553 41 0.015 8.6 % + PW_Basis gatherp_scatters 0.26031 41 0.0063 3.6 % + ORB_control set_orb_tables 1.1219 1 1.1 16 % + ORB_gen_tables gen_tables 1.1219 1 1.1 16 % + ORB_table_phi init_Table 0.48612 1 0.49 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.48117 126 0.0038 6.7 % + ORB_table_beta init_Table_Beta 0.19534 1 0.2 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.19383 56 0.0035 2.7 % + ORB_table_alpha init_Table_Alpha 0.2598 1 0.26 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.25792 66 0.0039 3.6 % + LOOP_ions opt_ions 5.5336 1 5.5 77 % + ESolver_KS_LCAO Run 4.9531 1 5 69 % + HSolverLCAO solve 2.8183 12 0.23 39 % + HamiltLCAO updateHk 1.4249 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3944 12 0.12 19 % + Gint_interface cal_gint 0.57887 25 0.023 8.1 % + Gint_Gamma distri_vl_value 0.79306 12 0.066 11 % + Gint_Gamma distri_vl 2.5636 6 0.43 36 % + LCAO_Deepks cal_projected_DM 5.1332 14 0.37 71 % + LCAO_gen_fixedH add_v_delta 2.4344 6 0.41 34 % + LCAO_DESCRIPTOR add_v_delta 2.4345 6 0.41 34 % + ElecStateLCAO psiToRho 1.3728 12 0.11 19 % + Charge mix_rho 0.71518 11 0.065 9.9 % + LOOP_ions force_stress 0.58038 1 0.58 8.1 % + Force_Stress_LCAO getForceStress 0.58036 1 0.58 8.1 % + Force_LCAO_gamma ftable_gamma 0.36878 1 0.37 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.13755 1 0.14 1.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:07 2022 + FINISH Time : Wed Sep 28 11:06:14 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/291/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..755995aa4a6b704b6dd7b5b15304d528c3aabc80 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.846562 0.958467 0.406706 +H 0.848447 0.918369 0.354538 +H 0.783411 0.974853 0.409804 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e1142acf37ded7d26c2d7c6262918e5d2d19fd48 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3062 2 + 2 -12.9597 2 + 3 -9.1942 2 + 4 -6.74949 2 + 5 1.28783 0 + 6 4.39351 0 + 7 11.0756 0 + 8 11.3355 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4caa13810091e51f9dcafacec43794a25f55220f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:44 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 23.703742279 26.8370670028 11.3877802557 0 0 0 0 + tauc_H1 23.7565144998 25.7143190014 9.9270767187 0 0 0 0 + tauc_H2 21.9354995962 27.2958825553 11.4745212012 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0872518261918 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0986570234972 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117027832758 (SEC) + + DONE : INIT CHARGE Time : 0.16673412221 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449944 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000796 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00181 + + Density error is 0.214573233665 + + Energy Rydberg eV + E_KohnSham -34.1910408598 -465.192976244 + E_Harris -34.3822789178 -467.794903508 + E_Fermi -0.405148561732 -5.51232897606 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011571351375 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00143726730723 + + Density error is 0.0980025917181 + + Energy Rydberg eV + E_KohnSham -34.2809980196 -466.416906194 + E_Harris -34.2878059113 -466.509532312 + E_Fermi -0.213625042674 -2.90651781586 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110774037316 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013179850746 + + Density error is 0.0628780288748 + + Energy Rydberg eV + E_KohnSham -34.2813455099 -466.421634042 + E_Harris -34.2857507178 -466.48156997 + E_Fermi -0.203153464199 -2.76404468155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104316896896 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110376339909 + + Density error is 0.00197098426671 + + Energy Rydberg eV + E_KohnSham -34.2813220848 -466.421315327 + E_Harris -34.2813231159 -466.421329355 + E_Fermi -0.167530016164 -2.27936280587 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104562542411 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110263071325 + + Density error is 0.000944254525213 + + Energy Rydberg eV + E_KohnSham -34.2812604132 -466.420476241 + E_Harris -34.281261672 -466.420493369 + E_Fermi -0.166925738832 -2.27114119097 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104433795972 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110002949661 + + Density error is 0.000132238287202 + + Energy Rydberg eV + E_KohnSham -34.2812977667 -466.420984462 + E_Harris -34.281297784 -466.420984697 + E_Fermi -0.166859816959 -2.27024427787 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010444041981 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109980477546 + + Density error is 3.67394350038e-05 + + Energy Rydberg eV + E_KohnSham -34.2812852815 -466.420814592 + E_Harris -34.2812852887 -466.42081469 + E_Fermi -0.166750885304 -2.26876218667 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104433206664 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109981930199 + + Density error is 1.65589505733e-05 + + Energy Rydberg eV + E_KohnSham -34.2812885738 -466.420859386 + E_Harris -34.281288575 -466.420859402 + E_Fermi -0.166791592802 -2.2693160406 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104433916405 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109979302582 + + Density error is 2.53513956893e-06 + + Energy Rydberg eV + E_KohnSham -34.2812871606 -466.420840159 + E_Harris -34.2812871606 -466.420840159 + E_Fermi -0.166775376867 -2.26909541148 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104433835421 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109978438054 + + Density error is 3.16087007876e-07 + + Energy Rydberg eV + E_KohnSham -34.2812873948 -466.420843345 + E_Harris -34.2812873948 -466.420843345 + E_Fermi -0.166772725664 -2.26905934002 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104433921488 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109978470916 + + Density error is 1.16279334217e-07 + + Energy Rydberg eV + E_KohnSham -34.2812874327 -466.42084386 + E_Harris -34.2812874327 -466.42084386 + E_Fermi -0.166772632989 -2.26905807912 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00104433943485 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109978448001 + + Density error is 1.05072804818e-08 + + Energy Rydberg eV + E_KohnSham -34.2812874354 -466.420843898 + E_Harris -34.2812874354 -466.420843898 + E_band -7.96864923643 -108.419034979 + E_one_elec -69.2712406675 -942.483580607 + E_Hartree +36.0277331015 +490.182456204 + E_xc -8.20762914131 -111.670523393 + E_Ewald +7.29420924714 +99.2428081654 + E_demet -7.0664801702e-77 -9.61443951188e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194782624493 -2.6501535645 + E_Fermi -0.166772537148 -2.26905677513 + + charge density convergence is achieved + final etot is -466.420843898 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3062 2.00000 + 2 -12.9597 2.00000 + 3 -9.19420 2.00000 + 4 -6.74949 2.00000 + 5 1.28783 0.00000 + 6 4.39351 0.00000 + 7 11.0756 0.00000 + 8 11.3355 0.00000 + + EFERMI = -2.269056775129038 eV + OUT.ABACUS/ final etot is -466.4208438976997 eV + correction force for each atom along direction 1 is -0.000151725 + correction force for each atom along direction 2 is 6.12860e-05 + correction force for each atom along direction 3 is -7.82284e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.26325813 -0.13515374 -0.10681801 + H1 +0.13444432 -0.049080441 -0.022019389 + H2 -0.39770246 +0.18423418 +0.12883740 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4208438976997 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.1322 11 0.74 1.0e+02% + Run_lcao lcao_line 8.1230 1 8.1 1.e+02% + Potential init_pot 0.28691 2 0.14 3.5% + PW_Basis recip2real 0.28370 17 0.017 3.5% + PW_Basis gathers_scatterp 0.13268 17 0.0078 1.6% + Potential v_of_rho 1.1080 14 0.079 14.% + XC_Functional v_xc 0.38275 15 0.026 4.7% + H_Hartree_pw v_hartree 0.68487 14 0.049 8.4% + PW_Basis real2recip 0.71449 41 0.017 8.8% + PW_Basis gatherp_scatters 0.31659 41 0.0077 3.9% + ORB_control set_orb_tables 1.1115 1 1.1 14.% + ORB_gen_tables gen_tables 1.1115 1 1.1 14.% + ORB_table_phi init_Table 0.48337 1 0.48 5.9% + ORB_table_phi cal_ST_Phi12_R 0.47819 126 0.0038 5.9% + ORB_table_beta init_Table_Beta 0.18744 1 0.19 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18588 56 0.0033 2.3% + ORB_table_alpha init_Table_Alpha 0.25339 1 0.25 3.1% + ORB_table_alpha S_PhiAlpha_R 0.25142 66 0.0038 3.1% + LOOP_ions opt_ions 6.4831 1 6.5 80.% + ESolver_KS_LCAO Run 5.8795 1 5.9 72.% + HSolverLCAO solve 3.4123 12 0.28 42.% + HamiltLCAO updateHk 1.6869 12 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.6573 12 0.14 20.% + Gint_interface cal_gint 0.45875 25 0.018 5.6% + Gint_Gamma distri_vl_value 1.0541 12 0.088 13.% + Gint_Gamma distri_vl 3.0540 6 0.51 38.% + LCAO_Deepks cal_projected_DM 6.0415 14 0.43 74.% + LCAO_gen_fixedH add_v_delta 2.9254 6 0.49 36.% + LCAO_DESCRIPTOR add_v_delta 2.9255 6 0.49 36.% + ElecStateLCAO psiToRho 1.6830 12 0.14 21.% + Charge mix_rho 0.78458 11 0.071 9.6% + LOOP_ions force_stress 0.60341 1 0.60 7.4% + Force_Stress_LCAO getForceStress 0.60338 1 0.60 7.4% + Force_LCAO_gamma ftable_gamma 0.38934 1 0.39 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.12584 1 0.13 1.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:44 2022 + Finish Time : Wed Sep 28 11:02:52 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..43e19e5137a522d4efe0144a5eb8d1d286b00cc2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123731 ima = 3.71453e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123062266502 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111889921436 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112480553084 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112734321742 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112682769969 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112712185541 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112706898503 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112709740141 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011270902346 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112708921496 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112708908959 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112708903949 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9fd4a1e2d6a95ce76ac2a2dc83d32f63f55876a8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-4.296257721015 26.837067002772 11.387780255736 0 0 0 +H +0.0 +2 +-4.243485500247 25.714319001460 9.927076718718 0 0 0 +-6.064500403788 27.295882555274 11.474521201212 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/conv new file mode 100644 index 0000000000000000000000000000000000000000..0de0662295082793ceeb04cd06c0e488bc2af007 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/conv @@ -0,0 +1 @@ +292 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..455a47a288f50ca8ef93b39227415dfbb7b71043 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750488731 0.01270916475 1.271848485 1.358466835 1.469356014 0.008717175022 0.01807233266 0.03906217621 +3.276322932e-18 0.001014100108 0.00264907493 0.01254332283 0.04543552435 -6.038994321e-19 2.192250539e-06 6.215252305e-06 +0.001627478694 0.00601783491 + +H atom_index 1 n_descriptor 18 +1.239073507 0.03477036786 0.1049662597 0.1448245088 0.317116892 0.02190637567 0.02765182501 0.0379051606 +-2.482984584e-17 4.578239242e-05 0.09904337576 0.1146314906 0.1242580577 -1.098151063e-18 4.533835897e-06 0.01334191634 +0.02599550117 0.03024816812 + +H atom_index 2 n_descriptor 18 +1.250337827 0.03438363651 0.1088254602 0.1499854045 0.3208318771 0.02243721881 0.02830925017 0.03753438236 +2.497461638e-17 4.683312545e-05 0.1018254876 0.1151216325 0.1287243416 -2.851832247e-18 3.926343654e-06 0.01322428314 +0.02641960264 0.03077044313 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..18e3a5c5ac3be7a2ac628e3f51ef95eaf6733be3 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:44 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872768 SEC) : SETUP UNITCELL + DONE(0.0986756 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11705 SEC) : INIT PLANEWAVE + DONE(0.166869 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450006 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651930e+02 0.000000e+00 2.146e-01 5.923e-01 + GE2 -4.664169e+02 -1.223930e+00 9.800e-02 5.438e-01 + GE3 -4.664216e+02 -4.727848e-03 6.288e-02 6.116e-01 + GE4 -4.664213e+02 3.187146e-04 1.971e-03 4.752e-01 + GE5 -4.664205e+02 8.390857e-04 9.443e-04 4.757e-01 + GE6 -4.664210e+02 -5.082204e-04 1.322e-04 4.663e-01 + GE7 -4.664208e+02 1.698694e-04 3.674e-05 4.608e-01 + GE8 -4.664209e+02 -4.479352e-05 1.656e-05 4.562e-01 + GE9 -4.664208e+02 1.922714e-05 2.535e-06 4.536e-01 + GE10 -4.664208e+02 -3.185993e-06 3.161e-07 4.511e-01 + GE11 -4.664208e+02 -5.152322e-07 1.163e-07 4.488e-01 + GE12 -4.664208e+02 -3.771922e-08 1.051e-08 3.782e-01 +E_delta_band = -7.04226492e-02 Ry = -9.58149297e-01 eV +E_delta_NN= -1.94782624e-01 Ry = -2.65015356e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.1322 11 0.74 1e+02 % + Run_lcao lcao_line 8.123 1 8.1 1e+02 % + Potential init_pot 0.28691 2 0.14 3.5 % + PW_Basis recip2real 0.2837 17 0.017 3.5 % + PW_Basis gathers_scatterp 0.13268 17 0.0078 1.6 % + Potential v_of_rho 1.108 14 0.079 14 % + XC_Functional v_xc 0.38275 15 0.026 4.7 % + H_Hartree_pw v_hartree 0.68487 14 0.049 8.4 % + PW_Basis real2recip 0.71449 41 0.017 8.8 % + PW_Basis gatherp_scatters 0.31659 41 0.0077 3.9 % + ORB_control set_orb_tables 1.1115 1 1.1 14 % + ORB_gen_tables gen_tables 1.1115 1 1.1 14 % + ORB_table_phi init_Table 0.48337 1 0.48 5.9 % + ORB_table_phi cal_ST_Phi12_R 0.47819 126 0.0038 5.9 % + ORB_table_beta init_Table_Beta 0.18744 1 0.19 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.18588 56 0.0033 2.3 % + ORB_table_alpha init_Table_Alpha 0.25339 1 0.25 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.25142 66 0.0038 3.1 % + LOOP_ions opt_ions 6.4831 1 6.5 80 % + ESolver_KS_LCAO Run 5.8795 1 5.9 72 % + HSolverLCAO solve 3.4123 12 0.28 42 % + HamiltLCAO updateHk 1.6869 12 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.6573 12 0.14 20 % + Gint_interface cal_gint 0.45875 25 0.018 5.6 % + Gint_Gamma distri_vl_value 1.0541 12 0.088 13 % + Gint_Gamma distri_vl 3.054 6 0.51 38 % + LCAO_Deepks cal_projected_DM 6.0415 14 0.43 74 % + LCAO_gen_fixedH add_v_delta 2.9254 6 0.49 36 % + LCAO_DESCRIPTOR add_v_delta 2.9255 6 0.49 36 % + ElecStateLCAO psiToRho 1.683 12 0.14 21 % + Charge mix_rho 0.78458 11 0.071 9.6 % + LOOP_ions force_stress 0.60341 1 0.6 7.4 % + Force_Stress_LCAO getForceStress 0.60338 1 0.6 7.4 % + Force_LCAO_gamma ftable_gamma 0.38934 1 0.39 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.12584 1 0.13 1.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:44 2022 + FINISH Time : Wed Sep 28 11:02:52 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/292/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..58fb25ad88f73bed1a949474b0c5dc636f182128 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.835535 0.957095 0.435433 +H 0.818927 0.955231 0.370576 +H 0.781922 0.945196 0.469721 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..45119037009ad606f07be48c0908d8f7244646e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1625 2 + 2 -13.1567 2 + 3 -8.93002 2 + 4 -6.71306 2 + 5 1.24528 0 + 6 4.3641 0 + 7 11.0963 0 + 8 11.3285 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..739d2c8522133b214fa1a5f749af0128462ba6d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:55 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 23.3949913269 26.7986536224 12.192119681 0 0 0 0 + tauc_H1 22.9299443116 26.7464714404 10.3761401528 0 0 0 0 + tauc_H2 21.8938046798 26.4654835828 13.1521829636 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0742920031827 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0871160223007 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103000821573 (SEC) + + DONE : INIT CHARGE Time : 0.145371525135 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.387363 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 +receiver_size is 324 ; receiver_size of each process is: +81 81 81 81 +sender_size is 369 ; sender_size of each process is: +81 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000879 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000754 + + Density error is 0.215618095624 + + Energy Rydberg eV + E_KohnSham -34.1885572929 -465.159185583 + E_Harris -34.3816785563 -467.78673517 + E_Fermi -0.402090330786 -5.4707196094 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00129498635734 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00119041993433 + + Density error is 0.0985467373383 + + Energy Rydberg eV + E_KohnSham -34.2795892461 -466.397738846 + E_Harris -34.2864177117 -466.490644888 + E_Fermi -0.208955091543 -2.8429798711 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00124448133595 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115112158257 + + Density error is 0.0633685399566 + + Energy Rydberg eV + E_KohnSham -34.2799905526 -466.403198902 + E_Harris -34.2843847893 -466.462985559 + E_Fermi -0.19932225298 -2.71191837873 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118120184151 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00110887061723 + + Density error is 0.00205382120071 + + Energy Rydberg eV + E_KohnSham -34.2799565773 -466.402736643 + E_Harris -34.279959646 -466.402778395 + E_Fermi -0.163957415734 -2.23075508333 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118329709127 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00110925145039 + + Density error is 0.000961252370682 + + Energy Rydberg eV + E_KohnSham -34.2798989193 -466.401952167 + E_Harris -34.2798995325 -466.40196051 + E_Fermi -0.163378409165 -2.22287729482 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118219123143 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00110850621584 + + Density error is 0.000192689005726 + + Energy Rydberg eV + E_KohnSham -34.2799300012 -466.402375057 + E_Harris -34.27993022 -466.402378034 + E_Fermi -0.163234278338 -2.22091629432 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118250912728 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00110891224159 + + Density error is 3.81190531547e-05 + + Energy Rydberg eV + E_KohnSham -34.2799182938 -466.40221577 + E_Harris -34.279918301 -466.402215867 + E_Fermi -0.163117955843 -2.21933364558 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118242735491 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00110878496044 + + Density error is 1.83387606938e-05 + + Energy Rydberg eV + E_KohnSham -34.2799230162 -466.402280022 + E_Harris -34.2799230175 -466.40228004 + E_Fermi -0.1631572015 -2.21986761014 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118243075626 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00110879125051 + + Density error is 2.95377327983e-06 + + Energy Rydberg eV + E_KohnSham -34.2799215733 -466.40226039 + E_Harris -34.2799215733 -466.40226039 + E_Fermi -0.163139442809 -2.21962599075 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011824269359 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00110879401639 + + Density error is 5.2985409161e-07 + + Energy Rydberg eV + E_KohnSham -34.2799218091 -466.402263598 + E_Harris -34.2799218091 -466.402263598 + E_Fermi -0.16313647733 -2.21958564334 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118242804282 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00110879485164 + + Density error is 1.79053774545e-07 + + Energy Rydberg eV + E_KohnSham -34.279921844 -466.402264073 + E_Harris -34.279921844 -466.402264073 + E_Fermi -0.163136232879 -2.21958231741 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00118242831032 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00110879508692 + + Density error is 1.01682667718e-08 + + Energy Rydberg eV + E_KohnSham -34.2799218479 -466.402264126 + E_Harris -34.2799218479 -466.402264126 + E_band -7.9323061725 -107.924562227 + E_one_elec -69.1505467635 -940.841455798 + E_Hartree +35.9804722564 +489.539439418 + E_xc -8.19991125383 -111.565516146 + E_Ewald +7.21471623916 +98.1612503057 + E_demet -4.35922281675e-73 -5.93102691595e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194478133494 -2.64601075192 + E_Fermi -0.163136059613 -2.21957996 + + charge density convergence is achieved + final etot is -466.402264126 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1625 2.00000 + 2 -13.1567 2.00000 + 3 -8.93002 2.00000 + 4 -6.71306 2.00000 + 5 1.24528 0.00000 + 6 4.36410 0.00000 + 7 11.0963 0.00000 + 8 11.3285 0.00000 + + EFERMI = -2.219579959998820 eV + OUT.ABACUS/ final etot is -466.4022641257483 eV + correction force for each atom along direction 1 is -5.54066e-05 + correction force for each atom along direction 2 is -2.59823e-05 + correction force for each atom along direction 3 is -2.38060e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.80531656 +0.19259892 -1.1133616 + H1 -0.020877898 -0.026270671 +0.92424822 + H2 -0.78443867 -0.16632825 +0.18911338 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4022641257483 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4079 11 0.67 1.0e+02% + Run_lcao lcao_line 7.4009 1 7.4 1.e+02% + Potential init_pot 0.24039 2 0.12 3.2% + PW_Basis recip2real 0.23370 17 0.014 3.2% + PW_Basis gathers_scatterp 0.11025 17 0.0065 1.5% + Potential v_of_rho 1.0228 14 0.073 14.% + XC_Functional v_xc 0.38914 15 0.026 5.3% + H_Hartree_pw v_hartree 0.60282 14 0.043 8.1% + PW_Basis real2recip 0.66155 41 0.016 8.9% + PW_Basis gatherp_scatters 0.29166 41 0.0071 3.9% + ORB_control set_orb_tables 0.89344 1 0.89 12.% + ORB_gen_tables gen_tables 0.89343 1 0.89 12.% + ORB_table_phi init_Table 0.37432 1 0.37 5.1% + ORB_table_phi cal_ST_Phi12_R 0.37014 126 0.0029 5.0% + ORB_table_beta init_Table_Beta 0.15276 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15149 56 0.0027 2.0% + ORB_table_alpha init_Table_Alpha 0.20740 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20572 66 0.0031 2.8% + LOOP_ions opt_ions 6.0503 1 6.1 82.% + ESolver_KS_LCAO Run 5.5118 1 5.5 74.% + HSolverLCAO solve 3.1702 12 0.26 43.% + HamiltLCAO updateHk 1.5696 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.5442 12 0.13 21.% + Gint_interface cal_gint 0.26949 25 0.011 3.6% + Gint_Gamma distri_vl_value 1.0468 12 0.087 14.% + Gint_Gamma distri_vl 2.8561 6 0.48 39.% + LCAO_Deepks cal_projected_DM 5.6288 14 0.40 76.% + LCAO_gen_fixedH add_v_delta 2.7387 6 0.46 37.% + LCAO_DESCRIPTOR add_v_delta 2.7389 6 0.46 37.% + ElecStateLCAO psiToRho 1.5721 12 0.13 21.% + Charge mix_rho 0.74169 11 0.067 10.% + LOOP_ions force_stress 0.53828 1 0.54 7.3% + Force_Stress_LCAO getForceStress 0.53826 1 0.54 7.3% + Force_LCAO_gamma ftable_gamma 0.34662 1 0.35 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:55 2022 + Finish Time : Wed Sep 28 11:02:03 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4daf49927476004b66d1c4de8fedd33d5147fe85 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123698 ima = 3.70735e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012366922505 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112418173543 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113026109233 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113263884795 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113222073122 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113247246271 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113238825318 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113241736381 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113241005161 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113240900519 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113240881533 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113240872631 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/STRU new file mode 100644 index 0000000000000000000000000000000000000000..132f037f406516861ddba5c80839384fef6dd2f0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-4.605008673112 26.798653622376 12.192119681011 0 0 0 +H +0.0 +2 +-5.070055688406 26.746471440433 10.376140152850 0 0 0 +-6.106195320245 26.465483582809 13.152182963624 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/conv new file mode 100644 index 0000000000000000000000000000000000000000..fd979112c845089ee244aa8f2eaff2e0248cc1f4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/conv @@ -0,0 +1 @@ +293 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..387e812f663d850545381e15aff04774cb4de4b1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74626942 0.01257040725 1.268312003 1.363939378 1.468769093 0.007968089479 0.01948382699 0.0389413363 +-3.093660421e-18 0.001076668399 0.002416353643 0.01203986963 0.04293102584 -2.197524958e-19 1.603409458e-06 5.011777901e-06 +0.001714223559 0.005753066507 + +H atom_index 1 n_descriptor 18 +1.209155252 0.03531245762 0.09465499332 0.1328682607 0.308762325 0.02003844082 0.02605492022 0.03859476512 +-1.015706123e-17 3.682863678e-05 0.09031039567 0.1137906454 0.1138043187 2.585447649e-18 5.880529115e-06 0.01366487262 +0.02436446067 0.02886450219 + +H atom_index 2 n_descriptor 18 +1.258912383 0.0335863461 0.1110266039 0.1550519529 0.3252668483 0.02226348372 0.02894387469 0.03685816458 +1.027703254e-17 4.098570446e-05 0.1031289356 0.1154141656 0.1330765584 -2.333540324e-19 3.727800715e-06 0.01296055855 +0.02627943586 0.03121713627 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e2beaa1e764d041e5ef271d64b8ee9db7d568d08 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:55 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0743077 SEC) : SETUP UNITCELL + DONE(0.0871281 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103016 SEC) : INIT PLANEWAVE + DONE(0.14547 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.387405 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651592e+02 0.000000e+00 2.156e-01 5.331e-01 + GE2 -4.663977e+02 -1.238553e+00 9.855e-02 5.085e-01 + GE3 -4.664032e+02 -5.460055e-03 6.337e-02 5.700e-01 + GE4 -4.664027e+02 4.622585e-04 2.054e-03 4.471e-01 + GE5 -4.664020e+02 7.844764e-04 9.613e-04 4.450e-01 + GE6 -4.664024e+02 -4.228903e-04 1.927e-04 4.433e-01 + GE7 -4.664022e+02 1.592875e-04 3.812e-05 4.333e-01 + GE8 -4.664023e+02 -6.425192e-05 1.834e-05 4.301e-01 + GE9 -4.664023e+02 1.963167e-05 2.954e-06 4.302e-01 + GE10 -4.664023e+02 -3.208290e-06 5.299e-07 4.311e-01 + GE11 -4.664023e+02 -4.750203e-07 1.791e-07 4.322e-01 + GE12 -4.664023e+02 -5.249859e-08 1.017e-08 3.482e-01 +E_delta_band = -6.98258073e-02 Ry = -9.50028847e-01 eV +E_delta_NN= -1.94478133e-01 Ry = -2.64601075e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4079 11 0.67 1e+02 % + Run_lcao lcao_line 7.4009 1 7.4 1e+02 % + Potential init_pot 0.24039 2 0.12 3.2 % + PW_Basis recip2real 0.2337 17 0.014 3.2 % + PW_Basis gathers_scatterp 0.11025 17 0.0065 1.5 % + Potential v_of_rho 1.0228 14 0.073 14 % + XC_Functional v_xc 0.38914 15 0.026 5.3 % + H_Hartree_pw v_hartree 0.60282 14 0.043 8.1 % + PW_Basis real2recip 0.66155 41 0.016 8.9 % + PW_Basis gatherp_scatters 0.29166 41 0.0071 3.9 % + ORB_control set_orb_tables 0.89344 1 0.89 12 % + ORB_gen_tables gen_tables 0.89343 1 0.89 12 % + ORB_table_phi init_Table 0.37432 1 0.37 5.1 % + ORB_table_phi cal_ST_Phi12_R 0.37014 126 0.0029 5 % + ORB_table_beta init_Table_Beta 0.15276 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15149 56 0.0027 2 % + ORB_table_alpha init_Table_Alpha 0.2074 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20572 66 0.0031 2.8 % + LOOP_ions opt_ions 6.0503 1 6.1 82 % + ESolver_KS_LCAO Run 5.5118 1 5.5 74 % + HSolverLCAO solve 3.1702 12 0.26 43 % + HamiltLCAO updateHk 1.5696 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.5442 12 0.13 21 % + Gint_interface cal_gint 0.26949 25 0.011 3.6 % + Gint_Gamma distri_vl_value 1.0468 12 0.087 14 % + Gint_Gamma distri_vl 2.8561 6 0.48 39 % + LCAO_Deepks cal_projected_DM 5.6288 14 0.4 76 % + LCAO_gen_fixedH add_v_delta 2.7387 6 0.46 37 % + LCAO_DESCRIPTOR add_v_delta 2.7389 6 0.46 37 % + ElecStateLCAO psiToRho 1.5721 12 0.13 21 % + Charge mix_rho 0.74169 11 0.067 10 % + LOOP_ions force_stress 0.53828 1 0.54 7.3 % + Force_Stress_LCAO getForceStress 0.53826 1 0.54 7.3 % + Force_LCAO_gamma ftable_gamma 0.34662 1 0.35 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:55 2022 + FINISH Time : Wed Sep 28 11:02:03 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/293/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..553afa0676a079bdfa098512eb5a2823e0f0444c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.834976 0.964358 0.465567 +H 0.83235 0.986479 0.404357 +H 0.769939 0.960404 0.479977 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0eb9f4aa945532a74ef70358fb378d5124cfd02b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.289 2 + 2 -12.8086 2 + 3 -9.28901 2 + 4 -6.74618 2 + 5 1.21826 0 + 6 4.29807 0 + 7 11.0864 0 + 8 11.3545 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b0de477273276d3d25135fa074d9bf471baa9126 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:50 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 23.3793140078 27.0020176501 13.0358696547 0 0 0 0 + tauc_H1 23.3058119605 27.6214022002 11.3219842413 0 0 0 0 + tauc_H2 21.5582790325 26.8913098744 13.4393528598 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0740052284911 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0742931118861 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0899749502081 (SEC) + + DONE : INIT CHARGE Time : 0.131282583656 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.376594 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 +receiver_size is 324 ; receiver_size of each process is: +81 81 81 81 +sender_size is 369 ; sender_size of each process is: +81 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000755 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000955 + + Density error is 0.214042939932 + + Energy Rydberg eV + E_KohnSham -34.1896045232 -465.173433882 + E_Harris -34.3799626498 -467.763389064 + E_Fermi -0.40235892758 -5.47437405626 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00119959041081 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00132616613706 + + Density error is 0.0982051727979 + + Energy Rydberg eV + E_KohnSham -34.2800505196 -466.404014795 + E_Harris -34.2869967922 -466.498523681 + E_Fermi -0.210860987017 -2.86891090933 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115371317082 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00126659116683 + + Density error is 0.0632271571076 + + Energy Rydberg eV + E_KohnSham -34.2804946915 -466.410058063 + E_Harris -34.2849825191 -466.47111809 + E_Fermi -0.201772199624 -2.74525161288 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110532592928 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00118817249208 + + Density error is 0.00194084155703 + + Energy Rydberg eV + E_KohnSham -34.2804477273 -466.409419083 + E_Harris -34.2804481881 -466.409425353 + E_Fermi -0.166069858532 -2.25949634209 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110814588466 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00119070430233 + + Density error is 0.00102132652203 + + Energy Rydberg eV + E_KohnSham -34.2803856307 -466.408574215 + E_Harris -34.2803868224 -466.408590429 + E_Fermi -0.165681590062 -2.25421367855 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110700458208 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00118925568137 + + Density error is 0.000115054305665 + + Energy Rydberg eV + E_KohnSham -34.2804201699 -466.409044145 + E_Harris -34.280420175 -466.409044214 + E_Fermi -0.165500355435 -2.25174785495 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110709297423 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0011893271988 + + Density error is 3.5843892156e-05 + + Energy Rydberg eV + E_KohnSham -34.2804095468 -466.40889961 + E_Harris -34.2804095538 -466.408899705 + E_Fermi -0.165403162129 -2.25042547217 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011069957182 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00118924307967 + + Density error is 1.37263808681e-05 + + Energy Rydberg eV + E_KohnSham -34.2804121705 -466.408935307 + E_Harris -34.2804121713 -466.408935319 + E_Fermi -0.165441282873 -2.2509441315 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110700258213 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00118924136369 + + Density error is 1.12793977672e-06 + + Energy Rydberg eV + E_KohnSham -34.2804108457 -466.408917282 + E_Harris -34.2804108457 -466.408917282 + E_Fermi -0.165425822484 -2.25073378211 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110700466565 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00118924227546 + + Density error is 2.11124862259e-07 + + Energy Rydberg eV + E_KohnSham -34.2804110822 -466.408920501 + E_Harris -34.2804110822 -466.408920501 + E_Fermi -0.165425414531 -2.25072823164 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011070053879 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00118924311071 + + Density error is 3.16074461774e-08 + + Energy Rydberg eV + E_KohnSham -34.2804110917 -466.40892063 + E_Harris -34.2804110917 -466.40892063 + E_band -7.95736477329 -108.265501981 + E_one_elec -69.1580344125 -940.94333049 + E_Hartree +35.9707244581 +489.406813818 + E_xc -8.19846592779 -111.545851477 + E_Ewald +7.22994548232 +98.3684547889 + E_demet -2.9612554189e-73 -4.02899469305e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194607862312 -2.64777580304 + E_Fermi -0.165425343544 -2.2507272658 + + charge density convergence is achieved + final etot is -466.40892063 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2890 2.00000 + 2 -12.8086 2.00000 + 3 -9.28901 2.00000 + 4 -6.74618 2.00000 + 5 1.21826 0.00000 + 6 4.29807 0.00000 + 7 11.0864 0.00000 + 8 11.3545 0.00000 + + EFERMI = -2.250727265804075 eV + OUT.ABACUS/ final etot is -466.4089206299009 eV + correction force for each atom along direction 1 is -4.46598e-05 + correction force for each atom along direction 2 is -1.32898e-05 + correction force for each atom along direction 3 is -5.16135e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.82926925 -0.15958079 +0.48166794 + H1 +0.25217686 +0.21848969 -0.61654623 + H2 +0.57709239 -0.058908899 +0.13487828 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4089206299009 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8436 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8365 1 6.8 1.e+02% + Potential init_pot 0.24554 2 0.12 3.6% + PW_Basis recip2real 0.22411 16 0.014 3.3% + PW_Basis gathers_scatterp 0.10755 16 0.0067 1.6% + Potential v_of_rho 0.95506 13 0.073 14.% + XC_Functional v_xc 0.36814 14 0.026 5.4% + H_Hartree_pw v_hartree 0.55801 13 0.043 8.2% + PW_Basis real2recip 0.60637 38 0.016 8.9% + PW_Basis gatherp_scatters 0.27562 38 0.0073 4.0% + ORB_control set_orb_tables 0.90579 1 0.91 13.% + ORB_gen_tables gen_tables 0.90579 1 0.91 13.% + ORB_table_phi init_Table 0.38252 1 0.38 5.6% + ORB_table_phi cal_ST_Phi12_R 0.37824 126 0.0030 5.5% + ORB_table_beta init_Table_Beta 0.15603 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15467 56 0.0028 2.3% + ORB_table_alpha init_Table_Alpha 0.20935 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20777 66 0.0031 3.0% + LOOP_ions opt_ions 5.4845 1 5.5 80.% + ESolver_KS_LCAO Run 4.9416 1 4.9 72.% + HSolverLCAO solve 2.7712 11 0.25 40.% + HamiltLCAO updateHk 1.3941 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3702 11 0.12 20.% + Gint_interface cal_gint 0.12115 23 0.0053 1.8% + Gint_Gamma distri_vl_value 0.93881 11 0.085 14.% + Gint_Gamma distri_vl 2.3698 6 0.39 35.% + LCAO_Deepks cal_projected_DM 5.0571 13 0.39 74.% + LCAO_gen_fixedH add_v_delta 2.2505 6 0.38 33.% + LCAO_DESCRIPTOR add_v_delta 2.2507 6 0.38 33.% + ElecStateLCAO psiToRho 1.3508 11 0.12 20.% + Charge mix_rho 0.67021 10 0.067 9.8% + LOOP_ions force_stress 0.54280 1 0.54 7.9% + Force_Stress_LCAO getForceStress 0.54278 1 0.54 7.9% + Force_LCAO_gamma ftable_gamma 0.34485 1 0.34 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:50 2022 + Finish Time : Wed Sep 28 11:02:57 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..180322a24148b40ba775eddb731d508b918a4c4d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123993 ima = 3.71883e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123040725463 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111592678498 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112267907897 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112523235975 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112473554086 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112500568198 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112496611694 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112499342151 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112498698259 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112498667787 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112498655644 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/STRU new file mode 100644 index 0000000000000000000000000000000000000000..eee3fe1db792dfe5857236a6a62db3b3275755ab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-4.620685992220 27.002017650114 13.035869654717 0 0 0 +H +0.0 +2 +-4.694188039544 27.621402200197 11.321984241316 0 0 0 +-6.441720967488 26.891309874361 13.439352859765 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/conv new file mode 100644 index 0000000000000000000000000000000000000000..a1503f6aa707bed56a5979f51f7c3d2ccd9fe983 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/conv @@ -0,0 +1 @@ +294 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..907685846357246d3eb6cd7c2603ec1ecd1c0556 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752196907 0.01269649426 1.265385529 1.352143696 1.46925229 0.009008482844 0.01739030042 0.03911845321 +-1.510861518e-18 0.0009426678335 0.002691635733 0.01260726433 0.04541605384 7.198787435e-20 2.331091345e-06 6.509583718e-06 +0.001599007761 0.006066801563 + +H atom_index 1 n_descriptor 18 +1.255701547 0.03441124025 0.1113592473 0.1523482182 0.3221893153 0.02293039776 0.02859550178 0.03758039509 +-1.327738464e-17 4.786720727e-05 0.1028652515 0.1156504302 0.1306813454 -5.788450879e-18 3.315135383e-06 0.01326305415 +0.02668643462 0.03099408688 + +H atom_index 2 n_descriptor 18 +1.220541787 0.03559604443 0.09944393496 0.1364888344 0.3102026609 0.02123941336 0.02653408108 0.03879941007 +-7.484378619e-18 4.458940859e-05 0.09412242003 0.1140785744 0.1169198251 3.265126789e-18 5.161146978e-06 0.01375618558 +0.02533525521 0.02931434107 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..87dc6536ded28e9fbb51c617682100d84b12769a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:50 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0740201 SEC) : SETUP UNITCELL + DONE(0.074302 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0899894 SEC) : INIT PLANEWAVE + DONE(0.131384 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.376638 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651734e+02 0.000000e+00 2.140e-01 5.256e-01 + GE2 -4.664040e+02 -1.230581e+00 9.821e-02 4.975e-01 + GE3 -4.664101e+02 -6.043269e-03 6.323e-02 5.580e-01 + GE4 -4.664094e+02 6.389804e-04 1.941e-03 4.328e-01 + GE5 -4.664086e+02 8.448675e-04 1.021e-03 4.344e-01 + GE6 -4.664090e+02 -4.699299e-04 1.151e-04 4.318e-01 + GE7 -4.664089e+02 1.445355e-04 3.584e-05 4.196e-01 + GE8 -4.664089e+02 -3.569742e-05 1.373e-05 4.147e-01 + GE9 -4.664089e+02 1.802497e-05 1.128e-06 4.160e-01 + GE10 -4.664089e+02 -3.218360e-06 2.111e-07 4.137e-01 + GE11 -4.664089e+02 -1.292562e-07 3.161e-08 3.369e-01 +E_delta_band = -7.00271705e-02 Ry = -9.52768533e-01 eV +E_delta_NN= -1.94607862e-01 Ry = -2.64777580e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8436 11 0.62 1e+02 % + Run_lcao lcao_line 6.8365 1 6.8 1e+02 % + Potential init_pot 0.24554 2 0.12 3.6 % + PW_Basis recip2real 0.22411 16 0.014 3.3 % + PW_Basis gathers_scatterp 0.10755 16 0.0067 1.6 % + Potential v_of_rho 0.95506 13 0.073 14 % + XC_Functional v_xc 0.36814 14 0.026 5.4 % + H_Hartree_pw v_hartree 0.55801 13 0.043 8.2 % + PW_Basis real2recip 0.60637 38 0.016 8.9 % + PW_Basis gatherp_scatters 0.27562 38 0.0073 4 % + ORB_control set_orb_tables 0.90579 1 0.91 13 % + ORB_gen_tables gen_tables 0.90579 1 0.91 13 % + ORB_table_phi init_Table 0.38252 1 0.38 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.37824 126 0.003 5.5 % + ORB_table_beta init_Table_Beta 0.15603 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15467 56 0.0028 2.3 % + ORB_table_alpha init_Table_Alpha 0.20935 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20777 66 0.0031 3 % + LOOP_ions opt_ions 5.4845 1 5.5 80 % + ESolver_KS_LCAO Run 4.9416 1 4.9 72 % + HSolverLCAO solve 2.7712 11 0.25 40 % + HamiltLCAO updateHk 1.3941 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3702 11 0.12 20 % + Gint_interface cal_gint 0.12115 23 0.0053 1.8 % + Gint_Gamma distri_vl_value 0.93881 11 0.085 14 % + Gint_Gamma distri_vl 2.3698 6 0.39 35 % + LCAO_Deepks cal_projected_DM 5.0571 13 0.39 74 % + LCAO_gen_fixedH add_v_delta 2.2505 6 0.38 33 % + LCAO_DESCRIPTOR add_v_delta 2.2507 6 0.38 33 % + ElecStateLCAO psiToRho 1.3508 11 0.12 20 % + Charge mix_rho 0.67021 10 0.067 9.8 % + LOOP_ions force_stress 0.5428 1 0.54 7.9 % + Force_Stress_LCAO getForceStress 0.54278 1 0.54 7.9 % + Force_LCAO_gamma ftable_gamma 0.34485 1 0.34 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:50 2022 + FINISH Time : Wed Sep 28 11:02:57 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/294/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..966e155574ac28f5d316d3f11d7e1900afe0d411 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.830262 0.965443 0.485757 +H 0.848985 0.00557863 0.438371 +H 0.777233 0.995946 0.51387 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c27ce367f5c53eb1ebc6c1eacb3902bd4b54133f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1839 2 + 2 -12.9831 2 + 3 -9.07693 2 + 4 -6.7203 2 + 5 1.20314 0 + 6 4.29017 0 + 7 11.099 0 + 8 11.3458 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1103c51c3aabe13bc48d9bba90b7640f87a95f2f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:34 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 23.2473430754 27.0324031617 13.6011870317 0 0 0 0 + tauc_H1 23.7715871033 0.156201713238 12.2743994686 0 0 0 0 + tauc_H2 21.7625374345 27.8864763387 14.3883674393 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.087628293025 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0882139229846 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106196830895 (SEC) + + DONE : INIT CHARGE Time : 0.149357062888 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.432901 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 1 + Local orbitals number in sub-FFT-grid = 5 + lgd_last = 0 + lgd_now = 5 + allocate DM , the dimension is 5 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 2 + nCol_in_proc = 2 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 2 + nCol_in_proc = 3 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 3 + nCol_in_proc = 2 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 3 + nCol_in_proc = 3 +receiver_size is 25 ; receiver_size of each process is: +4 6 6 9 +sender_size is 292 ; sender_size of each process is: +4 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000747 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.00104 + + Density error is 0.213970621827 + + Energy Rydberg eV + E_KohnSham -34.1907234954 -465.188658279 + E_Harris -34.3804373748 -467.769848029 + E_Fermi -0.399218525025 -5.4316466875 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000948851031914 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.00114244199168 + + Density error is 0.0982779229688 + + Energy Rydberg eV + E_KohnSham -34.279986182 -466.403139437 + E_Harris -34.286838109 -466.496364686 + E_Fermi -0.20875682406 -2.84028230361 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000905351516054 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.00107790350037 + + Density error is 0.0631625385078 + + Energy Rydberg eV + E_KohnSham -34.2803258332 -466.407760628 + E_Harris -34.2847489524 -466.467940253 + E_Fermi -0.199104762656 -2.70895927106 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000849131023581 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000978475060004 + + Density error is 0.00199060013858 + + Energy Rydberg eV + E_KohnSham -34.280285913 -466.407217486 + E_Harris -34.280287566 -466.407239976 + E_Fermi -0.163667376293 -2.2268088943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000849738881694 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000979216013274 + + Density error is 0.000897391272042 + + Energy Rydberg eV + E_KohnSham -34.2802361211 -466.406540032 + E_Harris -34.2802369231 -466.406550945 + E_Fermi -0.163189751054 -2.22031046954 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000848946376184 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000977852422802 + + Density error is 0.000171932811859 + + Energy Rydberg eV + E_KohnSham -34.2802639391 -466.406918516 + E_Harris -34.2802639773 -466.406919035 + E_Fermi -0.163008578948 -2.21784549657 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000849183126506 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000978003164262 + + Density error is 3.63268269161e-05 + + Energy Rydberg eV + E_KohnSham -34.2802538016 -466.406780587 + E_Harris -34.2802538078 -466.406780672 + E_Fermi -0.162915155554 -2.21657440609 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000849113544527 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000977962260649 + + Density error is 1.50188282155e-05 + + Energy Rydberg eV + E_KohnSham -34.2802578402 -466.406835535 + E_Harris -34.2802578411 -466.406835548 + E_Fermi -0.16294759163 -2.21701572155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000849113224118 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000977954202719 + + Density error is 1.95859571691e-06 + + Energy Rydberg eV + E_KohnSham -34.2802565492 -466.406817971 + E_Harris -34.2802565492 -466.406817971 + E_Fermi -0.162932090309 -2.21680481525 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000849115055055 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.00097795143925 + + Density error is 3.71176758196e-07 + + Energy Rydberg eV + E_KohnSham -34.2802567446 -466.40682063 + E_Harris -34.2802567446 -466.40682063 + E_Fermi -0.162930424472 -2.21678215038 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000849115334967 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000977951810752 + + Density error is 1.31586855453e-07 + + Energy Rydberg eV + E_KohnSham -34.2802567724 -466.406821008 + E_Harris -34.2802567724 -466.406821008 + E_Fermi -0.162930305181 -2.21678052734 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000849115362399 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000977951848919 + + Density error is 1.08590718709e-08 + + Energy Rydberg eV + E_KohnSham -34.2802567746 -466.406821037 + E_Harris -34.2802567746 -466.406821037 + E_band -7.93258778548 -107.928393768 + E_one_elec -69.0857773817 -939.960223151 + E_Hartree +35.9442269163 +489.046296266 + E_xc -8.19427522638 -111.488834059 + E_Ewald +7.18032586612 +97.693345276 + E_demet -2.8449176391e-71 -3.87070902324e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194435150629 -2.64542594004 + E_Fermi -0.162930180157 -2.2167788263 + + charge density convergence is achieved + final etot is -466.406821037 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1839 2.00000 + 2 -12.9831 2.00000 + 3 -9.07693 2.00000 + 4 -6.72030 2.00000 + 5 1.20314 0.00000 + 6 4.29017 0.00000 + 7 11.0990 0.00000 + 8 11.3458 0.00000 + + EFERMI = -2.216778826301963 eV + OUT.ABACUS/ final etot is -466.4068210373230 eV + correction force for each atom along direction 1 is -0.000126314 + correction force for each atom along direction 2 is 0.000181104 + correction force for each atom along direction 3 is -9.54339e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0074335 -0.065963552 +1.0048270 + H1 +0.18658343 +0.50114374 -0.54443873 + H2 +0.82085007 -0.43518019 -0.46038825 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4068210373230 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4786 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4692 1 7.5 1.e+02% + Potential init_pot 0.28332 2 0.14 3.8% + PW_Basis recip2real 0.27472 17 0.016 3.7% + PW_Basis gathers_scatterp 0.12839 17 0.0076 1.7% + Potential v_of_rho 1.1141 14 0.080 15.% + XC_Functional v_xc 0.40600 15 0.027 5.4% + H_Hartree_pw v_hartree 0.66724 14 0.048 8.9% + PW_Basis real2recip 0.75106 41 0.018 10.% + PW_Basis gatherp_scatters 0.33179 41 0.0081 4.4% + ORB_control set_orb_tables 1.0985 1 1.1 15.% + ORB_gen_tables gen_tables 1.0985 1 1.1 15.% + ORB_table_phi init_Table 0.47619 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47089 126 0.0037 6.3% + ORB_table_beta init_Table_Beta 0.18531 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18380 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24775 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24570 66 0.0037 3.3% + LOOP_ions opt_ions 5.8566 1 5.9 78.% + ESolver_KS_LCAO Run 5.3108 1 5.3 71.% + HSolverLCAO solve 2.6903 12 0.22 36.% + HamiltLCAO updateHk 1.3777 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.3480 12 0.11 18.% + Gint_Gamma distri_vl_value 0.92266 12 0.077 12.% + Gint_Gamma distri_vl 2.7651 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.4399 14 0.39 73.% + LCAO_gen_fixedH add_v_delta 2.6312 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6313 6 0.44 35.% + ElecStateLCAO psiToRho 1.2802 12 0.11 17.% + Charge mix_rho 0.89018 11 0.081 12.% + LOOP_ions force_stress 0.54553 1 0.55 7.3% + Force_Stress_LCAO getForceStress 0.54547 1 0.55 7.3% + Force_LCAO_gamma ftable_gamma 0.33657 1 0.34 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:34 2022 + Finish Time : Wed Sep 28 11:06:41 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d3c57b47627aca7d65c2f4f42c0fcfc6696bf3bb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123637 ima = 3.66417e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 1 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123342007885 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112188408767 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112802467658 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113029084033 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112992907693 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113015036693 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113007902227 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113010567906 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113009969559 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113009891648 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113009879568 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113009873004 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/STRU new file mode 100644 index 0000000000000000000000000000000000000000..67477cdb612dadda22daf921880090cd4abb3f02 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-4.752656924563 27.032403161750 13.601187031631 0 0 0 +H +0.0 +2 +-4.228412896712 28.156201713215 12.274399468578 0 0 0 +-6.237462565445 27.886476338700 14.388367439260 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/conv new file mode 100644 index 0000000000000000000000000000000000000000..53ab609766eb2c07642637238a2b3f314c56cd76 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/conv @@ -0,0 +1 @@ +295 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5b71267b49341fb1ea1d2b519676229b564e0501 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748955279 0.0125923855 1.263277481 1.357444864 1.468864405 0.008385059245 0.01853096066 0.03903082735 +8.165395964e-19 0.001012291409 0.002514256433 0.0120618738 0.04379519983 1.274670781e-18 1.833926137e-06 5.508336255e-06 +0.001648165749 0.005893156178 + +H atom_index 1 n_descriptor 18 +1.259003514 0.03388888837 0.111103453 0.1544612085 0.3244059799 0.02250089219 0.02886690536 0.03713356038 +-9.427093474e-18 4.395290989e-05 0.10282211 0.115578584 0.1325388031 -4.457957614e-18 3.610188027e-06 0.01308690238 +0.02636313172 0.03117253151 + +H atom_index 2 n_descriptor 18 +1.204302352 0.03574743474 0.09315505261 0.1302205837 0.3057834718 0.01998214442 0.02567513178 0.03908395652 +2.148431114e-18 3.913221156e-05 0.08880999046 0.11145141 0.1136019216 -1.294471182e-17 6.110070368e-06 0.01396046549 +0.02423670493 0.02853618108 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3cddc84654d4861f706165fe3463791b005cd8f0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:34 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0876515 SEC) : SETUP UNITCELL + DONE(0.0882296 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106217 SEC) : INIT PLANEWAVE + DONE(0.14949 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.432968 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651887e+02 0.000000e+00 2.140e-01 5.388e-01 + GE2 -4.664031e+02 -1.214481e+00 9.828e-02 4.988e-01 + GE3 -4.664078e+02 -4.621191e-03 6.316e-02 5.681e-01 + GE4 -4.664072e+02 5.431415e-04 1.991e-03 4.282e-01 + GE5 -4.664065e+02 6.774545e-04 8.974e-04 4.270e-01 + GE6 -4.664069e+02 -3.784839e-04 1.719e-04 4.233e-01 + GE7 -4.664068e+02 1.379285e-04 3.633e-05 4.117e-01 + GE8 -4.664068e+02 -5.494807e-05 1.502e-05 4.047e-01 + GE9 -4.664068e+02 1.756441e-05 1.959e-06 4.053e-01 + GE10 -4.664068e+02 -2.659094e-06 3.712e-07 4.047e-01 + GE11 -4.664068e+02 -3.780742e-07 1.316e-07 4.048e-01 + GE12 -4.664068e+02 -2.912787e-08 1.086e-08 3.264e-01 +E_delta_band = -6.96782017e-02 Ry = -9.48020570e-01 eV +E_delta_NN= -1.94435151e-01 Ry = -2.64542594e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4786 11 0.68 1e+02 % + Run_lcao lcao_line 7.4692 1 7.5 1e+02 % + Potential init_pot 0.28332 2 0.14 3.8 % + PW_Basis recip2real 0.27472 17 0.016 3.7 % + PW_Basis gathers_scatterp 0.12839 17 0.0076 1.7 % + Potential v_of_rho 1.1141 14 0.08 15 % + XC_Functional v_xc 0.406 15 0.027 5.4 % + H_Hartree_pw v_hartree 0.66724 14 0.048 8.9 % + PW_Basis real2recip 0.75106 41 0.018 10 % + PW_Basis gatherp_scatters 0.33179 41 0.0081 4.4 % + ORB_control set_orb_tables 1.0985 1 1.1 15 % + ORB_gen_tables gen_tables 1.0985 1 1.1 15 % + ORB_table_phi init_Table 0.47619 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47089 126 0.0037 6.3 % + ORB_table_beta init_Table_Beta 0.18531 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.1838 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24775 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.2457 66 0.0037 3.3 % + LOOP_ions opt_ions 5.8566 1 5.9 78 % + ESolver_KS_LCAO Run 5.3108 1 5.3 71 % + HSolverLCAO solve 2.6903 12 0.22 36 % + HamiltLCAO updateHk 1.3777 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.348 12 0.11 18 % + Gint_Gamma distri_vl_value 0.92266 12 0.077 12 % + Gint_Gamma distri_vl 2.7651 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.4399 14 0.39 73 % + LCAO_gen_fixedH add_v_delta 2.6312 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6313 6 0.44 35 % + ElecStateLCAO psiToRho 1.2802 12 0.11 17 % + Charge mix_rho 0.89018 11 0.081 12 % + LOOP_ions force_stress 0.54553 1 0.55 7.3 % + Force_Stress_LCAO getForceStress 0.54547 1 0.55 7.3 % + Force_LCAO_gamma ftable_gamma 0.33657 1 0.34 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:34 2022 + FINISH Time : Wed Sep 28 11:06:41 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/295/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..49f4f03e6accadf1af97cd293c0e78a786fb64af --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.813725 0.960351 0.495959 +H 0.864287 0.988711 0.467953 +H 0.794434 0.00473118 0.537875 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..82ea54ee3c1b1ee2bf50122bb08e715a4e18772d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.549 2 + 2 -13.1502 2 + 3 -9.237 2 + 4 -6.80218 2 + 5 1.4768 0 + 6 4.73246 0 + 7 11.0178 0 + 8 11.2762 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..298cc4a8fcb8b83c25f624864a841b08d9aa4475 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/running_scf.log @@ -0,0 +1,777 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:52 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 22.7842916113 26.8898371429 13.8868484284 0 0 0 0 + tauc_H1 24.2000348802 27.6839022673 13.1026954816 0 0 0 0 + tauc_H2 22.2441514089 0.13247301527 15.0604869511 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0884533135228 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0980097640427 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116107398639 (SEC) + + DONE : INIT CHARGE Time : 0.164630135644 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445742 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 1 + Local orbitals number in sub-FFT-grid = 5 + lgd_last = 0 + lgd_now = 5 + allocate DM , the dimension is 5 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 2 + nCol_in_proc = 2 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 2 + nCol_in_proc = 3 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 3 + nCol_in_proc = 2 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 3 + nCol_in_proc = 3 +receiver_size is 25 ; receiver_size of each process is: +4 6 6 9 +sender_size is 301 ; sender_size of each process is: +4 144 144 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00115 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000779 + + Density error is 0.216960942277 + + Energy Rydberg eV + E_KohnSham -34.1880262989 -465.151961039 + E_Harris -34.3845005578 -467.82513047 + E_Fermi -0.419233789669 -5.70396833363 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00120034672763 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000989999090539 + + Density error is 0.0973826128092 + + Energy Rydberg eV + E_KohnSham -34.2787007052 -466.385649627 + E_Harris -34.2853473943 -466.476082472 + E_Fermi -0.226961377147 -3.08796795512 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00112186432546 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000941568574027 + + Density error is 0.0621939714346 + + Energy Rydberg eV + E_KohnSham -34.2789606548 -466.389186423 + E_Harris -34.2832284293 -466.447252473 + E_Fermi -0.213001897752 -2.89803949424 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000999068159816 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000876070129953 + + Density error is 0.00202525266434 + + Energy Rydberg eV + E_KohnSham -34.2789998656 -466.389719913 + E_Harris -34.2790012837 -466.389739208 + E_Fermi -0.177172914781 -2.41056117229 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00099952141244 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000878833064057 + + Density error is 0.000925006007162 + + Energy Rydberg eV + E_KohnSham -34.278921778 -466.388657477 + E_Harris -34.2789247123 -466.3886974 + E_Fermi -0.175978142042 -2.39430545522 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00099815764099 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000877511911441 + + Density error is 9.77414230911e-05 + + Energy Rydberg eV + E_KohnSham -34.2789770343 -466.389409278 + E_Harris -34.278977043 -466.389409397 + E_Fermi -0.176277627759 -2.39838016744 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000998070175225 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000877440476689 + + Density error is 4.8215802295e-05 + + Energy Rydberg eV + E_KohnSham -34.2789593354 -466.389168471 + E_Harris -34.2789593472 -466.389168633 + E_Fermi -0.176143989112 -2.39656192037 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000998065712934 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000877415128838 + + Density error is 9.53457981496e-06 + + Energy Rydberg eV + E_KohnSham -34.2789617761 -466.38920168 + E_Harris -34.2789617765 -466.389201685 + E_Fermi -0.176200419549 -2.39732969586 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000998058452692 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000877427110382 + + Density error is 1.827235619e-06 + + Energy Rydberg eV + E_KohnSham -34.2789604915 -466.389184201 + E_Harris -34.2789604915 -466.389184201 + E_Fermi -0.176192123786 -2.39721682621 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000998056892797 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.00087742603201 + + Density error is 1.20272674355e-07 + + Energy Rydberg eV + E_KohnSham -34.2789606276 -466.389186053 + E_Harris -34.2789606276 -466.389186053 + E_Fermi -0.176190024871 -2.397188269 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000998057084477 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000877426199224 + + Density error is 4.72197111165e-08 + + Energy Rydberg eV + E_KohnSham -34.2789606632 -466.389186538 + E_Harris -34.2789606632 -466.389186538 + E_band -8.04637946155 -109.476608947 + E_one_elec -69.7533935892 -949.043607649 + E_Hartree +36.2541196287 +493.262602924 + E_xc -8.24427091125 -112.169060249 + E_Ewald +7.58794203922 +103.239247827 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195692443326 -2.66253228478 + E_Fermi -0.176190129315 -2.39718969004 + + charge density convergence is achieved + final etot is -466.389186538 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5490 2.00000 + 2 -13.1502 2.00000 + 3 -9.23700 2.00000 + 4 -6.80218 2.00000 + 5 1.47680 0.00000 + 6 4.73246 0.00000 + 7 11.0178 0.00000 + 8 11.2762 0.00000 + + EFERMI = -2.397189690035502 eV + OUT.ABACUS/ final etot is -466.3891865377022 eV + correction force for each atom along direction 1 is -2.78073e-05 + correction force for each atom along direction 2 is 0.000108519 + correction force for each atom along direction 3 is 2.25082e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.35073184 -1.2589914 -0.41009234 + H1 +0.96259287 +0.34774771 -0.64040658 + H2 -0.61186103 +0.91124372 +1.0504989 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3891865377022 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1571 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1467 1 6.1 1.e+02% + Potential init_pot 0.28769 2 0.14 4.7% + PW_Basis recip2real 0.27101 16 0.017 4.4% + PW_Basis gathers_scatterp 0.12421 16 0.0078 2.0% + Potential v_of_rho 0.85577 13 0.066 14.% + XC_Functional v_xc 0.22373 14 0.016 3.6% + H_Hartree_pw v_hartree 0.59730 13 0.046 9.7% + PW_Basis real2recip 0.58953 38 0.016 9.6% + PW_Basis gatherp_scatters 0.25537 38 0.0067 4.1% + ORB_control set_orb_tables 1.1135 1 1.1 18.% + ORB_gen_tables gen_tables 1.1135 1 1.1 18.% + ORB_table_phi init_Table 0.48462 1 0.48 7.9% + ORB_table_phi cal_ST_Phi12_R 0.47956 126 0.0038 7.8% + ORB_table_beta init_Table_Beta 0.19022 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18874 56 0.0034 3.1% + ORB_table_alpha init_Table_Alpha 0.25784 1 0.26 4.2% + ORB_table_alpha S_PhiAlpha_R 0.25592 66 0.0039 4.2% + LOOP_ions opt_ions 4.5110 1 4.5 73.% + ESolver_KS_LCAO Run 3.9881 1 4.0 65.% + HSolverLCAO solve 2.0163 11 0.18 33.% + HamiltLCAO updateHk 1.0596 11 0.096 17.% + LCAO_Hamilt cal_Hgamma 1.0312 11 0.094 17.% + Gint_Gamma distri_vl_value 0.66753 11 0.061 11.% + Gint_Gamma distri_vl 1.9315 6 0.32 31.% + LCAO_Deepks cal_projected_DM 4.1348 13 0.32 67.% + LCAO_gen_fixedH add_v_delta 1.8001 6 0.30 29.% + LCAO_DESCRIPTOR add_v_delta 1.8001 6 0.30 29.% + ElecStateLCAO psiToRho 0.93886 11 0.085 15.% + Charge mix_rho 0.65332 10 0.065 11.% + LOOP_ions force_stress 0.52275 1 0.52 8.5% + Force_Stress_LCAO getForceStress 0.52272 1 0.52 8.5% + Force_LCAO_gamma ftable_gamma 0.31068 1 0.31 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:52 2022 + Finish Time : Wed Sep 28 11:01:58 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d37c753eb651a37171f7126281dbd18ed83843d6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/OUT.ABACUS/warning.log @@ -0,0 +1,73 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123986 ima = 3.66197e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 1 + 2 3 + 3 3 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122729417516 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111841715335 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112278417522 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112565544065 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112487861474 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112531267064 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112527961083 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112530779567 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112530356313 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112530275003 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112530276743 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/STRU new file mode 100644 index 0000000000000000000000000000000000000000..f5e70920bbb5fd7bc05f442afaa5a283042081b1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-5.215708388692 26.889837142951 13.886848428382 0 0 0 +H +0.0 +2 +-3.799965119821 27.683902267316 13.102695481624 0 0 0 +-5.755848591070 28.132473015265 15.060486951138 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/conv new file mode 100644 index 0000000000000000000000000000000000000000..07fd70a749dc078f7c6b168a2e67afc272d512f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/conv @@ -0,0 +1 @@ +296 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..81c90fc52f8198a3f9fd55e2346846b4b381a643 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750599709 0.01284631344 1.291111466 1.374434227 1.470483527 0.008927621894 0.01849465761 0.03905726327 +5.888572794e-18 0.001121324608 0.002812933425 0.01325198739 0.0480811525 3.359579396e-19 2.555580507e-06 6.904455742e-06 +0.001631367873 0.006037949681 + +H atom_index 1 n_descriptor 18 +1.270771697 0.03370137034 0.1168864541 0.159581999 0.3266496832 0.02365721773 0.02947166537 0.03693774026 +-2.660477096e-17 5.348619474e-05 0.1075823539 0.11728538 0.1371445214 1.097076232e-17 2.770279311e-06 0.0132560009 +0.02771450826 0.03167490241 + +H atom_index 2 n_descriptor 18 +1.278767979 0.03344041252 0.1198965703 0.1635604829 0.3290199428 0.02403432449 0.02993168089 0.03678134869 +4.479765228e-17 5.42694669e-05 0.1082359271 0.1189242032 0.1405335549 -9.390084553e-18 2.312371875e-06 0.01332659149 +0.02798209819 0.03199587986 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a980378acf966fef2a4600f20e87bb9fa97eca26 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/e_base.npy new file mode 100644 index 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TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:52 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0884766 SEC) : SETUP UNITCELL + DONE(0.0980271 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116128 SEC) : INIT PLANEWAVE + DONE(0.16476 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445807 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651520e+02 0.000000e+00 2.170e-01 4.800e-01 + GE2 -4.663856e+02 -1.233689e+00 9.738e-02 4.098e-01 + GE3 -4.663892e+02 -3.536797e-03 6.219e-02 4.568e-01 + GE4 -4.663897e+02 -5.334897e-04 2.025e-03 3.487e-01 + GE5 -4.663887e+02 1.062436e-03 9.250e-04 3.483e-01 + GE6 -4.663894e+02 -7.518008e-04 9.774e-05 3.238e-01 + GE7 -4.663892e+02 2.408071e-04 4.822e-05 3.303e-01 + GE8 -4.663892e+02 -3.320861e-05 9.535e-06 3.220e-01 + GE9 -4.663892e+02 1.747857e-05 1.827e-06 3.204e-01 + GE10 -4.663892e+02 -1.851493e-06 1.203e-07 3.214e-01 + GE11 -4.663892e+02 -4.849607e-07 4.722e-08 2.654e-01 +E_delta_band = -7.23346126e-02 Ry = -9.84162894e-01 eV +E_delta_NN= -1.95692443e-01 Ry = -2.66253228e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1571 11 0.56 1e+02 % + Run_lcao lcao_line 6.1467 1 6.1 1e+02 % + Potential init_pot 0.28769 2 0.14 4.7 % + PW_Basis recip2real 0.27101 16 0.017 4.4 % + PW_Basis gathers_scatterp 0.12421 16 0.0078 2 % + Potential v_of_rho 0.85577 13 0.066 14 % + XC_Functional v_xc 0.22373 14 0.016 3.6 % + H_Hartree_pw v_hartree 0.5973 13 0.046 9.7 % + PW_Basis real2recip 0.58953 38 0.016 9.6 % + PW_Basis gatherp_scatters 0.25537 38 0.0067 4.1 % + ORB_control set_orb_tables 1.1135 1 1.1 18 % + ORB_gen_tables gen_tables 1.1135 1 1.1 18 % + ORB_table_phi init_Table 0.48462 1 0.48 7.9 % + ORB_table_phi cal_ST_Phi12_R 0.47956 126 0.0038 7.8 % + ORB_table_beta init_Table_Beta 0.19022 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18874 56 0.0034 3.1 % + ORB_table_alpha init_Table_Alpha 0.25784 1 0.26 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.25592 66 0.0039 4.2 % + LOOP_ions opt_ions 4.511 1 4.5 73 % + ESolver_KS_LCAO Run 3.9881 1 4 65 % + HSolverLCAO solve 2.0163 11 0.18 33 % + HamiltLCAO updateHk 1.0596 11 0.096 17 % + LCAO_Hamilt cal_Hgamma 1.0312 11 0.094 17 % + Gint_Gamma distri_vl_value 0.66753 11 0.061 11 % + Gint_Gamma distri_vl 1.9315 6 0.32 31 % + LCAO_Deepks cal_projected_DM 4.1348 13 0.32 67 % + LCAO_gen_fixedH add_v_delta 1.8001 6 0.3 29 % + LCAO_DESCRIPTOR add_v_delta 1.8001 6 0.3 29 % + ElecStateLCAO psiToRho 0.93886 11 0.085 15 % + Charge mix_rho 0.65332 10 0.065 11 % + LOOP_ions force_stress 0.52275 1 0.52 8.5 % + Force_Stress_LCAO getForceStress 0.52272 1 0.52 8.5 % + Force_LCAO_gamma ftable_gamma 0.31068 1 0.31 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:52 2022 + FINISH Time : Wed Sep 28 11:01:58 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/296/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5ec2481a16b6fb7c473ea67c63aa6d8d0e8be7c1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.80394 0.96361 0.504064 +H 0.818272 0.900349 0.521267 +H 0.77012 0.988735 0.556488 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..98981e15a6d50d135d7ef16e8ea0f6152e7df143 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9902 2 + 2 -12.8521 2 + 3 -9.02643 2 + 4 -6.67772 2 + 5 1.06408 0 + 6 4.01448 0 + 7 11.1437 0 + 8 11.39 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..efb1065705a181b065eb200f42f6669e8b47fb92 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:34 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 22.5103182668 26.9810739697 14.1138007879 0 0 0 0 + tauc_H1 22.9116153859 25.2097786305 14.5954676447 0 0 0 0 + tauc_H2 21.5633470797 27.6845685555 15.5816723467 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0732055064432 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0737409365421 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0896129583157 (SEC) + + DONE : INIT CHARGE Time : 0.132660061887 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.395206 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + No atoms on this sub-FFT-mesh. + Atom number in sub-FFT-grid = 0 + Local orbitals number in sub-FFT-grid = 0 + lgd_last = 0 + lgd_now = 0 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 +receiver_size is 0 ; receiver_size of each process is: +0 0 0 0 +sender_size is 297 ; sender_size of each process is: +0 144 144 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000703 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63e-322 + + Density error is 0.211391190678 + + Energy Rydberg eV + E_KohnSham -34.1931079423 -465.221100344 + E_Harris -34.3769699964 -467.722671926 + E_Fermi -0.387449049086 -5.27151475225 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000901606218079 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0986038987698 + + Energy Rydberg eV + E_KohnSham -34.2798861119 -466.401777913 + E_Harris -34.2868651153 -466.496732126 + E_Fermi -0.199251349683 -2.71095368987 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0008601738934 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0635169702551 + + Energy Rydberg eV + E_KohnSham -34.2801528622 -466.405407237 + E_Harris -34.2846390765 -466.466445314 + E_Fermi -0.191266363492 -2.60231237923 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000798283576679 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.00200608052771 + + Energy Rydberg eV + E_KohnSham -34.2800763668 -466.404366463 + E_Harris -34.2800789713 -466.4044019 + E_Fermi -0.156183297444 -2.12498277766 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000796842937882 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000823508518429 + + Energy Rydberg eV + E_KohnSham -34.2800501957 -466.404010387 + E_Harris -34.2800505199 -466.404014799 + E_Fermi -0.155957456667 -2.12191005625 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000796140469701 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000175620491995 + + Energy Rydberg eV + E_KohnSham -34.2800631368 -466.404186461 + E_Harris -34.2800629786 -466.404184307 + E_Fermi -0.155587462576 -2.11687602839 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000796253088053 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 2.48823454418e-05 + + Energy Rydberg eV + E_KohnSham -34.2800597403 -466.404140248 + E_Harris -34.2800597419 -466.40414027 + E_Fermi -0.155558705641 -2.11648477022 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0007962064216 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.15572045674e-05 + + Energy Rydberg eV + E_KohnSham -34.2800620601 -466.404171811 + E_Harris -34.2800620607 -466.404171819 + E_Fermi -0.155572196338 -2.11666832057 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000796206699278 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.91348012952e-06 + + Energy Rydberg eV + E_KohnSham -34.2800611677 -466.40415967 + E_Harris -34.2800611677 -466.40415967 + E_Fermi -0.155561133745 -2.11651780627 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000796205094653 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 4.94661844904e-07 + + Energy Rydberg eV + E_KohnSham -34.2800613739 -466.404162475 + E_Harris -34.2800613739 -466.404162475 + E_Fermi -0.155559763617 -2.11649916473 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000796205753253 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.68763782064e-07 + + Energy Rydberg eV + E_KohnSham -34.2800613768 -466.404162514 + E_Harris -34.2800613768 -466.404162514 + E_Fermi -0.155559522349 -2.11649588211 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000796205911496 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.07711343832e-08 + + Energy Rydberg eV + E_KohnSham -34.2800613807 -466.404162567 + E_Harris -34.2800613807 -466.404162567 + E_band -7.87118815954 -107.093009 + E_one_elec -68.7101337634 -934.849329524 + E_Hartree +35.7683927686 +486.653949954 + E_xc -8.16591054957 -111.102912833 + E_Ewald +6.95311817595 +94.6020260603 + E_demet -5.24524921917e-62 -7.13652768107e-61 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193737932575 -2.63593980175 + E_Fermi -0.155559359243 -2.11649366294 + + charge density convergence is achieved + final etot is -466.404162567 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9902 2.00000 + 2 -12.8521 2.00000 + 3 -9.02643 2.00000 + 4 -6.67772 2.00000 + 5 1.06408 0.00000 + 6 4.01448 0.00000 + 7 11.1437 0.00000 + 8 11.3900 0.00000 + + EFERMI = -2.116493662935446 eV + OUT.ABACUS/ final etot is -466.4041625669941 eV + correction force for each atom along direction 1 is 4.76320e-05 + correction force for each atom along direction 2 is -0.000109374 + correction force for each atom along direction 3 is 0.000143804 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.25147645 -0.37204288 +0.81630745 + H1 -0.24825512 +0.84620839 -0.11502771 + H2 +0.49973157 -0.47416551 -0.70127974 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4041625669941 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1771 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1700 1 7.2 1.e+02% + Potential init_pot 0.26125 2 0.13 3.6% + PW_Basis recip2real 0.25802 17 0.015 3.6% + PW_Basis gathers_scatterp 0.13569 17 0.0080 1.9% + Potential v_of_rho 1.0383 14 0.074 14.% + XC_Functional v_xc 0.39253 15 0.026 5.5% + H_Hartree_pw v_hartree 0.61509 14 0.044 8.6% + PW_Basis real2recip 0.64979 41 0.016 9.1% + PW_Basis gatherp_scatters 0.38729 41 0.0094 5.4% + ORB_control set_orb_tables 0.90649 1 0.91 13.% + ORB_gen_tables gen_tables 0.90649 1 0.91 13.% + ORB_table_phi init_Table 0.38223 1 0.38 5.3% + ORB_table_phi cal_ST_Phi12_R 0.37787 126 0.0030 5.3% + ORB_table_beta init_Table_Beta 0.15827 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15693 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.20838 1 0.21 2.9% + ORB_table_alpha S_PhiAlpha_R 0.20677 66 0.0031 2.9% + LOOP_ions opt_ions 5.7933 1 5.8 81.% + ESolver_KS_LCAO Run 5.2651 1 5.3 73.% + HSolverLCAO solve 2.9068 12 0.24 41.% + HamiltLCAO updateHk 1.3505 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.3187 12 0.11 18.% + Gint_Gamma distri_vl_value 1.0391 12 0.087 14.% + Gint_Gamma distri_vl 2.7300 6 0.46 38.% + LCAO_Deepks cal_projected_DM 5.3697 14 0.38 75.% + LCAO_gen_fixedH add_v_delta 2.6297 6 0.44 37.% + LCAO_DESCRIPTOR add_v_delta 2.6296 6 0.44 37.% + DiagoElpa elpa_solve 0.13026 12 0.011 1.8% + ElecStateLCAO psiToRho 1.4252 12 0.12 20.% + Charge mix_rho 0.72111 11 0.066 10.% + LOOP_ions force_stress 0.52802 1 0.53 7.4% + Force_Stress_LCAO getForceStress 0.52800 1 0.53 7.4% + Force_LCAO_gamma ftable_gamma 0.33200 1 0.33 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1028. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:34 2022 + Finish Time : Wed Sep 28 11:10:42 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..eff4116917066164c0124875141fa83f338b8cb6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/OUT.ABACUS/warning.log @@ -0,0 +1,79 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012354 ima = 3.665e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 0 + 2 3 + 3 3 + 4 1 + Grid_Technique::init_atoms_on_grid2 warning : no atom on this sub FFT grid. + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012345739065 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112348019461 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113025112638 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011320358145 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113191309012 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113199838235 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113196170035 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113197862251 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113197292749 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113197269923 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113197250893 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113197242242 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e036f8d0762c2917fddd3dfd81a274556aed7477 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-5.489681733175 26.981073969677 14.113800787860 0 0 0 +H +0.0 +2 +-5.088384614142 25.209778630503 14.595467644709 0 0 0 +-6.436652920254 27.684568555456 15.581672346708 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/conv new file mode 100644 index 0000000000000000000000000000000000000000..c5484651933ad5d4746443a78cc6599243394d56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/conv @@ -0,0 +1 @@ +297 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..12107ea90e8e8611a3e25b5281383f9c6173d025 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748773774 0.0124474701 1.250355032 1.343214267 1.468029325 0.008211771693 0.01833772473 0.03904106713 +8.079729048e-18 0.0009371177274 0.002377988779 0.01154566608 0.04156981523 -2.102626943e-19 1.581042974e-06 4.902925945e-06 +0.001644581995 0.005829440122 + +H atom_index 1 n_descriptor 18 +1.209013185 0.03558292981 0.09415626924 0.1324038034 0.3080631687 0.02001938623 0.02598373231 0.03892954575 +-1.100446668e-17 3.629711069e-05 0.08862999827 0.113255449 0.1140348414 -2.567653159e-18 5.696012411e-06 0.01379784691 +0.02405048988 0.02878272731 + +H atom_index 2 n_descriptor 18 +1.205694486 0.03569128702 0.09314622626 0.1310262761 0.30685646 0.01986793973 0.02578984148 0.03906480518 +-2.230784478e-17 3.602701592e-05 0.08776404642 0.1120449631 0.1139176743 8.502694478e-19 5.806660198e-06 0.01388520433 +0.02391466162 0.02861058252 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..2da27d8bf8cb6a3bbc15ee965a142dd4ea8e621a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:34 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0732205 SEC) : SETUP UNITCELL + DONE(0.0737517 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0896266 SEC) : INIT PLANEWAVE + DONE(0.132763 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.395251 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652211e+02 0.000000e+00 2.114e-01 5.173e-01 + GE2 -4.664018e+02 -1.180678e+00 9.860e-02 4.889e-01 + GE3 -4.664054e+02 -3.629324e-03 6.352e-02 5.498e-01 + GE4 -4.664044e+02 1.040774e-03 2.006e-03 4.282e-01 + GE5 -4.664040e+02 3.560761e-04 8.235e-04 4.259e-01 + GE6 -4.664042e+02 -1.760733e-04 1.756e-04 4.224e-01 + GE7 -4.664041e+02 4.621227e-05 2.488e-05 4.029e-01 + GE8 -4.664042e+02 -3.156260e-05 1.156e-05 4.105e-01 + GE9 -4.664042e+02 1.214111e-05 1.913e-06 4.104e-01 + GE10 -4.664042e+02 -2.804941e-06 4.947e-07 4.067e-01 + GE11 -4.664042e+02 -3.883629e-08 1.688e-07 4.074e-01 + GE12 -4.664042e+02 -5.334207e-08 1.077e-08 3.350e-01 +E_delta_band = -6.82099203e-02 Ry = -9.28043577e-01 eV +E_delta_NN= -1.93737933e-01 Ry = -2.63593980e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1771 11 0.65 1e+02 % + Run_lcao lcao_line 7.17 1 7.2 1e+02 % + Potential init_pot 0.26125 2 0.13 3.6 % + PW_Basis recip2real 0.25802 17 0.015 3.6 % + PW_Basis gathers_scatterp 0.13569 17 0.008 1.9 % + Potential v_of_rho 1.0383 14 0.074 14 % + XC_Functional v_xc 0.39253 15 0.026 5.5 % + H_Hartree_pw v_hartree 0.61509 14 0.044 8.6 % + PW_Basis real2recip 0.64979 41 0.016 9.1 % + PW_Basis gatherp_scatters 0.38729 41 0.0094 5.4 % + ORB_control set_orb_tables 0.90649 1 0.91 13 % + ORB_gen_tables gen_tables 0.90649 1 0.91 13 % + ORB_table_phi init_Table 0.38223 1 0.38 5.3 % + ORB_table_phi cal_ST_Phi12_R 0.37787 126 0.003 5.3 % + ORB_table_beta init_Table_Beta 0.15827 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15693 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.20838 1 0.21 2.9 % + ORB_table_alpha S_PhiAlpha_R 0.20677 66 0.0031 2.9 % + LOOP_ions opt_ions 5.7933 1 5.8 81 % + ESolver_KS_LCAO Run 5.2651 1 5.3 73 % + HSolverLCAO solve 2.9068 12 0.24 41 % + HamiltLCAO updateHk 1.3505 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.3187 12 0.11 18 % + Gint_Gamma distri_vl_value 1.0391 12 0.087 14 % + Gint_Gamma distri_vl 2.73 6 0.46 38 % + LCAO_Deepks cal_projected_DM 5.3697 14 0.38 75 % + LCAO_gen_fixedH add_v_delta 2.6297 6 0.44 37 % + LCAO_DESCRIPTOR add_v_delta 2.6296 6 0.44 37 % + DiagoElpa elpa_solve 0.13026 12 0.011 1.8 % + ElecStateLCAO psiToRho 1.4252 12 0.12 20 % + Charge mix_rho 0.72111 11 0.066 10 % + LOOP_ions force_stress 0.52802 1 0.53 7.4 % + Force_Stress_LCAO getForceStress 0.528 1 0.53 7.4 % + Force_LCAO_gamma ftable_gamma 0.332 1 0.33 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:34 2022 + FINISH Time : Wed Sep 28 11:10:42 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/297/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..378e0957855e21570fc0a0278dbf7cb0c0497b80 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.807907 0.953394 0.503681 +H 0.767316 0.912366 0.478991 +H 0.765889 0.00147836 0.522848 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..83b484ade766214ab0ee5e08a214ffaebba3f6b2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5249 2 + 2 -12.9566 2 + 3 -9.33983 2 + 4 -6.79414 2 + 5 1.34461 0 + 6 4.62532 0 + 7 11.0328 0 + 8 11.293 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f0e4eddc5d7be9ca2c963b950058a4a8528062fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:24 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 22.621403428 26.6950378578 14.103070548 0 0 0 0 + tauc_H1 21.4848383998 25.5462487631 13.4117597067 0 0 0 0 + tauc_H2 21.4448974425 0.0413942123705 14.6397313256 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0730580567466 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0733716408953 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0896399566541 (SEC) + + DONE : INIT CHARGE Time : 0.13312237135 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374402 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + No atoms on this sub-FFT-mesh. + Atom number in sub-FFT-grid = 0 + Local orbitals number in sub-FFT-grid = 0 + lgd_last = 0 + lgd_now = 0 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 +receiver_size is 0 ; receiver_size of each process is: +0 0 0 0 +sender_size is 288 ; sender_size of each process is: +0 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00119 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63e-322 + + Density error is 0.215585485002 + + Energy Rydberg eV + E_KohnSham -34.1858407993 -465.122225792 + E_Harris -34.379963702 -467.763403381 + E_Fermi -0.416062794297 -5.66082472824 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00125674275235 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0974528421819 + + Energy Rydberg eV + E_KohnSham -34.2758134386 -466.34636635 + E_Harris -34.2825477332 -466.437991128 + E_Fermi -0.224540915906 -3.05503589047 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00117260847669 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0623001360439 + + Energy Rydberg eV + E_KohnSham -34.2760280531 -466.34928633 + E_Harris -34.2803672963 -466.408324762 + E_Fermi -0.21157237104 -2.87858978552 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00103213471137 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.00199279769058 + + Energy Rydberg eV + E_KohnSham -34.2760445409 -466.349510658 + E_Harris -34.2760459283 -466.349529534 + E_Fermi -0.175612655324 -2.38933275332 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00103132207938 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000869283612791 + + Energy Rydberg eV + E_KohnSham -34.2759789134 -466.348617751 + E_Harris -34.2759809063 -466.348644865 + E_Fermi -0.174736719044 -2.37741502883 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00102962072744 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000117161901238 + + Energy Rydberg eV + E_KohnSham -34.2760231573 -466.349219719 + E_Harris -34.2760231919 -466.34922019 + E_Fermi -0.174848708338 -2.37893872134 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00102948512472 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 4.33909283377e-05 + + Energy Rydberg eV + E_KohnSham -34.2760081546 -466.349015597 + E_Harris -34.2760081651 -466.34901574 + E_Fermi -0.174723285996 -2.37723226284 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0010294598479 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.85796780401e-05 + + Energy Rydberg eV + E_KohnSham -34.2760116752 -466.349063498 + E_Harris -34.2760116766 -466.349063516 + E_Fermi -0.174774702511 -2.37793182041 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00102943677546 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 2.07061229301e-06 + + Energy Rydberg eV + E_KohnSham -34.2760100824 -466.349041826 + E_Harris -34.2760100824 -466.349041826 + E_Fermi -0.174754151577 -2.3776522106 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00102943854205 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 3.25104158044e-07 + + Energy Rydberg eV + E_KohnSham -34.276010328 -466.349045168 + E_Harris -34.276010328 -466.349045168 + E_Fermi -0.174752826839 -2.37763418662 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0010294383175 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.28220567094e-07 + + Energy Rydberg eV + E_KohnSham -34.2760103626 -466.349045638 + E_Harris -34.2760103626 -466.349045638 + E_Fermi -0.174752644162 -2.37763170117 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00102943819325 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.08286716146e-08 + + Energy Rydberg eV + E_KohnSham -34.2760103644 -466.349045662 + E_Harris -34.2760103644 -466.349045662 + E_band -8.02832335596 -109.230943027 + E_one_elec -69.5940032243 -946.874990481 + E_Hartree +36.1751991201 +492.188834318 + E_xc -8.23176112955 -111.998855937 + E_Ewald +7.49825625501 +102.019010132 + E_demet -6.16426352486e-84 -8.38691079117e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195464807608 -2.65943514194 + E_Fermi -0.174752502219 -2.37762976994 + + charge density convergence is achieved + final etot is -466.349045662 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5249 2.00000 + 2 -12.9566 2.00000 + 3 -9.33983 2.00000 + 4 -6.79414 2.00000 + 5 1.34461 0.00000 + 6 4.62532 0.00000 + 7 11.0328 0.00000 + 8 11.2930 0.00000 + + EFERMI = -2.377629769940081 eV + OUT.ABACUS/ final etot is -466.3490456623260 eV + correction force for each atom along direction 1 is -0.000180208 + correction force for each atom along direction 2 is -6.54290e-06 + correction force for each atom along direction 3 is -3.92957e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.90085325 +2.2088079 +1.1883530 + H1 -1.4953156 -2.0473899 -1.1741841 + H2 +0.59446232 -0.16141799 -0.014168975 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3490456623260 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8376 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8304 1 6.8 1.e+02% + Potential init_pot 0.23827 2 0.12 3.5% + PW_Basis recip2real 0.23787 17 0.014 3.5% + PW_Basis gathers_scatterp 0.11468 17 0.0067 1.7% + Potential v_of_rho 1.0305 14 0.074 15.% + XC_Functional v_xc 0.39280 15 0.026 5.7% + H_Hartree_pw v_hartree 0.60652 14 0.043 8.9% + PW_Basis real2recip 0.63442 41 0.015 9.3% + PW_Basis gatherp_scatters 0.36927 41 0.0090 5.4% + ORB_control set_orb_tables 0.89757 1 0.90 13.% + ORB_gen_tables gen_tables 0.89757 1 0.90 13.% + ORB_table_phi init_Table 0.37486 1 0.37 5.5% + ORB_table_phi cal_ST_Phi12_R 0.37058 126 0.0029 5.4% + ORB_table_beta init_Table_Beta 0.15620 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15489 56 0.0028 2.3% + ORB_table_alpha init_Table_Alpha 0.20944 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20782 66 0.0031 3.0% + LOOP_ions opt_ions 5.4882 1 5.5 80.% + ESolver_KS_LCAO Run 4.9901 1 5.0 73.% + HSolverLCAO solve 2.6446 12 0.22 39.% + HamiltLCAO updateHk 1.2339 12 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.2022 12 0.10 18.% + Gint_Gamma distri_vl_value 0.93196 12 0.078 14.% + Gint_Gamma distri_vl 2.6051 6 0.43 38.% + LCAO_Deepks cal_projected_DM 5.0985 14 0.36 75.% + LCAO_gen_fixedH add_v_delta 2.5053 6 0.42 37.% + LCAO_DESCRIPTOR add_v_delta 2.5052 6 0.42 37.% + DiagoElpa elpa_solve 0.13276 12 0.011 1.9% + ElecStateLCAO psiToRho 1.2754 12 0.11 19.% + Charge mix_rho 0.72291 11 0.066 11.% + LOOP_ions force_stress 0.49792 1 0.50 7.3% + Force_Stress_LCAO getForceStress 0.49790 1 0.50 7.3% + Force_LCAO_gamma ftable_gamma 0.30512 1 0.31 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1028. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:24 2022 + Finish Time : Wed Sep 28 11:09:30 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3d18b88d9327d4ee29fad4624827d6c4853bdf1c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/OUT.ABACUS/warning.log @@ -0,0 +1,79 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124139 ima = 3.65546e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 0 + 2 3 + 3 3 + 4 0 + Grid_Technique::init_atoms_on_grid2 warning : no atom on this sub FFT grid. + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122656373235 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111674093653 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112170083785 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112445760367 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112382238832 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112417953442 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011241253923 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011241574818 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112415020153 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112414927339 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112414916555 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112414909993 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/STRU new file mode 100644 index 0000000000000000000000000000000000000000..28dece56445829dfeed1881adb3e9b2d5151e406 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-5.378596571934 26.695037857811 14.103070548003 0 0 0 +H +0.0 +2 +-6.515161600225 25.546248763051 13.411759706661 0 0 0 +-6.555102557552 28.041394212351 14.639731325602 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/conv new file mode 100644 index 0000000000000000000000000000000000000000..50974bafa0a8254a17dc01ff01ce2aa7e1787082 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/conv @@ -0,0 +1 @@ +298 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..84c31e113dc8e28cd761f725908b00a0c2eae4ec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752603482 0.01278947207 1.277156483 1.371478955 1.470333409 0.009276863096 0.01773825789 0.03913184437 +1.26239322e-18 0.001022817216 0.002864275548 0.01321468374 0.04800206216 1.011799053e-19 2.677331155e-06 7.192615362e-06 +0.001591362594 0.006058768979 + +H atom_index 1 n_descriptor 18 +1.307560191 0.03285779025 0.1321700273 0.178613352 0.3368413851 0.02568739278 0.03155207693 0.03680437943 +-9.75382428e-17 5.701869924e-05 0.1080832763 0.1270928664 0.1530823366 -1.004466335e-17 6.538648732e-07 0.01404569507 +0.02888879211 0.0330188507 + +H atom_index 2 n_descriptor 18 +1.221820048 0.03559628342 0.1004926255 0.1369172914 0.3101432567 0.02154160759 0.02659170401 0.03874959238 +-1.60762556e-17 4.875770311e-05 0.09656599017 0.1137753968 0.117440472 5.605921009e-18 5.182470719e-06 0.01377600955 +0.02591336007 0.02940064999 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d19fad11dabfdb8d1dcfe2bb1650068093d615c8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/e_base.npy 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0000000000000000000000000000000000000000..5cbf668c2037a17af44eb41a8c9c410fd376351c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..e70e2d2adccdec0374623482176008b558b8728b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..7cf24fc69b093bf97a7218d6d76740f146fa4543 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:24 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0730727 SEC) : SETUP UNITCELL + DONE(0.0733807 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0896533 SEC) : INIT PLANEWAVE + DONE(0.133227 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374455 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651222e+02 0.000000e+00 2.156e-01 4.961e-01 + GE2 -4.663464e+02 -1.224141e+00 9.745e-02 4.651e-01 + GE3 -4.663493e+02 -2.919980e-03 6.230e-02 5.283e-01 + GE4 -4.663495e+02 -2.243279e-04 1.993e-03 4.067e-01 + GE5 -4.663486e+02 8.929072e-04 8.693e-04 4.015e-01 + GE6 -4.663492e+02 -6.019682e-04 1.172e-04 3.978e-01 + GE7 -4.663490e+02 2.041214e-04 4.339e-05 3.977e-01 + GE8 -4.663491e+02 -4.790030e-05 1.858e-05 3.772e-01 + GE9 -4.663490e+02 2.167165e-05 2.071e-06 3.861e-01 + GE10 -4.663490e+02 -3.341882e-06 3.251e-07 3.828e-01 + GE11 -4.663490e+02 -4.697860e-07 1.282e-07 3.854e-01 + GE12 -4.663490e+02 -2.452492e-08 1.083e-08 3.064e-01 +E_delta_band = -7.17634220e-02 Ry = -9.76391447e-01 eV +E_delta_NN= -1.95464808e-01 Ry = -2.65943514e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8376 11 0.62 1e+02 % + Run_lcao lcao_line 6.8304 1 6.8 1e+02 % + Potential init_pot 0.23827 2 0.12 3.5 % + PW_Basis recip2real 0.23787 17 0.014 3.5 % + PW_Basis gathers_scatterp 0.11468 17 0.0067 1.7 % + Potential v_of_rho 1.0305 14 0.074 15 % + XC_Functional v_xc 0.3928 15 0.026 5.7 % + H_Hartree_pw v_hartree 0.60652 14 0.043 8.9 % + PW_Basis real2recip 0.63442 41 0.015 9.3 % + PW_Basis gatherp_scatters 0.36927 41 0.009 5.4 % + ORB_control set_orb_tables 0.89757 1 0.9 13 % + ORB_gen_tables gen_tables 0.89757 1 0.9 13 % + ORB_table_phi init_Table 0.37486 1 0.37 5.5 % + ORB_table_phi cal_ST_Phi12_R 0.37058 126 0.0029 5.4 % + ORB_table_beta init_Table_Beta 0.1562 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15489 56 0.0028 2.3 % + ORB_table_alpha init_Table_Alpha 0.20944 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20782 66 0.0031 3 % + LOOP_ions opt_ions 5.4882 1 5.5 80 % + ESolver_KS_LCAO Run 4.9901 1 5 73 % + HSolverLCAO solve 2.6446 12 0.22 39 % + HamiltLCAO updateHk 1.2339 12 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.2022 12 0.1 18 % + Gint_Gamma distri_vl_value 0.93196 12 0.078 14 % + Gint_Gamma distri_vl 2.6051 6 0.43 38 % + LCAO_Deepks cal_projected_DM 5.0985 14 0.36 75 % + LCAO_gen_fixedH add_v_delta 2.5053 6 0.42 37 % + LCAO_DESCRIPTOR add_v_delta 2.5052 6 0.42 37 % + DiagoElpa elpa_solve 0.13276 12 0.011 1.9 % + ElecStateLCAO psiToRho 1.2754 12 0.11 19 % + Charge mix_rho 0.72291 11 0.066 11 % + LOOP_ions force_stress 0.49792 1 0.5 7.3 % + Force_Stress_LCAO getForceStress 0.4979 1 0.5 7.3 % + Force_LCAO_gamma ftable_gamma 0.30512 1 0.31 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:24 2022 + FINISH Time : Wed Sep 28 11:09:30 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/298/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e58f441a05b9317546732a117239340fb9b889cf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.797538 0.941152 0.491258 +H 0.834117 0.939239 0.433413 +H 0.766366 0.999832 0.488637 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..4e6b9eee2d8b2737b5171fd30fac13ad01c88e9a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.967 2 + 2 -12.7618 2 + 3 -9.07379 2 + 4 -6.67313 2 + 5 1.00601 0 + 6 3.94339 0 + 7 11.1519 0 + 8 11.4001 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..00185353da19297c42d0147104deef3e9f06086c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/running_scf.log @@ -0,0 +1,777 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:13 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 22.3310592367 26.3522652626 13.7552230327 0 0 0 0 + tauc_H1 23.3552627294 26.2987038106 12.1355646103 0 0 0 0 + tauc_H2 21.458242482 27.9952980159 13.6818250669 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0873406188583 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0990256567976 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117087382956 (SEC) + + DONE : INIT CHARGE Time : 0.16554928027 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447954 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 1 + Local orbitals number in sub-FFT-grid = 5 + lgd_last = 0 + lgd_now = 5 + allocate DM , the dimension is 5 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 2 + nCol_in_proc = 2 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 2 + nCol_in_proc = 3 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 3 + nCol_in_proc = 2 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 3 + nCol_in_proc = 3 +receiver_size is 25 ; receiver_size of each process is: +4 6 6 9 +sender_size is 292 ; sender_size of each process is: +4 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00145 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000511 + + Density error is 0.211219848685 + + Energy Rydberg eV + E_KohnSham -34.1912325117 -465.195583802 + E_Harris -34.3749159144 -467.694724707 + E_Fermi -0.385238055529 -5.24143264163 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00135641246158 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000804961529376 + + Density error is 0.0987728595973 + + Energy Rydberg eV + E_KohnSham -34.2786242271 -466.384609089 + E_Harris -34.2857357126 -466.481365814 + E_Fermi -0.196957094367 -2.67973874492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00126022596 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000778105467449 + + Density error is 0.0637331867124 + + Energy Rydberg eV + E_KohnSham -34.2789904551 -466.389591878 + E_Harris -34.2835432788 -466.451536221 + E_Fermi -0.190123523914 -2.58676324907 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00108177376236 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755751947436 + + Density error is 0.00199179829131 + + Energy Rydberg eV + E_KohnSham -34.2788946623 -466.38828855 + E_Harris -34.2788970134 -466.388320538 + E_Fermi -0.155002323882 -2.10891480804 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010804637872 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755260298176 + + Density error is 0.000882424399777 + + Energy Rydberg eV + E_KohnSham -34.2788679834 -466.387925564 + E_Harris -34.2788681563 -466.387927916 + E_Fermi -0.154910921213 -2.10767121092 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107798690167 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755108416446 + + Density error is 0.000180912020558 + + Energy Rydberg eV + E_KohnSham -34.2788786215 -466.388070302 + E_Harris -34.2788786179 -466.388070254 + E_Fermi -0.154478992003 -2.10179451254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107803409593 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755265191526 + + Density error is 2.54268356664e-05 + + Energy Rydberg eV + E_KohnSham -34.2788762122 -466.388037522 + E_Harris -34.2788762138 -466.388037544 + E_Fermi -0.15445702563 -2.1014956447 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107797698168 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755212967827 + + Density error is 1.09216295365e-05 + + Energy Rydberg eV + E_KohnSham -34.2788783254 -466.388066274 + E_Harris -34.278878326 -466.388066282 + E_Fermi -0.154467672422 -2.10164050174 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.001077964243 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755219072676 + + Density error is 1.61064924169e-06 + + Energy Rydberg eV + E_KohnSham -34.2788774596 -466.388054495 + E_Harris -34.2788774596 -466.388054495 + E_Fermi -0.154457145281 -2.10149727263 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107796054689 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755220701731 + + Density error is 2.6512293597e-07 + + Energy Rydberg eV + E_KohnSham -34.2788776344 -466.388056873 + E_Harris -34.2788776344 -466.388056873 + E_Fermi -0.15445581468 -2.10147916888 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107796076406 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755221211879 + + Density error is 4.46277719931e-08 + + Energy Rydberg eV + E_KohnSham -34.2788776515 -466.388057105 + E_Harris -34.2788776514 -466.388057105 + E_band -7.86077645793 -106.951350532 + E_one_elec -68.61791838 -933.594674867 + E_Hartree +35.7227746291 +486.033283325 + E_xc -8.15876189958 -111.00565046 + E_Ewald +6.90071865835 +93.8890940485 + E_demet -2.60299264375e-59 -3.5415531807e-58 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193617223862 -2.63429747546 + E_Fermi -0.154455669506 -2.10147719369 + + charge density convergence is achieved + final etot is -466.388057105 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9670 2.00000 + 2 -12.7618 2.00000 + 3 -9.07379 2.00000 + 4 -6.67313 2.00000 + 5 1.00601 0.00000 + 6 3.94339 0.00000 + 7 11.1519 0.00000 + 8 11.4001 0.00000 + + EFERMI = -2.101477193692980 eV + OUT.ABACUS/ final etot is -466.3880571045808 eV + correction force for each atom along direction 1 is -4.01947e-05 + correction force for each atom along direction 2 is 9.70773e-05 + correction force for each atom along direction 3 is -1.55970e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.68455745 +0.26918326 -1.3599485 + H1 -0.91648805 +0.10163727 +1.4000482 + H2 +0.23193060 -0.37082053 -0.040099790 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3880571045808 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3156 11 0.57 1.0e+02% + Run_lcao lcao_line 6.3061 1 6.3 1.e+02% + Potential init_pot 0.28829 2 0.14 4.6% + PW_Basis recip2real 0.26955 16 0.017 4.3% + PW_Basis gathers_scatterp 0.12774 16 0.0080 2.0% + Potential v_of_rho 0.86391 13 0.066 14.% + XC_Functional v_xc 0.24471 14 0.017 3.9% + H_Hartree_pw v_hartree 0.58274 13 0.045 9.2% + PW_Basis real2recip 0.57325 38 0.015 9.1% + PW_Basis gatherp_scatters 0.24129 38 0.0063 3.8% + ORB_control set_orb_tables 1.1036 1 1.1 17.% + ORB_gen_tables gen_tables 1.1036 1 1.1 17.% + ORB_table_phi init_Table 0.48536 1 0.49 7.7% + ORB_table_phi cal_ST_Phi12_R 0.48050 126 0.0038 7.6% + ORB_table_beta init_Table_Beta 0.18706 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18559 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25084 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.24899 66 0.0038 3.9% + LOOP_ions opt_ions 4.6779 1 4.7 74.% + ESolver_KS_LCAO Run 4.1509 1 4.2 66.% + HSolverLCAO solve 2.1917 11 0.20 35.% + HamiltLCAO updateHk 1.1399 11 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1115 11 0.10 18.% + Gint_Gamma distri_vl_value 0.73030 11 0.066 12.% + Gint_Gamma distri_vl 1.9916 6 0.33 32.% + LCAO_Deepks cal_projected_DM 4.2881 13 0.33 68.% + LCAO_gen_fixedH add_v_delta 1.8585 6 0.31 29.% + LCAO_DESCRIPTOR add_v_delta 1.8585 6 0.31 29.% + ElecStateLCAO psiToRho 1.0339 11 0.094 16.% + Charge mix_rho 0.65054 10 0.065 10.% + LOOP_ions force_stress 0.52682 1 0.53 8.3% + Force_Stress_LCAO getForceStress 0.52680 1 0.53 8.3% + Force_LCAO_gamma ftable_gamma 0.31876 1 0.32 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:13 2022 + Finish Time : Wed Sep 28 11:13:19 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..fcaa54b7dfcf99cde1fdeb3a6f04b9ca00fac2b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123469 ima = 3.67412e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 1 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123543104326 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112259763147 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113005778604 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113189595598 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113179712791 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113186656187 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113183535764 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011318520736 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113184685738 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113184632204 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113184617071 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e0a127c17545c929f453822be6c9a78ac32c0536 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-5.668940763312 26.352265262625 13.755223032649 0 0 0 +H +0.0 +2 +-4.644737270577 26.298703810592 12.135564610266 0 0 0 +-6.541757518019 27.995298015847 13.681825066905 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/conv new file mode 100644 index 0000000000000000000000000000000000000000..c4755f2c86aa9bd063c52869a8c5a5e9c8f50ccb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/conv @@ -0,0 +1 @@ +299 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f0cc208da41d025c57287e64b5cad608359dd1b6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749839543 0.01241258512 1.244711171 1.339448553 1.467969442 0.008373597426 0.01796949565 0.0390870582 +-1.317664218e-18 0.0008984163421 0.002389521444 0.01145272369 0.0414648212 -4.5961591e-19 1.601700708e-06 4.966436352e-06 +0.001616144468 0.005842756051 + +H atom_index 1 n_descriptor 18 +1.180009394 0.03656740936 0.08562068687 0.1205832413 0.2967656108 0.01873168944 0.02426238361 0.04023194857 +-3.374904049e-18 3.420789495e-05 0.08087787872 0.1027922439 0.1127616098 1.220091403e-18 6.459151943e-06 0.01472156974 +0.02279554512 0.02720366594 + +H atom_index 2 n_descriptor 18 +1.223469889 0.03520082269 0.09867782358 0.1383886981 0.3129364922 0.02072785037 0.02680377482 0.03847058703 +2.633220924e-17 3.776119131e-05 0.09206973146 0.1145620377 0.1184648458 3.036563073e-18 5.088274601e-06 0.01351176618 +0.02459092465 0.02949358169 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0ff22b1e5861974feb6c87994158dec39e61bd0b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/log.scf @@ -0,0 +1,100 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:13 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087363 SEC) : SETUP UNITCELL + DONE(0.0990428 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.117107 SEC) : INIT PLANEWAVE + DONE(0.16568 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448021 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651956e+02 0.000000e+00 2.112e-01 4.906e-01 + GE2 -4.663846e+02 -1.189025e+00 9.877e-02 4.166e-01 + GE3 -4.663896e+02 -4.982788e-03 6.373e-02 4.703e-01 + GE4 -4.663883e+02 1.303328e-03 1.992e-03 3.629e-01 + GE5 -4.663879e+02 3.629855e-04 8.824e-04 3.579e-01 + GE6 -4.663881e+02 -1.447379e-04 1.809e-04 3.588e-01 + GE7 -4.663880e+02 3.278016e-05 2.543e-05 3.384e-01 + GE8 -4.663881e+02 -2.875235e-05 1.092e-05 3.391e-01 + GE9 -4.663881e+02 1.177946e-05 1.611e-06 3.397e-01 + GE10 -4.663881e+02 -2.377859e-06 2.651e-07 3.365e-01 + GE11 -4.663881e+02 -2.318829e-07 4.463e-08 2.802e-01 +E_delta_band = -6.79265646e-02 Ry = -9.24188324e-01 eV +E_delta_NN= -1.93617224e-01 Ry = -2.63429748e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3156 11 0.57 1e+02 % + Run_lcao lcao_line 6.3061 1 6.3 1e+02 % + Potential init_pot 0.28829 2 0.14 4.6 % + PW_Basis recip2real 0.26955 16 0.017 4.3 % + PW_Basis gathers_scatterp 0.12774 16 0.008 2 % + Potential v_of_rho 0.86391 13 0.066 14 % + XC_Functional v_xc 0.24471 14 0.017 3.9 % + H_Hartree_pw v_hartree 0.58274 13 0.045 9.2 % + PW_Basis real2recip 0.57325 38 0.015 9.1 % + PW_Basis gatherp_scatters 0.24129 38 0.0063 3.8 % + ORB_control set_orb_tables 1.1036 1 1.1 17 % + ORB_gen_tables gen_tables 1.1036 1 1.1 17 % + ORB_table_phi init_Table 0.48536 1 0.49 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.4805 126 0.0038 7.6 % + ORB_table_beta init_Table_Beta 0.18706 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18559 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.25084 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.24899 66 0.0038 3.9 % + LOOP_ions opt_ions 4.6779 1 4.7 74 % + ESolver_KS_LCAO Run 4.1509 1 4.2 66 % + HSolverLCAO solve 2.1917 11 0.2 35 % + HamiltLCAO updateHk 1.1399 11 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1115 11 0.1 18 % + Gint_Gamma distri_vl_value 0.7303 11 0.066 12 % + Gint_Gamma distri_vl 1.9916 6 0.33 32 % + LCAO_Deepks cal_projected_DM 4.2881 13 0.33 68 % + LCAO_gen_fixedH add_v_delta 1.8585 6 0.31 29 % + LCAO_DESCRIPTOR add_v_delta 1.8585 6 0.31 29 % + ElecStateLCAO psiToRho 1.0339 11 0.094 16 % + Charge mix_rho 0.65054 10 0.065 10 % + LOOP_ions force_stress 0.52682 1 0.53 8.3 % + Force_Stress_LCAO getForceStress 0.5268 1 0.53 8.3 % + Force_LCAO_gamma ftable_gamma 0.31876 1 0.32 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:13 2022 + FINISH Time : Wed Sep 28 11:13:19 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/299/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..52c7a95f28d575a94e1edb5f42adff44e8719f59 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.659842 0.0421791 0.291949 +H 0.632541 0.997652 0.249948 +H 0.720673 0.0464153 0.269965 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1e9c81ed2b53ece0fdf5e0b1f4716d8096709ee2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.258 2 + 2 -12.8961 2 + 3 -9.1999 2 + 4 -6.73836 2 + 5 1.22266 0 + 6 4.31568 0 + 7 11.0881 0 + 8 11.3466 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0afe6872bc952c227b99ca441e5763c5c311ce6d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:18 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.4755826355 1.18101440408 8.17457636807 0 0 0 0 + tauc_H1 17.711147798 27.9342597677 6.99854959507 0 0 0 0 + tauc_H2 20.1788331207 1.29962704668 7.55900974392 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.100100048428 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100508629893 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118794558716 (SEC) + + DONE : INIT CHARGE Time : 0.163504937305 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445959 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 337 ; sender_size of each process is: +144 144 49 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000456 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00182 + + Density error is 0.214107725431 + + Energy Rydberg eV + E_KohnSham -34.1903163863 -465.183119276 + E_Harris -34.3804346114 -467.769810431 + E_Fermi -0.40177494478 -5.46642856264 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000658945687987 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0014728777428 + + Density error is 0.098151400476 + + Energy Rydberg eV + E_KohnSham -34.2800815588 -466.404437104 + E_Harris -34.2869596943 -466.498018938 + E_Fermi -0.210895084343 -2.86937482726 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000692977659299 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00135248235617 + + Density error is 0.0631139347767 + + Energy Rydberg eV + E_KohnSham -34.2804583338 -466.409563391 + E_Harris -34.2849036365 -466.470044838 + E_Fermi -0.201240862544 -2.73802240103 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000768963023192 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113087583501 + + Density error is 0.00196033658055 + + Energy Rydberg eV + E_KohnSham -34.2804192016 -466.40903097 + E_Harris -34.2804202671 -466.409045467 + E_Fermi -0.16563474467 -2.25357631429 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000765530453006 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112961842687 + + Density error is 0.000940961853431 + + Energy Rydberg eV + E_KohnSham -34.2803631289 -466.408268062 + E_Harris -34.2803642349 -466.408283111 + E_Fermi -0.165173030338 -2.24729436852 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000766357049382 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112672944396 + + Density error is 0.000146804875927 + + Energy Rydberg eV + E_KohnSham -34.280394943 -466.408700915 + E_Harris -34.2803949641 -466.408701203 + E_Fermi -0.165015181143 -2.24514672005 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000766483087426 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112655706877 + + Density error is 3.50410035154e-05 + + Energy Rydberg eV + E_KohnSham -34.2803841159 -466.408553605 + E_Harris -34.2803841214 -466.40855368 + E_Fermi -0.164921384645 -2.24387055323 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000766461075621 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011265421063 + + Density error is 1.74879831838e-05 + + Energy Rydberg eV + E_KohnSham -34.2803875448 -466.408600258 + E_Harris -34.2803875462 -466.408600276 + E_Fermi -0.16495540505 -2.24433342458 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000766471573798 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112651649678 + + Density error is 3.0000821572e-06 + + Energy Rydberg eV + E_KohnSham -34.2803861598 -466.408581413 + E_Harris -34.2803861598 -466.408581414 + E_Fermi -0.164939246841 -2.24411358087 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00076646943671 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112650642037 + + Density error is 3.84857627456e-07 + + Energy Rydberg eV + E_KohnSham -34.2803864076 -466.408584786 + E_Harris -34.2803864076 -466.408584786 + E_Fermi -0.164936067986 -2.24407033032 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000766470494899 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112650672953 + + Density error is 1.48630126843e-07 + + Energy Rydberg eV + E_KohnSham -34.2803864503 -466.408585367 + E_Harris -34.2803864503 -466.408585367 + E_Fermi -0.164935943707 -2.24406863943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000766470837172 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011265064708 + + Density error is 1.07608941335e-08 + + Energy Rydberg eV + E_KohnSham -34.2803864528 -466.408585399 + E_Harris -34.2803864528 -466.408585399 + E_band -7.95142667105 -108.184709955 + E_one_elec -69.1553771365 -940.907176395 + E_Hartree +35.9726190114 +489.432590538 + E_xc -8.19884634139 -111.551027269 + E_Ewald +7.22581764467 +98.3122926765 + E_demet -3.66039737426e-73 -4.98022612342e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19459412987 -2.64758896358 + E_Fermi -0.164935811574 -2.24406684167 + + charge density convergence is achieved + final etot is -466.408585399 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2580 2.00000 + 2 -12.8961 2.00000 + 3 -9.19990 2.00000 + 4 -6.73836 2.00000 + 5 1.22266 0.00000 + 6 4.31568 0.00000 + 7 11.0881 0.00000 + 8 11.3466 0.00000 + + EFERMI = -2.244066841665029 eV + OUT.ABACUS/ final etot is -466.4085853994692 eV + correction force for each atom along direction 1 is 4.71385e-05 + correction force for each atom along direction 2 is -0.000133153 + correction force for each atom along direction 3 is -0.000176063 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0282052 -0.67951404 -0.36791441 + H1 +0.19778772 +0.52813583 +0.55442859 + H2 +0.83041749 +0.15137821 -0.18651418 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4085853994692 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4194 11 0.58 1.0e+02% + Run_lcao lcao_line 6.4094 1 6.4 1.e+02% + Potential init_pot 0.28337 2 0.14 4.4% + PW_Basis recip2real 0.28982 17 0.017 4.5% + PW_Basis gathers_scatterp 0.12724 17 0.0075 2.0% + Potential v_of_rho 1.0738 14 0.077 17.% + XC_Functional v_xc 0.32071 15 0.021 5.0% + H_Hartree_pw v_hartree 0.70452 14 0.050 11.% + PW_Basis real2recip 0.75651 41 0.018 12.% + PW_Basis gatherp_scatters 0.29817 41 0.0073 4.6% + ORB_control set_orb_tables 1.0987 1 1.1 17.% + ORB_gen_tables gen_tables 1.0987 1 1.1 17.% + ORB_table_phi init_Table 0.47740 1 0.48 7.4% + ORB_table_phi cal_ST_Phi12_R 0.47221 126 0.0037 7.4% + ORB_table_beta init_Table_Beta 0.18409 1 0.18 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18257 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.24748 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.24550 66 0.0037 3.8% + LOOP_ions opt_ions 4.7860 1 4.8 75.% + ESolver_KS_LCAO Run 4.3293 1 4.3 67.% + HSolverLCAO solve 1.6549 12 0.14 26.% + HamiltLCAO updateHk 0.94060 12 0.078 15.% + LCAO_Hamilt cal_Hgamma 0.91101 12 0.076 14.% + Gint_interface cal_gint 1.1818 25 0.047 18.% + Gint_Gamma distri_vl 2.2690 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.6270 14 0.33 72.% + LCAO_gen_fixedH add_v_delta 2.1219 6 0.35 33.% + LCAO_DESCRIPTOR add_v_delta 2.1220 6 0.35 33.% + ElecStateLCAO psiToRho 0.69436 12 0.058 11.% + Charge mix_rho 0.98724 11 0.090 15.% + LOOP_ions force_stress 0.45652 1 0.46 7.1% + Force_Stress_LCAO getForceStress 0.45649 1 0.46 7.1% + Force_LCAO_gamma ftable_gamma 0.24108 1 0.24 3.8% + Force_LCAO_gamma cal_fvl_dphi 0.20879 1 0.21 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:18 2022 + Finish Time : Wed Sep 28 11:10:24 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..015060e57c31f53937bf1b45c20f90db6d7c1f47 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123994 ima = 3.65828e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123116905102 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111824185812 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011245754876 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011269998572 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112656262576 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112681563645 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112675894146 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112678619616 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112677838779 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011267772222 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112677708591 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011267770156 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/STRU new file mode 100644 index 0000000000000000000000000000000000000000..30694d5ff3dd1ad05c47d96401abdbe030f4eca6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.524417364530 1.181014404066 8.174576368055 0 0 0 +H +0.0 +2 +-10.288852201958 -0.065740232350 6.998549595062 0 0 0 +-7.821166879247 1.299627046683 7.559009743911 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/conv new file mode 100644 index 0000000000000000000000000000000000000000..57fe534564c694257d2bf5413ba64ea8cf8348e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/conv @@ -0,0 +1 @@ +3 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0726c2e941bc9b8005580b68fc98c8287695a770 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750836444 0.01265930872 1.265203567 1.355741645 1.469161233 0.008745217615 0.01790537576 0.03908336729 +-1.165518243e-18 0.0009813019866 0.00262500355 0.01237157778 0.04492886596 4.164614502e-19 2.123217456e-06 6.099363083e-06 +0.001615797328 0.006000187897 + +H atom_index 1 n_descriptor 18 +1.212879898 0.03567944767 0.09635747203 0.1334037786 0.3079786765 0.0206426348 0.02611551162 0.03893778948 +1.254622581e-17 4.256405682e-05 0.09167508973 0.1138179589 0.1142490482 -1.397485548e-18 5.715961922e-06 0.01385787869 +0.02484077456 0.02894224419 + +H atom_index 2 n_descriptor 18 +1.261581666 0.03403237204 0.112715494 0.1553185386 0.3244891298 0.0229411806 0.02896418282 0.03725794397 +-5.473486979e-18 4.704385268e-05 0.1038140308 0.115932087 0.1332688049 -3.056405695e-18 3.254315793e-06 0.01318133705 +0.02671227385 0.03126256584 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..971cae8cf78b3ed67e3f19d297050eea30aff01a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/e_base.npy 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/dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..d3e75ac23381503c9e67c1eeee57b5ba07ced586 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..f5d6bf0eca66c261da3d4d2fe12cc0b6a8a3d329 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:18 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.100124 SEC) : SETUP UNITCELL + DONE(0.100527 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118817 SEC) : INIT PLANEWAVE + DONE(0.163658 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44606 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651831e+02 0.000000e+00 2.141e-01 4.703e-01 + GE2 -4.664044e+02 -1.221318e+00 9.815e-02 4.180e-01 + GE3 -4.664096e+02 -5.126287e-03 6.311e-02 4.882e-01 + GE4 -4.664090e+02 5.324213e-04 1.960e-03 3.458e-01 + GE5 -4.664083e+02 7.629080e-04 9.410e-04 3.453e-01 + GE6 -4.664087e+02 -4.328530e-04 1.468e-04 3.388e-01 + GE7 -4.664086e+02 1.473102e-04 3.504e-05 3.288e-01 + GE8 -4.664086e+02 -4.665341e-05 1.749e-05 3.221e-01 + GE9 -4.664086e+02 1.884464e-05 3.000e-06 3.206e-01 + GE10 -4.664086e+02 -3.372312e-06 3.849e-07 3.206e-01 + GE11 -4.664086e+02 -5.809923e-07 1.486e-07 3.196e-01 + GE12 -4.664086e+02 -3.275847e-08 1.076e-08 2.484e-01 +E_delta_band = -6.99944989e-02 Ry = -9.52324014e-01 eV +E_delta_NN= -1.94594130e-01 Ry = -2.64758896e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4194 11 0.58 1e+02 % + Run_lcao lcao_line 6.4094 1 6.4 1e+02 % + Potential init_pot 0.28337 2 0.14 4.4 % + PW_Basis recip2real 0.28982 17 0.017 4.5 % + PW_Basis gathers_scatterp 0.12724 17 0.0075 2 % + Potential v_of_rho 1.0738 14 0.077 17 % + XC_Functional v_xc 0.32071 15 0.021 5 % + H_Hartree_pw v_hartree 0.70452 14 0.05 11 % + PW_Basis real2recip 0.75651 41 0.018 12 % + PW_Basis gatherp_scatters 0.29817 41 0.0073 4.6 % + ORB_control set_orb_tables 1.0987 1 1.1 17 % + ORB_gen_tables gen_tables 1.0987 1 1.1 17 % + ORB_table_phi init_Table 0.4774 1 0.48 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.47221 126 0.0037 7.4 % + ORB_table_beta init_Table_Beta 0.18409 1 0.18 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18257 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.24748 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.2455 66 0.0037 3.8 % + LOOP_ions opt_ions 4.786 1 4.8 75 % + ESolver_KS_LCAO Run 4.3293 1 4.3 67 % + HSolverLCAO solve 1.6549 12 0.14 26 % + HamiltLCAO updateHk 0.9406 12 0.078 15 % + LCAO_Hamilt cal_Hgamma 0.91101 12 0.076 14 % + Gint_interface cal_gint 1.1818 25 0.047 18 % + Gint_Gamma distri_vl 2.269 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.627 14 0.33 72 % + LCAO_gen_fixedH add_v_delta 2.1219 6 0.35 33 % + LCAO_DESCRIPTOR add_v_delta 2.122 6 0.35 33 % + ElecStateLCAO psiToRho 0.69436 12 0.058 11 % + Charge mix_rho 0.98724 11 0.09 15 % + LOOP_ions force_stress 0.45652 1 0.46 7.1 % + Force_Stress_LCAO getForceStress 0.45649 1 0.46 7.1 % + Force_LCAO_gamma ftable_gamma 0.24108 1 0.24 3.8 % + Force_LCAO_gamma cal_fvl_dphi 0.20879 1 0.21 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:18 2022 + FINISH Time : Wed Sep 28 11:10:24 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/3/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c46287bda3c6ab344fd4256a7949bcc6d0ce35d6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.504727 0.475208 0.434 +H 0.481128 0.448568 0.379333 +H 0.552544 0.513135 0.414916 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..10174ba5d1709f03de3965474804af5de77b346f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4232 2 + 2 -13.2312 2 + 3 -9.08536 2 + 4 -6.77414 2 + 5 1.43347 0 + 6 4.65095 0 + 7 11.0389 0 + 8 11.2829 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..2edd4f52c4f46113840d729da30fb4ce0a9155be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:11 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.1323531576 13.3058306085 12.1519926032 0 0 0 0 + tauc_H1 13.4715967342 12.5599004408 10.6213202824 0 0 0 0 + tauc_H2 15.471239078 14.3677842883 11.6176542104 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0731716944639 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877975531835 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104307433135 (SEC) + + DONE : INIT CHARGE Time : 0.146276475099 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.390534 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0015 + + Density error is 0.216878054519 + + Energy Rydberg eV + E_KohnSham -34.1887829278 -465.162255503 + E_Harris -34.3847809123 -467.828944889 + E_Fermi -0.414612014134 -5.64108585148 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00137598631942 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00143646263881 + + Density error is 0.0977711111429 + + Energy Rydberg eV + E_KohnSham -34.2796071148 -466.397981962 + E_Harris -34.2862477061 -466.488331842 + E_Fermi -0.222067692119 -3.02138595453 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00129578474422 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133745501362 + + Density error is 0.0625293344742 + + Energy Rydberg eV + E_KohnSham -34.2798876806 -466.401799256 + E_Harris -34.2841561958 -466.459875384 + E_Fermi -0.209036812812 -2.844091746 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116688537147 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117359875745 + + Density error is 0.00203470810104 + + Energy Rydberg eV + E_KohnSham -34.2799103803 -466.402108101 + E_Harris -34.279912346 -466.402134846 + E_Fermi -0.173385375745 -2.35902906 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116761765136 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117301741433 + + Density error is 0.00091168106506 + + Energy Rydberg eV + E_KohnSham -34.2798385669 -466.401131029 + E_Harris -34.2798405178 -466.401157573 + E_Fermi -0.172349210784 -2.34493131247 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116592809335 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117119102224 + + Density error is 0.00014651395797 + + Energy Rydberg eV + E_KohnSham -34.2798863317 -466.401780903 + E_Harris -34.279886384 -466.401781615 + E_Fermi -0.172539091413 -2.34751477096 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116591257956 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117107441221 + + Density error is 4.34849878542e-05 + + Energy Rydberg eV + E_KohnSham -34.2798691489 -466.40154712 + E_Harris -34.2798691594 -466.401547263 + E_Fermi -0.172383351237 -2.34539581716 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116587554842 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117106397519 + + Density error is 1.57160210217e-05 + + Energy Rydberg eV + E_KohnSham -34.2798734351 -466.401605436 + E_Harris -34.279873436 -466.401605449 + E_Fermi -0.172435387153 -2.34610380212 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116585909539 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117103881988 + + Density error is 1.88559370815e-06 + + Energy Rydberg eV + E_KohnSham -34.2798719822 -466.401585669 + E_Harris -34.2798719822 -466.401585669 + E_Fermi -0.172418614915 -2.34587560411 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116585711697 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117103557042 + + Density error is 1.99545420915e-07 + + Energy Rydberg eV + E_KohnSham -34.2798721782 -466.401588335 + E_Harris -34.2798721782 -466.401588335 + E_Fermi -0.172416782159 -2.34585066819 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116585779415 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117103617327 + + Density error is 8.49132552309e-08 + + Energy Rydberg eV + E_KohnSham -34.2798722112 -466.401588785 + E_Harris -34.2798722112 -466.401588785 + E_band -8.01339429372 -109.027822715 + E_one_elec -69.6025752121 -946.991618357 + E_Hartree +36.1881433868 +492.364950102 + E_xc -8.23356396192 -112.02338473 + E_Ewald +7.49181666646 +101.931395035 + E_demet -1.90813749694e-86 -2.59615425259e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195369086332 -2.65813278717 + E_Fermi -0.172416793586 -2.34585082366 + + charge density convergence is achieved + final etot is -466.401588785 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4232 2.00000 + 2 -13.2312 2.00000 + 3 -9.08536 2.00000 + 4 -6.77414 2.00000 + 5 1.43347 0.00000 + 6 4.65095 0.00000 + 7 11.0389 0.00000 + 8 11.2829 0.00000 + + EFERMI = -2.345850823658635 eV + OUT.ABACUS/ final etot is -466.4015887847899 eV + correction force for each atom along direction 1 is 9.96367e-05 + correction force for each atom along direction 2 is 8.99613e-05 + correction force for each atom along direction 3 is -0.000117358 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.98271178 -0.72419119 +0.83044470 + H1 -0.13453138 -0.15812961 -0.35897259 + H2 +1.1172432 +0.88232080 -0.47147211 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4015887847899 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6982 11 0.52 1.0e+02% + Run_lcao lcao_line 5.6903 1 5.7 1.e+02% + Potential init_pot 0.24213 2 0.12 4.2% + PW_Basis recip2real 0.22698 16 0.014 4.0% + PW_Basis gathers_scatterp 0.10806 16 0.0068 1.9% + Potential v_of_rho 0.89345 13 0.069 16.% + XC_Functional v_xc 0.29316 14 0.021 5.1% + H_Hartree_pw v_hartree 0.56657 13 0.044 9.9% + PW_Basis real2recip 0.59501 38 0.016 10.% + PW_Basis gatherp_scatters 0.25113 38 0.0066 4.4% + ORB_control set_orb_tables 0.89172 1 0.89 16.% + ORB_gen_tables gen_tables 0.89172 1 0.89 16.% + ORB_table_phi init_Table 0.37100 1 0.37 6.5% + ORB_table_phi cal_ST_Phi12_R 0.36682 126 0.0029 6.4% + ORB_table_beta init_Table_Beta 0.15323 1 0.15 2.7% + ORB_table_beta VNL_PhiBeta_R 0.15193 56 0.0027 2.7% + ORB_table_alpha init_Table_Alpha 0.20879 1 0.21 3.7% + ORB_table_alpha S_PhiAlpha_R 0.20712 66 0.0031 3.6% + LOOP_ions opt_ions 4.3367 1 4.3 76.% + ESolver_KS_LCAO Run 3.8808 1 3.9 68.% + HSolverLCAO solve 1.7013 11 0.15 30.% + HamiltLCAO updateHk 0.93481 11 0.085 16.% + LCAO_Hamilt cal_Hgamma 0.90561 11 0.082 16.% + Gint_interface cal_gint 0.12185 23 0.0053 2.1% + Gint_Gamma distri_vl_value 0.49185 11 0.045 8.6% + Gint_Gamma distri_vl 1.8828 6 0.31 33.% + LCAO_Deepks cal_projected_DM 4.0293 13 0.31 71.% + LCAO_gen_fixedH add_v_delta 1.7543 6 0.29 31.% + LCAO_DESCRIPTOR add_v_delta 1.7544 6 0.29 31.% + ElecStateLCAO psiToRho 0.75055 11 0.068 13.% + Charge mix_rho 0.74968 10 0.075 13.% + LOOP_ions force_stress 0.45571 1 0.46 8.0% + Force_Stress_LCAO getForceStress 0.45569 1 0.46 8.0% + Force_LCAO_gamma ftable_gamma 0.25829 1 0.26 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:11 2022 + Finish Time : Wed Sep 28 11:12:17 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..48940e98af8646992768b7ec706eb0f53172a1aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124021 ima = 3.68782e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123062472163 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112133544543 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112595984777 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001128654057 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112800108723 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112838533917 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112831045508 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112834090465 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112833503671 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112833421585 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112833415904 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/STRU new file mode 100644 index 0000000000000000000000000000000000000000..2fd881dd8082d259a903d3cc5c7f76dc7a0ad605 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.867646842429 13.305830608538 12.151992603234 0 0 0 +H +0.0 +2 +-14.528403265768 12.559900440809 10.621320282346 0 0 0 +-12.528760922024 14.367784288333 11.617654210414 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/conv new file mode 100644 index 0000000000000000000000000000000000000000..3e63a8a7995e00081393d748f8a10dd58a4816fb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/conv @@ -0,0 +1 @@ +30 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..40590bacb368f10cfc97356e994e29a6d584f6de --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748286095 0.012761391 1.286374906 1.374013908 1.469981637 0.008456165687 0.01917296812 0.03899682884 +2.538025004e-19 0.001145905909 0.002647087998 0.01279285232 0.04626223693 4.607577992e-19 2.105374268e-06 6.063200603e-06 +0.001675164569 0.00591222194 + +H atom_index 1 n_descriptor 18 +1.249959286 0.03410859685 0.1085375379 0.1500788215 0.3211350459 0.0222657609 0.02832714497 0.03723690982 +1.342056462e-17 4.699624495e-05 0.1028481745 0.1148339688 0.1289620646 -2.394962782e-18 4.243991234e-06 0.01313645215 +0.02655049028 0.03079618938 + +H atom_index 2 n_descriptor 18 +1.278475534 0.0331412922 0.1188492854 0.1638538675 0.3297887184 0.02356639373 0.02997098028 0.03654764985 +1.114383426e-17 4.967292521e-05 0.1076239627 0.1182364523 0.1407629988 -1.169526299e-17 2.645487211e-06 0.01320194991 +0.02754816401 0.03199445298 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e3a5b3c32f0b4caf823069ff5c83f6b65c48b842 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:11 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0731877 SEC) : SETUP UNITCELL + DONE(0.0878116 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104321 SEC) : INIT PLANEWAVE + DONE(0.146386 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.390577 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651623e+02 0.000000e+00 2.169e-01 4.422e-01 + GE2 -4.663980e+02 -1.235726e+00 9.777e-02 3.946e-01 + GE3 -4.664018e+02 -3.817294e-03 6.253e-02 4.593e-01 + GE4 -4.664021e+02 -3.088446e-04 2.035e-03 3.384e-01 + GE5 -4.664011e+02 9.770717e-04 9.117e-04 3.390e-01 + GE6 -4.664018e+02 -6.498735e-04 1.465e-04 3.293e-01 + GE7 -4.664015e+02 2.337833e-04 4.348e-05 3.235e-01 + GE8 -4.664016e+02 -5.831643e-05 1.572e-05 3.169e-01 + GE9 -4.664016e+02 1.976718e-05 1.886e-06 3.183e-01 + GE10 -4.664016e+02 -2.666287e-06 1.995e-07 3.174e-01 + GE11 -4.664016e+02 -4.496397e-07 8.491e-08 2.490e-01 +E_delta_band = -7.16759958e-02 Ry = -9.75201952e-01 eV +E_delta_NN= -1.95369086e-01 Ry = -2.65813279e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6982 11 0.52 1e+02 % + Run_lcao lcao_line 5.6903 1 5.7 1e+02 % + Potential init_pot 0.24213 2 0.12 4.2 % + PW_Basis recip2real 0.22698 16 0.014 4 % + PW_Basis gathers_scatterp 0.10806 16 0.0068 1.9 % + Potential v_of_rho 0.89345 13 0.069 16 % + XC_Functional v_xc 0.29316 14 0.021 5.1 % + H_Hartree_pw v_hartree 0.56657 13 0.044 9.9 % + PW_Basis real2recip 0.59501 38 0.016 10 % + PW_Basis gatherp_scatters 0.25113 38 0.0066 4.4 % + ORB_control set_orb_tables 0.89172 1 0.89 16 % + ORB_gen_tables gen_tables 0.89172 1 0.89 16 % + ORB_table_phi init_Table 0.371 1 0.37 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.36682 126 0.0029 6.4 % + ORB_table_beta init_Table_Beta 0.15323 1 0.15 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.15193 56 0.0027 2.7 % + ORB_table_alpha init_Table_Alpha 0.20879 1 0.21 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.20712 66 0.0031 3.6 % + LOOP_ions opt_ions 4.3367 1 4.3 76 % + ESolver_KS_LCAO Run 3.8808 1 3.9 68 % + HSolverLCAO solve 1.7013 11 0.15 30 % + HamiltLCAO updateHk 0.93481 11 0.085 16 % + LCAO_Hamilt cal_Hgamma 0.90561 11 0.082 16 % + Gint_interface cal_gint 0.12185 23 0.0053 2.1 % + Gint_Gamma distri_vl_value 0.49185 11 0.045 8.6 % + Gint_Gamma distri_vl 1.8828 6 0.31 33 % + LCAO_Deepks cal_projected_DM 4.0293 13 0.31 71 % + LCAO_gen_fixedH add_v_delta 1.7543 6 0.29 31 % + LCAO_DESCRIPTOR add_v_delta 1.7544 6 0.29 31 % + ElecStateLCAO psiToRho 0.75055 11 0.068 13 % + Charge mix_rho 0.74968 10 0.075 13 % + LOOP_ions force_stress 0.45571 1 0.46 8 % + Force_Stress_LCAO getForceStress 0.45569 1 0.46 8 % + Force_LCAO_gamma ftable_gamma 0.25829 1 0.26 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:11 2022 + FINISH Time : Wed Sep 28 11:12:17 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/30/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..31b4364aaae0f1947e6128b6e0c9971a9f666639 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.511072 0.512486 0.438707 +H 0.464371 0.468809 0.443985 +H 0.525326 0.516251 0.37075 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..a3a1e43034985f5f51b428c2fe8b8bd80b057f44 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0694 2 + 2 -12.9157 2 + 3 -9.01321 2 + 4 -6.6897 2 + 5 1.02403 0 + 6 4.16862 0 + 7 11.1253 0 + 8 11.3557 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..2f99e645b60d23425c6fd627771b1f579dcce82b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:13 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.310028745 14.3496116354 12.2838012053 0 0 0 0 + tauc_H1 13.0023840705 13.1266483132 12.4315687001 0 0 0 0 + tauc_H2 14.7091363034 14.4550370646 10.3809862986 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0863061652411 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0983379135371 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116812676208 (SEC) + + DONE : INIT CHARGE Time : 0.166836515854 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448804 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000561 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000673 + + Density error is 0.21356465299 + + Energy Rydberg eV + E_KohnSham -34.1852021867 -465.113537021 + E_Harris -34.3745771916 -467.690116147 + E_Fermi -0.393593874212 -5.35511938718 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000915358441568 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000927604252167 + + Density error is 0.098885444454 + + Energy Rydberg eV + E_KohnSham -34.2749479094 -466.334590221 + E_Harris -34.281995435 -466.430476726 + E_Fermi -0.203168583594 -2.76425039147 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000886590959606 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0008955999345 + + Density error is 0.0637447356324 + + Energy Rydberg eV + E_KohnSham -34.2753463084 -466.340010717 + E_Harris -34.2798595724 -466.401416824 + E_Fermi -0.195342508151 -2.65777117246 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00086320276923 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000863249186348 + + Density error is 0.00202211198701 + + Energy Rydberg eV + E_KohnSham -34.2752723229 -466.339004093 + E_Harris -34.2752749785 -466.339040224 + E_Fermi -0.159962232616 -2.17639782838 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000862208671955 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000861934639801 + + Density error is 0.000920017437347 + + Energy Rydberg eV + E_KohnSham -34.2752328104 -466.338466498 + E_Harris -34.2752331097 -466.33847057 + E_Fermi -0.159716958133 -2.17306069784 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000861955491728 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000861515660751 + + Density error is 0.000186544691841 + + Energy Rydberg eV + E_KohnSham -34.2752504739 -466.338706823 + E_Harris -34.2752505008 -466.338707188 + E_Fermi -0.159351578417 -2.16808945176 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000862207308303 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000861737658915 + + Density error is 3.49415065839e-05 + + Energy Rydberg eV + E_KohnSham -34.2752445687 -466.338626477 + E_Harris -34.2752445725 -466.33862653 + E_Fermi -0.159317159474 -2.16762115802 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000862111742823 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000861647003869 + + Density error is 1.33427219496e-05 + + Energy Rydberg eV + E_KohnSham -34.2752479027 -466.33867184 + E_Harris -34.2752479035 -466.338671849 + E_Fermi -0.159335141158 -2.16786581139 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000862120573736 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000861653604883 + + Density error is 2.34840301636e-06 + + Energy Rydberg eV + E_KohnSham -34.2752467901 -466.338656702 + E_Harris -34.2752467901 -466.338656702 + E_Fermi -0.159322222625 -2.16769004573 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000862121881855 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000861654340767 + + Density error is 5.80913690095e-07 + + Energy Rydberg eV + E_KohnSham -34.2752469897 -466.338659418 + E_Harris -34.2752469897 -466.338659418 + E_Fermi -0.15932035586 -2.16766464709 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000862122743762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00086165518212 + + Density error is 2.00896888211e-07 + + Energy Rydberg eV + E_KohnSham -34.2752469986 -466.338659539 + E_Harris -34.2752469986 -466.338659539 + E_Fermi -0.159320080685 -2.16766090313 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00086212305369 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000861655465851 + + Density error is 1.18182472392e-08 + + Energy Rydberg eV + E_KohnSham -34.2752470023 -466.338659589 + E_Harris -34.2752470023 -466.338659589 + E_band -7.89200009004 -107.376169841 + E_one_elec -68.8433279771 -936.661529771 + E_Hartree +35.8316816958 +487.515039986 + E_xc -8.17666056185 -111.249174253 + E_Ewald +7.03828752354 +95.7608144824 + E_demet -2.01514704835e-62 -2.74174821654e-61 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194068774789 -2.64044114101 + E_Fermi -0.159319883578 -2.16765822135 + + charge density convergence is achieved + final etot is -466.338659589 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0694 2.00000 + 2 -12.9157 2.00000 + 3 -9.01321 2.00000 + 4 -6.68970 2.00000 + 5 1.02403 0.00000 + 6 4.16862 0.00000 + 7 11.1253 0.00000 + 8 11.3557 0.00000 + + EFERMI = -2.167658221351176 eV + OUT.ABACUS/ final etot is -466.3386595892669 eV + correction force for each atom along direction 1 is -0.000109980 + correction force for each atom along direction 2 is -2.75317e-05 + correction force for each atom along direction 3 is -0.000113412 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.5561982 +1.1693304 -2.1931539 + H1 -0.98590611 -0.94616050 -0.039061646 + H2 -0.57029204 -0.22316992 +2.2322155 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3386595892669 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4608 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4516 1 6.5 1.e+02% + Potential init_pot 0.28450 2 0.14 4.4% + PW_Basis recip2real 0.29281 17 0.017 4.5% + PW_Basis gathers_scatterp 0.13900 17 0.0082 2.2% + Potential v_of_rho 1.0544 14 0.075 16.% + XC_Functional v_xc 0.31852 15 0.021 4.9% + H_Hartree_pw v_hartree 0.69434 14 0.050 11.% + PW_Basis real2recip 0.70986 41 0.017 11.% + PW_Basis gatherp_scatters 0.31447 41 0.0077 4.9% + ORB_control set_orb_tables 1.1049 1 1.1 17.% + ORB_gen_tables gen_tables 1.1049 1 1.1 17.% + ORB_table_phi init_Table 0.48309 1 0.48 7.5% + ORB_table_phi cal_ST_Phi12_R 0.47781 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18928 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18770 56 0.0034 2.9% + ORB_table_alpha init_Table_Alpha 0.24840 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24645 66 0.0037 3.8% + LOOP_ions opt_ions 4.8198 1 4.8 75.% + ESolver_KS_LCAO Run 4.3337 1 4.3 67.% + HSolverLCAO solve 1.8474 12 0.15 29.% + HamiltLCAO updateHk 1.0087 12 0.084 16.% + LCAO_Hamilt cal_Hgamma 0.97927 12 0.082 15.% + Gint_interface cal_gint 0.16350 25 0.0065 2.5% + Gint_Gamma distri_vl_value 0.51519 12 0.043 8.0% + Gint_Gamma distri_vl 2.2722 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.5111 14 0.32 70.% + LCAO_gen_fixedH add_v_delta 2.1292 6 0.35 33.% + LCAO_DESCRIPTOR add_v_delta 2.1293 6 0.35 33.% + ElecStateLCAO psiToRho 0.80916 12 0.067 13.% + Charge mix_rho 0.83613 11 0.076 13.% + LOOP_ions force_stress 0.48590 1 0.49 7.5% + Force_Stress_LCAO getForceStress 0.48588 1 0.49 7.5% + Force_LCAO_gamma ftable_gamma 0.26835 1 0.27 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:13 2022 + Finish Time : Wed Sep 28 11:10:19 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..5011b46942c399295ecf6ca0aee27b58f8a49163 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123806 ima = 3.67554e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123678367883 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112332305449 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113044034145 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113259086483 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113237609422 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113251430261 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113245692271 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113247922968 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113247351204 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113247312269 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113247292028 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113247281413 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/STRU new file mode 100644 index 0000000000000000000000000000000000000000..fa6fdb802d63a5399cc7314f65416f01bdf9ad48 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.689971255008 14.349611635388 12.283801205269 0 0 0 +H +0.0 +2 +-14.997615929458 13.126648313187 12.431568700139 0 0 0 +-13.290863696629 14.455037064618 10.380986298615 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/conv new file mode 100644 index 0000000000000000000000000000000000000000..281c64199c87334032e1561e600b16b7a8a18685 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/conv @@ -0,0 +1 @@ +31 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..296249e8f2e1d90dbbc9484cc04fd01818554bc6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748679798 0.01241583412 1.246505563 1.357503894 1.4684615 0.008297691775 0.01867339129 0.03905830581 +-2.795103567e-18 0.0009692251344 0.002419580746 0.01149149162 0.04238640647 5.318307656e-19 1.544400118e-06 4.993090029e-06 +0.001631377471 0.005743809027 + +H atom_index 1 n_descriptor 18 +1.273895015 0.03331579911 0.115886146 0.1620255104 0.3295049769 0.02293140812 0.02976408476 0.03677611839 +-6.334178288e-18 4.211422293e-05 0.1047588292 0.1167351391 0.1389350678 1.721750596e-17 2.852470091e-06 0.0130848448 +0.02653267489 0.03180209015 + +H atom_index 2 n_descriptor 18 +1.154916395 0.03709127028 0.0787440411 0.1114301615 0.2872689384 0.01755236053 0.0228530229 0.04107351296 +-4.692454788e-18 3.234334078e-05 0.07525612978 0.09471987316 0.1111073161 -2.148754276e-18 7.016817195e-06 0.01552269108 +0.02179299821 0.02584711883 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..8fc1a96e73c07319e6e7ed2bce859eec0b6e55f7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:13 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0863303 SEC) : SETUP UNITCELL + DONE(0.0983611 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116834 SEC) : INIT PLANEWAVE + DONE(0.166967 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448866 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651135e+02 0.000000e+00 2.136e-01 4.821e-01 + GE2 -4.663346e+02 -1.221053e+00 9.889e-02 4.159e-01 + GE3 -4.663400e+02 -5.420496e-03 6.374e-02 4.850e-01 + GE4 -4.663390e+02 1.006624e-03 2.022e-03 3.438e-01 + GE5 -4.663385e+02 5.375951e-04 9.200e-04 3.430e-01 + GE6 -4.663387e+02 -2.403243e-04 1.865e-04 3.386e-01 + GE7 -4.663386e+02 8.034520e-05 3.494e-05 3.241e-01 + GE8 -4.663387e+02 -4.536210e-05 1.334e-05 3.222e-01 + GE9 -4.663387e+02 1.513796e-05 2.348e-06 3.209e-01 + GE10 -4.663387e+02 -2.715931e-06 5.809e-07 3.211e-01 + GE11 -4.663387e+02 -1.211640e-07 2.009e-07 3.201e-01 + GE12 -4.663387e+02 -5.059362e-08 1.182e-08 2.552e-01 +E_delta_band = -6.88410920e-02 Ry = -9.36631107e-01 eV +E_delta_NN= -1.94068775e-01 Ry = -2.64044114e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4608 11 0.59 1e+02 % + Run_lcao lcao_line 6.4516 1 6.5 1e+02 % + Potential init_pot 0.2845 2 0.14 4.4 % + PW_Basis recip2real 0.29281 17 0.017 4.5 % + PW_Basis gathers_scatterp 0.139 17 0.0082 2.2 % + Potential v_of_rho 1.0544 14 0.075 16 % + XC_Functional v_xc 0.31852 15 0.021 4.9 % + H_Hartree_pw v_hartree 0.69434 14 0.05 11 % + PW_Basis real2recip 0.70986 41 0.017 11 % + PW_Basis gatherp_scatters 0.31447 41 0.0077 4.9 % + ORB_control set_orb_tables 1.1049 1 1.1 17 % + ORB_gen_tables gen_tables 1.1049 1 1.1 17 % + ORB_table_phi init_Table 0.48309 1 0.48 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.47781 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18928 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.1877 56 0.0034 2.9 % + ORB_table_alpha init_Table_Alpha 0.2484 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24645 66 0.0037 3.8 % + LOOP_ions opt_ions 4.8198 1 4.8 75 % + ESolver_KS_LCAO Run 4.3337 1 4.3 67 % + HSolverLCAO solve 1.8474 12 0.15 29 % + HamiltLCAO updateHk 1.0087 12 0.084 16 % + LCAO_Hamilt cal_Hgamma 0.97927 12 0.082 15 % + Gint_interface cal_gint 0.1635 25 0.0065 2.5 % + Gint_Gamma distri_vl_value 0.51519 12 0.043 8 % + Gint_Gamma distri_vl 2.2722 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.5111 14 0.32 70 % + LCAO_gen_fixedH add_v_delta 2.1292 6 0.35 33 % + LCAO_DESCRIPTOR add_v_delta 2.1293 6 0.35 33 % + ElecStateLCAO psiToRho 0.80916 12 0.067 13 % + Charge mix_rho 0.83613 11 0.076 13 % + LOOP_ions force_stress 0.4859 1 0.49 7.5 % + Force_Stress_LCAO getForceStress 0.48588 1 0.49 7.5 % + Force_LCAO_gamma ftable_gamma 0.26835 1 0.27 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:13 2022 + FINISH Time : Wed Sep 28 11:10:19 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/31/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a922823e60766feee87c703e02d0a895e5158fe5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.512995 0.56089 0.429952 +H 0.500338 0.533567 0.490312 +H 0.474826 0.528019 0.391544 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..4bcafe8f3ec77b8a170f115eab33d2b1a2c28833 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3543 2 + 2 -12.9872 2 + 3 -9.19375 2 + 4 -6.75667 2 + 5 1.26142 0 + 6 4.47182 0 + 7 11.0649 0 + 8 11.3135 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..315f447ba4ea71526f5f037f160d3a39a804f076 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:25 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.3638693699 15.7049272712 12.038647551 0 0 0 0 + tauc_H1 14.0094759488 14.9398687866 13.728744512 0 0 0 0 + tauc_H2 13.2951353735 14.7845404459 10.9632284132 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870091822504 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0945020430916 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.112766874476 (SEC) + + DONE : INIT CHARGE Time : 0.161756102718 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.439858 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 10 + nCol_in_proc = 10 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 10 + nCol_in_proc = 8 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 8 + nCol_in_proc = 10 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 8 + nCol_in_proc = 8 +receiver_size is 324 ; receiver_size of each process is: +100 80 80 64 +sender_size is 388 ; sender_size of each process is: +100 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00104 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0013 + + Density error is 0.2152095321 + + Energy Rydberg eV + E_KohnSham -34.1869977255 -465.13796658 + E_Harris -34.3800008908 -467.763909359 + E_Fermi -0.408114787635 -5.55268654989 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00124098804604 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00135615609222 + + Density error is 0.0980050635417 + + Energy Rydberg eV + E_KohnSham -34.277356672 -466.367363118 + E_Harris -34.2841574386 -466.459892295 + E_Fermi -0.216702578668 -2.94838984118 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00117500476798 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00127644301244 + + Density error is 0.0628594857672 + + Energy Rydberg eV + E_KohnSham -34.2776815749 -466.371783648 + E_Harris -34.2820733452 -466.431536749 + E_Fermi -0.205661819354 -2.79817260427 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107754453111 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115465868476 + + Density error is 0.00198504862117 + + Energy Rydberg eV + E_KohnSham -34.2776657219 -466.371567957 + E_Harris -34.2776669802 -466.371585077 + E_Fermi -0.169895402947 -2.31154554408 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00108014926515 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115682470687 + + Density error is 0.000898566040056 + + Energy Rydberg eV + E_KohnSham -34.2776066179 -466.370763806 + E_Harris -34.2776076663 -466.370778071 + E_Fermi -0.169264151401 -2.30295692619 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107858658113 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115498797246 + + Density error is 0.000147444720683 + + Energy Rydberg eV + E_KohnSham -34.2776419503 -466.371244528 + E_Harris -34.2776419948 -466.371245133 + E_Fermi -0.169201678628 -2.3021069405 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107865326295 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115502161806 + + Density error is 4.00695818126e-05 + + Energy Rydberg eV + E_KohnSham -34.2776292677 -466.371071972 + E_Harris -34.2776292757 -466.371072081 + E_Fermi -0.169090846965 -2.30059899837 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107861629195 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115498517506 + + Density error is 1.6802055038e-05 + + Energy Rydberg eV + E_KohnSham -34.2776333197 -466.371127102 + E_Harris -34.2776333207 -466.371127116 + E_Fermi -0.169130608025 -2.30113997535 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107861192774 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115497562177 + + Density error is 3.00654184776e-06 + + Energy Rydberg eV + E_KohnSham -34.2776319022 -466.371107816 + E_Harris -34.2776319022 -466.371107817 + E_Fermi -0.169114352167 -2.30091880306 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107860776034 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115497027748 + + Density error is 2.16900891864e-07 + + Energy Rydberg eV + E_KohnSham -34.2776320817 -466.371110259 + E_Harris -34.2776320817 -466.371110259 + E_Fermi -0.169111043818 -2.30087379065 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107860827742 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115497083434 + + Density error is 1.25566070291e-07 + + Energy Rydberg eV + E_KohnSham -34.2776321374 -466.371111016 + E_Harris -34.2776321374 -466.371111016 + E_Fermi -0.169111085293 -2.30087435495 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107860835543 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00115497087568 + + Density error is 1.05766643228e-08 + + Energy Rydberg eV + E_KohnSham -34.2776321361 -466.371110999 + E_Harris -34.2776321361 -466.371110999 + E_band -7.9807595105 -108.58380371 + E_one_elec -69.3443252366 -943.477947183 + E_Hartree +36.0621369769 +490.650544942 + E_xc -8.21356043352 -111.751222763 + E_Ewald +7.34233747531 +99.8976263032 + E_demet -4.20258917983e-77 -5.71791591988e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194982473299 -2.652872647 + E_Fermi -0.1691109789 -2.3008729074 + + charge density convergence is achieved + final etot is -466.371110999 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3543 2.00000 + 2 -12.9872 2.00000 + 3 -9.19375 2.00000 + 4 -6.75667 2.00000 + 5 1.26142 0.00000 + 6 4.47182 0.00000 + 7 11.0649 0.00000 + 8 11.3135 0.00000 + + EFERMI = -2.300872907399362 eV + OUT.ABACUS/ final etot is -466.3711109986347 eV + correction force for each atom along direction 1 is 4.65011e-06 + correction force for each atom along direction 2 is 2.00500e-05 + correction force for each atom along direction 3 is 1.13667e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.96570534 +0.53005186 +2.3172943 + H1 +0.28553881 +0.51386090 -0.90764421 + H2 -1.2512442 -1.0439128 -1.4096501 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3711109986347 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8980 11 0.54 1.0e+02% + Run_lcao lcao_line 5.8878 1 5.9 1.e+02% + Potential init_pot 0.28363 2 0.14 4.8% + PW_Basis recip2real 0.27489 17 0.016 4.7% + PW_Basis gathers_scatterp 0.12133 17 0.0071 2.1% + Charge atomic_rho 0.10013 1 0.10 1.7% + Potential v_of_rho 0.92011 14 0.066 16.% + XC_Functional v_xc 0.25672 15 0.017 4.4% + H_Hartree_pw v_hartree 0.62585 14 0.045 11.% + PW_Basis real2recip 0.60653 41 0.015 10.% + PW_Basis gatherp_scatters 0.24242 41 0.0059 4.1% + ORB_control set_orb_tables 1.1103 1 1.1 19.% + ORB_gen_tables gen_tables 1.1103 1 1.1 19.% + ORB_table_phi init_Table 0.48665 1 0.49 8.3% + ORB_table_phi cal_ST_Phi12_R 0.48177 126 0.0038 8.2% + ORB_table_beta init_Table_Beta 0.18913 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18764 56 0.0034 3.2% + ORB_table_alpha init_Table_Alpha 0.25604 1 0.26 4.3% + ORB_table_alpha S_PhiAlpha_R 0.25419 66 0.0039 4.3% + LOOP_ions opt_ions 4.2601 1 4.3 72.% + ESolver_KS_LCAO Run 3.7813 1 3.8 64.% + HSolverLCAO solve 1.6541 12 0.14 28.% + HamiltLCAO updateHk 0.90315 12 0.075 15.% + LCAO_Hamilt cal_Hgamma 0.87244 12 0.073 15.% + Gint_Gamma distri_vl_value 0.49145 12 0.041 8.3% + Gint_Gamma distri_vl 1.9905 6 0.33 34.% + LCAO_Deepks cal_projected_DM 3.9662 14 0.28 67.% + LCAO_gen_fixedH add_v_delta 1.8565 6 0.31 31.% + LCAO_DESCRIPTOR add_v_delta 1.8565 6 0.31 31.% + ElecStateLCAO psiToRho 0.72934 12 0.061 12.% + Charge mix_rho 0.71330 11 0.065 12.% + LOOP_ions force_stress 0.47862 1 0.48 8.1% + Force_Stress_LCAO getForceStress 0.47859 1 0.48 8.1% + Force_LCAO_gamma ftable_gamma 0.25234 1 0.25 4.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:25 2022 + Finish Time : Wed Sep 28 11:10:31 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..04ab8b1e152db50c2df4967051ed3658c5b2d762 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123801 ima = 3.68637e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123102792955 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111976660866 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112548284155 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112805430304 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756745617 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112785375287 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112778341891 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112781271702 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112780651617 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112780516332 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112780513344 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112780507673 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c95429488830cb482ea1899fb1ad1035b631b14a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.636130630143 15.704927271247 12.038647551024 0 0 0 +H +0.0 +2 +-13.990524051156 14.939868786593 13.728744512012 0 0 0 +-14.704864626486 14.784540445909 10.963228413245 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/conv new file mode 100644 index 0000000000000000000000000000000000000000..1c629c6613399db2138ae12aecd14ad67905fdc5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/conv @@ -0,0 +1 @@ +32 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c66f623b1b12cf5220f1a4c06da35275e066211c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750638721 0.01267440768 1.268434811 1.367043533 1.46963747 0.008800722944 0.01823886574 0.03908497253 +-1.611856517e-18 0.001028966154 0.002678287782 0.01251360678 0.04592313395 -5.433910807e-19 2.170466899e-06 6.246935394e-06 +0.001613738324 0.005958473136 + +H atom_index 1 n_descriptor 18 +1.202889169 0.03595646428 0.09331806375 0.1292645606 0.3042912688 0.02019324535 0.02553264194 0.03928026045 +-6.322945773e-19 4.281994467e-05 0.0896884732 0.110677955 0.1133163226 -1.419001874e-18 6.2555127e-06 0.01411391373 +0.02456879672 0.02843702199 + +H atom_index 2 n_descriptor 18 +1.293731881 0.03295422427 0.1248987255 0.1714617102 0.3338485823 0.02445187032 0.0308084591 0.03664047582 +3.967204071e-17 5.129129857e-05 0.1078485834 0.1215577668 0.1470597117 -1.520535899e-18 1.60229064e-06 0.01353298705 +0.02791873224 0.03254020282 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5a04a3cb3cb38d9dff114a476f8d60c835201ee6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:25 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870318 SEC) : SETUP UNITCELL + DONE(0.0945213 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.112787 SEC) : INIT PLANEWAVE + DONE(0.161885 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.439926 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651380e+02 0.000000e+00 2.152e-01 4.349e-01 + GE2 -4.663674e+02 -1.229397e+00 9.801e-02 3.576e-01 + GE3 -4.663718e+02 -4.420531e-03 6.286e-02 4.126e-01 + GE4 -4.663716e+02 2.156908e-04 1.985e-03 3.024e-01 + GE5 -4.663708e+02 8.041510e-04 8.986e-04 3.038e-01 + GE6 -4.663712e+02 -4.807215e-04 1.474e-04 2.938e-01 + GE7 -4.663711e+02 1.725563e-04 4.007e-05 2.857e-01 + GE8 -4.663711e+02 -5.513024e-05 1.680e-05 2.758e-01 + GE9 -4.663711e+02 1.928586e-05 3.007e-06 2.799e-01 + GE10 -4.663711e+02 -2.442915e-06 2.169e-07 2.771e-01 + GE11 -4.663711e+02 -7.569048e-07 1.256e-07 2.772e-01 + GE12 -4.663711e+02 1.729010e-08 1.058e-08 2.192e-01 +E_delta_band = -7.07615552e-02 Ry = -9.62760349e-01 eV +E_delta_NN= -1.94982473e-01 Ry = -2.65287265e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.898 11 0.54 1e+02 % + Run_lcao lcao_line 5.8878 1 5.9 1e+02 % + Potential init_pot 0.28363 2 0.14 4.8 % + PW_Basis recip2real 0.27489 17 0.016 4.7 % + PW_Basis gathers_scatterp 0.12133 17 0.0071 2.1 % + Charge atomic_rho 0.10013 1 0.1 1.7 % + Potential v_of_rho 0.92011 14 0.066 16 % + XC_Functional v_xc 0.25672 15 0.017 4.4 % + H_Hartree_pw v_hartree 0.62585 14 0.045 11 % + PW_Basis real2recip 0.60653 41 0.015 10 % + PW_Basis gatherp_scatters 0.24242 41 0.0059 4.1 % + ORB_control set_orb_tables 1.1103 1 1.1 19 % + ORB_gen_tables gen_tables 1.1103 1 1.1 19 % + ORB_table_phi init_Table 0.48665 1 0.49 8.3 % + ORB_table_phi cal_ST_Phi12_R 0.48177 126 0.0038 8.2 % + ORB_table_beta init_Table_Beta 0.18913 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18764 56 0.0034 3.2 % + ORB_table_alpha init_Table_Alpha 0.25604 1 0.26 4.3 % + ORB_table_alpha S_PhiAlpha_R 0.25419 66 0.0039 4.3 % + LOOP_ions opt_ions 4.2601 1 4.3 72 % + ESolver_KS_LCAO Run 3.7813 1 3.8 64 % + HSolverLCAO solve 1.6541 12 0.14 28 % + HamiltLCAO updateHk 0.90315 12 0.075 15 % + LCAO_Hamilt cal_Hgamma 0.87244 12 0.073 15 % + Gint_Gamma distri_vl_value 0.49145 12 0.041 8.3 % + Gint_Gamma distri_vl 1.9905 6 0.33 34 % + LCAO_Deepks cal_projected_DM 3.9662 14 0.28 67 % + LCAO_gen_fixedH add_v_delta 1.8565 6 0.31 31 % + LCAO_DESCRIPTOR add_v_delta 1.8565 6 0.31 31 % + ElecStateLCAO psiToRho 0.72934 12 0.061 12 % + Charge mix_rho 0.7133 11 0.065 12 % + LOOP_ions force_stress 0.47862 1 0.48 8.1 % + Force_Stress_LCAO getForceStress 0.47859 1 0.48 8.1 % + Force_LCAO_gamma ftable_gamma 0.25234 1 0.25 4.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:25 2022 + FINISH Time : Wed Sep 28 11:10:31 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/32/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..de7ec694980a3c08a98a6b5ba9e5f98a165da658 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.509592 0.588078 0.433214 +H 0.476453 0.63169 0.463651 +H 0.467074 0.537621 0.430365 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e8134c7a8cb01b648d8492663045eeda59a89fa7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5409 2 + 2 -13.1161 2 + 3 -9.24355 2 + 4 -6.79803 2 + 5 1.4211 0 + 6 4.71523 0 + 7 11.0215 0 + 8 11.273 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..634e3bf6a5a28cd1fc4f881c44c667c0994e79d5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:49 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.268575191 16.4661955993 12.1299795753 0 0 0 0 + tauc_H1 13.3406825732 17.6873300302 12.9822188835 0 0 0 0 + tauc_H2 13.0780785859 15.0533794435 12.0502124493 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.139969041437 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.140989481857 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.159068177042 (SEC) + + DONE : INIT CHARGE Time : 0.231997858292 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.573195 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00126 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106 + + Density error is 0.216494021386 + + Energy Rydberg eV + E_KohnSham -34.186432407 -465.130275027 + E_Harris -34.3821195782 -467.79273558 + E_Fermi -0.419009621768 -5.70091837287 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127543782227 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106944735996 + + Density error is 0.097425012887 + + Energy Rydberg eV + E_KohnSham -34.2764629512 -466.355203423 + E_Harris -34.2831225716 -466.445812206 + E_Fermi -0.227018499025 -3.08874513815 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001183858325 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100432925686 + + Density error is 0.0621774147652 + + Energy Rydberg eV + E_KohnSham -34.2766345509 -466.357538156 + E_Harris -34.2809048796 -466.415638959 + E_Fermi -0.212929208424 -2.89705050519 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010294032258 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000905850631017 + + Density error is 0.00202349865032 + + Energy Rydberg eV + E_KohnSham -34.2766729197 -466.35806019 + E_Harris -34.2766744026 -466.358080366 + E_Fermi -0.177093091426 -2.40947511983 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102758846927 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906063094767 + + Density error is 0.000873658917976 + + Energy Rydberg eV + E_KohnSham -34.2766025813 -466.357103188 + E_Harris -34.2766048447 -466.357133983 + E_Fermi -0.175982911817 -2.39437035135 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010260449545 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904942051457 + + Density error is 0.000120770643754 + + Energy Rydberg eV + E_KohnSham -34.2766521067 -466.357777015 + E_Harris -34.2766519877 -466.357775396 + E_Fermi -0.176226721885 -2.3976875575 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102585495448 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000905047222284 + + Density error is 4.66163985672e-05 + + Energy Rydberg eV + E_KohnSham -34.2766350825 -466.357545389 + E_Harris -34.2766350949 -466.357545557 + E_Fermi -0.176079369274 -2.39568272237 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102585841832 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000905003622464 + + Density error is 1.65270323561e-05 + + Energy Rydberg eV + E_KohnSham -34.2766388999 -466.357597327 + E_Harris -34.2766389009 -466.35759734 + E_Fermi -0.176136510945 -2.39646017469 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102583075656 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904989199307 + + Density error is 2.20214614618e-06 + + Energy Rydberg eV + E_KohnSham -34.2766373634 -466.357576422 + E_Harris -34.2766373634 -466.357576422 + E_Fermi -0.176118726874 -2.39621820999 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102583054486 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904989829374 + + Density error is 1.13599988212e-07 + + Energy Rydberg eV + E_KohnSham -34.2766375406 -466.357578833 + E_Harris -34.2766375406 -466.357578833 + E_Fermi -0.176116676301 -2.39619031051 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102583048505 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904989822936 + + Density error is 7.00455538326e-08 + + Energy Rydberg eV + E_KohnSham -34.2766375893 -466.357579495 + E_Harris -34.2766375893 -466.357579495 + E_band -8.04054165439 -109.397181506 + E_one_elec -69.7102987065 -948.45727169 + E_Hartree +36.2334449208 +492.981309092 + E_xc -8.24116466481 -112.126797598 + E_Ewald +7.56485240386 +102.925097222 + E_demet -4.95198309565e-88 -6.73751865005e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195656218923 -2.66203942649 + E_Fermi -0.176116738957 -2.39619116299 + + charge density convergence is achieved + final etot is -466.357579495 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5409 2.00000 + 2 -13.1161 2.00000 + 3 -9.24355 2.00000 + 4 -6.79803 2.00000 + 5 1.42110 0.00000 + 6 4.71523 0.00000 + 7 11.0215 0.00000 + 8 11.2730 0.00000 + + EFERMI = -2.396191162992968 eV + OUT.ABACUS/ final etot is -466.3575794951221 eV + correction force for each atom along direction 1 is -0.000173776 + correction force for each atom along direction 2 is -5.83047e-05 + correction force for each atom along direction 3 is 2.24663e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.0792841 -2.0840860 -1.2541313 + H1 -1.3098323 +2.1079572 +1.3553351 + H2 +0.23054815 -0.023871181 -0.10120380 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3575794951221 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9910 11 0.73 1.0e+02% + Run_lcao lcao_line 7.9788 1 8.0 1.e+02% + Potential init_pot 0.29902 2 0.15 3.7% + PW_Basis recip2real 0.26968 16 0.017 3.4% + PW_Basis gathers_scatterp 0.12090 16 0.0076 1.5% + Potential v_of_rho 1.0725 13 0.082 13.% + XC_Functional v_xc 0.39004 14 0.028 4.9% + H_Hartree_pw v_hartree 0.64528 13 0.050 8.1% + PW_Basis real2recip 0.69468 38 0.018 8.7% + PW_Basis gatherp_scatters 0.30894 38 0.0081 3.9% + ORB_control set_orb_tables 1.1771 1 1.2 15.% + ORB_gen_tables gen_tables 1.1771 1 1.2 15.% + ORB_table_phi init_Table 0.47344 1 0.47 5.9% + ORB_table_phi cal_ST_Phi12_R 0.46712 126 0.0037 5.8% + ORB_table_beta init_Table_Beta 0.18402 1 0.18 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18119 56 0.0032 2.3% + ORB_table_alpha init_Table_Alpha 0.25246 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24864 66 0.0038 3.1% + LOOP_ions opt_ions 6.1295 1 6.1 77.% + ESolver_KS_LCAO Run 5.5571 1 5.6 70.% + HSolverLCAO solve 3.0483 11 0.28 38.% + HamiltLCAO updateHk 1.5321 11 0.14 19.% + LCAO_Hamilt cal_Hgamma 1.5007 11 0.14 19.% + Gint_interface cal_gint 0.10884 23 0.0047 1.4% + Gint_Gamma distri_vl_value 0.97458 11 0.089 12.% + Gint_Gamma distri_vl 2.7605 6 0.46 35.% + LCAO_Deepks cal_projected_DM 5.6664 13 0.44 71.% + LCAO_gen_fixedH add_v_delta 2.5755 6 0.43 32.% + LCAO_DESCRIPTOR add_v_delta 2.5757 6 0.43 32.% + ElecStateLCAO psiToRho 1.4123 11 0.13 18.% + Charge mix_rho 0.89255 10 0.089 11.% + LOOP_ions force_stress 0.57217 1 0.57 7.2% + Force_Stress_LCAO getForceStress 0.57215 1 0.57 7.2% + Force_LCAO_gamma ftable_gamma 0.36189 1 0.36 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:49 2022 + Finish Time : Wed Sep 28 11:01:57 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4a8014aa2844834e4287c7b65f5158469c701b29 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124094 ima = 3.68283e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122708250462 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111863926159 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112295017536 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112573390921 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112503411225 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011254316428 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112537021519 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112540245005 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011253967177 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112539558812 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112539560035 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/STRU new file mode 100644 index 0000000000000000000000000000000000000000..2c2681ae8d65a08f69604a4f443c110f34bad228 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.731424809030 16.466195599299 12.129979575349 0 0 0 +H +0.0 +2 +-14.659317426791 17.687330030195 12.982218883456 0 0 0 +-14.921921414136 15.053379443440 12.050212449273 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/conv new file mode 100644 index 0000000000000000000000000000000000000000..c2980d84b78aafd4018db0947a4d2c3efc0d4d01 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/conv @@ -0,0 +1 @@ +33 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b6517ae9e73c9cd2bd7607b648b049d05a6d0774 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750930342 0.01279656872 1.284593611 1.376987941 1.470470901 0.008989044313 0.01844605214 0.03908073019 +4.881179649e-19 0.001103050751 0.002813954703 0.01312772409 0.04799049077 5.659238879e-20 2.503855944e-06 6.846346228e-06 +0.001616769098 0.006002255125 + +H atom_index 1 n_descriptor 18 +1.308750793 0.03258433286 0.1317837975 0.1793374867 0.3373125897 0.02541959686 0.03162979969 0.03660740253 +9.764159938e-18 5.677251681e-05 0.1080756314 0.1273287004 0.1537834272 4.063714832e-18 8.390241978e-07 0.0140437416 +0.02882948358 0.03305555236 + +H atom_index 2 n_descriptor 18 +1.234162907 0.03496453717 0.103898522 0.1424525158 0.3149032671 0.0219023359 0.02734078758 0.03805713529 +3.411880043e-17 4.952596388e-05 0.09980109297 0.1141319571 0.1223543169 2.692653533e-18 4.87387916e-06 0.01346284176 +0.02631130505 0.03003108656 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..7a45542c958a880d9de4c51eb66b581ef33bc6e0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:49 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.139993 SEC) : SETUP UNITCELL + DONE(0.141004 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.159089 SEC) : INIT PLANEWAVE + DONE(0.232123 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.573271 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651303e+02 0.000000e+00 2.165e-01 7.681e-01 + GE2 -4.663552e+02 -1.224928e+00 9.743e-02 5.455e-01 + GE3 -4.663575e+02 -2.334734e-03 6.218e-02 6.170e-01 + GE4 -4.663581e+02 -5.220337e-04 2.023e-03 4.675e-01 + GE5 -4.663571e+02 9.570024e-04 8.737e-04 4.673e-01 + GE6 -4.663578e+02 -6.738277e-04 1.208e-04 4.553e-01 + GE7 -4.663575e+02 2.316262e-04 4.662e-05 4.569e-01 + GE8 -4.663576e+02 -5.193822e-05 1.653e-05 4.456e-01 + GE9 -4.663576e+02 2.090566e-05 2.202e-06 4.458e-01 + GE10 -4.663576e+02 -2.411077e-06 1.136e-07 4.470e-01 + GE11 -4.663576e+02 -6.622480e-07 7.005e-08 3.657e-01 +E_delta_band = -7.21846763e-02 Ry = -9.82122906e-01 eV +E_delta_NN= -1.95656219e-01 Ry = -2.66203943e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.991 11 0.73 1e+02 % + Run_lcao lcao_line 7.9788 1 8 1e+02 % + Potential init_pot 0.29902 2 0.15 3.7 % + PW_Basis recip2real 0.26968 16 0.017 3.4 % + PW_Basis gathers_scatterp 0.1209 16 0.0076 1.5 % + Potential v_of_rho 1.0725 13 0.082 13 % + XC_Functional v_xc 0.39004 14 0.028 4.9 % + H_Hartree_pw v_hartree 0.64528 13 0.05 8.1 % + PW_Basis real2recip 0.69468 38 0.018 8.7 % + PW_Basis gatherp_scatters 0.30894 38 0.0081 3.9 % + ORB_control set_orb_tables 1.1771 1 1.2 15 % + ORB_gen_tables gen_tables 1.1771 1 1.2 15 % + ORB_table_phi init_Table 0.47344 1 0.47 5.9 % + ORB_table_phi cal_ST_Phi12_R 0.46712 126 0.0037 5.8 % + ORB_table_beta init_Table_Beta 0.18402 1 0.18 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.18119 56 0.0032 2.3 % + ORB_table_alpha init_Table_Alpha 0.25246 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24864 66 0.0038 3.1 % + LOOP_ions opt_ions 6.1295 1 6.1 77 % + ESolver_KS_LCAO Run 5.5571 1 5.6 70 % + HSolverLCAO solve 3.0483 11 0.28 38 % + HamiltLCAO updateHk 1.5321 11 0.14 19 % + LCAO_Hamilt cal_Hgamma 1.5007 11 0.14 19 % + Gint_interface cal_gint 0.10884 23 0.0047 1.4 % + Gint_Gamma distri_vl_value 0.97458 11 0.089 12 % + Gint_Gamma distri_vl 2.7605 6 0.46 35 % + LCAO_Deepks cal_projected_DM 5.6664 13 0.44 71 % + LCAO_gen_fixedH add_v_delta 2.5755 6 0.43 32 % + LCAO_DESCRIPTOR add_v_delta 2.5757 6 0.43 32 % + ElecStateLCAO psiToRho 1.4123 11 0.13 18 % + Charge mix_rho 0.89255 10 0.089 11 % + LOOP_ions force_stress 0.57217 1 0.57 7.2 % + Force_Stress_LCAO getForceStress 0.57215 1 0.57 7.2 % + Force_LCAO_gamma ftable_gamma 0.36189 1 0.36 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:49 2022 + FINISH Time : Wed Sep 28 11:01:57 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/33/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9fb14b3176704c50658882bd6927ca964c9e35a2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.499246 0.598229 0.441869 +H 0.478152 0.659193 0.458948 +H 0.454857 0.557269 0.470151 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d585d879e1d2bc31253cdd6dc2fd849b3ff1e3e9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0862 2 + 2 -12.8685 2 + 3 -9.09193 2 + 4 -6.7001 2 + 5 1.13051 0 + 6 4.12014 0 + 7 11.1239 0 + 8 11.3759 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0055383fb466a82d33302e15789050962ce75f31 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:09 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.9788845211 16.7504063453 12.3723456062 0 0 0 0 + tauc_H1 13.3882580959 18.4574156871 12.8505346762 0 0 0 0 + tauc_H2 12.7360023465 15.6035434692 13.1642344085 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0854679415125 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0983225478049 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116682376523 (SEC) + + DONE : INIT CHARGE Time : 0.166041091574 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446969 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 +receiver_size is 324 ; receiver_size of each process is: +81 81 81 81 +sender_size is 369 ; sender_size of each process is: +81 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000985 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00148 + + Density error is 0.211674263631 + + Energy Rydberg eV + E_KohnSham -34.1938719978 -465.231495853 + E_Harris -34.3788088479 -467.747690784 + E_Fermi -0.392606567783 -5.34168639407 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00105250459192 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00134836523402 + + Density error is 0.0983097961019 + + Energy Rydberg eV + E_KohnSham -34.2807913138 -466.414093816 + E_Harris -34.2876788651 -466.507803759 + E_Fermi -0.20380506137 -2.77291011587 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000986971155312 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00124173529656 + + Density error is 0.063200851399 + + Energy Rydberg eV + E_KohnSham -34.2810167152 -466.417160559 + E_Harris -34.2854623294 -466.477646244 + E_Fermi -0.194741513374 -2.64959421904 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000872559947516 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.001040566853 + + Density error is 0.00197343673094 + + Energy Rydberg eV + E_KohnSham -34.280958773 -466.416372216 + E_Harris -34.2809607958 -466.416399737 + E_Fermi -0.159513165542 -2.17028795738 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000870454710198 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103737207542 + + Density error is 0.000807889006148 + + Energy Rydberg eV + E_KohnSham -34.2809256109 -466.415921022 + E_Harris -34.2809259273 -466.415925327 + E_Fermi -0.159180244575 -2.16575833525 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000869049907598 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0010348458095 + + Density error is 0.000164035267091 + + Energy Rydberg eV + E_KohnSham -34.2809444717 -466.416177636 + E_Harris -34.2809444983 -466.416177999 + E_Fermi -0.158890104351 -2.16181077499 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000869162706696 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103491689136 + + Density error is 2.82253238348e-05 + + Energy Rydberg eV + E_KohnSham -34.2809381197 -466.416091214 + E_Harris -34.2809381226 -466.416091252 + E_Fermi -0.158847878334 -2.16123626056 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000869116094076 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103487772227 + + Density error is 1.35715054709e-05 + + Energy Rydberg eV + E_KohnSham -34.2809411665 -466.416132667 + E_Harris -34.2809411673 -466.416132678 + E_Fermi -0.15886889543 -2.16152221281 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000869105214391 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0010348522993 + + Density error is 1.84826076777e-06 + + Energy Rydberg eV + E_KohnSham -34.2809400932 -466.416118064 + E_Harris -34.2809400932 -466.416118064 + E_Fermi -0.15885522424 -2.16133620674 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000869103417579 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103484794603 + + Density error is 4.39734997127e-07 + + Energy Rydberg eV + E_KohnSham -34.280940315 -466.416121082 + E_Harris -34.280940315 -466.416121082 + E_Fermi -0.158853715093 -2.16131567373 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000869103897071 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103484801783 + + Density error is 1.40005644794e-07 + + Energy Rydberg eV + E_KohnSham -34.2809403289 -466.416121271 + E_Harris -34.2809403289 -466.416121271 + E_Fermi -0.158853505824 -2.16131282649 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000869103914099 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103484777531 + + Density error is 1.05151136548e-08 + + Energy Rydberg eV + E_KohnSham -34.2809403331 -466.416121328 + E_Harris -34.2809403331 -466.416121328 + E_band -7.90062970199 -107.493581735 + E_one_elec -68.8726762097 -937.060832961 + E_Hartree +35.8428245285 +487.666646002 + E_xc -8.17786174498 -111.265517188 + E_Ewald +7.05196708047 +95.9469344028 + E_demet -3.1370544869e-66 -4.26818159582e-65 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194043150491 -2.64009250454 + E_Fermi -0.158853372196 -2.16131100838 + + charge density convergence is achieved + final etot is -466.416121328 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0862 2.00000 + 2 -12.8685 2.00000 + 3 -9.09193 2.00000 + 4 -6.70010 2.00000 + 5 1.13051 0.00000 + 6 4.12014 0.00000 + 7 11.1239 0.00000 + 8 11.3759 0.00000 + + EFERMI = -2.161311008376322 eV + OUT.ABACUS/ final etot is -466.4161213275050 eV + correction force for each atom along direction 1 is -1.98266e-05 + correction force for each atom along direction 2 is 5.45365e-05 + correction force for each atom along direction 3 is 0.000140220 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.54226210 +0.19032225 +0.38268569 + H1 +0.16913182 -0.57315116 -0.14373771 + H2 +0.37313029 +0.38282892 -0.23894798 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4161213275050 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4177 11 0.58 1.0e+02% + Run_lcao lcao_line 6.4094 1 6.4 1.e+02% + Potential init_pot 0.28443 2 0.14 4.4% + PW_Basis recip2real 0.28015 17 0.016 4.4% + PW_Basis gathers_scatterp 0.12886 17 0.0076 2.0% + Potential v_of_rho 1.0381 14 0.074 16.% + XC_Functional v_xc 0.31043 15 0.021 4.8% + H_Hartree_pw v_hartree 0.68534 14 0.049 11.% + PW_Basis real2recip 0.69938 41 0.017 11.% + PW_Basis gatherp_scatters 0.30224 41 0.0074 4.7% + ORB_control set_orb_tables 1.0897 1 1.1 17.% + ORB_gen_tables gen_tables 1.0897 1 1.1 17.% + ORB_table_phi init_Table 0.47192 1 0.47 7.4% + ORB_table_phi cal_ST_Phi12_R 0.46678 126 0.0037 7.3% + ORB_table_beta init_Table_Beta 0.18304 1 0.18 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18150 56 0.0032 2.8% + ORB_table_alpha init_Table_Alpha 0.24783 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.24592 66 0.0037 3.8% + LOOP_ions opt_ions 4.7938 1 4.8 75.% + ESolver_KS_LCAO Run 4.3087 1 4.3 67.% + HSolverLCAO solve 1.8580 12 0.15 29.% + HamiltLCAO updateHk 1.0132 12 0.084 16.% + LCAO_Hamilt cal_Hgamma 0.98354 12 0.082 15.% + Gint_Gamma distri_vl_value 0.57477 12 0.048 9.0% + Gint_Gamma distri_vl 2.2569 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.4688 14 0.32 70.% + LCAO_gen_fixedH add_v_delta 2.1129 6 0.35 33.% + LCAO_DESCRIPTOR add_v_delta 2.1129 6 0.35 33.% + ElecStateLCAO psiToRho 0.82130 12 0.068 13.% + Charge mix_rho 0.83775 11 0.076 13.% + LOOP_ions force_stress 0.48492 1 0.48 7.6% + Force_Stress_LCAO getForceStress 0.48490 1 0.48 7.6% + Force_LCAO_gamma ftable_gamma 0.27107 1 0.27 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:09 2022 + Finish Time : Wed Sep 28 11:06:15 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..bd6f921c15d75953bf8c2b451cd7ba67fe571bc4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123679 ima = 3.66389e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123242537577 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112205684062 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112835788912 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113028876298 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113007375373 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113021639406 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113016226459 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113018304435 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113017672509 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113017623639 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113017605646 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001130175986 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/STRU new file mode 100644 index 0000000000000000000000000000000000000000..2b6f2d0d17d6f730417457789d76cc7f2268ed3f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.021115478878 16.750406345333 12.372345606149 0 0 0 +H +0.0 +2 +-14.611741904110 18.457415687118 12.850534676234 0 0 0 +-15.263997653559 15.603543469200 13.164234408524 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/conv new file mode 100644 index 0000000000000000000000000000000000000000..501bb87cf148d861e35308a1051db302d48d2488 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/conv @@ -0,0 +1 @@ +34 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..804ba5e64cb1311f57582b7fac4bf2b3a4627ac0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749518827 0.01253563791 1.256521082 1.347037173 1.468419993 0.008394813648 0.01815761242 0.03905204036 +4.601349322e-19 0.000954665501 0.00246664466 0.01184541832 0.04280464224 3.908130609e-19 1.774292777e-06 5.337520002e-06 +0.001634667365 0.005907576707 + +H atom_index 1 n_descriptor 18 +1.218095012 0.03536337769 0.09729691411 0.1359717995 0.3107512226 0.02059163836 0.02647546898 0.03862424647 +-2.68092355e-17 3.927222854e-05 0.09168796876 0.1142180588 0.1164252018 -9.996778875e-18 5.449601099e-06 0.01363677474 +0.0246371503 0.02922769604 + +H atom_index 2 n_descriptor 18 +1.218987987 0.035333726 0.09758087647 0.1363564057 0.3110741821 0.02063331802 0.02652815375 0.03858937993 +-2.599716933e-17 3.93511341e-05 0.09192432182 0.1142482787 0.1167619253 -6.274400202e-18 5.413378862e-06 0.01361660343 +0.02467318456 0.0292731394 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..1915e0d96a141e44fa330dd5e4302a777c59918e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:09 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0854911 SEC) : SETUP UNITCELL + DONE(0.0983409 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116705 SEC) : INIT PLANEWAVE + DONE(0.16617 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447033 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652315e+02 0.000000e+00 2.117e-01 4.711e-01 + GE2 -4.664141e+02 -1.182598e+00 9.831e-02 4.111e-01 + GE3 -4.664172e+02 -3.066743e-03 6.320e-02 4.792e-01 + GE4 -4.664164e+02 7.883431e-04 1.973e-03 3.419e-01 + GE5 -4.664159e+02 4.511943e-04 8.079e-04 3.409e-01 + GE6 -4.664162e+02 -2.566142e-04 1.640e-04 3.364e-01 + GE7 -4.664161e+02 8.642268e-05 2.823e-05 3.263e-01 + GE8 -4.664161e+02 -4.145330e-05 1.357e-05 3.213e-01 + GE9 -4.664161e+02 1.460308e-05 1.848e-06 3.210e-01 + GE10 -4.664161e+02 -3.018460e-06 4.397e-07 3.201e-01 + GE11 -4.664161e+02 -1.884921e-07 1.400e-07 3.213e-01 + GE12 -4.664161e+02 -5.674975e-08 1.052e-08 2.561e-01 +E_delta_band = -6.88491631e-02 Ry = -9.36740921e-01 eV +E_delta_NN= -1.94043150e-01 Ry = -2.64009250e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4177 11 0.58 1e+02 % + Run_lcao lcao_line 6.4094 1 6.4 1e+02 % + Potential init_pot 0.28443 2 0.14 4.4 % + PW_Basis recip2real 0.28015 17 0.016 4.4 % + PW_Basis gathers_scatterp 0.12886 17 0.0076 2 % + Potential v_of_rho 1.0381 14 0.074 16 % + XC_Functional v_xc 0.31043 15 0.021 4.8 % + H_Hartree_pw v_hartree 0.68534 14 0.049 11 % + PW_Basis real2recip 0.69938 41 0.017 11 % + PW_Basis gatherp_scatters 0.30224 41 0.0074 4.7 % + ORB_control set_orb_tables 1.0897 1 1.1 17 % + ORB_gen_tables gen_tables 1.0897 1 1.1 17 % + ORB_table_phi init_Table 0.47192 1 0.47 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.46678 126 0.0037 7.3 % + ORB_table_beta init_Table_Beta 0.18304 1 0.18 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.1815 56 0.0032 2.8 % + ORB_table_alpha init_Table_Alpha 0.24783 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.24592 66 0.0037 3.8 % + LOOP_ions opt_ions 4.7938 1 4.8 75 % + ESolver_KS_LCAO Run 4.3087 1 4.3 67 % + HSolverLCAO solve 1.858 12 0.15 29 % + HamiltLCAO updateHk 1.0132 12 0.084 16 % + LCAO_Hamilt cal_Hgamma 0.98354 12 0.082 15 % + Gint_Gamma distri_vl_value 0.57477 12 0.048 9 % + Gint_Gamma distri_vl 2.2569 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.4688 14 0.32 70 % + LCAO_gen_fixedH add_v_delta 2.1129 6 0.35 33 % + LCAO_DESCRIPTOR add_v_delta 2.1129 6 0.35 33 % + ElecStateLCAO psiToRho 0.8213 12 0.068 13 % + Charge mix_rho 0.83775 11 0.076 13 % + LOOP_ions force_stress 0.48492 1 0.48 7.6 % + Force_Stress_LCAO getForceStress 0.4849 1 0.48 7.6 % + Force_LCAO_gamma ftable_gamma 0.27107 1 0.27 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:09 2022 + FINISH Time : Wed Sep 28 11:06:15 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/34/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..28981ded674f4c5de431a49ecac27791ff38ed9b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.502394 0.616204 0.454223 +H 0.456455 0.662427 0.44817 +H 0.481388 0.578123 0.500632 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..426b17fe4a3d14c358bf4eff2ffa77c451a2637b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4415 2 + 2 -13.2285 2 + 3 -9.09947 2 + 4 -6.77784 2 + 5 1.43606 0 + 6 4.66855 0 + 7 11.0353 0 + 8 11.2792 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e22c6dc7d920286be9188596cb4d67eef78b790b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/running_scf.log @@ -0,0 +1,777 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.0670270096 17.2536993438 12.7182556509 0 0 0 0 + tauc_H1 12.7807432408 18.5479658745 12.5487561708 0 0 0 0 + tauc_H2 13.4788679298 16.1874563682 14.0176826223 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.104465600531 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.104826709787 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.122957864181 (SEC) + + DONE : INIT CHARGE Time : 0.166208567114 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447299 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 +receiver_size is 324 ; receiver_size of each process is: +81 81 81 81 +sender_size is 369 ; sender_size of each process is: +81 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00123 + + Density error is 0.216593691093 + + Energy Rydberg eV + E_KohnSham -34.1890092799 -465.165335182 + E_Harris -34.3844681809 -467.82468996 + E_Fermi -0.415650054148 -5.65520911042 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00127196934572 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0013099529704 + + Density error is 0.097625437019 + + Energy Rydberg eV + E_KohnSham -34.2791427745 -466.391664289 + E_Harris -34.2857652306 -466.481767426 + E_Fermi -0.223298654541 -3.03813405748 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00119141457507 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00122397134676 + + Density error is 0.0623439728986 + + Energy Rydberg eV + E_KohnSham -34.2793530799 -466.394525641 + E_Harris -34.2836029361 -466.452347901 + E_Fermi -0.209708082244 -2.85322483517 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00106072580109 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107978921344 + + Density error is 0.0020340625584 + + Energy Rydberg eV + E_KohnSham -34.2793838147 -466.394943809 + E_Harris -34.2793855418 -466.394967307 + E_Fermi -0.174080641029 -2.36848862949 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00106060397572 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107830694644 + + Density error is 0.00087889905735 + + Energy Rydberg eV + E_KohnSham -34.2793141512 -466.393995988 + E_Harris -34.2793161199 -466.394022773 + E_Fermi -0.172983102339 -2.35355584952 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00105911115167 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107681394132 + + Density error is 0.000144195282637 + + Energy Rydberg eV + E_KohnSham -34.2793622807 -466.394650824 + E_Harris -34.2793623389 -466.394651615 + E_Fermi -0.173213279846 -2.35668757517 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00105905209116 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107674424991 + + Density error is 4.33455228766e-05 + + Energy Rydberg eV + E_KohnSham -34.2793448668 -466.394413895 + E_Harris -34.2793448773 -466.394414039 + E_Fermi -0.173053445047 -2.35451291118 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00105903145954 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107672460881 + + Density error is 1.54489226039e-05 + + Energy Rydberg eV + E_KohnSham -34.2793491816 -466.394472601 + E_Harris -34.2793491824 -466.394472613 + E_Fermi -0.173106484867 -2.35523455494 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00105901227914 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107669850265 + + Density error is 1.95891698073e-06 + + Energy Rydberg eV + E_KohnSham -34.279347747 -466.394453083 + E_Harris -34.279347747 -466.394453083 + E_Fermi -0.173089916125 -2.35500912564 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00105901069011 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107669779269 + + Density error is 1.85523626292e-07 + + Energy Rydberg eV + E_KohnSham -34.279347929 -466.394455559 + E_Harris -34.279347929 -466.394455559 + E_Fermi -0.173088005714 -2.35498313317 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0010590112692 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107669823206 + + Density error is 8.8298520456e-08 + + Energy Rydberg eV + E_KohnSham -34.2793479654 -466.394456054 + E_Harris -34.2793479654 -466.394456054 + E_band -8.01830993965 -109.094703509 + E_one_elec -69.6278870968 -947.336004217 + E_Hartree +36.1996134559 +492.521008397 + E_xc -8.23549188191 -112.049615427 + E_Ewald +7.50806091067 +102.152409316 + E_demet -5.83324191711e-87 -7.93653278851e-86 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195429057259 -2.65894873349 + E_Fermi -0.173088031809 -2.35498348821 + + charge density convergence is achieved + final etot is -466.394456054 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4415 2.00000 + 2 -13.2285 2.00000 + 3 -9.09947 2.00000 + 4 -6.77784 2.00000 + 5 1.43606 0.00000 + 6 4.66855 0.00000 + 7 11.0353 0.00000 + 8 11.2792 0.00000 + + EFERMI = -2.354983488209402 eV + OUT.ABACUS/ final etot is -466.3944560540162 eV + correction force for each atom along direction 1 is -0.000198285 + correction force for each atom along direction 2 is 5.43712e-05 + correction force for each atom along direction 3 is -3.37780e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.77434473 +0.92050509 -1.3158316 + H1 -0.17190538 +0.17163119 -0.018561024 + H2 -0.60243935 -1.0921363 +1.3343926 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3944560540162 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2737 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2646 1 7.3 1.e+02% + Potential init_pot 0.28174 2 0.14 3.9% + PW_Basis recip2real 0.25229 16 0.016 3.5% + PW_Basis gathers_scatterp 0.11343 16 0.0071 1.6% + Potential v_of_rho 0.98479 13 0.076 14.% + XC_Functional v_xc 0.36079 14 0.026 5.0% + H_Hartree_pw v_hartree 0.58607 13 0.045 8.1% + PW_Basis real2recip 0.67994 38 0.018 9.3% + PW_Basis gatherp_scatters 0.29479 38 0.0078 4.1% + ORB_control set_orb_tables 1.1025 1 1.1 15.% + ORB_gen_tables gen_tables 1.1025 1 1.1 15.% + ORB_table_phi init_Table 0.47911 1 0.48 6.6% + ORB_table_phi cal_ST_Phi12_R 0.47372 126 0.0038 6.5% + ORB_table_beta init_Table_Beta 0.18445 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18290 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24867 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24665 66 0.0037 3.4% + LOOP_ions opt_ions 5.6385 1 5.6 78.% + ESolver_KS_LCAO Run 5.0845 1 5.1 70.% + HSolverLCAO solve 2.7301 11 0.25 38.% + HamiltLCAO updateHk 1.4002 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.3725 11 0.12 19.% + Gint_Gamma distri_vl_value 0.94291 11 0.086 13.% + Gint_Gamma distri_vl 2.4506 6 0.41 34.% + LCAO_Deepks cal_projected_DM 5.2016 13 0.40 72.% + LCAO_gen_fixedH add_v_delta 2.3215 6 0.39 32.% + LCAO_DESCRIPTOR add_v_delta 2.3216 6 0.39 32.% + ElecStateLCAO psiToRho 1.2928 11 0.12 18.% + Charge mix_rho 0.81096 10 0.081 11.% + LOOP_ions force_stress 0.55380 1 0.55 7.6% + Force_Stress_LCAO getForceStress 0.55377 1 0.55 7.6% + Force_LCAO_gamma ftable_gamma 0.35224 1 0.35 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:17 2022 + Finish Time : Wed Sep 28 11:06:25 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1259f262d2bc6b25f6565a10ac8b5e9db1ba5444 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123763 ima = 3.7125e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122991183677 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112176752319 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112611063565 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112877850582 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112812199585 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112850997149 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112843396623 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112846399537 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112845847132 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011284575866 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011284575432 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4d34a9ecbbf8daf20f1a1ed675812185af09caba --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.932972990431 17.253699343792 12.718255650880 0 0 0 +H +0.0 +2 +-15.219256759183 18.547965874486 12.548756170840 0 0 0 +-14.521132070182 16.187456368175 14.017682622242 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/conv new file mode 100644 index 0000000000000000000000000000000000000000..eaa88ab9307df4916db53fbc7b92b093665c242b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/conv @@ -0,0 +1 @@ +35 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..1e4a926bb1f7879d4ff31a52857af2d498c5fcfd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748519472 0.01276540026 1.286515041 1.375150963 1.470068396 0.008510860465 0.01913550635 0.03900546356 +-7.826960589e-19 0.001146916695 0.002666204828 0.01282895179 0.04650430329 -1.097503237e-19 2.141648397e-06 6.141392256e-06 +0.001668722705 0.005917048541 + +H atom_index 1 n_descriptor 18 +1.245287255 0.03429433686 0.106976293 0.1478703833 0.3195225151 0.02208302812 0.02804844793 0.03740396382 +7.16518647e-17 4.705728513e-05 0.1018361233 0.1145926405 0.1270609922 1.038860093e-17 4.493017391e-06 0.01318746644 +0.02641713712 0.0305815522 + +H atom_index 2 n_descriptor 18 +1.286289659 0.0329175963 0.1218932831 0.1677774616 0.3319213102 0.02395723333 0.03041015541 0.03645606296 +1.539790599e-17 5.092761458e-05 0.1081141878 0.1200840915 0.144095548 -3.955781073e-18 2.200746454e-06 0.01333154917 +0.02784171233 0.03229011946 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4ff6d348835793da13460727b8db42a6f5cd0840 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/log.scf @@ -0,0 +1,100 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.104489 SEC) : SETUP UNITCELL + DONE(0.104841 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.122977 SEC) : INIT PLANEWAVE + DONE(0.166347 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447363 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651653e+02 0.000000e+00 2.166e-01 5.483e-01 + GE2 -4.663917e+02 -1.226329e+00 9.763e-02 5.133e-01 + GE3 -4.663945e+02 -2.861352e-03 6.234e-02 5.871e-01 + GE4 -4.663949e+02 -4.181682e-04 2.034e-03 4.446e-01 + GE5 -4.663940e+02 9.478206e-04 8.789e-04 4.435e-01 + GE6 -4.663947e+02 -6.548359e-04 1.442e-04 4.303e-01 + GE7 -4.663944e+02 2.369292e-04 4.335e-05 4.322e-01 + GE8 -4.663945e+02 -5.870585e-05 1.545e-05 4.226e-01 + GE9 -4.663945e+02 1.951769e-05 1.959e-06 4.235e-01 + GE10 -4.663945e+02 -2.476158e-06 1.855e-07 4.211e-01 + GE11 -4.663945e+02 -4.947349e-07 8.830e-08 3.485e-01 +E_delta_band = -7.17857040e-02 Ry = -9.76694610e-01 eV +E_delta_NN= -1.95429057e-01 Ry = -2.65894873e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2737 11 0.66 1e+02 % + Run_lcao lcao_line 7.2646 1 7.3 1e+02 % + Potential init_pot 0.28174 2 0.14 3.9 % + PW_Basis recip2real 0.25229 16 0.016 3.5 % + PW_Basis gathers_scatterp 0.11343 16 0.0071 1.6 % + Potential v_of_rho 0.98479 13 0.076 14 % + XC_Functional v_xc 0.36079 14 0.026 5 % + H_Hartree_pw v_hartree 0.58607 13 0.045 8.1 % + PW_Basis real2recip 0.67994 38 0.018 9.3 % + PW_Basis gatherp_scatters 0.29479 38 0.0078 4.1 % + ORB_control set_orb_tables 1.1025 1 1.1 15 % + ORB_gen_tables gen_tables 1.1025 1 1.1 15 % + ORB_table_phi init_Table 0.47911 1 0.48 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.47372 126 0.0038 6.5 % + ORB_table_beta init_Table_Beta 0.18445 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.1829 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24867 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24665 66 0.0037 3.4 % + LOOP_ions opt_ions 5.6385 1 5.6 78 % + ESolver_KS_LCAO Run 5.0845 1 5.1 70 % + HSolverLCAO solve 2.7301 11 0.25 38 % + HamiltLCAO updateHk 1.4002 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.3725 11 0.12 19 % + Gint_Gamma distri_vl_value 0.94291 11 0.086 13 % + Gint_Gamma distri_vl 2.4506 6 0.41 34 % + LCAO_Deepks cal_projected_DM 5.2016 13 0.4 72 % + LCAO_gen_fixedH add_v_delta 2.3215 6 0.39 32 % + LCAO_DESCRIPTOR add_v_delta 2.3216 6 0.39 32 % + ElecStateLCAO psiToRho 1.2928 11 0.12 18 % + Charge mix_rho 0.81096 10 0.081 11 % + LOOP_ions force_stress 0.5538 1 0.55 7.6 % + Force_Stress_LCAO getForceStress 0.55377 1 0.55 7.6 % + Force_LCAO_gamma ftable_gamma 0.35224 1 0.35 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:17 2022 + FINISH Time : Wed Sep 28 11:06:25 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/35/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..6659b06a75d38a047677b000e65829e5506b0878 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.492348 0.649522 0.470769 +H 0.450324 0.646325 0.42082 +H 0.47761 0.594632 0.507471 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6461db323967aa65479a7e5479dcc6c1eb8cec96 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1348 2 + 2 -12.8769 2 + 3 -9.11901 2 + 4 -6.71041 2 + 5 1.14305 0 + 6 4.18155 0 + 7 11.1134 0 + 8 11.365 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b9044a60ccf93437063187cf81b616d00b4d1ebc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:12 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.7857360187 18.1866124088 13.1815232386 0 0 0 0 + tauc_H1 12.6090683014 18.0971001397 11.7829587161 0 0 0 0 + tauc_H2 13.3730934882 16.6497014554 14.2091933302 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101600352597 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101940992579 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119992151512 (SEC) + + DONE : INIT CHARGE Time : 0.162970169127 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446885 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 1 + Local orbitals number in sub-FFT-grid = 5 + lgd_last = 0 + lgd_now = 5 + allocate DM , the dimension is 5 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 2 + nCol_in_proc = 2 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 2 + nCol_in_proc = 3 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 3 + nCol_in_proc = 2 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 3 + nCol_in_proc = 3 +receiver_size is 25 ; receiver_size of each process is: +4 6 6 9 +sender_size is 292 ; sender_size of each process is: +4 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00129 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000613 + + Density error is 0.212721614615 + + Energy Rydberg eV + E_KohnSham -34.1916368081 -465.201084537 + E_Harris -34.3788540553 -467.748305862 + E_Fermi -0.395474081191 -5.38070091551 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00128369795644 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000933429556226 + + Density error is 0.0983787347014 + + Energy Rydberg eV + E_KohnSham -34.2799743977 -466.402979103 + E_Harris -34.2868921563 -466.497100037 + E_Fermi -0.205647965725 -2.79798411597 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00119847350779 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000898733070542 + + Density error is 0.0632875110639 + + Energy Rydberg eV + E_KohnSham -34.2802948986 -466.407339742 + E_Harris -34.2847563707 -466.468041184 + E_Fermi -0.196724826353 -2.67657857646 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00104992446389 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000861883145263 + + Density error is 0.00197562119762 + + Energy Rydberg eV + E_KohnSham -34.2802385143 -466.406572593 + E_Harris -34.2802402606 -466.406596353 + E_Fermi -0.16136057034 -2.19542318916 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00104825256231 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000863534415801 + + Density error is 0.000867217838832 + + Energy Rydberg eV + E_KohnSham -34.2801973648 -466.406012726 + E_Harris -34.2801978219 -466.406018944 + E_Fermi -0.161010799287 -2.19066430984 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00104645899806 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000862976751079 + + Density error is 0.00016803383399 + + Energy Rydberg eV + E_KohnSham -34.2802194831 -466.406313661 + E_Harris -34.2802195004 -466.406313897 + E_Fermi -0.160753144358 -2.18715873468 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00104656422574 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.00086315349664 + + Density error is 3.01175347529e-05 + + Energy Rydberg eV + E_KohnSham -34.2802120257 -466.406212197 + E_Harris -34.2802120288 -466.406212239 + E_Fermi -0.160686604061 -2.1862534075 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00104650426889 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000863111592432 + + Density error is 1.51590763897e-05 + + Energy Rydberg eV + E_KohnSham -34.2802152033 -466.406255431 + E_Harris -34.2802152044 -466.406255446 + E_Fermi -0.160710368366 -2.18657673746 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00104649603796 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000863121005516 + + Density error is 2.72538592337e-06 + + Energy Rydberg eV + E_KohnSham -34.2802140501 -466.406239741 + E_Harris -34.2802140501 -466.406239741 + E_Fermi -0.160696492884 -2.18638795184 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010464913929 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000863117959627 + + Density error is 4.73240967256e-07 + + Energy Rydberg eV + E_KohnSham -34.2802142919 -466.406243031 + E_Harris -34.2802142919 -466.406243031 + E_Fermi -0.160693870905 -2.18635227799 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00104649131242 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000863118833909 + + Density error is 1.81993995748e-07 + + Energy Rydberg eV + E_KohnSham -34.280214314 -466.406243332 + E_Harris -34.280214314 -466.406243332 + E_Fermi -0.160693692943 -2.18634985669 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00104649113437 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000863119075935 + + Density error is 1.06591498575e-08 + + Energy Rydberg eV + E_KohnSham -34.2802143162 -466.406243361 + E_Harris -34.2802143162 -466.406243361 + E_band -7.91450312084 -107.682339282 + E_one_elec -68.9499938835 -938.11279388 + E_Hartree +35.8784219942 +488.150974369 + E_xc -8.18373363523 -111.345408353 + E_Ewald +7.10011496438 +96.6020199706 + E_demet -1.09037766568e-67 -1.48353492252e-66 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194207877089 -2.6423337249 + E_Fermi -0.160693516903 -2.18634746154 + + charge density convergence is achieved + final etot is -466.406243361 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1348 2.00000 + 2 -12.8769 2.00000 + 3 -9.11901 2.00000 + 4 -6.71041 2.00000 + 5 1.14305 0.00000 + 6 4.18155 0.00000 + 7 11.1134 0.00000 + 8 11.3650 0.00000 + + EFERMI = -2.186347461536479 eV + OUT.ABACUS/ final etot is -466.4062433614978 eV + correction force for each atom along direction 1 is -5.38263e-05 + correction force for each atom along direction 2 is -0.000127772 + correction force for each atom along direction 3 is -9.87744e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.015106162 -0.97223813 +0.95340163 + H1 -0.25446774 -0.0089059353 -0.30899476 + H2 +0.26957390 +0.98114407 -0.64440687 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4062433614978 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3771 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3687 1 7.4 1.e+02% + Potential init_pot 0.28530 2 0.14 3.9% + PW_Basis recip2real 0.27245 17 0.016 3.7% + PW_Basis gathers_scatterp 0.12381 17 0.0073 1.7% + Potential v_of_rho 0.85094 14 0.061 12.% + XC_Functional v_xc 0.20315 15 0.014 2.8% + H_Hartree_pw v_hartree 0.60812 14 0.043 8.2% + PW_Basis real2recip 0.70528 41 0.017 9.6% + PW_Basis gatherp_scatters 0.28016 41 0.0068 3.8% + ORB_control set_orb_tables 1.0936 1 1.1 15.% + ORB_gen_tables gen_tables 1.0936 1 1.1 15.% + ORB_table_phi init_Table 0.47443 1 0.47 6.4% + ORB_table_phi cal_ST_Phi12_R 0.46922 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18396 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18246 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24551 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24360 66 0.0037 3.3% + LOOP_ions opt_ions 5.7480 1 5.7 78.% + ESolver_KS_LCAO Run 5.2083 1 5.2 71.% + HSolverLCAO solve 2.8679 12 0.24 39.% + HamiltLCAO updateHk 1.4846 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.4549 12 0.12 20.% + Gint_Gamma distri_vl_index 0.12184 1 0.12 1.7% + Gint_Gamma distri_vl_value 0.96233 12 0.080 13.% + Gint_Gamma distri_vl 2.6785 6 0.45 36.% + LCAO_Deepks cal_projected_DM 5.2823 14 0.38 72.% + LCAO_gen_fixedH add_v_delta 2.5512 6 0.43 35.% + LCAO_DESCRIPTOR add_v_delta 2.5514 6 0.43 35.% + ElecStateLCAO psiToRho 1.3521 12 0.11 18.% + Charge mix_rho 0.88971 11 0.081 12.% + LOOP_ions force_stress 0.53953 1 0.54 7.3% + Force_Stress_LCAO getForceStress 0.53950 1 0.54 7.3% + Force_LCAO_gamma ftable_gamma 0.34481 1 0.34 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:12 2022 + Finish Time : Wed Sep 28 11:04:19 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..428bca0c32f0ea0d984388bf85464b126d47844f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123329 ima = 3.71632e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 1 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123300906018 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011214897752 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112797709621 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113010459282 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112982685702 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112999646511 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112994283727 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112996474923 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112995766855 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011299570005 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112995684897 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112995675588 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1735cd79aa9b8063d3e6c9625e6bbf27f5529efd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.214263981291 18.186612408853 13.181523238639 0 0 0 +H +0.0 +2 +-15.390931698552 18.097100139764 11.782958716154 0 0 0 +-14.626906511796 16.649701455364 14.209193330203 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/conv new file mode 100644 index 0000000000000000000000000000000000000000..e628df175b5094d5e4629f6e48e91885dbca12df --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/conv @@ -0,0 +1 @@ +36 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..38f0620de2a9b4a3eded1a57ea7bd6fa6bb42561 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749886919 0.01255927559 1.257469259 1.350874463 1.46865095 0.008499324959 0.01811488335 0.03906631194 +8.603265624e-19 0.0009626813336 0.002509793444 0.01194957122 0.04340905764 -2.071093311e-19 1.847996774e-06 5.527881389e-06 +0.001626026897 0.005920616082 + +H atom_index 1 n_descriptor 18 +1.248940337 0.03434382534 0.1076138474 0.1496109592 0.3210500998 0.02209059109 0.02826509393 0.03754356343 +-2.033141432e-17 4.295170591e-05 0.09997363614 0.1151753194 0.1283072412 3.631943556e-18 4.026809123e-06 0.01317164928 +0.02592752392 0.03070928251 + +H atom_index 2 n_descriptor 18 +1.198031079 0.03604399967 0.091275288 0.1275305895 0.3031815884 0.01972612576 0.02528634234 0.03945880345 +4.090501404e-17 3.849248937e-05 0.08674519589 0.1090303961 0.1134116723 8.543027811e-18 6.221364268e-06 0.01418712762 +0.02390586059 0.02817966605 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..280f04fdd1dd2fdf27003490c24f5acb2a9975aa Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:12 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101623 SEC) : SETUP UNITCELL + DONE(0.101957 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.120015 SEC) : INIT PLANEWAVE + DONE(0.163113 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446953 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652011e+02 0.000000e+00 2.127e-01 5.737e-01 + GE2 -4.664030e+02 -1.201895e+00 9.838e-02 4.805e-01 + GE3 -4.664073e+02 -4.360639e-03 6.329e-02 5.426e-01 + GE4 -4.664066e+02 7.671485e-04 1.976e-03 4.130e-01 + GE5 -4.664060e+02 5.598667e-04 8.672e-04 4.143e-01 + GE6 -4.664063e+02 -3.009350e-04 1.680e-04 4.108e-01 + GE7 -4.664062e+02 1.014642e-04 3.012e-05 3.979e-01 + GE8 -4.664063e+02 -4.323441e-05 1.516e-05 3.936e-01 + GE9 -4.664062e+02 1.569082e-05 2.725e-06 3.936e-01 + GE10 -4.664062e+02 -3.290037e-06 4.732e-07 3.927e-01 + GE11 -4.664062e+02 -3.009168e-07 1.820e-07 3.948e-01 + GE12 -4.664062e+02 -2.987042e-08 1.066e-08 3.391e-01 +E_delta_band = -6.91841210e-02 Ry = -9.41298257e-01 eV +E_delta_NN= -1.94207877e-01 Ry = -2.64233372e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3771 11 0.67 1e+02 % + Run_lcao lcao_line 7.3687 1 7.4 1e+02 % + Potential init_pot 0.2853 2 0.14 3.9 % + PW_Basis recip2real 0.27245 17 0.016 3.7 % + PW_Basis gathers_scatterp 0.12381 17 0.0073 1.7 % + Potential v_of_rho 0.85094 14 0.061 12 % + XC_Functional v_xc 0.20315 15 0.014 2.8 % + H_Hartree_pw v_hartree 0.60812 14 0.043 8.2 % + PW_Basis real2recip 0.70528 41 0.017 9.6 % + PW_Basis gatherp_scatters 0.28016 41 0.0068 3.8 % + ORB_control set_orb_tables 1.0936 1 1.1 15 % + ORB_gen_tables gen_tables 1.0936 1 1.1 15 % + ORB_table_phi init_Table 0.47443 1 0.47 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.46922 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18396 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18246 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24551 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.2436 66 0.0037 3.3 % + LOOP_ions opt_ions 5.748 1 5.7 78 % + ESolver_KS_LCAO Run 5.2083 1 5.2 71 % + HSolverLCAO solve 2.8679 12 0.24 39 % + HamiltLCAO updateHk 1.4846 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.4549 12 0.12 20 % + Gint_Gamma distri_vl_index 0.12184 1 0.12 1.7 % + Gint_Gamma distri_vl_value 0.96233 12 0.08 13 % + Gint_Gamma distri_vl 2.6785 6 0.45 36 % + LCAO_Deepks cal_projected_DM 5.2823 14 0.38 72 % + LCAO_gen_fixedH add_v_delta 2.5512 6 0.43 35 % + LCAO_DESCRIPTOR add_v_delta 2.5514 6 0.43 35 % + ElecStateLCAO psiToRho 1.3521 12 0.11 18 % + Charge mix_rho 0.88971 11 0.081 12 % + LOOP_ions force_stress 0.53953 1 0.54 7.3 % + Force_Stress_LCAO getForceStress 0.5395 1 0.54 7.3 % + Force_LCAO_gamma ftable_gamma 0.34481 1 0.34 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:12 2022 + FINISH Time : Wed Sep 28 11:04:19 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/36/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..08178b2fc0844a9d97c723a4568c87605201d450 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.483083 0.683931 0.470981 +H 0.459959 0.629987 0.438952 +H 0.502199 0.660418 0.527541 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..a52a3ebd19c54824bb5914bcd397e64fc512aa5f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3103 2 + 2 -13.0011 2 + 3 -9.16008 2 + 4 -6.74885 2 + 5 1.27752 0 + 6 4.42642 0 + 7 11.0728 0 + 8 11.3249 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..791ed30498503a79baf547a9a2626f2420b5035c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:23 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.5263286169 19.1500654233 13.1874632887 0 0 0 0 + tauc_H1 12.8788601939 17.6396308937 12.2906662471 0 0 0 0 + tauc_H2 14.0615673323 18.4917072821 14.7711423325 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870077795944 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0985731945934 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116773859486 (SEC) + + DONE : INIT CHARGE Time : 0.166245536842 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447257 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 1 + Local orbitals number in sub-FFT-grid = 5 + lgd_last = 0 + lgd_now = 5 + allocate DM , the dimension is 5 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 2 + nCol_in_proc = 2 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 2 + nCol_in_proc = 3 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 3 + nCol_in_proc = 2 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 3 + nCol_in_proc = 3 +receiver_size is 25 ; receiver_size of each process is: +4 6 6 9 +sender_size is 292 ; sender_size of each process is: +4 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000695 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.00121 + + Density error is 0.214371270582 + + Energy Rydberg eV + E_KohnSham -34.1908110376 -465.189849353 + E_Harris -34.3814691819 -467.783886485 + E_Fermi -0.405205110832 -5.51309836603 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000900866358781 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.0011635398714 + + Density error is 0.0978713856489 + + Energy Rydberg eV + E_KohnSham -34.2796543564 -466.398624718 + E_Harris -34.2864060327 -466.490485986 + E_Fermi -0.215116625691 -2.92681184393 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000860392365455 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.00108020858443 + + Density error is 0.0627275602497 + + Energy Rydberg eV + E_KohnSham -34.2799063324 -466.402053027 + E_Harris -34.2842656673 -466.461364821 + E_Fermi -0.203746925287 -2.77211913389 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0008101371625 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000941656711509 + + Density error is 0.0019808202046 + + Energy Rydberg eV + E_KohnSham -34.2798945714 -466.401893011 + E_Harris -34.2798957424 -466.401908943 + E_Fermi -0.168183837267 -2.28825849834 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000812444459197 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000940337819256 + + Density error is 0.000841280068534 + + Energy Rydberg eV + E_KohnSham -34.2798405544 -466.401158071 + E_Harris -34.2798416107 -466.401172444 + E_Fermi -0.167488541289 -2.27879851123 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000811486551479 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000938922886078 + + Density error is 0.000161916348815 + + Energy Rydberg eV + E_KohnSham -34.2798759996 -466.401640327 + E_Harris -34.2798760575 -466.401641116 + E_Fermi -0.167472448654 -2.27857955971 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000811640148648 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000939040154495 + + Density error is 3.77709923433e-05 + + Energy Rydberg eV + E_KohnSham -34.2798624779 -466.401456355 + E_Harris -34.2798624849 -466.401456452 + E_Fermi -0.167355036516 -2.27698208562 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000811605647406 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000938999836607 + + Density error is 1.74310474742e-05 + + Energy Rydberg eV + E_KohnSham -34.2798668479 -466.401515813 + E_Harris -34.2798668492 -466.40151583 + E_Fermi -0.16739369163 -2.27750801542 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000811613452505 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000938985870076 + + Density error is 2.99069672471e-06 + + Energy Rydberg eV + E_KohnSham -34.2798654085 -466.401496229 + E_Harris -34.2798654086 -466.40149623 + E_Fermi -0.16737709352 -2.27728218655 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000811611439177 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000938982310602 + + Density error is 3.9570744278e-07 + + Energy Rydberg eV + E_KohnSham -34.2798656406 -466.401499386 + E_Harris -34.2798656406 -466.401499386 + E_Fermi -0.167373947184 -2.27723937846 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000811612006481 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000938982234626 + + Density error is 1.50533390316e-07 + + Energy Rydberg eV + E_KohnSham -34.2798656836 -466.401499972 + E_Harris -34.2798656836 -466.401499972 + E_Fermi -0.167373809803 -2.27723750928 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00081161213042 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000938982068282 + + Density error is 1.05779998645e-08 + + Energy Rydberg eV + E_KohnSham -34.2798656859 -466.401500003 + E_Harris -34.2798656859 -466.401500003 + E_band -7.97023134736 -108.440560702 + E_one_elec -69.2932602603 -942.783172537 + E_Hartree +36.039286425 +490.339647234 + E_xc -8.20964891796 -111.698003864 + E_Ewald +7.30808179644 +99.4315538816 + E_demet -8.66961627837e-77 -1.17956180859e-75 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194841588447 -2.65095581025 + E_Fermi -0.167373671991 -2.27723563426 + + charge density convergence is achieved + final etot is -466.401500003 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3103 2.00000 + 2 -13.0011 2.00000 + 3 -9.16008 2.00000 + 4 -6.74885 2.00000 + 5 1.27752 0.00000 + 6 4.42642 0.00000 + 7 11.0728 0.00000 + 8 11.3249 0.00000 + + EFERMI = -2.277235634260345 eV + OUT.ABACUS/ final etot is -466.4015000032933 eV + correction force for each atom along direction 1 is 0.000106694 + correction force for each atom along direction 2 is -0.000124898 + correction force for each atom along direction 3 is -1.54825e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.65431178 -0.18614937 -1.5146350 + H1 +0.22291255 +0.61413072 +0.27541660 + H2 +0.43139924 -0.42798135 +1.2392184 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4015000032933 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3228 11 0.57 1.0e+02% + Run_lcao lcao_line 6.3137 1 6.3 1.e+02% + Potential init_pot 0.28243 2 0.14 4.5% + PW_Basis recip2real 0.28810 17 0.017 4.6% + PW_Basis gathers_scatterp 0.13692 17 0.0081 2.2% + Potential v_of_rho 1.0487 14 0.075 17.% + XC_Functional v_xc 0.31107 15 0.021 4.9% + H_Hartree_pw v_hartree 0.69481 14 0.050 11.% + PW_Basis real2recip 0.70618 41 0.017 11.% + PW_Basis gatherp_scatters 0.30485 41 0.0074 4.8% + ORB_control set_orb_tables 1.1005 1 1.1 17.% + ORB_gen_tables gen_tables 1.1005 1 1.1 17.% + ORB_table_phi init_Table 0.47442 1 0.47 7.5% + ORB_table_phi cal_ST_Phi12_R 0.46922 126 0.0037 7.4% + ORB_table_beta init_Table_Beta 0.18729 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18569 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25263 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25059 66 0.0038 4.0% + LOOP_ions opt_ions 4.6884 1 4.7 74.% + ESolver_KS_LCAO Run 4.2210 1 4.2 67.% + HSolverLCAO solve 1.7343 12 0.14 27.% + HamiltLCAO updateHk 0.95522 12 0.080 15.% + LCAO_Hamilt cal_Hgamma 0.92570 12 0.077 15.% + Gint_Gamma distri_vl_value 0.52455 12 0.044 8.3% + Gint_Gamma distri_vl 2.2158 6 0.37 35.% + LCAO_Deepks cal_projected_DM 4.3883 14 0.31 69.% + LCAO_gen_fixedH add_v_delta 2.0715 6 0.35 33.% + LCAO_DESCRIPTOR add_v_delta 2.0716 6 0.35 33.% + ElecStateLCAO psiToRho 0.75509 12 0.063 12.% + Charge mix_rho 0.83950 11 0.076 13.% + LOOP_ions force_stress 0.46723 1 0.47 7.4% + Force_Stress_LCAO getForceStress 0.46720 1 0.47 7.4% + Force_LCAO_gamma ftable_gamma 0.24891 1 0.25 3.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:23 2022 + Finish Time : Wed Sep 28 11:13:29 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ed7dff352f8bbc2ef61aee8be29bd1bb30f110b8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123846 ima = 3.71826e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 1 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122988706242 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112004950993 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112544040054 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112782848692 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112736378195 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112765521697 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112757663437 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011276055296 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112759816522 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112759700075 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112759686465 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112759679176 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/STRU new file mode 100644 index 0000000000000000000000000000000000000000..690e298f71c04c4b9ca150e59239cc6aed9d5f5e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.473671383135 19.150065423229 13.187463288654 0 0 0 +H +0.0 +2 +-15.121139806056 17.639630893726 12.290666247121 0 0 0 +-13.938432667719 18.491707282118 14.771142332472 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/conv new file mode 100644 index 0000000000000000000000000000000000000000..4a0c146ec920005e155c743bf8b2bf4e1dc95251 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/conv @@ -0,0 +1 @@ +37 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c21faaf83cf900ceaf890e08c66f3f3a2309a653 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750015483 0.01268191439 1.270365942 1.362864635 1.469425052 0.008650006437 0.01832444365 0.0390590382 +-2.01491454e-18 0.001032588234 0.002632678183 0.01245422887 0.04538050074 4.220605899e-19 2.103400096e-06 6.071558334e-06 +0.001631053284 0.005966805043 + +H atom_index 1 n_descriptor 18 +1.21557592 0.0354933808 0.09709965918 0.1346331612 0.3091579262 0.02071771198 0.02628951727 0.0387169856 +3.705185278e-17 4.309663079e-05 0.092793047 0.1138292314 0.1153876105 4.506147286e-18 5.741895943e-06 0.01375238691 +0.02501061651 0.02910100327 + +H atom_index 2 n_descriptor 18 +1.275254283 0.03346998908 0.1175919135 0.1620829896 0.3287400397 0.02350555015 0.02976510323 0.0368370939 +-3.237761174e-17 4.862939348e-05 0.106498982 0.1174684283 0.1391154825 6.256517898e-18 2.631602208e-06 0.01321164368 +0.02724308807 0.03184300566 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..2e24fe98fc95f08d176ad6b94929721288f69eb9 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:23 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870307 SEC) : SETUP UNITCELL + DONE(0.0985921 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116795 SEC) : INIT PLANEWAVE + DONE(0.166379 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447323 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651898e+02 0.000000e+00 2.144e-01 4.669e-01 + GE2 -4.663986e+02 -1.208775e+00 9.787e-02 4.024e-01 + GE3 -4.664021e+02 -3.428309e-03 6.273e-02 4.707e-01 + GE4 -4.664019e+02 1.600161e-04 1.981e-03 3.353e-01 + GE5 -4.664012e+02 7.349396e-04 8.413e-04 3.354e-01 + GE6 -4.664016e+02 -4.822560e-04 1.619e-04 3.294e-01 + GE7 -4.664015e+02 1.839722e-04 3.777e-05 3.222e-01 + GE8 -4.664015e+02 -5.945756e-05 1.743e-05 3.131e-01 + GE9 -4.664015e+02 1.958359e-05 2.991e-06 3.131e-01 + GE10 -4.664015e+02 -3.157012e-06 3.957e-07 3.130e-01 + GE11 -4.664015e+02 -5.856166e-07 1.505e-07 3.111e-01 + GE12 -4.664015e+02 -3.146565e-08 1.058e-08 2.456e-01 +E_delta_band = -7.05168593e-02 Ry = -9.59431092e-01 eV +E_delta_NN= -1.94841588e-01 Ry = -2.65095581e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3228 11 0.57 1e+02 % + Run_lcao lcao_line 6.3137 1 6.3 1e+02 % + Potential init_pot 0.28243 2 0.14 4.5 % + PW_Basis recip2real 0.2881 17 0.017 4.6 % + PW_Basis gathers_scatterp 0.13692 17 0.0081 2.2 % + Potential v_of_rho 1.0487 14 0.075 17 % + XC_Functional v_xc 0.31107 15 0.021 4.9 % + H_Hartree_pw v_hartree 0.69481 14 0.05 11 % + PW_Basis real2recip 0.70618 41 0.017 11 % + PW_Basis gatherp_scatters 0.30485 41 0.0074 4.8 % + ORB_control set_orb_tables 1.1005 1 1.1 17 % + ORB_gen_tables gen_tables 1.1005 1 1.1 17 % + ORB_table_phi init_Table 0.47442 1 0.47 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.46922 126 0.0037 7.4 % + ORB_table_beta init_Table_Beta 0.18729 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18569 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.25263 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.25059 66 0.0038 4 % + LOOP_ions opt_ions 4.6884 1 4.7 74 % + ESolver_KS_LCAO Run 4.221 1 4.2 67 % + HSolverLCAO solve 1.7343 12 0.14 27 % + HamiltLCAO updateHk 0.95522 12 0.08 15 % + LCAO_Hamilt cal_Hgamma 0.9257 12 0.077 15 % + Gint_Gamma distri_vl_value 0.52455 12 0.044 8.3 % + Gint_Gamma distri_vl 2.2158 6 0.37 35 % + LCAO_Deepks cal_projected_DM 4.3883 14 0.31 69 % + LCAO_gen_fixedH add_v_delta 2.0715 6 0.35 33 % + LCAO_DESCRIPTOR add_v_delta 2.0716 6 0.35 33 % + ElecStateLCAO psiToRho 0.75509 12 0.063 12 % + Charge mix_rho 0.8395 11 0.076 13 % + LOOP_ions force_stress 0.46723 1 0.47 7.4 % + Force_Stress_LCAO getForceStress 0.4672 1 0.47 7.4 % + Force_LCAO_gamma ftable_gamma 0.24891 1 0.25 3.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:23 2022 + FINISH Time : Wed Sep 28 11:13:29 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/37/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..bb13c75eb55ca36b1c6b89ff2a7a7239a28e3cda --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.473188 0.706079 0.468712 +H 0.423215 0.663457 0.459897 +H 0.482258 0.699543 0.534023 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1b80d0f11137742a6cf603833cde31aed9650aa1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2454 2 + 2 -12.7255 2 + 3 -9.32006 2 + 4 -6.73791 2 + 5 1.1754 0 + 6 4.20555 0 + 7 11.0985 0 + 8 11.3722 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9cb6576d85c402af0f98641037f819dedda96efe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/running_scf.log @@ -0,0 +1,777 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:08 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.2492529158 19.7702162238 13.1239322576 0 0 0 0 + tauc_H1 11.8500138627 18.5767978768 12.877106894 0 0 0 0 + tauc_H2 13.503210137 19.5871998667 14.9526351241 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0884588141764 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0888090434519 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107207859633 (SEC) + + DONE : INIT CHARGE Time : 0.156893486276 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441923 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 +receiver_size is 324 ; receiver_size of each process is: +81 81 81 81 +sender_size is 378 ; sender_size of each process is: +81 144 144 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.000675 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00116 + + Density error is 0.212704761618 + + Energy Rydberg eV + E_KohnSham -34.1913592056 -465.197307561 + E_Harris -34.3788253847 -467.74791578 + E_Fermi -0.398199292077 -5.41777931181 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.00105312242853 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00130887173223 + + Density error is 0.0980450695894 + + Energy Rydberg eV + E_KohnSham -34.280293096 -466.407315216 + E_Harris -34.287254243 -466.50202648 + E_Fermi -0.208431991097 -2.83586272441 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.00101335006984 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00123297967692 + + Density error is 0.0631112458619 + + Energy Rydberg eV + E_KohnSham -34.2806822003 -466.412609251 + E_Harris -34.2851808646 -466.473816719 + E_Fermi -0.199606105379 -2.71578038874 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.000973113374877 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0011125308025 + + Density error is 0.00191622657976 + + Energy Rydberg eV + E_KohnSham -34.2806252663 -466.411834624 + E_Harris -34.2806258401 -466.411842432 + E_Fermi -0.164012142803 -2.2314996833 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.000975351276859 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00111352254245 + + Density error is 0.000952657378842 + + Energy Rydberg eV + E_KohnSham -34.2805729351 -466.411122622 + E_Harris -34.2805739502 -466.411136433 + E_Fermi -0.163700755329 -2.22726303938 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.000974445488897 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00111170145602 + + Density error is 0.000120999151735 + + Energy Rydberg eV + E_KohnSham -34.2806035529 -466.411539199 + E_Harris -34.2806035625 -466.41153933 + E_Fermi -0.163477613282 -2.22422703607 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.000974580947112 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00111176678241 + + Density error is 3.25890768826e-05 + + Energy Rydberg eV + E_KohnSham -34.2805935537 -466.411403153 + E_Harris -34.2805935589 -466.411403223 + E_Fermi -0.163398382164 -2.22314904141 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.000974507234729 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00111170879127 + + Density error is 1.26877521941e-05 + + Energy Rydberg eV + E_KohnSham -34.2805962063 -466.411439243 + E_Harris -34.280596207 -466.411439252 + E_Fermi -0.163428961546 -2.22356509525 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.000974511986864 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00111169697387 + + Density error is 1.54288269735e-06 + + Energy Rydberg eV + E_KohnSham -34.2805950472 -466.411423473 + E_Harris -34.2805950472 -466.411423473 + E_Fermi -0.163415414794 -2.22338078223 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.000974513564679 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00111169681727 + + Density error is 1.48367924875e-07 + + Energy Rydberg eV + E_KohnSham -34.2805952241 -466.411425879 + E_Harris -34.2805952241 -466.411425879 + E_Fermi -0.16341409641 -2.22336284469 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 378 + sender_size = 378 + last sender_buffer = 0.000974514091382 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00111169727796 + + Density error is 3.64178597218e-08 + + Energy Rydberg eV + E_KohnSham -34.2805952507 -466.411426242 + E_Harris -34.2805952507 -466.411426242 + E_band -7.94210138277 -108.057832899 + E_one_elec -69.0465137349 -939.42601383 + E_Hartree +35.9168402497 +488.673681551 + E_xc -8.18974421794 -111.427186526 + E_Ewald +7.16362722599 +97.4661486214 + E_demet -1.99570360488e-70 -2.71529405455e-69 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194404306143 -2.64500627928 + E_Fermi -0.163414103309 -2.22336293857 + + charge density convergence is achieved + final etot is -466.411426242 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2454 2.00000 + 2 -12.7255 2.00000 + 3 -9.32006 2.00000 + 4 -6.73791 2.00000 + 5 1.17540 0.00000 + 6 4.20555 0.00000 + 7 11.0985 0.00000 + 8 11.3722 0.00000 + + EFERMI = -2.223362938566563 eV + OUT.ABACUS/ final etot is -466.4114262415835 eV + correction force for each atom along direction 1 is -4.68545e-05 + correction force for each atom along direction 2 is -0.000158942 + correction force for each atom along direction 3 is 6.08856e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.34821820 -0.42209027 +0.47379122 + H1 +0.13544246 +0.18796463 -0.28766045 + H2 +0.21277574 +0.23412564 -0.18613077 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4114262415835 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1771 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1677 1 6.2 1.e+02% + Potential init_pot 0.28740 2 0.14 4.7% + PW_Basis recip2real 0.28011 16 0.018 4.5% + PW_Basis gathers_scatterp 0.13502 16 0.0084 2.2% + Potential v_of_rho 1.0066 13 0.077 16.% + XC_Functional v_xc 0.30986 14 0.022 5.0% + H_Hartree_pw v_hartree 0.65594 13 0.050 11.% + PW_Basis real2recip 0.66658 38 0.018 11.% + PW_Basis gatherp_scatters 0.29867 38 0.0079 4.8% + ORB_control set_orb_tables 1.1016 1 1.1 18.% + ORB_gen_tables gen_tables 1.1016 1 1.1 18.% + ORB_table_phi init_Table 0.47678 1 0.48 7.7% + ORB_table_phi cal_ST_Phi12_R 0.47152 126 0.0037 7.6% + ORB_table_beta init_Table_Beta 0.18767 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18608 56 0.0033 3.0% + ORB_table_alpha init_Table_Alpha 0.25208 1 0.25 4.1% + ORB_table_alpha S_PhiAlpha_R 0.25003 66 0.0038 4.0% + LOOP_ions opt_ions 4.5455 1 4.5 74.% + ESolver_KS_LCAO Run 4.0574 1 4.1 66.% + HSolverLCAO solve 1.7425 11 0.16 28.% + HamiltLCAO updateHk 0.95576 11 0.087 15.% + LCAO_Hamilt cal_Hgamma 0.92813 11 0.084 15.% + Gint_Gamma distri_vl_value 0.53079 11 0.048 8.6% + Gint_Gamma distri_vl 1.9704 6 0.33 32.% + LCAO_Deepks cal_projected_DM 4.2239 13 0.32 68.% + LCAO_gen_fixedH add_v_delta 1.8274 6 0.30 30.% + LCAO_DESCRIPTOR add_v_delta 1.8274 6 0.30 30.% + ElecStateLCAO psiToRho 0.76278 11 0.069 12.% + Charge mix_rho 0.77017 10 0.077 12.% + LOOP_ions force_stress 0.48796 1 0.49 7.9% + Force_Stress_LCAO getForceStress 0.48794 1 0.49 7.9% + Force_LCAO_gamma ftable_gamma 0.26983 1 0.27 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:08 2022 + Finish Time : Wed Sep 28 11:03:15 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..209465e5eb233aaee0f455ab40d45ee7b65d7584 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/OUT.ABACUS/warning.log @@ -0,0 +1,73 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123805 ima = 3.72572e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 2 + 2 3 + 3 3 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122954491452 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111614504626 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112295628172 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112532459769 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112491173294 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112515326539 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112510982326 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112513399154 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112512865245 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011251279704 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112512790267 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/STRU new file mode 100644 index 0000000000000000000000000000000000000000..dafd469c65b0105290b118891d3ff971ae0998e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.750747084194 19.770216223808 13.123932257638 0 0 0 +H +0.0 +2 +-16.149986137237 18.576797876857 12.877106894027 0 0 0 +-14.496789863008 19.587199866713 14.952635124146 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/conv new file mode 100644 index 0000000000000000000000000000000000000000..8105b199da0a3f58fca60cff6600e74539ce22e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/conv @@ -0,0 +1 @@ +38 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..3ab8eab137ec8c470680d162b55ba97d03ffcf22 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752818466 0.01267770251 1.261733614 1.345899498 1.469058307 0.009090863514 0.01706506031 0.03914189314 +-2.882346165e-18 0.0009020264644 0.002681054024 0.01257144065 0.04496611703 3.66853192e-20 2.337940548e-06 6.519281146e-06 +0.001591509139 0.006082190656 + +H atom_index 1 n_descriptor 18 +1.231303455 0.03531346832 0.1031965506 0.1411496228 0.3139066368 0.02182476241 0.02715859961 0.03847653799 +5.243164238e-19 4.508508664e-05 0.09661870963 0.1145682046 0.1209363545 8.623853062e-18 4.463420809e-06 0.01356476534 +0.02572801866 0.02984003668 + +H atom_index 2 n_descriptor 18 +1.231478064 0.03530754468 0.1032611332 0.1412347537 0.3139794254 0.02183383426 0.02716971525 0.03846986235 +-1.415834885e-17 4.510160601e-05 0.09666601217 0.1145790898 0.1210095277 -3.755804594e-18 4.454189075e-06 0.01356137579 +0.0257349403 0.02984934316 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e60a24182dfb693527b25a49f820a9ec04a57644 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/log.scf @@ -0,0 +1,100 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:08 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0884806 SEC) : SETUP UNITCELL + DONE(0.0888235 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.10723 SEC) : INIT PLANEWAVE + DONE(0.157027 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.441991 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651973e+02 0.000000e+00 2.127e-01 4.769e-01 + GE2 -4.664073e+02 -1.210008e+00 9.805e-02 4.161e-01 + GE3 -4.664126e+02 -5.294035e-03 6.311e-02 4.838e-01 + GE4 -4.664118e+02 7.746269e-04 1.916e-03 3.484e-01 + GE5 -4.664111e+02 7.120021e-04 9.527e-04 3.470e-01 + GE6 -4.664115e+02 -4.165767e-04 1.210e-04 3.433e-01 + GE7 -4.664114e+02 1.360459e-04 3.259e-05 3.343e-01 + GE8 -4.664114e+02 -3.609044e-05 1.269e-05 3.322e-01 + GE9 -4.664114e+02 1.577084e-05 1.543e-06 3.268e-01 + GE10 -4.664114e+02 -2.406503e-06 1.484e-07 3.312e-01 + GE11 -4.664114e+02 -3.625332e-07 3.642e-08 2.565e-01 +E_delta_band = -6.95995326e-02 Ry = -9.46950222e-01 eV +E_delta_NN= -1.94404306e-01 Ry = -2.64500628e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1771 11 0.56 1e+02 % + Run_lcao lcao_line 6.1677 1 6.2 1e+02 % + Potential init_pot 0.2874 2 0.14 4.7 % + PW_Basis recip2real 0.28011 16 0.018 4.5 % + PW_Basis gathers_scatterp 0.13502 16 0.0084 2.2 % + Potential v_of_rho 1.0066 13 0.077 16 % + XC_Functional v_xc 0.30986 14 0.022 5 % + H_Hartree_pw v_hartree 0.65594 13 0.05 11 % + PW_Basis real2recip 0.66658 38 0.018 11 % + PW_Basis gatherp_scatters 0.29867 38 0.0079 4.8 % + ORB_control set_orb_tables 1.1016 1 1.1 18 % + ORB_gen_tables gen_tables 1.1016 1 1.1 18 % + ORB_table_phi init_Table 0.47678 1 0.48 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.47152 126 0.0037 7.6 % + ORB_table_beta init_Table_Beta 0.18767 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18608 56 0.0033 3 % + ORB_table_alpha init_Table_Alpha 0.25208 1 0.25 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.25003 66 0.0038 4 % + LOOP_ions opt_ions 4.5455 1 4.5 74 % + ESolver_KS_LCAO Run 4.0574 1 4.1 66 % + HSolverLCAO solve 1.7425 11 0.16 28 % + HamiltLCAO updateHk 0.95576 11 0.087 15 % + LCAO_Hamilt cal_Hgamma 0.92813 11 0.084 15 % + Gint_Gamma distri_vl_value 0.53079 11 0.048 8.6 % + Gint_Gamma distri_vl 1.9704 6 0.33 32 % + LCAO_Deepks cal_projected_DM 4.2239 13 0.32 68 % + LCAO_gen_fixedH add_v_delta 1.8274 6 0.3 30 % + LCAO_DESCRIPTOR add_v_delta 1.8274 6 0.3 30 % + ElecStateLCAO psiToRho 0.76278 11 0.069 12 % + Charge mix_rho 0.77017 10 0.077 12 % + LOOP_ions force_stress 0.48796 1 0.49 7.9 % + Force_Stress_LCAO getForceStress 0.48794 1 0.49 7.9 % + Force_LCAO_gamma ftable_gamma 0.26983 1 0.27 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:08 2022 + FINISH Time : Wed Sep 28 11:03:15 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/38/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e9641376b82a3cfc6b9dd6e41a6dfa2f0e541b1e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.462046 0.710761 0.483813 +H 0.394825 0.716991 0.481375 +H 0.479378 0.753575 0.531123 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..33158b8a2d1f4e9e754b5862c1066dcf2109ed23 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0857 2 + 2 -12.8089 2 + 3 -9.13502 2 + 4 -6.70061 2 + 5 1.10387 0 + 6 4.08914 0 + 7 11.1262 0 + 8 11.3811 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f5e4e9c7ad0fbe45b84d4f45bf57d8fac3fe2511 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/running_scf.log @@ -0,0 +1,776 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:56 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.9372898458 19.9013199361 13.5467535057 0 0 0 0 + tauc_H1 11.0550869007 20.0757529323 13.4784863409 0 0 0 0 + tauc_H2 13.4225838811 21.100109814 14.8714310369 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0868687532529 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0988879697157 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11814064209 (SEC) + + DONE : INIT CHARGE Time : 0.167092443625 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449333 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + No atoms on this sub-FFT-mesh. + Atom number in sub-FFT-grid = 0 + Local orbitals number in sub-FFT-grid = 0 + lgd_last = 0 + lgd_now = 0 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 +receiver_size is 0 ; receiver_size of each process is: +0 0 0 0 +sender_size is 288 ; sender_size of each process is: +0 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00116 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63e-322 + + Density error is 0.21260716595 + + Energy Rydberg eV + E_KohnSham -34.1910483062 -465.193077558 + E_Harris -34.3779567057 -467.736096795 + E_Fermi -0.392187961355 -5.33599096144 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00129363255897 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0985632094951 + + Energy Rydberg eV + E_KohnSham -34.2801075363 -466.404790546 + E_Harris -34.2871538991 -466.50066123 + E_Fermi -0.202107439709 -2.74981278824 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00122085128074 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0635244823768 + + Energy Rydberg eV + E_KohnSham -34.2805456088 -466.410750829 + E_Harris -34.2850710019 -466.47232196 + E_Fermi -0.194538245134 -2.64682861274 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110356295468 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.00196364546377 + + Energy Rydberg eV + E_KohnSham -34.2804687797 -466.409705515 + E_Harris -34.2804706835 -466.409731417 + E_Fermi -0.159194031101 -2.16594591056 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110352631006 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000957872694656 + + Energy Rydberg eV + E_KohnSham -34.2804244361 -466.409102189 + E_Harris -34.2804248952 -466.409108435 + E_Fermi -0.158988569446 -2.16315046133 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0011018792009 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000168425500181 + + Energy Rydberg eV + E_KohnSham -34.2804452409 -466.409385254 + E_Harris -34.2804452501 -466.409385378 + E_Fermi -0.158656642588 -2.15863436475 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110203324749 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 3.12226314034e-05 + + Energy Rydberg eV + E_KohnSham -34.2804386833 -466.409296032 + E_Harris -34.2804386871 -466.409296084 + E_Fermi -0.158592965824 -2.15776799792 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110196450461 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.40973451089e-05 + + Energy Rydberg eV + E_KohnSham -34.2804417377 -466.40933759 + E_Harris -34.2804417386 -466.409337602 + E_Fermi -0.158617102165 -2.15809638969 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110195562078 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.79578034172e-06 + + Energy Rydberg eV + E_KohnSham -34.2804405767 -466.409321794 + E_Harris -34.2804405767 -466.409321794 + E_Fermi -0.158602830441 -2.15790221293 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110195423591 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 3.02677755769e-07 + + Energy Rydberg eV + E_KohnSham -34.2804407925 -466.409324729 + E_Harris -34.2804407925 -466.409324729 + E_Fermi -0.158601228739 -2.15788042066 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0011019546465 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 7.95531120061e-08 + + Energy Rydberg eV + E_KohnSham -34.2804408132 -466.409325011 + E_Harris -34.2804408132 -466.409325011 + E_band -7.89819618687 -107.460472063 + E_one_elec -68.8373121253 -936.579679908 + E_Hartree +35.8244953822 +487.417265172 + E_xc -8.17503410744 -111.227045206 + E_Ewald +7.03266226576 +95.6842789239 + E_demet -4.49518321778e-65 -6.11601053158e-64 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194004861623 -2.63957155778 + E_Fermi -0.158601102889 -2.15787870837 + + charge density convergence is achieved + final etot is -466.409325011 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0857 2.00000 + 2 -12.8089 2.00000 + 3 -9.13502 2.00000 + 4 -6.70061 2.00000 + 5 1.10387 0.00000 + 6 4.08914 0.00000 + 7 11.1262 0.00000 + 8 11.3811 0.00000 + + EFERMI = -2.157878708370386 eV + OUT.ABACUS/ final etot is -466.4093250112617 eV + correction force for each atom along direction 1 is -0.000103431 + correction force for each atom along direction 2 is 4.93951e-05 + correction force for each atom along direction 3 is 8.33575e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.1073169 +0.23327711 +0.099383019 + H1 +1.1164946 -0.12475029 +0.017022010 + H2 -0.0091776763 -0.10852682 -0.11640503 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4093250112617 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6387 11 0.51 1.0e+02% + Run_lcao lcao_line 5.6294 1 5.6 1.e+02% + Potential init_pot 0.28801 2 0.14 5.1% + PW_Basis recip2real 0.26048 16 0.016 4.6% + PW_Basis gathers_scatterp 0.11865 16 0.0074 2.1% + Potential v_of_rho 0.88204 13 0.068 16.% + XC_Functional v_xc 0.26243 14 0.019 4.7% + H_Hartree_pw v_hartree 0.58401 13 0.045 10.% + PW_Basis real2recip 0.56574 38 0.015 10.% + PW_Basis gatherp_scatters 0.26237 38 0.0069 4.7% + ORB_control set_orb_tables 1.1071 1 1.1 20.% + ORB_gen_tables gen_tables 1.1071 1 1.1 20.% + ORB_table_phi init_Table 0.48373 1 0.48 8.6% + ORB_table_phi cal_ST_Phi12_R 0.47889 126 0.0038 8.5% + ORB_table_beta init_Table_Beta 0.19035 1 0.19 3.4% + ORB_table_beta VNL_PhiBeta_R 0.18884 56 0.0034 3.3% + ORB_table_alpha init_Table_Alpha 0.25379 1 0.25 4.5% + ORB_table_alpha S_PhiAlpha_R 0.25194 66 0.0038 4.5% + LOOP_ions opt_ions 3.9962 1 4.0 71.% + ESolver_KS_LCAO Run 3.5327 1 3.5 63.% + HSolverLCAO solve 1.5587 11 0.14 28.% + HamiltLCAO updateHk 0.80489 11 0.073 14.% + LCAO_Hamilt cal_Hgamma 0.77636 11 0.071 14.% + Gint_Gamma distri_vl_value 0.49346 11 0.045 8.8% + Gint_Gamma distri_vl 1.7123 6 0.29 30.% + LCAO_Deepks cal_projected_DM 3.6894 13 0.28 65.% + LCAO_gen_fixedH add_v_delta 1.5956 6 0.27 28.% + LCAO_DESCRIPTOR add_v_delta 1.5956 6 0.27 28.% + ElecStateLCAO psiToRho 0.67736 11 0.062 12.% + Charge mix_rho 0.63990 10 0.064 11.% + LOOP_ions force_stress 0.46328 1 0.46 8.2% + Force_Stress_LCAO getForceStress 0.46325 1 0.46 8.2% + Force_LCAO_gamma ftable_gamma 0.25592 1 0.26 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1028. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:56 2022 + Finish Time : Wed Sep 28 11:07:02 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..35e6da7051b3f93daa5dc5f47f5907b70b38ebc8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/OUT.ABACUS/warning.log @@ -0,0 +1,75 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123214 ima = 3.67604e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 0 + 2 3 + 3 3 + 4 0 + Grid_Technique::init_atoms_on_grid2 warning : no atom on this sub FFT grid. + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123455184267 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112068753233 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112790647902 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113007271107 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011298015843 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112995996365 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112990991505 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112993302925 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011299266604 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112992603304 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112992588428 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c011594a7ef3b9ac5bb976b509df9504b6bed6b1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.062710154208 19.901319936077 13.546753505762 0 0 0 +H +0.0 +2 +-16.944913099358 20.075752932237 13.478486340899 0 0 0 +-14.577416118863 21.100109814041 14.871431036908 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/conv new file mode 100644 index 0000000000000000000000000000000000000000..12986671dd3dc511c796707f4abf65c84de23a76 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/conv @@ -0,0 +1 @@ +39 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..58811a234bbcf9a34b2d01ce227f09bfd1665753 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750322877 0.01253064137 1.253889528 1.345007724 1.468441387 0.00853394949 0.01787334969 0.03908478174 +-2.80408666e-18 0.0009295772229 0.002489388742 0.01185233609 0.04291891017 -4.704008634e-19 1.827648485e-06 5.463397575e-06 +0.001616546637 0.005930255202 + +H atom_index 1 n_descriptor 18 +1.200733537 0.03600688503 0.09207022531 0.1285868984 0.3041154747 0.01985403522 0.02543640344 0.03940925759 +2.645710058e-17 3.828074544e-05 0.08707987467 0.1099229016 0.1135894193 -2.441800616e-18 6.04055405e-06 0.01412831122 +0.0239454078 0.02831020133 + +H atom_index 2 n_descriptor 18 +1.232430369 0.0349625586 0.1020482459 0.1420872357 0.3155105613 0.02133156694 0.02729505017 0.03816688264 +-3.953953539e-19 4.102931456e-05 0.09536720361 0.1146974727 0.1217456575 3.776646581e-18 4.759492285e-06 0.01339326964 +0.02522565108 0.02992372529 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..cf4ff71a140f989eb0e8aacd7fd3bfcfbc8385e0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/log.scf @@ -0,0 +1,100 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:56 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0868917 SEC) : SETUP UNITCELL + DONE(0.0989072 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118166 SEC) : INIT PLANEWAVE + DONE(0.167227 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449397 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651931e+02 0.000000e+00 2.126e-01 4.341e-01 + GE2 -4.664048e+02 -1.211713e+00 9.856e-02 3.599e-01 + GE3 -4.664108e+02 -5.960283e-03 6.352e-02 4.119e-01 + GE4 -4.664097e+02 1.045314e-03 1.964e-03 3.073e-01 + GE5 -4.664091e+02 6.033259e-04 9.579e-04 3.029e-01 + GE6 -4.664094e+02 -2.830642e-04 1.684e-04 3.010e-01 + GE7 -4.664093e+02 8.922179e-05 3.122e-05 2.822e-01 + GE8 -4.664093e+02 -4.155835e-05 1.410e-05 2.842e-01 + GE9 -4.664093e+02 1.579639e-05 1.796e-06 2.857e-01 + GE10 -4.664093e+02 -2.935598e-06 3.027e-07 2.841e-01 + GE11 -4.664093e+02 -2.818872e-07 7.955e-08 2.178e-01 +E_delta_band = -6.87526332e-02 Ry = -9.35427564e-01 eV +E_delta_NN= -1.94004862e-01 Ry = -2.63957156e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6387 11 0.51 1e+02 % + Run_lcao lcao_line 5.6294 1 5.6 1e+02 % + Potential init_pot 0.28801 2 0.14 5.1 % + PW_Basis recip2real 0.26048 16 0.016 4.6 % + PW_Basis gathers_scatterp 0.11865 16 0.0074 2.1 % + Potential v_of_rho 0.88204 13 0.068 16 % + XC_Functional v_xc 0.26243 14 0.019 4.7 % + H_Hartree_pw v_hartree 0.58401 13 0.045 10 % + PW_Basis real2recip 0.56574 38 0.015 10 % + PW_Basis gatherp_scatters 0.26237 38 0.0069 4.7 % + ORB_control set_orb_tables 1.1071 1 1.1 20 % + ORB_gen_tables gen_tables 1.1071 1 1.1 20 % + ORB_table_phi init_Table 0.48373 1 0.48 8.6 % + ORB_table_phi cal_ST_Phi12_R 0.47889 126 0.0038 8.5 % + ORB_table_beta init_Table_Beta 0.19035 1 0.19 3.4 % + ORB_table_beta VNL_PhiBeta_R 0.18884 56 0.0034 3.3 % + ORB_table_alpha init_Table_Alpha 0.25379 1 0.25 4.5 % + ORB_table_alpha S_PhiAlpha_R 0.25194 66 0.0038 4.5 % + LOOP_ions opt_ions 3.9962 1 4 71 % + ESolver_KS_LCAO Run 3.5327 1 3.5 63 % + HSolverLCAO solve 1.5587 11 0.14 28 % + HamiltLCAO updateHk 0.80489 11 0.073 14 % + LCAO_Hamilt cal_Hgamma 0.77636 11 0.071 14 % + Gint_Gamma distri_vl_value 0.49346 11 0.045 8.8 % + Gint_Gamma distri_vl 1.7123 6 0.29 30 % + LCAO_Deepks cal_projected_DM 3.6894 13 0.28 65 % + LCAO_gen_fixedH add_v_delta 1.5956 6 0.27 28 % + LCAO_DESCRIPTOR add_v_delta 1.5956 6 0.27 28 % + ElecStateLCAO psiToRho 0.67736 11 0.062 12 % + Charge mix_rho 0.6399 10 0.064 11 % + LOOP_ions force_stress 0.46328 1 0.46 8.2 % + Force_Stress_LCAO getForceStress 0.46325 1 0.46 8.2 % + Force_LCAO_gamma ftable_gamma 0.25592 1 0.26 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:56 2022 + FINISH Time : Wed Sep 28 11:07:02 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/39/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..dbb4c9b4d6f315f5c5550b50c335681e16f6b2c3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.647121 0.0617126 0.311896 +H 0.646862 0.0148911 0.269255 +H 0.69809 0.0472683 0.350521 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..4cc96c8bfe5259928ce9ae3eb7150fea146112ce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4846 2 + 2 -13.1769 2 + 3 -9.16665 2 + 4 -6.78722 2 + 5 1.4364 0 + 6 4.68585 0 + 7 11.0292 0 + 8 11.2784 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e743cd3fb509adcb925372e0563d925b7c5dcec3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:23 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.1193924912 1.72795253148 8.73309297646 0 0 0 0 + tauc_H1 18.1121257998 0.416951424668 7.53914656161 0 0 0 0 + tauc_H2 19.5465061962 1.3235133421 9.81458110803 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0876038458377 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.103148611935 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.121401147084 (SEC) + + DONE : INIT CHARGE Time : 0.170367753795 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.45039 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 100 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000612 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00147 + + Density error is 0.21692086936 + + Energy Rydberg eV + E_KohnSham -34.1876019357 -465.146187281 + E_Harris -34.3839365378 -467.817456584 + E_Fermi -0.416882338387 -5.67197519762 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000931854352748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00136900610933 + + Density error is 0.0976197170404 + + Energy Rydberg eV + E_KohnSham -34.2784682543 -466.38248697 + E_Harris -34.2851247115 -466.473052717 + E_Fermi -0.224417732293 -3.05335989143 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000897881306977 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127424747866 + + Density error is 0.0624093856354 + + Energy Rydberg eV + E_KohnSham -34.2787373621 -466.38614837 + E_Harris -34.283016444 -466.444368266 + E_Fermi -0.21105201481 -2.8715099758 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000858445457059 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112025418966 + + Density error is 0.00202989037288 + + Energy Rydberg eV + E_KohnSham -34.2787657848 -466.38653508 + E_Harris -34.2787674106 -466.386557201 + E_Fermi -0.175275109939 -2.38474021275 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000861130890192 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111989366803 + + Density error is 0.000908797150479 + + Energy Rydberg eV + E_KohnSham -34.2786930783 -466.385545858 + E_Harris -34.2786950292 -466.385572401 + E_Fermi -0.174228768913 -2.37050401274 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000860111012353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001118211746 + + Density error is 0.000114682256522 + + Energy Rydberg eV + E_KohnSham -34.2787409217 -466.386196802 + E_Harris -34.2787409398 -466.386197047 + E_Fermi -0.174413639929 -2.37301931196 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000860211702502 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111806721382 + + Density error is 4.66055459587e-05 + + Energy Rydberg eV + E_KohnSham -34.2787252833 -466.385984029 + E_Harris -34.2787252955 -466.385984195 + E_Fermi -0.174273274939 -2.37110954829 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000860137277754 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111805625678 + + Density error is 1.1919252372e-05 + + Energy Rydberg eV + E_KohnSham -34.2787285831 -466.386028926 + E_Harris -34.2787285837 -466.386028934 + E_Fermi -0.174327245752 -2.37184385887 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000860141414152 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111803720803 + + Density error is 1.11545735511e-06 + + Energy Rydberg eV + E_KohnSham -34.2787271661 -466.386009646 + E_Harris -34.2787271661 -466.386009646 + E_Fermi -0.174313749366 -2.37166023112 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000860143573285 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111803694388 + + Density error is 1.39372000744e-07 + + Energy Rydberg eV + E_KohnSham -34.2787273418 -466.386012037 + E_Harris -34.2787273418 -466.386012037 + E_Fermi -0.174312935834 -2.37164916245 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00086014380487 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111803729823 + + Density error is 4.35925324678e-08 + + Energy Rydberg eV + E_KohnSham -34.2787273626 -466.386012319 + E_Harris -34.2787273626 -466.386012319 + E_band -8.02830639215 -109.230712223 + E_one_elec -69.664356628 -947.832197645 + E_Hartree +36.2144829054 +492.723317636 + E_xc -8.23796834083 -112.083309379 + E_Ewald +7.53267733776 +102.487332989 + E_demet -1.10916085798e-87 -1.50909076671e-86 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195525179191 -2.66025653946 + E_Fermi -0.174313033814 -2.37165049554 + + charge density convergence is achieved + final etot is -466.386012319 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4846 2.00000 + 2 -13.1769 2.00000 + 3 -9.16665 2.00000 + 4 -6.78722 2.00000 + 5 1.43640 0.00000 + 6 4.68585 0.00000 + 7 11.0292 0.00000 + 8 11.2784 0.00000 + + EFERMI = -2.371650495535414 eV + OUT.ABACUS/ final etot is -466.3860123193419 eV + correction force for each atom along direction 1 is 0.000137815 + correction force for each atom along direction 2 is -2.42810e-07 + correction force for each atom along direction 3 is 2.79920e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.038127969 +1.4876894 +1.3021701 + H1 -0.093561739 -1.5244093 -1.4716039 + H2 +0.13168971 +0.036719871 +0.16943381 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3860123193419 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6258 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6156 1 6.6 1.e+02% + Potential init_pot 0.28404 2 0.14 4.3% + PW_Basis recip2real 0.26565 16 0.017 4.0% + PW_Basis gathers_scatterp 0.12442 16 0.0078 1.9% + Potential v_of_rho 0.86327 13 0.066 13.% + XC_Functional v_xc 0.24348 14 0.017 3.7% + H_Hartree_pw v_hartree 0.58484 13 0.045 8.8% + PW_Basis real2recip 0.57753 38 0.015 8.7% + PW_Basis gatherp_scatters 0.24192 38 0.0064 3.7% + ORB_control set_orb_tables 1.1066 1 1.1 17.% + ORB_gen_tables gen_tables 1.1066 1 1.1 17.% + ORB_table_phi init_Table 0.48710 1 0.49 7.4% + ORB_table_phi cal_ST_Phi12_R 0.48215 126 0.0038 7.3% + ORB_table_beta init_Table_Beta 0.18621 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18476 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25258 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.25075 66 0.0038 3.8% + LOOP_ions opt_ions 4.9812 1 5.0 75.% + ESolver_KS_LCAO Run 4.4157 1 4.4 67.% + HSolverLCAO solve 2.4291 11 0.22 37.% + HamiltLCAO updateHk 1.2517 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2233 11 0.11 18.% + Gint_interface cal_gint 1.0852 23 0.047 16.% + Gint_Gamma distri_vl_value 0.46035 11 0.042 6.9% + Gint_Gamma distri_vl 2.1199 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.6774 13 0.36 71.% + LCAO_gen_fixedH add_v_delta 1.9898 6 0.33 30.% + LCAO_DESCRIPTOR add_v_delta 1.9898 6 0.33 30.% + ElecStateLCAO psiToRho 1.1590 11 0.11 17.% + Charge mix_rho 0.66150 10 0.066 10.% + LOOP_ions force_stress 0.56536 1 0.57 8.5% + Force_Stress_LCAO getForceStress 0.56533 1 0.57 8.5% + Force_LCAO_gamma ftable_gamma 0.35263 1 0.35 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.21108 1 0.21 3.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:23 2022 + Finish Time : Wed Sep 28 11:05:29 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0f59161c3528ac7cb4fb0e12ec659923a9e8366b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123655 ima = 3.65997e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122951435091 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112035088324 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011249153717 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112768596146 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112700970244 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112738159149 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112733046922 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112736111184 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112735623726 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112735577221 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112735577409 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3bb80d7a90b860150d4535063590b06d54527795 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.880607508796 1.727952531460 8.733092976482 0 0 0 +H +0.0 +2 +-9.887874200220 0.416951424678 7.539146561629 0 0 0 +-8.453493803754 1.323513342123 9.814581108039 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/conv new file mode 100644 index 0000000000000000000000000000000000000000..ec04b1df1677af42c7a274704c11bb2eb7f60c8e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/conv @@ -0,0 +1 @@ +4 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..29b55ecce77024cd05911b27418463ef7622c4fa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749623201 0.01278804402 1.286409882 1.375124781 1.470241192 0.008721834731 0.01879844264 0.0390385716 +-4.577664973e-18 0.001128203699 0.002733060573 0.01296335276 0.04719703379 -4.642367194e-20 2.312494946e-06 6.469755467e-06 +0.001644725018 0.005968984377 + +H atom_index 1 n_descriptor 18 +1.29320073 0.03284940344 0.1249248401 0.1711601854 0.33349842 0.02445988629 0.0307772546 0.03650007781 +2.110854809e-17 5.341840926e-05 0.1083414447 0.1221770745 0.1469479274 -5.015425993e-18 1.710621644e-06 0.01352398508 +0.02819925248 0.0325355336 + +H atom_index 2 n_descriptor 18 +1.243815579 0.03447956482 0.1067414797 0.1469860138 0.3186029066 0.02216813512 0.02793286853 0.03757570094 +-4.042811537e-17 4.866851922e-05 0.1017965578 0.1145320352 0.1262963088 4.893641219e-18 4.486302481e-06 0.01326508053 +0.02650339635 0.0304995604 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..47dc5646183a3a5dcddd5a40f0a24dae4c567f2f Binary files /dev/null and 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0000000000000000000000000000000000000000..57d0bfd2355003f6a58a5e6a15e71d8cb421638e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:23 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0876262 SEC) : SETUP UNITCELL + DONE(0.103166 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.121428 SEC) : INIT PLANEWAVE + DONE(0.170508 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450456 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651462e+02 0.000000e+00 2.169e-01 5.154e-01 + GE2 -4.663825e+02 -1.236300e+00 9.762e-02 4.413e-01 + GE3 -4.663861e+02 -3.661400e-03 6.241e-02 4.952e-01 + GE4 -4.663865e+02 -3.867104e-04 2.030e-03 3.891e-01 + GE5 -4.663855e+02 9.892222e-04 9.088e-04 3.829e-01 + GE6 -4.663862e+02 -6.509435e-04 1.147e-04 3.678e-01 + GE7 -4.663860e+02 2.127721e-04 4.661e-05 3.687e-01 + GE8 -4.663860e+02 -4.489641e-05 1.192e-05 3.622e-01 + GE9 -4.663860e+02 1.927936e-05 1.115e-06 3.598e-01 + GE10 -4.663860e+02 -2.390258e-06 1.394e-07 3.619e-01 + GE11 -4.663860e+02 -2.826723e-07 4.359e-08 3.103e-01 +E_delta_band = -7.19625424e-02 Ry = -9.79100619e-01 eV +E_delta_NN= -1.95525179e-01 Ry = -2.66025654e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6258 11 0.6 1e+02 % + Run_lcao lcao_line 6.6156 1 6.6 1e+02 % + Potential init_pot 0.28404 2 0.14 4.3 % + PW_Basis recip2real 0.26565 16 0.017 4 % + PW_Basis gathers_scatterp 0.12442 16 0.0078 1.9 % + Potential v_of_rho 0.86327 13 0.066 13 % + XC_Functional v_xc 0.24348 14 0.017 3.7 % + H_Hartree_pw v_hartree 0.58484 13 0.045 8.8 % + PW_Basis real2recip 0.57753 38 0.015 8.7 % + PW_Basis gatherp_scatters 0.24192 38 0.0064 3.7 % + ORB_control set_orb_tables 1.1066 1 1.1 17 % + ORB_gen_tables gen_tables 1.1066 1 1.1 17 % + ORB_table_phi init_Table 0.4871 1 0.49 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.48215 126 0.0038 7.3 % + ORB_table_beta init_Table_Beta 0.18621 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18476 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25258 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.25075 66 0.0038 3.8 % + LOOP_ions opt_ions 4.9812 1 5 75 % + ESolver_KS_LCAO Run 4.4157 1 4.4 67 % + HSolverLCAO solve 2.4291 11 0.22 37 % + HamiltLCAO updateHk 1.2517 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.2233 11 0.11 18 % + Gint_interface cal_gint 1.0852 23 0.047 16 % + Gint_Gamma distri_vl_value 0.46035 11 0.042 6.9 % + Gint_Gamma distri_vl 2.1199 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.6774 13 0.36 71 % + LCAO_gen_fixedH add_v_delta 1.9898 6 0.33 30 % + LCAO_DESCRIPTOR add_v_delta 1.9898 6 0.33 30 % + ElecStateLCAO psiToRho 1.159 11 0.11 17 % + Charge mix_rho 0.6615 10 0.066 10 % + LOOP_ions force_stress 0.56536 1 0.57 8.5 % + Force_Stress_LCAO getForceStress 0.56533 1 0.57 8.5 % + Force_LCAO_gamma ftable_gamma 0.35263 1 0.35 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.21108 1 0.21 3.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:23 2022 + FINISH Time : Wed Sep 28 11:05:29 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/4/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d61154bf28441db7750e428141a997ca6fc0bfa2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.450025 0.716601 0.495355 +H 0.39268 0.721887 0.524539 +H 0.477325 0.773726 0.495723 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..01cc8e88dd79c534a7202b1416d1803972541c41 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4833 2 + 2 -13.4563 2 + 3 -8.97141 2 + 4 -6.78705 2 + 5 1.53436 0 + 6 4.81971 0 + 7 11.0156 0 + 8 11.2428 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..603db2fa80ab4ff27540d0a66faf1e1e018d81d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/running_scf.log @@ -0,0 +1,777 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:24 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.6006885693 20.0648190906 13.8699463922 0 0 0 0 + tauc_H1 10.9950304968 20.2128390348 14.6870987216 0 0 0 0 + tauc_H2 13.3651076418 21.6643197869 13.8802436517 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.100569953186 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100912531552 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118933919891 (SEC) + + DONE : INIT CHARGE Time : 0.162501268962 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.439564 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + No atoms on this sub-FFT-mesh. + Atom number in sub-FFT-grid = 0 + Local orbitals number in sub-FFT-grid = 0 + lgd_last = 0 + lgd_now = 0 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 +receiver_size is 0 ; receiver_size of each process is: +0 0 0 0 +sender_size is 288 ; sender_size of each process is: +0 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00154 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63e-322 + + Density error is 0.218627469557 + + Energy Rydberg eV + E_KohnSham -34.1862605589 -465.127936914 + E_Harris -34.3856531225 -467.840811918 + E_Fermi -0.420898081826 -5.72661219011 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00141428789405 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.097476153213 + + Energy Rydberg eV + E_KohnSham -34.2775779964 -466.370374391 + E_Harris -34.284126953 -466.459477516 + E_Fermi -0.227472737432 -3.09492536873 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00130054713856 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0621792323698 + + Energy Rydberg eV + E_KohnSham -34.2778157685 -466.373609446 + E_Harris -34.2819800689 -466.430267659 + E_Fermi -0.212610225557 -2.89271052064 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0011127403564 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0021046492775 + + Energy Rydberg eV + E_KohnSham -34.2778714755 -466.374367379 + E_Harris -34.2778744206 -466.374407448 + E_Fermi -0.177054093329 -2.4089445235 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00111015805692 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000903913544684 + + Energy Rydberg eV + E_KohnSham -34.2777945597 -466.373320885 + E_Harris -34.27779692 -466.373352999 + E_Fermi -0.175718007909 -2.39076614877 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110878398307 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000166657575906 + + Energy Rydberg eV + E_KohnSham -34.2778471123 -466.3740359 + E_Harris -34.2778471887 -466.37403694 + E_Fermi -0.176070656152 -2.39556417427 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110854909066 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 5.05105165321e-05 + + Energy Rydberg eV + E_KohnSham -34.2778279283 -466.373774888 + E_Harris -34.2778279426 -466.373775083 + E_Fermi -0.17587445667 -2.39289474337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110857229643 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.69210618077e-05 + + Energy Rydberg eV + E_KohnSham -34.2778329553 -466.373843285 + E_Harris -34.2778329565 -466.373843301 + E_Fermi -0.175935310449 -2.39372270151 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110853927072 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.6373001432e-06 + + Energy Rydberg eV + E_KohnSham -34.2778313117 -466.373820922 + E_Harris -34.2778313117 -466.373820922 + E_Fermi -0.175917061048 -2.39347440567 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110853509824 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.65936075518e-07 + + Energy Rydberg eV + E_KohnSham -34.2778315566 -466.373824254 + E_Harris -34.2778315566 -466.373824254 + E_Fermi -0.175915448851 -2.39345247061 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00110853539299 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 8.00291261407e-08 + + Energy Rydberg eV + E_KohnSham -34.2778315806 -466.373824581 + E_Harris -34.2778315806 -466.373824581 + E_band -8.04046236168 -109.396102673 + E_one_elec -69.8208405141 -949.961270141 + E_Hartree +36.2951476401 +493.820817657 + E_xc -8.25084508483 -112.258506469 + E_Ewald +7.62197059158 +103.702230034 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195739253364 -2.66316916801 + E_Fermi -0.175915484111 -2.39345295034 + + charge density convergence is achieved + final etot is -466.373824581 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4833 2.00000 + 2 -13.4563 2.00000 + 3 -8.97141 2.00000 + 4 -6.78705 2.00000 + 5 1.53436 0.00000 + 6 4.81971 0.00000 + 7 11.0156 0.00000 + 8 11.2428 0.00000 + + EFERMI = -2.393452950338111 eV + OUT.ABACUS/ final etot is -466.3738245806865 eV + correction force for each atom along direction 1 is -1.70138e-05 + correction force for each atom along direction 2 is 0.000159729 + correction force for each atom along direction 3 is -8.83932e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.037306647 -2.1401216 -0.53284851 + H1 -0.74580888 +0.25747924 +0.42632278 + H2 +0.70850223 +1.8826424 +0.10652574 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3738245806865 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7855 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7755 1 6.8 1.e+02% + Potential init_pot 0.27788 2 0.14 4.1% + PW_Basis recip2real 0.25936 16 0.016 3.8% + PW_Basis gathers_scatterp 0.12088 16 0.0076 1.8% + Potential v_of_rho 1.0715 13 0.082 16.% + XC_Functional v_xc 0.40896 14 0.029 6.0% + H_Hartree_pw v_hartree 0.62640 13 0.048 9.2% + PW_Basis real2recip 0.66957 38 0.018 9.9% + PW_Basis gatherp_scatters 0.38039 38 0.010 5.6% + ORB_control set_orb_tables 1.0929 1 1.1 16.% + ORB_gen_tables gen_tables 1.0928 1 1.1 16.% + ORB_table_phi init_Table 0.47600 1 0.48 7.0% + ORB_table_phi cal_ST_Phi12_R 0.47082 126 0.0037 6.9% + ORB_table_beta init_Table_Beta 0.18163 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18006 56 0.0032 2.7% + ORB_table_alpha init_Table_Alpha 0.24771 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.24571 66 0.0037 3.6% + LOOP_ions opt_ions 5.1683 1 5.2 76.% + ESolver_KS_LCAO Run 4.6320 1 4.6 68.% + HSolverLCAO solve 2.2156 11 0.20 33.% + HamiltLCAO updateHk 1.0514 11 0.096 15.% + LCAO_Hamilt cal_Hgamma 1.0170 11 0.092 15.% + Gint_Gamma distri_vl_value 0.72799 11 0.066 11.% + Gint_Gamma distri_vl 2.2404 6 0.37 33.% + LCAO_Deepks cal_projected_DM 4.7697 13 0.37 70.% + LCAO_gen_fixedH add_v_delta 2.1246 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.1245 6 0.35 31.% + DiagoElpa elpa_solve 0.14538 11 0.013 2.1% + ElecStateLCAO psiToRho 1.0176 11 0.093 15.% + Charge mix_rho 0.79259 10 0.079 12.% + LOOP_ions force_stress 0.53621 1 0.54 7.9% + Force_Stress_LCAO getForceStress 0.53619 1 0.54 7.9% + Force_LCAO_gamma ftable_gamma 0.32537 1 0.33 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1028. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:24 2022 + Finish Time : Wed Sep 28 11:07:31 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3d33633bad152770fd7552cd94bd569115ff0726 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/OUT.ABACUS/warning.log @@ -0,0 +1,75 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124168 ima = 3.66789e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 0 + 2 3 + 3 3 + 4 0 + Grid_Technique::init_atoms_on_grid2 warning : no atom on this sub FFT grid. + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012315583055 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112420445535 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112789951317 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113068509579 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112996578777 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011303842028 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113029642815 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113033072404 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113032391065 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113032332572 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011303232813 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/STRU new file mode 100644 index 0000000000000000000000000000000000000000..57391aa783cfbc2d9be25186a16d88a092d3d5f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.399311430726 20.064819090641 13.869946392135 0 0 0 +H +0.0 +2 +-17.004969503232 20.212839034780 14.687098721594 0 0 0 +-14.634892358150 21.664319786880 13.880243651706 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/conv new file mode 100644 index 0000000000000000000000000000000000000000..97cd915fbbd53f8b361350499ec4a59242a298e7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/conv @@ -0,0 +1 @@ +40 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5bc5ac9bb9b50215c1aca9e1cfb5e976b42ce97c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746081557 0.01277505799 1.297443932 1.384549325 1.470379437 0.008190400592 0.02018836357 0.03893763249 +4.0441193e-19 0.001245204892 0.002598750005 0.01301457309 0.04621758139 -2.774324573e-19 1.940881986e-06 5.758462544e-06 +0.001731769445 0.00576520188 + +H atom_index 1 n_descriptor 18 +1.26240561 0.03337968228 0.113133171 0.1564018188 0.325601881 0.02269614724 0.02910309276 0.03659201706 +7.652000358e-18 4.669142558e-05 0.1061637396 0.1157500692 0.1345044962 7.846754885e-18 3.682049848e-06 0.01300190726 +0.0270730009 0.03138443502 + +H atom_index 2 n_descriptor 18 +1.290130503 0.0324638395 0.1235060486 0.1702449263 0.3334789976 0.0239076571 0.03068123229 0.03613138111 +2.002765928e-17 4.921851048e-05 0.1083409896 0.1214691927 0.1462780355 -3.385362667e-18 2.178123047e-06 0.01332691032 +0.02798931282 0.03245986896 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..26b2b199d2115c61f46ccd7b395ce02613465614 Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..eccedc7887158fa5150828e4cdb01724fb0e53c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:24 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.100594 SEC) : SETUP UNITCELL + DONE(0.100928 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118954 SEC) : INIT PLANEWAVE + DONE(0.162644 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.439628 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651279e+02 0.000000e+00 2.186e-01 5.156e-01 + GE2 -4.663704e+02 -1.242437e+00 9.748e-02 4.772e-01 + GE3 -4.663736e+02 -3.235055e-03 6.218e-02 5.463e-01 + GE4 -4.663744e+02 -7.579331e-04 2.105e-03 4.038e-01 + GE5 -4.663733e+02 1.046493e-03 9.039e-04 4.028e-01 + GE6 -4.663740e+02 -7.150150e-04 1.667e-04 3.902e-01 + GE7 -4.663738e+02 2.610127e-04 5.051e-05 3.887e-01 + GE8 -4.663738e+02 -6.839685e-05 1.692e-05 3.789e-01 + GE9 -4.663738e+02 2.236285e-05 1.637e-06 3.785e-01 + GE10 -4.663738e+02 -3.332104e-06 1.659e-07 3.804e-01 + GE11 -4.663738e+02 -3.268501e-07 8.003e-08 2.997e-01 +E_delta_band = -7.24750399e-02 Ry = -9.86073506e-01 eV +E_delta_NN= -1.95739253e-01 Ry = -2.66316917e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7855 11 0.62 1e+02 % + Run_lcao lcao_line 6.7755 1 6.8 1e+02 % + Potential init_pot 0.27788 2 0.14 4.1 % + PW_Basis recip2real 0.25936 16 0.016 3.8 % + PW_Basis gathers_scatterp 0.12088 16 0.0076 1.8 % + Potential v_of_rho 1.0715 13 0.082 16 % + XC_Functional v_xc 0.40896 14 0.029 6 % + H_Hartree_pw v_hartree 0.6264 13 0.048 9.2 % + PW_Basis real2recip 0.66957 38 0.018 9.9 % + PW_Basis gatherp_scatters 0.38039 38 0.01 5.6 % + ORB_control set_orb_tables 1.0929 1 1.1 16 % + ORB_gen_tables gen_tables 1.0928 1 1.1 16 % + ORB_table_phi init_Table 0.476 1 0.48 7 % + ORB_table_phi cal_ST_Phi12_R 0.47082 126 0.0037 6.9 % + ORB_table_beta init_Table_Beta 0.18163 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18006 56 0.0032 2.7 % + ORB_table_alpha init_Table_Alpha 0.24771 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.24571 66 0.0037 3.6 % + LOOP_ions opt_ions 5.1683 1 5.2 76 % + ESolver_KS_LCAO Run 4.632 1 4.6 68 % + HSolverLCAO solve 2.2156 11 0.2 33 % + HamiltLCAO updateHk 1.0514 11 0.096 15 % + LCAO_Hamilt cal_Hgamma 1.017 11 0.092 15 % + Gint_Gamma distri_vl_value 0.72799 11 0.066 11 % + Gint_Gamma distri_vl 2.2404 6 0.37 33 % + LCAO_Deepks cal_projected_DM 4.7697 13 0.37 70 % + LCAO_gen_fixedH add_v_delta 2.1246 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.1245 6 0.35 31 % + DiagoElpa elpa_solve 0.14538 11 0.013 2.1 % + ElecStateLCAO psiToRho 1.0176 11 0.093 15 % + Charge mix_rho 0.79259 10 0.079 12 % + LOOP_ions force_stress 0.53621 1 0.54 7.9 % + Force_Stress_LCAO getForceStress 0.53619 1 0.54 7.9 % + Force_LCAO_gamma ftable_gamma 0.32537 1 0.33 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:24 2022 + FINISH Time : Wed Sep 28 11:07:31 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/40/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4edec86f47495a4cded219acf470032873e511dc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.444397 0.739349 0.499804 +H 0.430258 0.742641 0.565739 +H 0.435229 0.803591 0.482913 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..07d93eee86ad23d78496b45a61cb76b0cb69fab0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0763 2 + 2 -12.5887 2 + 3 -9.29602 2 + 4 -6.70198 2 + 5 1.0311 0 + 6 3.95173 0 + 7 11.1374 0 + 8 11.4074 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..6f31364195a346395f487d8b12ba97c1ac5fe7ac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/running_scf.log @@ -0,0 +1,798 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:34 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.4431244486 20.7017610376 13.9945238441 0 0 0 0 + tauc_H1 12.0472282602 20.7939513377 15.8406914261 0 0 0 0 + tauc_H2 12.1864014315 22.500561122 13.5215676472 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0876443240785 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0890453318419 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107103351302 (SEC) + + DONE : INIT CHARGE Time : 0.155638538201 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.433338 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + No atoms on this sub-FFT-mesh. + Atom number in sub-FFT-grid = 0 + Local orbitals number in sub-FFT-grid = 0 + lgd_last = 0 + lgd_now = 0 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 +receiver_size is 0 ; receiver_size of each process is: +0 0 0 0 +sender_size is 292 ; sender_size of each process is: +0 144 144 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00089 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63e-322 + + Density error is 0.210143683243 + + Energy Rydberg eV + E_KohnSham -34.19273988 -465.2160926 + E_Harris -34.3746762135 -467.691463409 + E_Fermi -0.387380431322 -5.27058115968 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00121540449504 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0982847275664 + + Energy Rydberg eV + E_KohnSham -34.2791983332 -466.392420204 + E_Harris -34.286275771 -466.488713685 + E_Fermi -0.200294644924 -2.72514844986 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116663405615 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0632884853395 + + Energy Rydberg eV + E_KohnSham -34.2795201811 -466.396799169 + E_Harris -34.2840759202 -466.45878318 + E_Fermi -0.192909397958 -2.62466700997 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111568758559 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0019120460084 + + Energy Rydberg eV + E_KohnSham -34.2794281557 -466.395547099 + E_Harris -34.279428653 -466.395553865 + E_Fermi -0.157611752664 -2.14441790799 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011170612393 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000828573931397 + + Energy Rydberg eV + E_KohnSham -34.2794029221 -466.395203779 + E_Harris -34.2794033328 -466.395209367 + E_Fermi -0.157586615564 -2.14407590021 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111648637662 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000147270763359 + + Energy Rydberg eV + E_KohnSham -34.2794136737 -466.395350061 + E_Harris -34.2794136685 -466.395349991 + E_Fermi -0.157169004448 -2.13839400948 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111657339249 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 2.30594342013e-05 + + Energy Rydberg eV + E_KohnSham -34.2794116755 -466.395322874 + E_Harris -34.2794116765 -466.395322888 + E_Fermi -0.157138537774 -2.13797948912 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111651416879 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 9.62732728967e-06 + + Energy Rydberg eV + E_KohnSham -34.2794131874 -466.395343445 + E_Harris -34.2794131878 -466.395343451 + E_Fermi -0.157147676466 -2.1381038274 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111652195878 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.99593510857e-06 + + Energy Rydberg eV + E_KohnSham -34.2794124291 -466.395333128 + E_Harris -34.2794124291 -466.395333128 + E_Fermi -0.157139073728 -2.13798678114 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111651913315 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 4.2155307193e-07 + + Energy Rydberg eV + E_KohnSham -34.2794125943 -466.395335375 + E_Harris -34.2794125943 -466.395335375 + E_Fermi -0.157137508112 -2.13796547984 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111652008958 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.49129074632e-07 + + Energy Rydberg eV + E_KohnSham -34.2794126031 -466.395335496 + E_Harris -34.2794126031 -466.395335496 + E_Fermi -0.157137312488 -2.13796281824 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111652037548 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.13322416354e-08 + + Energy Rydberg eV + E_KohnSham -34.2794126067 -466.395335545 + E_Harris -34.2794126067 -466.395335545 + E_band -7.8883132661 -107.326008028 + E_one_elec -68.7018072912 -934.736042058 + E_Hartree +35.7542406232 +486.461400139 + E_xc -8.16375789923 -111.073624522 + E_Ewald +6.95741526365 +94.6604909378 + E_demet -1.4075339096e-61 -1.91504812988e-60 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193806968211 -2.63687907977 + E_Fermi -0.15713718031 -2.13796101987 + + charge density convergence is achieved + final etot is -466.395335545 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0763 2.00000 + 2 -12.5887 2.00000 + 3 -9.29602 2.00000 + 4 -6.70198 2.00000 + 5 1.03110 0.00000 + 6 3.95173 0.00000 + 7 11.1374 0.00000 + 8 11.4074 0.00000 + + EFERMI = -2.137961019869684 eV + OUT.ABACUS/ final etot is -466.3953355445374 eV + correction force for each atom along direction 1 is 9.52960e-05 + correction force for each atom along direction 2 is 0.000162622 + correction force for each atom along direction 3 is 5.96030e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.40916657 +1.0470709 +1.0278404 + H1 +0.25255105 -0.31103944 -0.95269854 + H2 +0.15661552 -0.73603149 -0.075141873 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3953355445374 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0826 11 0.55 1.0e+02% + Run_lcao lcao_line 6.0731 1 6.1 1.e+02% + Potential init_pot 0.28430 2 0.14 4.7% + PW_Basis recip2real 0.27887 17 0.016 4.6% + PW_Basis gathers_scatterp 0.12694 17 0.0075 2.1% + Potential v_of_rho 0.93533 14 0.067 15.% + XC_Functional v_xc 0.26494 15 0.018 4.4% + H_Hartree_pw v_hartree 0.63192 14 0.045 10.% + PW_Basis real2recip 0.61303 41 0.015 10.% + PW_Basis gatherp_scatters 0.28215 41 0.0069 4.6% + ORB_control set_orb_tables 1.1020 1 1.1 18.% + ORB_gen_tables gen_tables 1.1020 1 1.1 18.% + ORB_table_phi init_Table 0.48029 1 0.48 7.9% + ORB_table_phi cal_ST_Phi12_R 0.47541 126 0.0038 7.8% + ORB_table_beta init_Table_Beta 0.18897 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18748 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25253 1 0.25 4.2% + ORB_table_alpha S_PhiAlpha_R 0.25064 66 0.0038 4.1% + LOOP_ions opt_ions 4.4607 1 4.5 73.% + ESolver_KS_LCAO Run 3.9763 1 4.0 65.% + HSolverLCAO solve 1.8352 12 0.15 30.% + HamiltLCAO updateHk 0.92600 12 0.077 15.% + LCAO_Hamilt cal_Hgamma 0.89522 12 0.075 15.% + Gint_Gamma distri_vl_value 0.60417 12 0.050 9.9% + Gint_Gamma distri_vl 2.0724 6 0.35 34.% + LCAO_Deepks cal_projected_DM 4.1316 14 0.30 68.% + LCAO_gen_fixedH add_v_delta 1.9552 6 0.33 32.% + LCAO_DESCRIPTOR add_v_delta 1.9551 6 0.33 32.% + ElecStateLCAO psiToRho 0.83072 12 0.069 14.% + Charge mix_rho 0.70492 11 0.064 12.% + LOOP_ions force_stress 0.48418 1 0.48 8.0% + Force_Stress_LCAO getForceStress 0.48415 1 0.48 8.0% + Force_LCAO_gamma ftable_gamma 0.27441 1 0.27 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1028. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:34 2022 + Finish Time : Wed Sep 28 11:06:40 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..620d01cdf0000d278592ad7c38748ddfae0b6ebd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/OUT.ABACUS/warning.log @@ -0,0 +1,79 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123442 ima = 3.66623e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 0 + 2 3 + 3 3 + 4 1 + Grid_Technique::init_atoms_on_grid2 warning : no atom on this sub FFT grid. + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123058854263 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111827383237 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011256417721 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755063886 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011274433866 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112750696949 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112748558398 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112750005956 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112749530483 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112749495703 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112749478992 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112749471843 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/STRU new file mode 100644 index 0000000000000000000000000000000000000000..36688d00dc6693d215ea4d8b2b0ce9a39ec35396 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.556875551363 20.701761037582 13.994523844149 0 0 0 +H +0.0 +2 +-15.952771739780 20.793951337718 15.840691426085 0 0 0 +-15.813598568524 22.500561122047 13.521567647178 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/conv new file mode 100644 index 0000000000000000000000000000000000000000..4802d59808b67163ca2aede83512d9a1eb2cdaa9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/conv @@ -0,0 +1 @@ +41 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f3eea27360e30f59e373f3324bb925f47149bdb2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753122391 0.01253483465 1.247984456 1.333551354 1.468426165 0.009027758453 0.01679629399 0.03918472238 +5.398004066e-18 0.0008328220519 0.002562496059 0.01205684877 0.04304030844 -1.303818625e-19 2.056302663e-06 5.956515545e-06 +0.001574314654 0.006014525344 + +H atom_index 1 n_descriptor 18 +1.204153816 0.03619519578 0.0940823534 0.1296351555 0.3044005047 0.02036012085 0.02557140655 0.03957777633 +-4.225107448e-18 3.977597156e-05 0.08803559969 0.1107579475 0.1137614647 -9.343373545e-18 5.525880331e-06 0.01417825721 +0.02424325624 0.02843848543 + +H atom_index 2 n_descriptor 18 +1.214212471 0.03587667609 0.09721450219 0.1338360363 0.308139309 0.02084123672 0.02616310372 0.03917447524 +-2.033047938e-18 4.065117959e-05 0.09062548137 0.1141858394 0.1144476075 7.365919985e-19 5.122090466e-06 0.013911492 +0.02465721076 0.02896512012 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..89d3d5760629c2917e66b32d02657e6bee7dc136 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:34 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087671 SEC) : SETUP UNITCELL + DONE(0.0890597 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107123 SEC) : INIT PLANEWAVE + DONE(0.155771 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.433398 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652161e+02 0.000000e+00 2.101e-01 4.460e-01 + GE2 -4.663924e+02 -1.176328e+00 9.828e-02 3.708e-01 + GE3 -4.663968e+02 -4.378965e-03 6.329e-02 4.255e-01 + GE4 -4.663955e+02 1.252070e-03 1.912e-03 3.220e-01 + GE5 -4.663952e+02 3.433201e-04 8.286e-04 3.189e-01 + GE6 -4.663954e+02 -1.462823e-04 1.473e-04 3.182e-01 + GE7 -4.663953e+02 2.718708e-05 2.306e-05 2.963e-01 + GE8 -4.663953e+02 -2.057098e-05 9.627e-06 2.953e-01 + GE9 -4.663953e+02 1.031712e-05 1.996e-06 2.973e-01 + GE10 -4.663953e+02 -2.247188e-06 4.216e-07 2.947e-01 + GE11 -4.663953e+02 -1.205822e-07 1.491e-07 2.942e-01 + GE12 -4.663953e+02 -4.888694e-08 1.133e-08 2.354e-01 +E_delta_band = -6.83036650e-02 Ry = -9.29319038e-01 eV +E_delta_NN= -1.93806968e-01 Ry = -2.63687908e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0826 11 0.55 1e+02 % + Run_lcao lcao_line 6.0731 1 6.1 1e+02 % + Potential init_pot 0.2843 2 0.14 4.7 % + PW_Basis recip2real 0.27887 17 0.016 4.6 % + PW_Basis gathers_scatterp 0.12694 17 0.0075 2.1 % + Potential v_of_rho 0.93533 14 0.067 15 % + XC_Functional v_xc 0.26494 15 0.018 4.4 % + H_Hartree_pw v_hartree 0.63192 14 0.045 10 % + PW_Basis real2recip 0.61303 41 0.015 10 % + PW_Basis gatherp_scatters 0.28215 41 0.0069 4.6 % + ORB_control set_orb_tables 1.102 1 1.1 18 % + ORB_gen_tables gen_tables 1.102 1 1.1 18 % + ORB_table_phi init_Table 0.48029 1 0.48 7.9 % + ORB_table_phi cal_ST_Phi12_R 0.47541 126 0.0038 7.8 % + ORB_table_beta init_Table_Beta 0.18897 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18748 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.25253 1 0.25 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.25064 66 0.0038 4.1 % + LOOP_ions opt_ions 4.4607 1 4.5 73 % + ESolver_KS_LCAO Run 3.9763 1 4 65 % + HSolverLCAO solve 1.8352 12 0.15 30 % + HamiltLCAO updateHk 0.926 12 0.077 15 % + LCAO_Hamilt cal_Hgamma 0.89522 12 0.075 15 % + Gint_Gamma distri_vl_value 0.60417 12 0.05 9.9 % + Gint_Gamma distri_vl 2.0724 6 0.35 34 % + LCAO_Deepks cal_projected_DM 4.1316 14 0.3 68 % + LCAO_gen_fixedH add_v_delta 1.9552 6 0.33 32 % + LCAO_DESCRIPTOR add_v_delta 1.9551 6 0.33 32 % + ElecStateLCAO psiToRho 0.83072 12 0.069 14 % + Charge mix_rho 0.70492 11 0.064 12 % + LOOP_ions force_stress 0.48418 1 0.48 8 % + Force_Stress_LCAO getForceStress 0.48415 1 0.48 8 % + Force_LCAO_gamma ftable_gamma 0.27441 1 0.27 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:34 2022 + FINISH Time : Wed Sep 28 11:06:40 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/41/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..cce14166de45796b7f3f9338e36010deb8e22884 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.448031 0.751457 0.492652 +H 0.478949 0.757231 0.548085 +H 0.419203 0.808544 0.481969 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e533a49ab3188efca5937e8927420e8eb60a3fd9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4551 2 + 2 -13.3244 2 + 3 -9.04371 2 + 4 -6.78099 2 + 5 1.48088 0 + 6 4.72803 0 + 7 11.0279 0 + 8 11.2656 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..459371c9b2ad0779ebae4b6da4ca261813817064 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/running_scf.log @@ -0,0 +1,798 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:21 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.5448786801 21.0407990057 13.7942657697 0 0 0 0 + tauc_H1 13.4105818891 21.2024545286 15.3463812073 0 0 0 0 + tauc_H2 11.737673731 22.6392397826 13.4951360743 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874239034271 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0961553161746 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.114267160235 (SEC) + + DONE : INIT CHARGE Time : 0.161918210164 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441396 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + No atoms on this sub-FFT-mesh. + Atom number in sub-FFT-grid = 0 + Local orbitals number in sub-FFT-grid = 0 + lgd_last = 0 + lgd_now = 0 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 +receiver_size is 0 ; receiver_size of each process is: +0 0 0 0 +sender_size is 292 ; sender_size of each process is: +0 144 144 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00118 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63e-322 + + Density error is 0.21733525379 + + Energy Rydberg eV + E_KohnSham -34.1886246258 -465.160101694 + E_Harris -34.38533454 -467.83647738 + E_Fermi -0.417236373717 -5.6767920954 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00133765180841 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0974872482472 + + Energy Rydberg eV + E_KohnSham -34.2789862027 -466.389534021 + E_Harris -34.2855712969 -466.479128823 + E_Fermi -0.224918972676 -3.0601796167 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00126705134473 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0622269538052 + + Energy Rydberg eV + E_KohnSham -34.2792029387 -466.392482865 + E_Harris -34.2834101683 -466.449725159 + E_Fermi -0.210710236595 -2.86685984463 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00115873255638 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.00206176289784 + + Energy Rydberg eV + E_KohnSham -34.2792456396 -466.39306384 + E_Harris -34.2792479066 -466.393094684 + E_Fermi -0.175151565723 -2.38305930745 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116040868055 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.00088308359129 + + Energy Rydberg eV + E_KohnSham -34.2791734479 -466.392081621 + E_Harris -34.279175689 -466.392112113 + E_Fermi -0.173923985034 -2.36635721532 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00115882981595 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000167491261981 + + Energy Rydberg eV + E_KohnSham -34.2792244388 -466.392775389 + E_Harris -34.2792245262 -466.392776578 + E_Fermi -0.174237667508 -2.37062508433 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00115885624282 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 4.49594142558e-05 + + Energy Rydberg eV + E_KohnSham -34.2792052116 -466.392513788 + E_Harris -34.2792052224 -466.392513936 + E_Fermi -0.174053952201 -2.36812550935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00115881033829 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.6231758173e-05 + + Energy Rydberg eV + E_KohnSham -34.279210153 -466.39258102 + E_Harris -34.279210154 -466.392581034 + E_Fermi -0.174106969302 -2.36884684401 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00115880248454 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 2.62870471508e-06 + + Energy Rydberg eV + E_KohnSham -34.2792086958 -466.392561195 + E_Harris -34.2792086959 -466.392561195 + E_Fermi -0.174090672463 -2.36862511415 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00115879928795 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 2.69215860458e-07 + + Energy Rydberg eV + E_KohnSham -34.2792088744 -466.392563625 + E_Harris -34.2792088744 -466.392563625 + E_Fermi -0.174087813505 -2.36858621603 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00115880004209 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.25444736596e-07 + + Energy Rydberg eV + E_KohnSham -34.2792089173 -466.392564208 + E_Harris -34.2792089173 -466.392564208 + E_Fermi -0.174087780807 -2.36858577115 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011588001813 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 9.78665435175e-09 + + Energy Rydberg eV + E_KohnSham -34.2792089178 -466.392564215 + E_Harris -34.2792089178 -466.392564215 + E_band -8.0266587891 -109.208295434 + E_one_elec -69.7042108365 -948.37444197 + E_Hartree +36.2376029767 +493.037882345 + E_xc -8.24155828864 -112.132153125 + E_Ewald +7.55244705406 +102.756313779 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195544629718 -2.66052117746 + E_Fermi -0.174087673619 -2.36858431279 + + charge density convergence is achieved + final etot is -466.392564215 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4551 2.00000 + 2 -13.3244 2.00000 + 3 -9.04371 2.00000 + 4 -6.78099 2.00000 + 5 1.48088 0.00000 + 6 4.72803 0.00000 + 7 11.0279 0.00000 + 8 11.2656 0.00000 + + EFERMI = -2.368584312787656 eV + OUT.ABACUS/ final etot is -466.3925642145759 eV + correction force for each atom along direction 1 is -8.62266e-05 + correction force for each atom along direction 2 is 1.65590e-05 + correction force for each atom along direction 3 is 2.40309e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.50592305 -0.87865993 -1.4137734 + H1 +0.78064132 +0.23467779 +1.4536761 + H2 -0.27471827 +0.64398214 -0.039902687 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3925642145759 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8881 11 0.54 1.0e+02% + Run_lcao lcao_line 5.8787 1 5.9 1.e+02% + Potential init_pot 0.28450 2 0.14 4.8% + PW_Basis recip2real 0.27464 17 0.016 4.7% + PW_Basis gathers_scatterp 0.12492 17 0.0073 2.1% + Potential v_of_rho 0.92955 14 0.066 16.% + XC_Functional v_xc 0.27125 15 0.018 4.6% + H_Hartree_pw v_hartree 0.62129 14 0.044 11.% + PW_Basis real2recip 0.61187 41 0.015 10.% + PW_Basis gatherp_scatters 0.28286 41 0.0069 4.8% + ORB_control set_orb_tables 1.0973 1 1.1 19.% + ORB_gen_tables gen_tables 1.0973 1 1.1 19.% + ORB_table_phi init_Table 0.47910 1 0.48 8.1% + ORB_table_phi cal_ST_Phi12_R 0.47428 126 0.0038 8.1% + ORB_table_beta init_Table_Beta 0.18568 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18418 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25336 1 0.25 4.3% + ORB_table_alpha S_PhiAlpha_R 0.25150 66 0.0038 4.3% + LOOP_ions opt_ions 4.2643 1 4.3 72.% + ESolver_KS_LCAO Run 3.8042 1 3.8 65.% + HSolverLCAO solve 1.6801 12 0.14 29.% + HamiltLCAO updateHk 0.86342 12 0.072 15.% + LCAO_Hamilt cal_Hgamma 0.83208 12 0.069 14.% + Gint_Gamma distri_vl_value 0.54326 12 0.045 9.2% + Gint_Gamma distri_vl 1.9987 6 0.33 34.% + LCAO_Deepks cal_projected_DM 3.9618 14 0.28 67.% + LCAO_gen_fixedH add_v_delta 1.8815 6 0.31 32.% + LCAO_DESCRIPTOR add_v_delta 1.8815 6 0.31 32.% + ElecStateLCAO psiToRho 0.74210 12 0.062 13.% + Charge mix_rho 0.69476 11 0.063 12.% + LOOP_ions force_stress 0.45990 1 0.46 7.8% + Force_Stress_LCAO getForceStress 0.45987 1 0.46 7.8% + Force_LCAO_gamma ftable_gamma 0.25143 1 0.25 4.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1028. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:21 2022 + Finish Time : Wed Sep 28 11:02:27 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..87242741f249b5b838b7b7046d4481b298bdd1e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/OUT.ABACUS/warning.log @@ -0,0 +1,79 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123884 ima = 3.67322e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 0 + 2 3 + 3 3 + 4 1 + Grid_Technique::init_atoms_on_grid2 warning : no atom on this sub FFT grid. + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123020627698 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112258880955 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112658987117 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112927074432 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112858281214 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112899948198 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112890932817 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112894007939 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112893429648 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011289332158 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112893314381 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112893308967 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5aca02429194dcbfc098c7379a9df0da47cb831a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.455121319910 21.040799005767 13.794265769702 0 0 0 +H +0.0 +2 +-14.589418110953 21.202454528595 15.346381207311 0 0 0 +-16.262326268999 22.639239782590 13.495136074330 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/conv new file mode 100644 index 0000000000000000000000000000000000000000..54a289566abdd15ca324d79e8ab5de9756de5018 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/conv @@ -0,0 +1 @@ +42 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..dc8409cabed8ef130750c032600e7670057f4c45 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747454635 0.01277325901 1.291439586 1.378538104 1.47016774 0.008359090803 0.01957186638 0.03897247659 +6.640319508e-19 0.001189281682 0.002635529869 0.01289186761 0.04637180044 3.976025594e-19 2.056015124e-06 5.973226929e-06 +0.001695780822 0.005862345996 + +H atom_index 1 n_descriptor 18 +1.28230245 0.03290277434 0.1203431775 0.1659293426 0.3310266813 0.02367684883 0.03020570511 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:21 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874465 SEC) : SETUP UNITCELL + DONE(0.0961782 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.114286 SEC) : INIT PLANEWAVE + DONE(0.162044 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.441465 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651601e+02 0.000000e+00 2.173e-01 4.327e-01 + GE2 -4.663895e+02 -1.229432e+00 9.749e-02 3.577e-01 + GE3 -4.663925e+02 -2.948844e-03 6.223e-02 4.158e-01 + GE4 -4.663931e+02 -5.809753e-04 2.062e-03 3.041e-01 + GE5 -4.663921e+02 9.822185e-04 8.831e-04 3.021e-01 + GE6 -4.663928e+02 -6.937676e-04 1.675e-04 2.964e-01 + GE7 -4.663925e+02 2.616005e-04 4.496e-05 2.933e-01 + GE8 -4.663926e+02 -6.723200e-05 1.623e-05 2.798e-01 + GE9 -4.663926e+02 1.982588e-05 2.629e-06 2.809e-01 + GE10 -4.663926e+02 -2.430028e-06 2.692e-07 2.837e-01 + GE11 -4.663926e+02 -5.834927e-07 1.254e-07 2.775e-01 + GE12 -4.663926e+02 -6.553261e-09 9.787e-09 2.188e-01 +E_delta_band = -7.20548063e-02 Ry = -9.80355934e-01 eV +E_delta_NN= -1.95544630e-01 Ry = -2.66052118e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8881 11 0.54 1e+02 % + Run_lcao lcao_line 5.8787 1 5.9 1e+02 % + Potential init_pot 0.2845 2 0.14 4.8 % + PW_Basis recip2real 0.27464 17 0.016 4.7 % + PW_Basis gathers_scatterp 0.12492 17 0.0073 2.1 % + Potential v_of_rho 0.92955 14 0.066 16 % + XC_Functional v_xc 0.27125 15 0.018 4.6 % + H_Hartree_pw v_hartree 0.62129 14 0.044 11 % + PW_Basis real2recip 0.61187 41 0.015 10 % + PW_Basis gatherp_scatters 0.28286 41 0.0069 4.8 % + ORB_control set_orb_tables 1.0973 1 1.1 19 % + ORB_gen_tables gen_tables 1.0973 1 1.1 19 % + ORB_table_phi init_Table 0.4791 1 0.48 8.1 % + ORB_table_phi cal_ST_Phi12_R 0.47428 126 0.0038 8.1 % + ORB_table_beta init_Table_Beta 0.18568 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18418 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.25336 1 0.25 4.3 % + ORB_table_alpha S_PhiAlpha_R 0.2515 66 0.0038 4.3 % + LOOP_ions opt_ions 4.2643 1 4.3 72 % + ESolver_KS_LCAO Run 3.8042 1 3.8 65 % + HSolverLCAO solve 1.6801 12 0.14 29 % + HamiltLCAO updateHk 0.86342 12 0.072 15 % + LCAO_Hamilt cal_Hgamma 0.83208 12 0.069 14 % + Gint_Gamma distri_vl_value 0.54326 12 0.045 9.2 % + Gint_Gamma distri_vl 1.9987 6 0.33 34 % + LCAO_Deepks cal_projected_DM 3.9618 14 0.28 67 % + LCAO_gen_fixedH add_v_delta 1.8815 6 0.31 32 % + LCAO_DESCRIPTOR add_v_delta 1.8815 6 0.31 32 % + ElecStateLCAO psiToRho 0.7421 12 0.062 13 % + Charge mix_rho 0.69476 11 0.063 12 % + LOOP_ions force_stress 0.4599 1 0.46 7.8 % + Force_Stress_LCAO getForceStress 0.45987 1 0.46 7.8 % + Force_LCAO_gamma ftable_gamma 0.25143 1 0.25 4.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:21 2022 + FINISH Time : Wed Sep 28 11:02:27 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/42/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..6b53ab70aef8bcd522844de9747724c4bbecd24b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.465247 0.769588 0.484509 +H 0.529596 0.754626 0.470479 +H 0.46218 0.825754 0.448752 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..21be670fa72e6a577186c074c43639af4b4a715b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1701 2 + 2 -12.4623 2 + 3 -9.45791 2 + 4 -6.72414 2 + 5 1.03464 0 + 6 3.98467 0 + 7 11.1247 0 + 8 11.4106 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b04074f1a41d864cffbc437d78b242b7996284ea --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/running_scf.log @@ -0,0 +1,777 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:37 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.0269155375 21.5484622359 13.5662509856 0 0 0 0 + tauc_H1 14.8286787914 21.1295186287 13.1734210227 0 0 0 0 + tauc_H2 12.9410359939 23.1211259826 12.5650468472 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871257462871 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0874849208312 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105549863866 (SEC) + + DONE : INIT CHARGE Time : 0.154973526624 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.436435 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 1 + Local orbitals number in sub-FFT-grid = 5 + lgd_last = 0 + lgd_now = 5 + allocate DM , the dimension is 5 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 3 + nCol_in_proc = 3 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 3 + nCol_in_proc = 2 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 2 + nCol_in_proc = 3 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 2 + nCol_in_proc = 2 +receiver_size is 25 ; receiver_size of each process is: +9 6 6 4 +sender_size is 297 ; sender_size of each process is: +9 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00143 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000638 + + Density error is 0.210400264445 + + Energy Rydberg eV + E_KohnSham -34.1902248015 -465.181873201 + E_Harris -34.3733434768 -467.673330596 + E_Fermi -0.390530038382 -5.31343376215 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00140150489169 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000875405267563 + + Density error is 0.0981565341257 + + Energy Rydberg eV + E_KohnSham -34.2778207777 -466.373677599 + E_Harris -34.2849765768 -466.471037242 + E_Fermi -0.202544733429 -2.75576247453 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00130177575822 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000842069467189 + + Density error is 0.0633493133826 + + Energy Rydberg eV + E_KohnSham -34.2782389611 -466.379367276 + E_Harris -34.2828393206 -466.441958379 + E_Fermi -0.195503623653 -2.65996326133 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111967112345 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000812819897891 + + Density error is 0.00187830994307 + + Energy Rydberg eV + E_KohnSham -34.2781435525 -466.378069176 + E_Harris -34.2781429024 -466.37806033 + E_Fermi -0.159979604756 -2.17663418847 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111957561783 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000813366619274 + + Density error is 0.000934817470373 + + Energy Rydberg eV + E_KohnSham -34.2781075185 -466.377578909 + E_Harris -34.2781083461 -466.377590169 + E_Fermi -0.160044551885 -2.17751783949 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111704784496 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000813098812218 + + Density error is 0.000112101808609 + + Energy Rydberg eV + E_KohnSham -34.2781236409 -466.377798265 + E_Harris -34.2781236389 -466.377798238 + E_Fermi -0.159633455492 -2.17192458613 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0011169351058 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000813229393935 + + Density error is 2.40675956357e-05 + + Energy Rydberg eV + E_KohnSham -34.2781203186 -466.377753063 + E_Harris -34.2781203205 -466.377753089 + E_Fermi -0.159567118547 -2.17102202568 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111688241073 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000813169334862 + + Density error is 1.10237791462e-05 + + Energy Rydberg eV + E_KohnSham -34.2781215481 -466.377769791 + E_Harris -34.2781215487 -466.377769798 + E_Fermi -0.159584509435 -2.17125864085 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111687456352 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000813176685039 + + Density error is 2.13618407753e-06 + + Energy Rydberg eV + E_KohnSham -34.2781206521 -466.377757601 + E_Harris -34.2781206522 -466.377757601 + E_Fermi -0.159575191268 -2.17113186068 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111686996171 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000813178535334 + + Density error is 3.33688180318e-07 + + Energy Rydberg eV + E_KohnSham -34.2781208279 -466.377759992 + E_Harris -34.2781208279 -466.377759992 + E_Fermi -0.159573206346 -2.17110485443 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111687012203 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.0008131790017 + + Density error is 9.30464100855e-08 + + Energy Rydberg eV + E_KohnSham -34.2781208513 -466.377760311 + E_Harris -34.2781208513 -466.377760311 + E_band -7.91057659491 -107.628916156 + E_one_elec -68.7817802152 -935.824129511 + E_Hartree +35.7864122936 +486.899118171 + E_xc -8.16879032462 -111.142094182 + E_Ewald +7.01135727327 +95.3944096303 + E_demet -5.9872986893e-63 -8.14613778024e-62 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193959210376 -2.63895044069 + E_Fermi -0.159573027673 -2.17110242347 + + charge density convergence is achieved + final etot is -466.377760311 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1701 2.00000 + 2 -12.4623 2.00000 + 3 -9.45791 2.00000 + 4 -6.72414 2.00000 + 5 1.03464 0.00000 + 6 3.98467 0.00000 + 7 11.1247 0.00000 + 8 11.4106 0.00000 + + EFERMI = -2.171102423470878 eV + OUT.ABACUS/ final etot is -466.3777603108591 eV + correction force for each atom along direction 1 is 0.000121690 + correction force for each atom along direction 2 is 7.82020e-05 + correction force for each atom along direction 3 is -4.60353e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.4052111 +0.45436054 -0.81726818 + H1 -0.92063003 -0.21998513 +0.48467978 + H2 -0.48458104 -0.23437541 +0.33258840 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3777603108591 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0089 11 0.55 1.0e+02% + Run_lcao lcao_line 5.9989 1 6.0 1.e+02% + Potential init_pot 0.28286 2 0.14 4.7% + PW_Basis recip2real 0.26665 16 0.017 4.4% + PW_Basis gathers_scatterp 0.12418 16 0.0078 2.1% + Potential v_of_rho 0.98243 13 0.076 16.% + XC_Functional v_xc 0.29948 14 0.021 5.0% + H_Hartree_pw v_hartree 0.64220 13 0.049 11.% + PW_Basis real2recip 0.64687 38 0.017 11.% + PW_Basis gatherp_scatters 0.27013 38 0.0071 4.5% + ORB_control set_orb_tables 1.0888 1 1.1 18.% + ORB_gen_tables gen_tables 1.0888 1 1.1 18.% + ORB_table_phi init_Table 0.47582 1 0.48 7.9% + ORB_table_phi cal_ST_Phi12_R 0.47068 126 0.0037 7.8% + ORB_table_beta init_Table_Beta 0.18293 1 0.18 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18137 56 0.0032 3.0% + ORB_table_alpha init_Table_Alpha 0.24353 1 0.24 4.1% + ORB_table_alpha S_PhiAlpha_R 0.24163 66 0.0037 4.0% + LOOP_ions opt_ions 4.3921 1 4.4 73.% + ESolver_KS_LCAO Run 3.9190 1 3.9 65.% + HSolverLCAO solve 1.6295 11 0.15 27.% + HamiltLCAO updateHk 0.91227 11 0.083 15.% + LCAO_Hamilt cal_Hgamma 0.88467 11 0.080 15.% + Gint_Gamma distri_vl_value 0.48884 11 0.044 8.1% + Gint_Gamma distri_vl 1.9082 6 0.32 32.% + LCAO_Deepks cal_projected_DM 4.0858 13 0.31 68.% + LCAO_gen_fixedH add_v_delta 1.7635 6 0.29 29.% + LCAO_DESCRIPTOR add_v_delta 1.7635 6 0.29 29.% + ElecStateLCAO psiToRho 0.69675 11 0.063 12.% + Charge mix_rho 0.76961 10 0.077 13.% + LOOP_ions force_stress 0.47299 1 0.47 7.9% + Force_Stress_LCAO getForceStress 0.47296 1 0.47 7.9% + Force_LCAO_gamma ftable_gamma 0.25399 1 0.25 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:37 2022 + Finish Time : Wed Sep 28 11:03:43 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ffd061671076668c995d8f56b84ba8d3788b4874 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123803 ima = 3.6565e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 1 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122887649149 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111456765446 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112239513041 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112460982843 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112439464957 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112450433226 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011244894461 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112450694877 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112450156017 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112450085632 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112450069066 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b2033aa8afb5f5c0cd98ce6d7e82fc3ff6cf1903 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.973084462433 21.548462235884 13.566250985599 0 0 0 +H +0.0 +2 +-13.171321208603 21.129518628667 13.173421022762 0 0 0 +-15.058964006114 23.121125982596 12.565046847237 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/conv new file mode 100644 index 0000000000000000000000000000000000000000..468f29ad8b25a18a4eb168f215ce0aa7fbb9e1fb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/conv @@ -0,0 +1 @@ +43 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5a957a3189720f049f0f6d9c8cef98fe72890717 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755358234 0.01262452483 1.250226395 1.331071029 1.468778297 0.009549694734 0.0159896507 0.03924580673 +-5.189337543e-18 0.0007777544564 0.002698422274 0.01269992441 0.04406453017 -3.262712529e-19 2.437232824e-06 6.804718981e-06 +0.001569717296 0.006092162794 + +H atom_index 1 n_descriptor 18 +1.205361187 0.03643566828 0.09629075449 0.1299732615 0.3039440217 0.02095679666 0.02560339618 0.03978669517 +-3.390886357e-18 4.144800945e-05 0.08968381868 0.1110010091 0.1136853788 9.843568758e-19 4.8933582e-06 0.01426481325 +0.02475511102 0.02848587117 + +H atom_index 2 n_descriptor 18 +1.224721598 0.03582223849 0.1025442064 0.1382130832 0.3111296899 0.02191505558 0.02674767629 0.03902687458 +-5.401669721e-17 4.314279909e-05 0.09462138837 0.1145776932 0.1182176139 2.900638918e-18 4.02057526e-06 0.01378538494 +0.02554561041 0.02949094627 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fc97d07ad82802cb2bfadbd2097fc899ac9236ed Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/log.scf @@ -0,0 +1,100 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:37 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871481 SEC) : SETUP UNITCELL + DONE(0.0874987 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105572 SEC) : INIT PLANEWAVE + DONE(0.155109 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.436499 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651819e+02 0.000000e+00 2.104e-01 4.702e-01 + GE2 -4.663737e+02 -1.191804e+00 9.816e-02 4.090e-01 + GE3 -4.663794e+02 -5.689677e-03 6.335e-02 4.721e-01 + GE4 -4.663781e+02 1.298101e-03 1.878e-03 3.369e-01 + GE5 -4.663776e+02 4.902670e-04 9.348e-04 3.360e-01 + GE6 -4.663778e+02 -2.193562e-04 1.121e-04 3.281e-01 + GE7 -4.663778e+02 4.520181e-05 2.407e-05 3.129e-01 + GE8 -4.663778e+02 -1.672788e-05 1.102e-05 3.142e-01 + GE9 -4.663778e+02 1.219009e-05 2.136e-06 3.161e-01 + GE10 -4.663778e+02 -2.390912e-06 3.337e-07 3.141e-01 + GE11 -4.663778e+02 -3.192976e-07 9.305e-08 2.470e-01 +E_delta_band = -6.86393320e-02 Ry = -9.33886021e-01 eV +E_delta_NN= -1.93959210e-01 Ry = -2.63895044e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0089 11 0.55 1e+02 % + Run_lcao lcao_line 5.9989 1 6 1e+02 % + Potential init_pot 0.28286 2 0.14 4.7 % + PW_Basis recip2real 0.26665 16 0.017 4.4 % + PW_Basis gathers_scatterp 0.12418 16 0.0078 2.1 % + Potential v_of_rho 0.98243 13 0.076 16 % + XC_Functional v_xc 0.29948 14 0.021 5 % + H_Hartree_pw v_hartree 0.6422 13 0.049 11 % + PW_Basis real2recip 0.64687 38 0.017 11 % + PW_Basis gatherp_scatters 0.27013 38 0.0071 4.5 % + ORB_control set_orb_tables 1.0888 1 1.1 18 % + ORB_gen_tables gen_tables 1.0888 1 1.1 18 % + ORB_table_phi init_Table 0.47582 1 0.48 7.9 % + ORB_table_phi cal_ST_Phi12_R 0.47068 126 0.0037 7.8 % + ORB_table_beta init_Table_Beta 0.18293 1 0.18 3 % + ORB_table_beta VNL_PhiBeta_R 0.18137 56 0.0032 3 % + ORB_table_alpha init_Table_Alpha 0.24353 1 0.24 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.24163 66 0.0037 4 % + LOOP_ions opt_ions 4.3921 1 4.4 73 % + ESolver_KS_LCAO Run 3.919 1 3.9 65 % + HSolverLCAO solve 1.6295 11 0.15 27 % + HamiltLCAO updateHk 0.91227 11 0.083 15 % + LCAO_Hamilt cal_Hgamma 0.88467 11 0.08 15 % + Gint_Gamma distri_vl_value 0.48884 11 0.044 8.1 % + Gint_Gamma distri_vl 1.9082 6 0.32 32 % + LCAO_Deepks cal_projected_DM 4.0858 13 0.31 68 % + LCAO_gen_fixedH add_v_delta 1.7635 6 0.29 29 % + LCAO_DESCRIPTOR add_v_delta 1.7635 6 0.29 29 % + ElecStateLCAO psiToRho 0.69675 11 0.063 12 % + Charge mix_rho 0.76961 10 0.077 13 % + LOOP_ions force_stress 0.47299 1 0.47 7.9 % + Force_Stress_LCAO getForceStress 0.47296 1 0.47 7.9 % + Force_LCAO_gamma ftable_gamma 0.25399 1 0.25 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:37 2022 + FINISH Time : Wed Sep 28 11:03:43 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/43/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fa33a86f49f6dfcbc7452f2a27658a736a444a17 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.481693 0.773873 0.47555 +H 0.486302 0.723029 0.438634 +H 0.471751 0.82755 0.441288 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8823634d132ef94d9922b2af417fb7903e0e8490 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4399 2 + 2 -13.6753 2 + 3 -8.7791 2 + 4 -6.77649 2 + 5 1.5689 0 + 6 4.88746 0 + 7 11.0136 0 + 8 11.2183 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..62d67c5c10de8d7007c00ae4598cbccdc5b57865 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:13 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.4873956496 21.6684542767 13.3153906867 0 0 0 0 + tauc_H1 13.6164559608 20.2448094342 12.2817575067 0 0 0 0 + tauc_H2 13.2090414971 23.171400047 12.3560715146 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0954433221825 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.113203536856 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.131468735055 (SEC) + + DONE : INIT CHARGE Time : 0.174669856566 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.454651 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 10 + lgd_last = 0 + lgd_now = 10 + allocate DM , the dimension is 10 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 5 + nCol_in_proc = 5 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 5 + nCol_in_proc = 5 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 5 + nCol_in_proc = 5 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 5 + nCol_in_proc = 5 +receiver_size is 100 ; receiver_size of each process is: +25 25 25 25 +sender_size is 313 ; sender_size of each process is: +25 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.0014 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.000949 + + Density error is 0.218842420943 + + Energy Rydberg eV + E_KohnSham -34.1851083359 -465.112260115 + E_Harris -34.3850625796 -467.832777169 + E_Fermi -0.421521853864 -5.73509904407 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.0013265500564 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.00129125643056 + + Density error is 0.0973619540798 + + Energy Rydberg eV + E_KohnSham -34.2752270419 -466.338388013 + E_Harris -34.2816990324 -466.426443961 + E_Fermi -0.22872590037 -3.11197552521 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00121950489549 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.00124955839424 + + Density error is 0.0618900446017 + + Energy Rydberg eV + E_KohnSham -34.2753349763 -466.339856536 + E_Harris -34.2793822618 -466.394922681 + E_Fermi -0.212315167366 -2.88869604801 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00103872997045 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.00118898886812 + + Density error is 0.00217136568514 + + Energy Rydberg eV + E_KohnSham -34.2754156433 -466.340954067 + E_Harris -34.2754196709 -466.341008866 + E_Fermi -0.177157907431 -2.41035698681 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00103342722922 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.00119072834044 + + Density error is 0.000885579649 + + Energy Rydberg eV + E_KohnSham -34.2753415143 -466.33994549 + E_Harris -34.2753442315 -466.33998246 + E_Fermi -0.175556015765 -2.38856213258 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00103250789403 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.00118945483632 + + Density error is 0.000255975999678 + + Energy Rydberg eV + E_KohnSham -34.2753977906 -466.340711169 + E_Harris -34.2753980597 -466.340714831 + E_Fermi -0.176097431523 -2.39592847188 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00103211085926 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.00118991365274 + + Density error is 4.14214059331e-05 + + Energy Rydberg eV + E_KohnSham -34.2753742475 -466.340390849 + E_Harris -34.275374256 -466.340390964 + E_Fermi -0.175810367669 -2.39202276778 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00103215216292 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.00118982541872 + + Density error is 1.78450348355e-05 + + Energy Rydberg eV + E_KohnSham -34.275381122 -466.340484381 + E_Harris -34.2753811231 -466.340484396 + E_Fermi -0.175864531225 -2.39275970076 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00103210311266 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.00118981178285 + + Density error is 1.83092193554e-06 + + Energy Rydberg eV + E_KohnSham -34.2753798084 -466.340466508 + E_Harris -34.2753798084 -466.340466509 + E_Fermi -0.175844847292 -2.39249188712 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00103210072639 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.0011898147641 + + Density error is 2.81065867669e-07 + + Energy Rydberg eV + E_KohnSham -34.2753800064 -466.340469202 + E_Harris -34.2753800064 -466.340469202 + E_Fermi -0.175843159391 -2.39246892205 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.0010321009627 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.00118981520157 + + Density error is 1.2084857663e-07 + + Energy Rydberg eV + E_KohnSham -34.2753800339 -466.340469577 + E_Harris -34.2753800339 -466.340469577 + E_Fermi -0.17584310839 -2.39246822813 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00103210081828 + number of non-zero elements in receiver_buffer = 100 + receiver_size = 100 + last receiver_buffer = 0.00118981529949 + + Density error is 9.07934453994e-09 + + Energy Rydberg eV + E_KohnSham -34.2753800342 -466.340469581 + E_Harris -34.2753800342 -466.340469581 + E_band -8.03645388017 -109.341564485 + E_one_elec -69.8777902815 -950.736111477 + E_Hartree +36.3290921626 +494.282656578 + E_xc -8.25609115822 -112.329882959 + E_Ewald +7.65259436817 +104.11888789 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195739745347 -2.66317586178 + E_Fermi -0.175842999458 -2.39246674604 + + charge density convergence is achieved + final etot is -466.340469581 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4399 2.00000 + 2 -13.6753 2.00000 + 3 -8.77910 2.00000 + 4 -6.77649 2.00000 + 5 1.56890 0.00000 + 6 4.88746 0.00000 + 7 11.0136 0.00000 + 8 11.2183 0.00000 + + EFERMI = -2.392466746037703 eV + OUT.ABACUS/ final etot is -466.3404695808026 eV + correction force for each atom along direction 1 is 0.000129562 + correction force for each atom along direction 2 is -1.24009e-05 + correction force for each atom along direction 3 is -2.63250e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.035162399 +1.0418113 +2.5317927 + H1 +0.092762580 -1.5063757 -1.6801833 + H2 -0.12792498 +0.46456445 -0.85160937 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3404695808026 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6329 11 0.69 1.0e+02% + Run_lcao lcao_line 7.6236 1 7.6 1.e+02% + Potential init_pot 0.28296 2 0.14 3.7% + PW_Basis recip2real 0.27059 17 0.016 3.5% + PW_Basis gathers_scatterp 0.12290 17 0.0072 1.6% + Potential v_of_rho 0.94426 14 0.067 12.% + XC_Functional v_xc 0.30157 15 0.020 4.0% + H_Hartree_pw v_hartree 0.60346 14 0.043 7.9% + PW_Basis real2recip 0.70206 41 0.017 9.2% + PW_Basis gatherp_scatters 0.28810 41 0.0070 3.8% + ORB_control set_orb_tables 1.0980 1 1.1 14.% + ORB_gen_tables gen_tables 1.0980 1 1.1 14.% + ORB_table_phi init_Table 0.47666 1 0.48 6.2% + ORB_table_phi cal_ST_Phi12_R 0.47140 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18598 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18440 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24736 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24536 66 0.0037 3.2% + LOOP_ions opt_ions 5.9936 1 6.0 79.% + ESolver_KS_LCAO Run 5.4520 1 5.5 71.% + HSolverLCAO solve 3.0172 12 0.25 40.% + HamiltLCAO updateHk 1.5059 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4761 12 0.12 19.% + Gint_Gamma distri_vl_value 1.0387 12 0.087 14.% + Gint_Gamma distri_vl 2.8553 6 0.48 37.% + LCAO_Deepks cal_projected_DM 5.5609 14 0.40 73.% + LCAO_gen_fixedH add_v_delta 2.7305 6 0.46 36.% + LCAO_DESCRIPTOR add_v_delta 2.7307 6 0.46 36.% + ElecStateLCAO psiToRho 1.4649 12 0.12 19.% + Charge mix_rho 0.87432 11 0.079 11.% + LOOP_ions force_stress 0.54138 1 0.54 7.1% + Force_Stress_LCAO getForceStress 0.54135 1 0.54 7.1% + Force_LCAO_gamma ftable_gamma 0.34835 1 0.35 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:13 2022 + Finish Time : Wed Sep 28 11:13:21 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3e56659053c836e672a2970f209e30e6bfe2dd1d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123858 ima = 3.67044e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123383974382 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113013946951 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113285124295 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113548726281 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113474971674 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011352208484 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113508242161 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113510881022 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113510318229 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113510248507 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113510242279 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113510237082 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8e6fd665e99fd860ed357278875e8e16df38d458 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.512604350343 21.668454276716 13.315390686704 0 0 0 +H +0.0 +2 +-14.383544039183 20.244809434206 12.281757506716 0 0 0 +-14.790958502904 23.171400047032 12.356071514554 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/conv new file mode 100644 index 0000000000000000000000000000000000000000..719879f30289eee388c8f7290dcc3a8f114ad2a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/conv @@ -0,0 +1 @@ +44 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..44eadc01ba13eb34b8dbbc8b674f829d43ea1d13 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742449684 0.01272940729 1.303332081 1.391651153 1.470317509 0.007701872247 0.02147097286 0.03884154164 +-8.770450347e-19 0.001302306749 0.002437258183 0.01319351329 0.04436816952 -1.957618493e-19 1.596202861e-06 5.032488976e-06 +0.001837039663 0.005500362842 + +H atom_index 1 n_descriptor 18 +1.293144412 0.03191502788 0.1256077594 0.1729566596 0.3353825682 0.02376508887 0.03097019675 0.03578373204 +7.830683415e-18 4.37248057e-05 0.1081787799 0.1229167594 0.1485746973 -2.238597925e-18 2.08667644e-06 0.01326271986 +0.02801087344 0.03261761799 + +H atom_index 2 n_descriptor 18 +1.260694108 0.03299683571 0.1134367517 0.1567194122 0.326507064 0.02243416255 0.02914087484 0.0362420301 +-4.727890547e-17 4.106255439e-05 0.1062026669 0.1156867072 0.1347859213 2.619113849e-18 3.680979221e-06 0.01281025482 +0.02695047749 0.03139603084 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0c5574fc46dfac9b66480a8019cbb8a409d9c853 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:13 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.095472 SEC) : SETUP UNITCELL + DONE(0.113223 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.131487 SEC) : INIT PLANEWAVE + DONE(0.174805 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.454721 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651123e+02 0.000000e+00 2.188e-01 5.777e-01 + GE2 -4.663384e+02 -1.226128e+00 9.736e-02 5.015e-01 + GE3 -4.663399e+02 -1.468523e-03 6.189e-02 5.725e-01 + GE4 -4.663410e+02 -1.097531e-03 2.171e-03 4.336e-01 + GE5 -4.663399e+02 1.008578e-03 8.856e-04 4.326e-01 + GE6 -4.663407e+02 -7.656791e-04 2.560e-04 4.201e-01 + GE7 -4.663404e+02 3.203200e-04 4.142e-05 4.261e-01 + GE8 -4.663405e+02 -9.353221e-05 1.785e-05 4.159e-01 + GE9 -4.663405e+02 1.787260e-05 1.831e-06 4.168e-01 + GE10 -4.663405e+02 -2.693972e-06 2.811e-07 4.164e-01 + GE11 -4.663405e+02 -3.741287e-07 1.208e-07 4.151e-01 + GE12 -4.663405e+02 -4.227664e-09 9.079e-09 3.536e-01 +E_delta_band = -7.25546200e-02 Ry = -9.87156249e-01 eV +E_delta_NN= -1.95739745e-01 Ry = -2.66317586e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6329 11 0.69 1e+02 % + Run_lcao lcao_line 7.6236 1 7.6 1e+02 % + Potential init_pot 0.28296 2 0.14 3.7 % + PW_Basis recip2real 0.27059 17 0.016 3.5 % + PW_Basis gathers_scatterp 0.1229 17 0.0072 1.6 % + Potential v_of_rho 0.94426 14 0.067 12 % + XC_Functional v_xc 0.30157 15 0.02 4 % + H_Hartree_pw v_hartree 0.60346 14 0.043 7.9 % + PW_Basis real2recip 0.70206 41 0.017 9.2 % + PW_Basis gatherp_scatters 0.2881 41 0.007 3.8 % + ORB_control set_orb_tables 1.098 1 1.1 14 % + ORB_gen_tables gen_tables 1.098 1 1.1 14 % + ORB_table_phi init_Table 0.47666 1 0.48 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.4714 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18598 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.1844 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24736 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24536 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9936 1 6 79 % + ESolver_KS_LCAO Run 5.452 1 5.5 71 % + HSolverLCAO solve 3.0172 12 0.25 40 % + HamiltLCAO updateHk 1.5059 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4761 12 0.12 19 % + Gint_Gamma distri_vl_value 1.0387 12 0.087 14 % + Gint_Gamma distri_vl 2.8553 6 0.48 37 % + LCAO_Deepks cal_projected_DM 5.5609 14 0.4 73 % + LCAO_gen_fixedH add_v_delta 2.7305 6 0.46 36 % + LCAO_DESCRIPTOR add_v_delta 2.7307 6 0.46 36 % + ElecStateLCAO psiToRho 1.4649 12 0.12 19 % + Charge mix_rho 0.87432 11 0.079 11 % + LOOP_ions force_stress 0.54138 1 0.54 7.1 % + Force_Stress_LCAO getForceStress 0.54135 1 0.54 7.1 % + Force_LCAO_gamma ftable_gamma 0.34835 1 0.35 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:13 2022 + FINISH Time : Wed Sep 28 11:13:21 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/44/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..6f9b4f832d664a2aa7ab3326147e3491e1926ba8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.491461 0.773677 0.466994 +H 0.457102 0.715547 0.470942 +H 0.446638 0.804019 0.432527 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1fe58543546a21183b126203394870a6d3d3967d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4331 2 + 2 -12.5068 2 + 3 -9.59544 2 + 4 -6.77712 2 + 5 1.14106 0 + 6 4.30806 0 + 7 11.0732 0 + 8 11.3647 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..571b3d81f46a8686dbd8c13aacc8a4f215451d71 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:37 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.7608955374 21.6629541993 13.0758386036 0 0 0 0 + tauc_H1 12.7988576053 20.0353135846 13.186366677 0 0 0 0 + tauc_H2 12.5058747451 22.5125435738 12.1107586539 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0858072849692 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100764449546 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119273566667 (SEC) + + DONE : INIT CHARGE Time : 0.168462170355 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.452592 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 10 + nCol_in_proc = 10 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 10 + nCol_in_proc = 8 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 8 + nCol_in_proc = 10 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 8 + nCol_in_proc = 8 +receiver_size is 324 ; receiver_size of each process is: +100 80 80 64 +sender_size is 388 ; sender_size of each process is: +100 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000944 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00132 + + Density error is 0.212105338454 + + Energy Rydberg eV + E_KohnSham -34.186295045 -465.128406122 + E_Harris -34.3736002951 -467.676824787 + E_Fermi -0.404163837849 -5.49893112029 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00115994001567 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00125202272995 + + Density error is 0.0975045260424 + + Energy Rydberg eV + E_KohnSham -34.2745028704 -466.328535154 + E_Harris -34.2814616537 -466.423214259 + E_Fermi -0.215511394444 -2.93218294836 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109064323007 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00116743236188 + + Density error is 0.0626139525484 + + Energy Rydberg eV + E_KohnSham -34.2747924853 -466.332475568 + E_Harris -34.2792938835 -466.393720232 + E_Fermi -0.205467475104 -2.79552841509 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00098772954663 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103340463354 + + Density error is 0.00191548388078 + + Energy Rydberg eV + E_KohnSham -34.2747474542 -466.331862888 + E_Harris -34.2747478599 -466.331868408 + E_Fermi -0.16948024237 -2.30589699466 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000990743866107 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0010360794282 + + Density error is 0.000837276263117 + + Energy Rydberg eV + E_KohnSham -34.2747021757 -466.331246843 + E_Harris -34.2747030627 -466.33125891 + E_Fermi -0.169209372661 -2.30221162319 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000988945223458 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103402214775 + + Density error is 0.000105594235937 + + Energy Rydberg eV + E_KohnSham -34.2747310217 -466.331639312 + E_Harris -34.2747310361 -466.331639508 + E_Fermi -0.16899827057 -2.29933943189 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000988727598927 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0010338339456 + + Density error is 3.35775027041e-05 + + Energy Rydberg eV + E_KohnSham -34.274722387 -466.331521832 + E_Harris -34.2747223906 -466.33152188 + E_Fermi -0.168926807682 -2.29836712943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00098865936297 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103379971321 + + Density error is 1.69662949091e-05 + + Energy Rydberg eV + E_KohnSham -34.2747243614 -466.331548695 + E_Harris -34.2747243627 -466.331548713 + E_Fermi -0.168950848982 -2.29869422809 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000988657956697 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0010337901796 + + Density error is 2.02885524138e-06 + + Energy Rydberg eV + E_KohnSham -34.2747230434 -466.331530762 + E_Harris -34.2747230434 -466.331530763 + E_Fermi -0.168933392846 -2.29845672518 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000988661954015 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103379060103 + + Density error is 7.152084975e-07 + + Energy Rydberg eV + E_KohnSham -34.2747233342 -466.331534719 + E_Harris -34.2747233343 -466.331534719 + E_Fermi -0.168932919661 -2.29845028716 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00098866254801 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00103379067304 + + Density error is 1.66927624137e-07 + + Energy Rydberg eV + E_KohnSham -34.2747233488 -466.331534917 + E_Harris -34.2747233488 -466.331534917 + E_Fermi -0.168932396593 -2.29844317047 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000988662564559 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0010337905038 + + Density error is 1.17569871179e-08 + + Energy Rydberg eV + E_KohnSham -34.2747233584 -466.331535047 + E_Harris -34.2747233584 -466.331535047 + E_band -7.98378795028 -108.625007748 + E_one_elec -69.2091840588 -941.63925713 + E_Hartree +35.9845147466 +489.594440318 + E_xc -8.20063577033 -111.575373699 + E_Ewald +7.27502247991 +98.9817588048 + E_demet -4.63791057797e-72 -6.31020106749e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194741097838 -2.64958856538 + E_Fermi -0.168932213486 -2.29844067916 + + charge density convergence is achieved + final etot is -466.331535047 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4331 2.00000 + 2 -12.5068 2.00000 + 3 -9.59544 2.00000 + 4 -6.77712 2.00000 + 5 1.14106 0.00000 + 6 4.30806 0.00000 + 7 11.0732 0.00000 + 8 11.3647 0.00000 + + EFERMI = -2.298440679158753 eV + OUT.ABACUS/ final etot is -466.3315350474306 eV + correction force for each atom along direction 1 is -3.29971e-05 + correction force for each atom along direction 2 is -3.31680e-05 + correction force for each atom along direction 3 is 9.06504e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.34634686 -1.9171892 +0.54143987 + H1 +1.0312375 +0.49402221 +0.34588305 + H2 -0.68489065 +1.4231670 -0.88732292 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3315350474306 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6174 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6082 1 6.6 1.e+02% + Potential init_pot 0.28532 2 0.14 4.3% + PW_Basis recip2real 0.28741 17 0.017 4.3% + PW_Basis gathers_scatterp 0.13489 17 0.0079 2.0% + Potential v_of_rho 1.0671 14 0.076 16.% + XC_Functional v_xc 0.33032 15 0.022 5.0% + H_Hartree_pw v_hartree 0.69445 14 0.050 10.% + PW_Basis real2recip 0.71441 41 0.017 11.% + PW_Basis gatherp_scatters 0.32050 41 0.0078 4.8% + ORB_control set_orb_tables 1.1033 1 1.1 17.% + ORB_gen_tables gen_tables 1.1033 1 1.1 17.% + ORB_table_phi init_Table 0.48362 1 0.48 7.3% + ORB_table_phi cal_ST_Phi12_R 0.47836 126 0.0038 7.2% + ORB_table_beta init_Table_Beta 0.18405 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18253 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25028 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24835 66 0.0038 3.8% + LOOP_ions opt_ions 4.9725 1 5.0 75.% + ESolver_KS_LCAO Run 4.4770 1 4.5 68.% + HSolverLCAO solve 1.9989 12 0.17 30.% + HamiltLCAO updateHk 1.0718 12 0.089 16.% + LCAO_Hamilt cal_Hgamma 1.0423 12 0.087 16.% + Gint_Gamma distri_vl_value 0.62347 12 0.052 9.4% + Gint_Gamma distri_vl 2.3442 6 0.39 35.% + LCAO_Deepks cal_projected_DM 4.6342 14 0.33 70.% + LCAO_gen_fixedH add_v_delta 2.2030 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2032 6 0.37 33.% + ElecStateLCAO psiToRho 0.89751 12 0.075 14.% + Charge mix_rho 0.83188 11 0.076 13.% + LOOP_ions force_stress 0.49537 1 0.50 7.5% + Force_Stress_LCAO getForceStress 0.49535 1 0.50 7.5% + Force_LCAO_gamma ftable_gamma 0.28158 1 0.28 4.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:37 2022 + Finish Time : Wed Sep 28 11:08:44 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..94d985396a9aa66b23fa12edf63d9c8c838afb5b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123672 ima = 3.69867e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122454704091 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111275240308 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111931051884 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112182016115 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112140116755 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112162706385 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112160417633 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112162868124 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112162044925 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112161976693 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112161944376 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112161935265 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e12f888bcb6694dc75cb32946c5301c733d68c2a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.239104462568 21.662954199351 13.075838603613 0 0 0 +H +0.0 +2 +-15.201142394653 20.035313584588 13.186366676994 0 0 0 +-15.494125254837 22.512543573803 12.110758653907 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/conv new file mode 100644 index 0000000000000000000000000000000000000000..3353160702e6e877e366fc90b0a77868e99f7027 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/conv @@ -0,0 +1 @@ +45 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..930da71ddd117c5fbfde5250e3f110d162fca588 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.756719025 0.01279233087 1.261047386 1.347942504 1.469787998 0.01005783151 0.01578004166 0.03925832569 +-5.764914717e-18 0.0007969854443 0.002943095755 0.01378523375 0.04685477216 6.274843234e-19 3.05913208e-06 8.112160889e-06 +0.001586842903 0.006149310339 + +H atom_index 1 n_descriptor 18 +1.20381957 0.03672395795 0.09792335991 0.1293498648 0.302578332 0.02149708719 0.02550274032 0.04004942516 +3.637850322e-17 4.46223882e-05 0.0923890014 0.110503116 0.113182191 1.995158338e-18 4.474678813e-06 0.01440579072 +0.02552998849 0.02843409332 + +H atom_index 2 n_descriptor 18 +1.279713471 0.03428372447 0.1249457201 0.1641624745 0.3287158951 0.02538358228 0.02996901836 0.03759241489 +1.329348252e-17 5.123158493e-05 0.1074747538 0.1205955792 0.140590122 5.843413863e-18 8.101397841e-07 0.01352189293 +0.02839816292 0.03203100702 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d4c13b8dbbad45d0ca5df94095bac1bac8ddcc02 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/e_base.npy new file mode 100644 index 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..4576c9e2c5902b9acd2c67483d0fcd08e26a3595 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..cc8ce2ae845766e32bed4b0b0b99e1bd2e908032 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:37 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0858324 SEC) : SETUP UNITCELL + DONE(0.100782 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119294 SEC) : INIT PLANEWAVE + DONE(0.168594 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.452659 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651284e+02 0.000000e+00 2.121e-01 4.863e-01 + GE2 -4.663285e+02 -1.200129e+00 9.750e-02 4.263e-01 + GE3 -4.663325e+02 -3.940413e-03 6.261e-02 4.962e-01 + GE4 -4.663319e+02 6.126792e-04 1.915e-03 3.569e-01 + GE5 -4.663312e+02 6.160452e-04 8.373e-04 3.537e-01 + GE6 -4.663316e+02 -3.924692e-04 1.056e-04 3.514e-01 + GE7 -4.663315e+02 1.174806e-04 3.358e-05 3.372e-01 + GE8 -4.663315e+02 -2.686282e-05 1.697e-05 3.357e-01 + GE9 -4.663315e+02 1.793213e-05 2.029e-06 3.376e-01 + GE10 -4.663315e+02 -3.956959e-06 7.152e-07 3.366e-01 + GE11 -4.663315e+02 -1.979419e-07 1.669e-07 3.348e-01 + GE12 -4.663315e+02 -1.301481e-07 1.176e-08 2.625e-01 +E_delta_band = -7.03003421e-02 Ry = -9.56485224e-01 eV +E_delta_NN= -1.94741098e-01 Ry = -2.64958857e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6174 11 0.6 1e+02 % + Run_lcao lcao_line 6.6082 1 6.6 1e+02 % + Potential init_pot 0.28532 2 0.14 4.3 % + PW_Basis recip2real 0.28741 17 0.017 4.3 % + PW_Basis gathers_scatterp 0.13489 17 0.0079 2 % + Potential v_of_rho 1.0671 14 0.076 16 % + XC_Functional v_xc 0.33032 15 0.022 5 % + H_Hartree_pw v_hartree 0.69445 14 0.05 10 % + PW_Basis real2recip 0.71441 41 0.017 11 % + PW_Basis gatherp_scatters 0.3205 41 0.0078 4.8 % + ORB_control set_orb_tables 1.1033 1 1.1 17 % + ORB_gen_tables gen_tables 1.1033 1 1.1 17 % + ORB_table_phi init_Table 0.48362 1 0.48 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.47836 126 0.0038 7.2 % + ORB_table_beta init_Table_Beta 0.18405 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18253 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25028 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24835 66 0.0038 3.8 % + LOOP_ions opt_ions 4.9725 1 5 75 % + ESolver_KS_LCAO Run 4.477 1 4.5 68 % + HSolverLCAO solve 1.9989 12 0.17 30 % + HamiltLCAO updateHk 1.0718 12 0.089 16 % + LCAO_Hamilt cal_Hgamma 1.0423 12 0.087 16 % + Gint_Gamma distri_vl_value 0.62347 12 0.052 9.4 % + Gint_Gamma distri_vl 2.3442 6 0.39 35 % + LCAO_Deepks cal_projected_DM 4.6342 14 0.33 70 % + LCAO_gen_fixedH add_v_delta 2.203 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2032 6 0.37 33 % + ElecStateLCAO psiToRho 0.89751 12 0.075 14 % + Charge mix_rho 0.83188 11 0.076 13 % + LOOP_ions force_stress 0.49537 1 0.5 7.5 % + Force_Stress_LCAO getForceStress 0.49535 1 0.5 7.5 % + Force_LCAO_gamma ftable_gamma 0.28158 1 0.28 4.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:37 2022 + FINISH Time : Wed Sep 28 11:08:44 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/45/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c89ed53a9a742baf9209c786041dcc04053e2635 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.481886 0.780575 0.454079 +H 0.476233 0.766461 0.517491 +H 0.420739 0.774801 0.426881 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..790eef57a753dfee670b2e7e12c9c379ff65fcec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1133 2 + 2 -13.0916 2 + 3 -8.93981 2 + 4 -6.70282 2 + 5 1.19983 0 + 6 4.27976 0 + 7 11.1087 0 + 8 11.3441 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..49b2571f4b0d5b117586c006c1f5ccb319393d30 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:06 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.492813594 21.856086189 12.714209467 0 0 0 0 + tauc_H1 13.3345142082 21.46091923 14.4897347979 0 0 0 0 + tauc_H2 11.7806850278 21.6944293203 11.952666663 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871056443316 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0974951695442 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115618278349 (SEC) + + DONE : INIT CHARGE Time : 0.164538121349 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446386 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 10 + nCol_in_proc = 10 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 10 + nCol_in_proc = 8 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 8 + nCol_in_proc = 10 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 8 + nCol_in_proc = 8 +receiver_size is 324 ; receiver_size of each process is: +100 80 80 64 +sender_size is 388 ; sender_size of each process is: +100 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000749 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00157 + + Density error is 0.215017904504 + + Energy Rydberg eV + E_KohnSham -34.1890921668 -465.166462916 + E_Harris -34.3807903276 -467.774650198 + E_Fermi -0.398544328868 -5.42247377819 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00117621858178 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00128389764684 + + Density error is 0.0986844474576 + + Energy Rydberg eV + E_KohnSham -34.279820802 -466.400889326 + E_Harris -34.2867158414 -466.49470115 + E_Fermi -0.205985954331 -2.80258268686 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00113550500011 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.0011880815337 + + Density error is 0.0635334682442 + + Energy Rydberg eV + E_KohnSham -34.2802455041 -466.406667695 + E_Harris -34.2846794569 -466.466994717 + E_Fermi -0.197144430992 -2.68228759046 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109260948599 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00101589275641 + + Density error is 0.00204175717703 + + Energy Rydberg eV + E_KohnSham -34.2801975342 -466.406015031 + E_Harris -34.280200618 -466.406056988 + E_Fermi -0.161832485647 -2.2018439263 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109343175427 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00101474027518 + + Density error is 0.000974604347791 + + Energy Rydberg eV + E_KohnSham -34.2801429898 -466.405272916 + E_Harris -34.280143631 -466.40528164 + E_Fermi -0.161357408391 -2.19538016862 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109267370286 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00101234094927 + + Density error is 0.000190200415706 + + Energy Rydberg eV + E_KohnSham -34.2801711162 -466.405655595 + E_Harris -34.2801711579 -466.405656163 + E_Fermi -0.16114908685 -2.19254580866 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109302692644 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00101232194965 + + Density error is 3.71682752607e-05 + + Energy Rydberg eV + E_KohnSham -34.2801609202 -466.405516872 + E_Harris -34.2801609268 -466.405516962 + E_Fermi -0.161047574286 -2.19116465937 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109291416414 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00101229831831 + + Density error is 1.6735799171e-05 + + Energy Rydberg eV + E_KohnSham -34.2801652837 -466.40557624 + E_Harris -34.2801652849 -466.405576256 + E_Fermi -0.161083026214 -2.19164700759 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109291763641 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00101227097522 + + Density error is 1.52932107457e-06 + + Energy Rydberg eV + E_KohnSham -34.2801639009 -466.405557426 + E_Harris -34.2801639009 -466.405557426 + E_Fermi -0.161064946728 -2.19140102356 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109292038948 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00101226907508 + + Density error is 3.88065939422e-07 + + Energy Rydberg eV + E_KohnSham -34.2801641507 -466.405560825 + E_Harris -34.2801641507 -466.405560825 + E_Fermi -0.161063954183 -2.1913875193 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109292114071 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00101226899238 + + Density error is 1.01182823191e-07 + + Energy Rydberg eV + E_KohnSham -34.2801641651 -466.405561021 + E_Harris -34.2801641651 -466.405561021 + E_Fermi -0.161063776373 -2.19138510007 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00109292119307 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00101226877493 + + Density error is 1.03344007668e-08 + + Energy Rydberg eV + E_KohnSham -34.2801641696 -466.405561083 + E_Harris -34.2801641696 -466.405561083 + E_band -7.91544826114 -107.695198576 + E_one_elec -69.0379505641 -939.309505914 + E_Hartree +35.9269284142 +488.810938071 + E_xc -8.19130930259 -111.448480596 + E_Ewald +7.14704631713 +97.2405537828 + E_demet -3.9881853039e-70 -5.42620448129e-69 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194277819577 -2.64328534126 + E_Fermi -0.161063683667 -2.19138383875 + + charge density convergence is achieved + final etot is -466.405561083 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1133 2.00000 + 2 -13.0916 2.00000 + 3 -8.93981 2.00000 + 4 -6.70282 2.00000 + 5 1.19983 0.00000 + 6 4.27976 0.00000 + 7 11.1087 0.00000 + 8 11.3441 0.00000 + + EFERMI = -2.191383838745339 eV + OUT.ABACUS/ final etot is -466.4055610825716 eV + correction force for each atom along direction 1 is -4.77908e-05 + correction force for each atom along direction 2 is 6.64183e-05 + correction force for each atom along direction 3 is 7.86860e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.53923153 +0.10919514 -0.99891892 + H1 -0.28081249 -0.13183347 +0.37701068 + H2 +0.82004403 +0.022638335 +0.62190824 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4055610825716 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0639 11 0.55 1.0e+02% + Run_lcao lcao_line 6.0539 1 6.1 1.e+02% + Potential init_pot 0.28686 2 0.14 4.7% + PW_Basis recip2real 0.27787 17 0.016 4.6% + PW_Basis gathers_scatterp 0.12684 17 0.0075 2.1% + Potential v_of_rho 0.92443 14 0.066 15.% + XC_Functional v_xc 0.25534 15 0.017 4.2% + H_Hartree_pw v_hartree 0.63126 14 0.045 10.% + PW_Basis real2recip 0.60604 41 0.015 10.% + PW_Basis gatherp_scatters 0.24517 41 0.0060 4.0% + ORB_control set_orb_tables 1.1116 1 1.1 18.% + ORB_gen_tables gen_tables 1.1116 1 1.1 18.% + ORB_table_phi init_Table 0.48877 1 0.49 8.1% + ORB_table_phi cal_ST_Phi12_R 0.48378 126 0.0038 8.0% + ORB_table_beta init_Table_Beta 0.18903 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18753 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25393 1 0.25 4.2% + ORB_table_alpha S_PhiAlpha_R 0.25201 66 0.0038 4.2% + LOOP_ions opt_ions 4.4196 1 4.4 73.% + ESolver_KS_LCAO Run 3.9395 1 3.9 65.% + HSolverLCAO solve 1.7949 12 0.15 30.% + HamiltLCAO updateHk 0.96842 12 0.081 16.% + LCAO_Hamilt cal_Hgamma 0.93774 12 0.078 15.% + Gint_Gamma distri_vl_value 0.56635 12 0.047 9.3% + Gint_Gamma distri_vl 2.0638 6 0.34 34.% + LCAO_Deepks cal_projected_DM 4.0990 14 0.29 68.% + LCAO_gen_fixedH add_v_delta 1.9331 6 0.32 32.% + LCAO_DESCRIPTOR add_v_delta 1.9331 6 0.32 32.% + ElecStateLCAO psiToRho 0.80645 12 0.067 13.% + Charge mix_rho 0.71735 11 0.065 12.% + LOOP_ions force_stress 0.47987 1 0.48 7.9% + Force_Stress_LCAO getForceStress 0.47984 1 0.48 7.9% + Force_LCAO_gamma ftable_gamma 0.26824 1 0.27 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:06 2022 + Finish Time : Wed Sep 28 11:11:12 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..00f0c5e4c7faefce328ed9d7be5540ecb3b670be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012351 ima = 3.6994e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123745084204 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112427072867 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113070623801 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113297431834 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113259965072 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113282279348 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113274628916 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113277422021 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113276714389 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113276665909 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113276649547 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113276644766 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0f0924c5d92a4fd4c342bd0eec0046a44f72f78f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.507186405955 21.856086188958 12.714209467001 0 0 0 +H +0.0 +2 +-14.665485791816 21.460919229980 14.489734797856 0 0 0 +-16.219314972159 21.694429320267 11.952666663032 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/conv new file mode 100644 index 0000000000000000000000000000000000000000..c85b9c5996ca2bc1615612098c5d563bfb50773c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/conv @@ -0,0 +1 @@ +46 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0f9eb833e6861e0f31f6715c7dee3dad5e42bb19 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746635421 0.01253798114 1.263779048 1.359251581 1.468567026 0.007982947553 0.01926682579 0.03896171404 +4.064883529e-18 0.001044966018 0.002397062029 0.01189639551 0.04249537324 -1.023408533e-19 1.577559432e-06 4.939225261e-06 +0.001702722553 0.005764572028 + +H atom_index 1 n_descriptor 18 +1.248955979 0.03398193956 0.1074113792 0.1503304597 0.3221613963 0.02180210414 0.02836364054 0.03720182803 +-6.889756338e-18 3.971816522e-05 0.1003459848 0.1149827853 0.128979194 5.683910295e-18 4.181414206e-06 0.01301180765 +0.02582473599 0.03077264091 + +H atom_index 2 n_descriptor 18 +1.205238037 0.03548639669 0.09331918635 0.131194178 0.307296807 0.01983756368 0.02581935678 0.03881562665 +2.357152146e-17 3.610073971e-05 0.08884898273 0.1123008064 0.1137258107 7.739355498e-18 5.95762968e-06 0.01378443026 +0.02411084349 0.02865028288 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ea7fd6f670af7907671dca8cc7649f76b11c34c4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:06 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871397 SEC) : SETUP UNITCELL + DONE(0.0975191 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115639 SEC) : INIT PLANEWAVE + DONE(0.164671 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446451 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651665e+02 0.000000e+00 2.150e-01 4.461e-01 + GE2 -4.664009e+02 -1.234426e+00 9.868e-02 3.720e-01 + GE3 -4.664067e+02 -5.778369e-03 6.353e-02 4.242e-01 + GE4 -4.664060e+02 6.526641e-04 2.042e-03 3.140e-01 + GE5 -4.664053e+02 7.421152e-04 9.746e-04 3.181e-01 + GE6 -4.664057e+02 -3.826796e-04 1.902e-04 3.083e-01 + GE7 -4.664055e+02 1.387236e-04 3.717e-05 2.975e-01 + GE8 -4.664056e+02 -5.936865e-05 1.674e-05 2.929e-01 + GE9 -4.664056e+02 1.881419e-05 1.529e-06 2.907e-01 + GE10 -4.664056e+02 -3.398531e-06 3.881e-07 2.916e-01 + GE11 -4.664056e+02 -1.964562e-07 1.012e-07 2.916e-01 + GE12 -4.664056e+02 -6.154383e-08 1.033e-08 2.313e-01 +E_delta_band = -6.93987853e-02 Ry = -9.44218914e-01 eV +E_delta_NN= -1.94277820e-01 Ry = -2.64328534e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0639 11 0.55 1e+02 % + Run_lcao lcao_line 6.0539 1 6.1 1e+02 % + Potential init_pot 0.28686 2 0.14 4.7 % + PW_Basis recip2real 0.27787 17 0.016 4.6 % + PW_Basis gathers_scatterp 0.12684 17 0.0075 2.1 % + Potential v_of_rho 0.92443 14 0.066 15 % + XC_Functional v_xc 0.25534 15 0.017 4.2 % + H_Hartree_pw v_hartree 0.63126 14 0.045 10 % + PW_Basis real2recip 0.60604 41 0.015 10 % + PW_Basis gatherp_scatters 0.24517 41 0.006 4 % + ORB_control set_orb_tables 1.1116 1 1.1 18 % + ORB_gen_tables gen_tables 1.1116 1 1.1 18 % + ORB_table_phi init_Table 0.48877 1 0.49 8.1 % + ORB_table_phi cal_ST_Phi12_R 0.48378 126 0.0038 8 % + ORB_table_beta init_Table_Beta 0.18903 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18753 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.25393 1 0.25 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.25201 66 0.0038 4.2 % + LOOP_ions opt_ions 4.4196 1 4.4 73 % + ESolver_KS_LCAO Run 3.9395 1 3.9 65 % + HSolverLCAO solve 1.7949 12 0.15 30 % + HamiltLCAO updateHk 0.96842 12 0.081 16 % + LCAO_Hamilt cal_Hgamma 0.93774 12 0.078 15 % + Gint_Gamma distri_vl_value 0.56635 12 0.047 9.3 % + Gint_Gamma distri_vl 2.0638 6 0.34 34 % + LCAO_Deepks cal_projected_DM 4.099 14 0.29 68 % + LCAO_gen_fixedH add_v_delta 1.9331 6 0.32 32 % + LCAO_DESCRIPTOR add_v_delta 1.9331 6 0.32 32 % + ElecStateLCAO psiToRho 0.80645 12 0.067 13 % + Charge mix_rho 0.71735 11 0.065 12 % + LOOP_ions force_stress 0.47987 1 0.48 7.9 % + Force_Stress_LCAO getForceStress 0.47984 1 0.48 7.9 % + Force_LCAO_gamma ftable_gamma 0.26824 1 0.27 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:06 2022 + FINISH Time : Wed Sep 28 11:11:12 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/46/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..1db6de7d508981b32b84230c7ba183d126706885 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.475153 0.798292 0.45203 +H 0.437628 0.841975 0.48003 +H 0.430531 0.757533 0.431565 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..860fb72f7d388077231aadf90c33c01e3832acc8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6658 2 + 2 -13.0377 2 + 3 -9.39477 2 + 4 -6.82686 2 + 5 1.49178 0 + 6 4.79491 0 + 7 11.0009 0 + 8 11.2752 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..2f9ac606f239d5f58a919933fb798bcb6e56a879 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/running_scf.log @@ -0,0 +1,777 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:34 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.3042737404 22.3521634657 12.6568438135 0 0 0 0 + tauc_H1 12.2535705574 23.5753076704 13.440848451 0 0 0 0 + tauc_H2 12.0548721748 21.2109159668 12.0838212201 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105931090665 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.106328504219 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.12446270853 (SEC) + + DONE : INIT CHARGE Time : 0.167818688221 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450628 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 10 + nCol_in_proc = 10 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 10 + nCol_in_proc = 8 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 8 + nCol_in_proc = 10 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 8 + nCol_in_proc = 8 +receiver_size is 324 ; receiver_size of each process is: +100 80 80 64 +sender_size is 388 ; sender_size of each process is: +100 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00117 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00121 + + Density error is 0.216799076854 + + Energy Rydberg eV + E_KohnSham -34.1861916432 -465.126999267 + E_Harris -34.3828061834 -467.802077324 + E_Fermi -0.423684008054 -5.76451666102 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00129981781049 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00113292541663 + + Density error is 0.0970828307866 + + Energy Rydberg eV + E_KohnSham -34.2766178761 -466.357311283 + E_Harris -34.2832917255 -466.448113662 + E_Fermi -0.231127831345 -3.14465547268 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00121269556284 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00105470416265 + + Density error is 0.0619028966214 + + Energy Rydberg eV + E_KohnSham -34.2768228254 -466.360099762 + E_Harris -34.2810920713 -466.418185833 + E_Fermi -0.216429556597 -2.94467518534 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107375621188 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00093387352221 + + Density error is 0.00204119255532 + + Energy Rydberg eV + E_KohnSham -34.2768728797 -466.360780786 + E_Harris -34.2768751323 -466.360811433 + E_Fermi -0.180440473483 -2.45501858918 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107507182943 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000934687865568 + + Density error is 0.00090811421992 + + Energy Rydberg eV + E_KohnSham -34.276795149 -466.359723206 + E_Harris -34.2767981076 -466.359763459 + E_Fermi -0.17921288794 -2.43831643102 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107325301484 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000933334948843 + + Density error is 0.000113495945681 + + Energy Rydberg eV + E_KohnSham -34.2768521169 -466.360498293 + E_Harris -34.2768521446 -466.36049867 + E_Fermi -0.179554440798 -2.44296349606 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107288066469 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000933203874101 + + Density error is 4.29254101567e-05 + + Energy Rydberg eV + E_KohnSham -34.2768335624 -466.360245847 + E_Harris -34.2768335729 -466.36024599 + E_Fermi -0.17941903097 -2.44112115083 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107290444917 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000933221546392 + + Density error is 2.40212081135e-05 + + Energy Rydberg eV + E_KohnSham -34.2768363379 -466.360283609 + E_Harris -34.2768363402 -466.360283641 + E_Fermi -0.179484392495 -2.44201044 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107287627759 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000933202140634 + + Density error is 1.70889924873e-06 + + Energy Rydberg eV + E_KohnSham -34.2768346473 -466.360260607 + E_Harris -34.2768346473 -466.360260607 + E_Fermi -0.179456798697 -2.44163500712 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107287645203 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000933200046177 + + Density error is 1.77344372836e-07 + + Energy Rydberg eV + E_KohnSham -34.276834995 -466.360265338 + E_Harris -34.276834995 -466.360265338 + E_Fermi -0.179455365581 -2.44161550858 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107287721323 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000933200649285 + + Density error is 3.47312520468e-08 + + Energy Rydberg eV + E_KohnSham -34.2768350257 -466.360265756 + E_Harris -34.2768350257 -466.360265756 + E_band -8.07383943079 -109.850220996 + E_one_elec -69.8704575515 -950.636344567 + E_Hartree +36.3042366783 +493.944480365 + E_xc -8.25233074398 -112.278719899 + E_Ewald +7.66481852357 +104.285206057 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195934259302 -2.66582235991 + E_Fermi -0.179455426134 -2.44161633244 + + charge density convergence is achieved + final etot is -466.360265756 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6658 2.00000 + 2 -13.0377 2.00000 + 3 -9.39477 2.00000 + 4 -6.82686 2.00000 + 5 1.49178 0.00000 + 6 4.79491 0.00000 + 7 11.0009 0.00000 + 8 11.2752 0.00000 + + EFERMI = -2.441616332442680 eV + OUT.ABACUS/ final etot is -466.3602657560083 eV + correction force for each atom along direction 1 is -3.25212e-05 + correction force for each atom along direction 2 is -6.20572e-05 + correction force for each atom along direction 3 is 0.000105025 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.4412891 +0.085763948 -0.045717906 + H1 -0.53665901 +1.3342399 +0.80846555 + H2 -0.90463014 -1.4200039 -0.76274764 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3602657560083 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1857 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1765 1 7.2 1.e+02% + Potential init_pot 0.28447 2 0.14 4.0% + PW_Basis recip2real 0.25587 16 0.016 3.6% + PW_Basis gathers_scatterp 0.11595 16 0.0072 1.6% + Potential v_of_rho 0.93170 13 0.072 13.% + XC_Functional v_xc 0.32462 14 0.023 4.5% + H_Hartree_pw v_hartree 0.56936 13 0.044 7.9% + PW_Basis real2recip 0.66251 38 0.017 9.2% + PW_Basis gatherp_scatters 0.27464 38 0.0072 3.8% + ORB_control set_orb_tables 1.0964 1 1.1 15.% + ORB_gen_tables gen_tables 1.0964 1 1.1 15.% + ORB_table_phi init_Table 0.47614 1 0.48 6.6% + ORB_table_phi cal_ST_Phi12_R 0.47088 126 0.0037 6.6% + ORB_table_beta init_Table_Beta 0.18382 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18225 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24665 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24472 66 0.0037 3.4% + LOOP_ions opt_ions 5.5494 1 5.5 77.% + ESolver_KS_LCAO Run 5.0061 1 5.0 70.% + HSolverLCAO solve 2.7136 11 0.25 38.% + HamiltLCAO updateHk 1.3717 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.3442 11 0.12 19.% + Gint_Gamma distri_vl_value 0.90212 11 0.082 13.% + Gint_Gamma distri_vl 2.4089 6 0.40 34.% + LCAO_Deepks cal_projected_DM 5.1245 13 0.39 71.% + LCAO_gen_fixedH add_v_delta 2.2781 6 0.38 32.% + LCAO_DESCRIPTOR add_v_delta 2.2782 6 0.38 32.% + ElecStateLCAO psiToRho 1.3061 11 0.12 18.% + Charge mix_rho 0.80445 10 0.080 11.% + LOOP_ions force_stress 0.54304 1 0.54 7.6% + Force_Stress_LCAO getForceStress 0.54301 1 0.54 7.6% + Force_LCAO_gamma ftable_gamma 0.34561 1 0.35 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:34 2022 + Finish Time : Wed Sep 28 11:12:41 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b88da85ac4fc85bc704782d03936e0b240eef76d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123951 ima = 3.68638e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122418201588 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111593636559 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112013877743 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112314268704 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112232268312 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112277724862 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112274448103 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112277577049 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112276615207 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112276541205 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112276535139 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b23066f3ba14ee330fe8bc6166f65eac5768efc5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.695726259602 22.352163465687 12.656843813542 0 0 0 +H +0.0 +2 +-15.746429442631 23.575307670394 13.440848451003 0 0 0 +-15.945127825196 21.210915966857 12.083821220084 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/conv new file mode 100644 index 0000000000000000000000000000000000000000..75ddfecc81453fa379e09d13b8d82854156d2045 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/conv @@ -0,0 +1 @@ +47 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..18b87fad0bfeac7b724c29441967252e4a887c82 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752947527 0.01291804382 1.293917702 1.374030342 1.470923266 0.009446863987 0.01774222923 0.03912147296 +4.38360448e-19 0.001069047774 0.00298147078 0.01384252659 0.04959867277 -8.719271089e-21 3.077972531e-06 7.828971981e-06 +0.0016016375 0.006132790203 + +H atom_index 1 n_descriptor 18 +1.280131678 0.03375102724 0.1220961063 0.1640624356 0.3287391209 0.02467859054 0.02998052715 0.03705845519 +-2.298265471e-17 5.785850827e-05 0.1088954617 0.1202771001 0.1409372833 7.249628142e-18 1.721474573e-06 0.01346138902 +0.02854237283 0.03205735181 + +H atom_index 2 n_descriptor 18 +1.285152402 0.03359489963 0.124060724 0.1666224059 0.330207635 0.02492458742 0.03026892828 0.03698065108 +-2.434854396e-17 5.834675262e-05 0.1089728869 0.1216443024 0.143106612 3.167039982e-18 1.461709858e-06 0.01353310948 +0.02870350495 0.03225128588 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..86cc0d5456318e37f55a9a81f18a5187f7656eea Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/log.scf @@ -0,0 +1,100 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:34 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105954 SEC) : SETUP UNITCELL + DONE(0.106344 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124484 SEC) : INIT PLANEWAVE + DONE(0.167949 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450695 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651270e+02 0.000000e+00 2.168e-01 5.435e-01 + GE2 -4.663573e+02 -1.230312e+00 9.708e-02 5.046e-01 + GE3 -4.663601e+02 -2.788479e-03 6.190e-02 5.750e-01 + GE4 -4.663608e+02 -6.810237e-04 2.041e-03 4.346e-01 + GE5 -4.663597e+02 1.057580e-03 9.081e-04 4.333e-01 + GE6 -4.663605e+02 -7.750872e-04 1.135e-04 4.226e-01 + GE7 -4.663602e+02 2.524463e-04 4.293e-05 4.269e-01 + GE8 -4.663603e+02 -3.776263e-05 2.402e-05 4.151e-01 + GE9 -4.663603e+02 2.300197e-05 1.709e-06 4.162e-01 + GE10 -4.663603e+02 -4.731211e-06 1.773e-07 4.145e-01 + GE11 -4.663603e+02 -4.176146e-07 3.473e-08 3.509e-01 +E_delta_band = -7.28323272e-02 Ry = -9.90934648e-01 eV +E_delta_NN= -1.95934259e-01 Ry = -2.66582236e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1857 11 0.65 1e+02 % + Run_lcao lcao_line 7.1765 1 7.2 1e+02 % + Potential init_pot 0.28447 2 0.14 4 % + PW_Basis recip2real 0.25587 16 0.016 3.6 % + PW_Basis gathers_scatterp 0.11595 16 0.0072 1.6 % + Potential v_of_rho 0.9317 13 0.072 13 % + XC_Functional v_xc 0.32462 14 0.023 4.5 % + H_Hartree_pw v_hartree 0.56936 13 0.044 7.9 % + PW_Basis real2recip 0.66251 38 0.017 9.2 % + PW_Basis gatherp_scatters 0.27464 38 0.0072 3.8 % + ORB_control set_orb_tables 1.0964 1 1.1 15 % + ORB_gen_tables gen_tables 1.0964 1 1.1 15 % + ORB_table_phi init_Table 0.47614 1 0.48 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.47088 126 0.0037 6.6 % + ORB_table_beta init_Table_Beta 0.18382 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18225 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24665 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24472 66 0.0037 3.4 % + LOOP_ions opt_ions 5.5494 1 5.5 77 % + ESolver_KS_LCAO Run 5.0061 1 5 70 % + HSolverLCAO solve 2.7136 11 0.25 38 % + HamiltLCAO updateHk 1.3717 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.3442 11 0.12 19 % + Gint_Gamma distri_vl_value 0.90212 11 0.082 13 % + Gint_Gamma distri_vl 2.4089 6 0.4 34 % + LCAO_Deepks cal_projected_DM 5.1245 13 0.39 71 % + LCAO_gen_fixedH add_v_delta 2.2781 6 0.38 32 % + LCAO_DESCRIPTOR add_v_delta 2.2782 6 0.38 32 % + ElecStateLCAO psiToRho 1.3061 11 0.12 18 % + Charge mix_rho 0.80445 10 0.08 11 % + LOOP_ions force_stress 0.54304 1 0.54 7.6 % + Force_Stress_LCAO getForceStress 0.54301 1 0.54 7.6 % + Force_LCAO_gamma ftable_gamma 0.34561 1 0.35 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:34 2022 + FINISH Time : Wed Sep 28 11:12:41 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/47/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3fb0f8f17f5194732be0cc655580cbc20d673822 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.460964 0.806224 0.466878 +H 0.405743 0.841779 0.466998 +H 0.455174 0.759447 0.420212 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..efddb315d609c2b90837d84ebbafcbd2d4e873ae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1245 2 + 2 -13.1559 2 + 3 -8.90386 2 + 4 -6.70524 2 + 5 1.23852 0 + 6 4.32305 0 + 7 11.1036 0 + 8 11.3368 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a09b59d70e34071d007125faf4ce02c62a67efee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:01 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.9070030716 22.5742741639 13.0725842809 0 0 0 0 + tauc_H1 11.3608164671 23.5697996244 13.0759543356 0 0 0 0 + tauc_H2 12.7448630247 21.264502567 11.7659498142 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0736178189493 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0739348250738 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.090269939254 (SEC) + + DONE : INIT CHARGE Time : 0.131921622461 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.379156 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000606 + + Density error is 0.214414656694 + + Energy Rydberg eV + E_KohnSham -34.1915165391 -465.199448193 + E_Harris -34.3818337788 -467.78884708 + E_Fermi -0.399247680213 -5.43204336419 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00129295080604 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000819120259755 + + Density error is 0.0983352227221 + + Energy Rydberg eV + E_KohnSham -34.2804644153 -466.409646134 + E_Harris -34.2872271979 -466.501658512 + E_Fermi -0.208031691988 -2.83041637562 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121300834081 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000794230148859 + + Density error is 0.0631812895943 + + Energy Rydberg eV + E_KohnSham -34.2807299323 -466.413258678 + E_Harris -34.2850847812 -466.472509438 + E_Fermi -0.197753529203 -2.69057479677 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107481183453 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000769929512074 + + Density error is 0.00205490402387 + + Energy Rydberg eV + E_KohnSham -34.2807020095 -466.412878769 + E_Harris -34.2807049222 -466.412918398 + E_Fermi -0.162546327417 -2.21155624184 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107241029763 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000769782347569 + + Density error is 0.000866370885645 + + Energy Rydberg eV + E_KohnSham -34.2806543628 -466.412230502 + E_Harris -34.2806551144 -466.412240729 + E_Fermi -0.1619277226 -2.20313969152 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107071596199 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000769439827525 + + Density error is 0.000192216221928 + + Energy Rydberg eV + E_KohnSham -34.2806829459 -466.412619396 + E_Harris -34.2806828546 -466.412618153 + E_Fermi -0.161799194695 -2.20139097966 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107082013762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000769727332212 + + Density error is 3.49964783173e-05 + + Energy Rydberg eV + E_KohnSham -34.2806718475 -466.412468395 + E_Harris -34.2806718535 -466.412468476 + E_Fermi -0.16168880055 -2.19988899027 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107076860878 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000769656352397 + + Density error is 1.68447231875e-05 + + Energy Rydberg eV + E_KohnSham -34.2806765132 -466.412531874 + E_Harris -34.2806765144 -466.41253189 + E_Fermi -0.161724652696 -2.20037678374 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107074788615 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000769661716682 + + Density error is 2.11201845403e-06 + + Energy Rydberg eV + E_KohnSham -34.280675173 -466.41251364 + E_Harris -34.280675173 -466.41251364 + E_Fermi -0.161707268836 -2.20014026419 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107074567192 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000769663610245 + + Density error is 4.69713565561e-07 + + Energy Rydberg eV + E_KohnSham -34.2806754196 -466.412516995 + E_Harris -34.2806754196 -466.412516995 + E_Fermi -0.161705369255 -2.20011441907 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107074597168 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00076966410117 + + Density error is 1.5697066616e-07 + + Energy Rydberg eV + E_KohnSham -34.2806754385 -466.412517252 + E_Harris -34.2806754385 -466.412517252 + E_Fermi -0.16170515566 -2.20011151296 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107074587553 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000769664254021 + + Density error is 9.9698669264e-09 + + Energy Rydberg eV + E_KohnSham -34.2806754421 -466.412517302 + E_Harris -34.2806754421 -466.412517302 + E_band -7.92159954916 -107.778891143 + E_one_elec -69.0954902876 -940.092374015 + E_Hartree +35.9555753499 +489.200699627 + E_xc -8.19578483872 -111.509373389 + E_Ewald +7.17979492287 +97.6861214225 + E_demet -5.0280075915e-72 -6.84095528317e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194347039969 -2.64422713301 + E_Fermi -0.161705003441 -2.20010944191 + + charge density convergence is achieved + final etot is -466.412517302 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1245 2.00000 + 2 -13.1559 2.00000 + 3 -8.90386 2.00000 + 4 -6.70524 2.00000 + 5 1.23852 0.00000 + 6 4.32305 0.00000 + 7 11.1036 0.00000 + 8 11.3368 0.00000 + + EFERMI = -2.200109441912931 eV + OUT.ABACUS/ final etot is -466.4125173017968 eV + correction force for each atom along direction 1 is -6.38041e-05 + correction force for each atom along direction 2 is -8.82629e-05 + correction force for each atom along direction 3 is 3.55788e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.36069669 -0.26910665 -0.026869893 + H1 -0.13221073 -0.15038876 -0.22118428 + H2 -0.22848597 +0.41949541 +0.24805417 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4125173017968 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3846 11 0.58 1.0e+02% + Run_lcao lcao_line 6.3771 1 6.4 1.e+02% + Potential init_pot 0.24811 2 0.12 3.9% + PW_Basis recip2real 0.24702 17 0.015 3.9% + PW_Basis gathers_scatterp 0.11968 17 0.0070 1.9% + Potential v_of_rho 0.96571 14 0.069 15.% + XC_Functional v_xc 0.30744 15 0.020 4.8% + H_Hartree_pw v_hartree 0.62370 14 0.045 9.8% + PW_Basis real2recip 0.66045 41 0.016 10.% + PW_Basis gatherp_scatters 0.30055 41 0.0073 4.7% + ORB_control set_orb_tables 0.90390 1 0.90 14.% + ORB_gen_tables gen_tables 0.90390 1 0.90 14.% + ORB_table_phi init_Table 0.37763 1 0.38 5.9% + ORB_table_phi cal_ST_Phi12_R 0.37332 126 0.0030 5.8% + ORB_table_beta init_Table_Beta 0.15643 1 0.16 2.5% + ORB_table_beta VNL_PhiBeta_R 0.15514 56 0.0028 2.4% + ORB_table_alpha init_Table_Alpha 0.21150 1 0.21 3.3% + ORB_table_alpha S_PhiAlpha_R 0.20982 66 0.0032 3.3% + LOOP_ions opt_ions 5.0246 1 5.0 79.% + ESolver_KS_LCAO Run 4.5287 1 4.5 71.% + HSolverLCAO solve 2.1481 12 0.18 34.% + HamiltLCAO updateHk 1.1391 12 0.095 18.% + LCAO_Hamilt cal_Hgamma 1.1135 12 0.093 17.% + Gint_Gamma distri_vl_value 0.70068 12 0.058 11.% + Gint_Gamma distri_vl 2.3677 6 0.39 37.% + LCAO_Deepks cal_projected_DM 4.6674 14 0.33 73.% + LCAO_gen_fixedH add_v_delta 2.2343 6 0.37 35.% + LCAO_DESCRIPTOR add_v_delta 2.2344 6 0.37 35.% + ElecStateLCAO psiToRho 0.99180 12 0.083 16.% + Charge mix_rho 0.82110 11 0.075 13.% + LOOP_ions force_stress 0.49572 1 0.50 7.8% + Force_Stress_LCAO getForceStress 0.49571 1 0.50 7.8% + Force_LCAO_gamma ftable_gamma 0.29917 1 0.30 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:01 2022 + Finish Time : Wed Sep 28 11:08:08 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a822b5ecbce4a9238267f497c9af9eff10e98a99 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123384 ima = 3.7104e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123595982153 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112611144965 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113169502546 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113382433597 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113346894367 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113369860798 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113361264945 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113363926239 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113363220098 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113363158493 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113363141077 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113363133245 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a736d70f83f01bb1f53632565d2f09489268e577 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.092996928410 22.574274163908 13.072584280932 0 0 0 +H +0.0 +2 +-16.639183532851 23.569799624432 13.075954335543 0 0 0 +-15.255136975315 21.264502566988 11.765949814194 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/conv new file mode 100644 index 0000000000000000000000000000000000000000..535aedaebef530444094f41923dcc9cc590a181f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/conv @@ -0,0 +1 @@ +48 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a6b35021aa280a7fa31fc9497fae1e3b73d8c83f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745827068 0.01255768726 1.267936341 1.361313007 1.468589028 0.007871944669 0.01954884108 0.03892635273 +-2.605651754e-18 0.001070182284 0.002380678781 0.01199461758 0.04241502076 3.618692431e-20 1.551938444e-06 4.866331937e-06 +0.001727519897 0.0057381633 + +H atom_index 1 n_descriptor 18 +1.237687111 0.03429414608 0.1037632334 0.145362116 0.3187628003 0.02128166494 0.02773443609 0.03748139946 +-1.342671161e-17 3.827373198e-05 0.09776874561 0.1145851773 0.1246956907 1.038866574e-18 4.703838003e-06 0.01308667971 +0.02543994564 0.03027476075 + +H atom_index 2 n_descriptor 18 +1.223181294 0.03480103488 0.09904353735 0.1389573168 0.3139001143 0.02063388524 0.02689083452 0.03801103187 +-2.139400083e-17 3.70827367e-05 0.09391632631 0.1142190044 0.1191206227 4.836816975e-18 5.306324811e-06 0.01332324234 +0.024875485 0.02957896994 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..30f4ed6514213804889c323e1984ca78fdb9d56c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:01 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.073634 SEC) : SETUP UNITCELL + DONE(0.0739442 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0902842 SEC) : INIT PLANEWAVE + DONE(0.132028 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.379207 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651994e+02 0.000000e+00 2.144e-01 4.698e-01 + GE2 -4.664096e+02 -1.210198e+00 9.834e-02 4.275e-01 + GE3 -4.664133e+02 -3.612544e-03 6.318e-02 4.885e-01 + GE4 -4.664129e+02 3.799089e-04 2.055e-03 3.661e-01 + GE5 -4.664122e+02 6.482671e-04 8.664e-04 3.657e-01 + GE6 -4.664126e+02 -3.888939e-04 1.922e-04 3.586e-01 + GE7 -4.664125e+02 1.510014e-04 3.500e-05 3.484e-01 + GE8 -4.664125e+02 -6.347945e-05 1.684e-05 3.405e-01 + GE9 -4.664125e+02 1.823464e-05 2.112e-06 3.458e-01 + GE10 -4.664125e+02 -3.355447e-06 4.697e-07 3.448e-01 + GE11 -4.664125e+02 -2.570457e-07 1.570e-07 3.444e-01 + GE12 -4.664125e+02 -4.965018e-08 9.970e-09 2.747e-01 +E_delta_band = -6.95764513e-02 Ry = -9.46636185e-01 eV +E_delta_NN= -1.94347040e-01 Ry = -2.64422713e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3846 11 0.58 1e+02 % + Run_lcao lcao_line 6.3771 1 6.4 1e+02 % + Potential init_pot 0.24811 2 0.12 3.9 % + PW_Basis recip2real 0.24702 17 0.015 3.9 % + PW_Basis gathers_scatterp 0.11968 17 0.007 1.9 % + Potential v_of_rho 0.96571 14 0.069 15 % + XC_Functional v_xc 0.30744 15 0.02 4.8 % + H_Hartree_pw v_hartree 0.6237 14 0.045 9.8 % + PW_Basis real2recip 0.66045 41 0.016 10 % + PW_Basis gatherp_scatters 0.30055 41 0.0073 4.7 % + ORB_control set_orb_tables 0.9039 1 0.9 14 % + ORB_gen_tables gen_tables 0.9039 1 0.9 14 % + ORB_table_phi init_Table 0.37763 1 0.38 5.9 % + ORB_table_phi cal_ST_Phi12_R 0.37332 126 0.003 5.8 % + ORB_table_beta init_Table_Beta 0.15643 1 0.16 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.15514 56 0.0028 2.4 % + ORB_table_alpha init_Table_Alpha 0.2115 1 0.21 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.20982 66 0.0032 3.3 % + LOOP_ions opt_ions 5.0246 1 5 79 % + ESolver_KS_LCAO Run 4.5287 1 4.5 71 % + HSolverLCAO solve 2.1481 12 0.18 34 % + HamiltLCAO updateHk 1.1391 12 0.095 18 % + LCAO_Hamilt cal_Hgamma 1.1135 12 0.093 17 % + Gint_Gamma distri_vl_value 0.70068 12 0.058 11 % + Gint_Gamma distri_vl 2.3677 6 0.39 37 % + LCAO_Deepks cal_projected_DM 4.6674 14 0.33 73 % + LCAO_gen_fixedH add_v_delta 2.2343 6 0.37 35 % + LCAO_DESCRIPTOR add_v_delta 2.2344 6 0.37 35 % + ElecStateLCAO psiToRho 0.9918 12 0.083 16 % + Charge mix_rho 0.8211 11 0.075 13 % + LOOP_ions force_stress 0.49572 1 0.5 7.8 % + Force_Stress_LCAO getForceStress 0.49571 1 0.5 7.8 % + Force_LCAO_gamma ftable_gamma 0.29917 1 0.3 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:01 2022 + FINISH Time : Wed Sep 28 11:08:08 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/48/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4cfa75132f208ee3e2d8847cfd6a85703af2f8c5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.447246 0.826739 0.478246 +H 0.38623 0.836808 0.503754 +H 0.437758 0.77106 0.442974 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f3ebd1ae7a25c6227bc8b2f1c95487fa7ff83948 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1331 2 + 2 -12.7391 2 + 3 -9.22611 2 + 4 -6.71272 2 + 5 1.11684 0 + 6 4.09584 0 + 7 11.1198 0 + 8 11.3843 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..193a3ef0e0d8874b22437b65e380e7387a805e47 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:43 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.5228756134 23.1486785725 13.3908946177 0 0 0 0 + tauc_H1 10.8144275394 23.4306229232 14.1051109734 0 0 0 0 + tauc_H2 12.2572114804 21.5896838347 12.4032715959 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.114743138466 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.11529468327 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.14601266514 (SEC) + + DONE : INIT CHARGE Time : 0.196789409219 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.492309 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 1 + Local orbitals number in sub-FFT-grid = 5 + lgd_last = 0 + lgd_now = 5 + allocate DM , the dimension is 5 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 3 + nCol_in_proc = 3 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 3 + nCol_in_proc = 2 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 2 + nCol_in_proc = 3 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 2 + nCol_in_proc = 2 +receiver_size is 25 ; receiver_size of each process is: +9 6 6 4 +sender_size is 297 ; sender_size of each process is: +9 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00141 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000604 + + Density error is 0.211892444045 + + Energy Rydberg eV + E_KohnSham -34.1923298645 -465.210514053 + E_Harris -34.377870837 -467.734928491 + E_Fermi -0.393292237182 -5.35101540484 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00137780925316 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000807451637914 + + Density error is 0.0983565166972 + + Energy Rydberg eV + E_KohnSham -34.2804290085 -466.4091644 + E_Harris -34.2874281245 -466.504392258 + E_Fermi -0.203862655013 -2.77369371759 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0012822044538 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000779386354155 + + Density error is 0.0633823661103 + + Energy Rydberg eV + E_KohnSham -34.2807884435 -466.414054764 + E_Harris -34.2853023592 -466.475469738 + E_Fermi -0.195731973849 -2.66307012514 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00111012820256 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000754983413971 + + Density error is 0.00193563088193 + + Energy Rydberg eV + E_KohnSham -34.2807175037 -466.413089579 + E_Harris -34.2807182064 -466.41309914 + E_Fermi -0.16033437813 -2.18146112785 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00110900418304 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755070368374 + + Density error is 0.000902986746252 + + Energy Rydberg eV + E_KohnSham -34.2806768032 -466.41253582 + E_Harris -34.2806772629 -466.412542075 + E_Fermi -0.160130573876 -2.17868822873 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00110676131882 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000754864354497 + + Density error is 0.000147195929449 + + Energy Rydberg eV + E_KohnSham -34.2806971324 -466.412812412 + E_Harris -34.2806971337 -466.412812431 + E_Fermi -0.159818229011 -2.17443855881 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00110676820461 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755091473136 + + Density error is 2.83097711294e-05 + + Energy Rydberg eV + E_KohnSham -34.2806912689 -466.412732636 + E_Harris -34.2806912718 -466.412732675 + E_Fermi -0.159753830721 -2.17356237514 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00110671215111 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.00075503003579 + + Density error is 1.39289986937e-05 + + Energy Rydberg eV + E_KohnSham -34.280693698 -466.412765685 + E_Harris -34.2806936989 -466.412765697 + E_Fermi -0.159776104558 -2.17386542623 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00110669940076 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755038465521 + + Density error is 2.22683114749e-06 + + Energy Rydberg eV + E_KohnSham -34.2806925968 -466.412750703 + E_Harris -34.2806925968 -466.412750703 + E_Fermi -0.159763091623 -2.17368837617 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00110669484145 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755040126242 + + Density error is 4.249442757e-07 + + Energy Rydberg eV + E_KohnSham -34.2806928262 -466.412753825 + E_Harris -34.2806928262 -466.412753824 + E_Fermi -0.159761050731 -2.1736606084 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00110669495332 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755040535904 + + Density error is 1.52443343612e-07 + + Energy Rydberg eV + E_KohnSham -34.2806928452 -466.412754082 + E_Harris -34.2806928452 -466.412754082 + E_Fermi -0.159760877529 -2.17365825187 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0011066947517 + number of non-zero elements in receiver_buffer = 25 + receiver_size = 25 + last receiver_buffer = 0.000755040709179 + + Density error is 1.11918608741e-08 + + Energy Rydberg eV + E_KohnSham -34.2806928486 -466.412754129 + E_Harris -34.2806928486 -466.412754129 + E_band -7.91007145583 -107.622043386 + E_one_elec -68.8758313572 -937.103760944 + E_Hartree +35.839349131 +487.619360793 + E_xc -8.17736286159 -111.258729531 + E_Ewald +7.05831931378 +96.0333609709 + E_demet -3.52981272009e-66 -4.80255658661e-65 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19408943868 -2.64072228767 + E_Fermi -0.159760739114 -2.17365636864 + + charge density convergence is achieved + final etot is -466.412754129 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1331 2.00000 + 2 -12.7391 2.00000 + 3 -9.22611 2.00000 + 4 -6.71272 2.00000 + 5 1.11684 0.00000 + 6 4.09584 0.00000 + 7 11.1198 0.00000 + 8 11.3843 0.00000 + + EFERMI = -2.173656368643045 eV + OUT.ABACUS/ final etot is -466.4127541287260 eV + correction force for each atom along direction 1 is -0.000163673 + correction force for each atom along direction 2 is 1.71987e-05 + correction force for each atom along direction 3 is -0.000120495 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.87926722 -0.41102258 -0.022807759 + H1 +0.65199935 +0.038169474 -0.16807602 + H2 +0.22726787 +0.37285311 +0.19088378 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4127541287260 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2802 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2702 1 7.3 1.e+02% + Potential init_pot 0.29452 2 0.15 4.0% + PW_Basis recip2real 0.27356 17 0.016 3.8% + PW_Basis gathers_scatterp 0.12261 17 0.0072 1.7% + Potential v_of_rho 1.0183 14 0.073 14.% + XC_Functional v_xc 0.35220 15 0.023 4.8% + H_Hartree_pw v_hartree 0.62524 14 0.045 8.6% + PW_Basis real2recip 0.73306 41 0.018 10.% + PW_Basis gatherp_scatters 0.31410 41 0.0077 4.3% + ORB_control set_orb_tables 1.0895 1 1.1 15.% + ORB_gen_tables gen_tables 1.0895 1 1.1 15.% + ORB_table_phi init_Table 0.47120 1 0.47 6.5% + ORB_table_phi cal_ST_Phi12_R 0.46591 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18145 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.17991 56 0.0032 2.5% + ORB_table_alpha init_Table_Alpha 0.24718 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24516 66 0.0037 3.4% + LOOP_ions opt_ions 5.6083 1 5.6 77.% + ESolver_KS_LCAO Run 5.0942 1 5.1 70.% + HSolverLCAO solve 2.5830 12 0.22 35.% + HamiltLCAO updateHk 1.3213 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2916 12 0.11 18.% + Gint_Gamma distri_vl_value 0.87079 12 0.073 12.% + Gint_Gamma distri_vl 2.6518 6 0.44 36.% + LCAO_Deepks cal_projected_DM 5.2195 14 0.37 72.% + LCAO_gen_fixedH add_v_delta 2.5161 6 0.42 35.% + LCAO_DESCRIPTOR add_v_delta 2.5162 6 0.42 35.% + ElecStateLCAO psiToRho 1.2289 12 0.10 17.% + Charge mix_rho 0.88660 11 0.081 12.% + LOOP_ions force_stress 0.51391 1 0.51 7.1% + Force_Stress_LCAO getForceStress 0.51388 1 0.51 7.1% + Force_LCAO_gamma ftable_gamma 0.31395 1 0.31 4.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:43 2022 + Finish Time : Wed Sep 28 11:08:50 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d9671251b71a232449981f592574580f43cb6a9c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123448 ima = 3.68982e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 1 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012315787958 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111852302494 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001125528056 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112767024865 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112740663809 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011275557067 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112751800544 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753930383 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011275326073 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753200243 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753183715 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753176344 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9d315b35091c6b27995216f1e984c714926e20b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.477124386670 23.148678572539 13.390894617666 0 0 0 +H +0.0 +2 +-17.185572460668 23.430622923168 14.105110973361 0 0 0 +-15.742788519590 21.589683834717 12.403271595897 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/conv new file mode 100644 index 0000000000000000000000000000000000000000..3742b6e94575489fb31c4d33f1aa26d0e6881bf4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/conv @@ -0,0 +1 @@ +49 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..984035d46c03d10081036adf080f1f30c29f8555 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751678601 0.01258189621 1.255493691 1.342650611 1.46862046 0.008799493082 0.01739235777 0.03912084069 +-3.04148632e-19 0.0009028549422 0.002563908751 0.01210254629 0.0436141359 -1.236089077e-19 2.030460391e-06 5.885905245e-06 +0.001598122772 0.006005326236 + +H atom_index 1 n_descriptor 18 +1.216543106 0.03565239299 0.09750304403 0.1349337571 0.3092997881 0.02081046709 0.02632324857 0.03891686766 +2.091000633e-17 4.130866886e-05 0.0916430133 0.1141521672 0.115486976 -1.058243275e-17 5.327593071e-06 0.01379558629 +0.02478253434 0.02910826637 + +H atom_index 2 n_descriptor 18 +1.223273936 0.03543029264 0.09965463436 0.1378254693 0.3117164136 0.02112977864 0.02671888642 0.03865522102 +-2.804107611e-17 4.190926428e-05 0.09340010112 0.1143927872 0.1180168058 5.422421251e-20 5.030745955e-06 0.0136447903 +0.02505346447 0.02944955872 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..cdb181eaade6e8c55bc4aa44840c971da3ddc2b6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:43 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.114783 SEC) : SETUP UNITCELL + DONE(0.115314 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.146039 SEC) : INIT PLANEWAVE + DONE(0.196942 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.492372 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652105e+02 0.000000e+00 2.119e-01 5.202e-01 + GE2 -4.664092e+02 -1.198650e+00 9.836e-02 4.791e-01 + GE3 -4.664141e+02 -4.890363e-03 6.338e-02 5.484e-01 + GE4 -4.664131e+02 9.651851e-04 1.936e-03 4.085e-01 + GE5 -4.664125e+02 5.537585e-04 9.030e-04 4.066e-01 + GE6 -4.664128e+02 -2.765923e-04 1.472e-04 4.029e-01 + GE7 -4.664127e+02 7.977651e-05 2.831e-05 3.896e-01 + GE8 -4.664128e+02 -3.304926e-05 1.393e-05 3.873e-01 + GE9 -4.664128e+02 1.498176e-05 2.227e-06 3.886e-01 + GE10 -4.664128e+02 -3.121188e-06 4.249e-07 3.873e-01 + GE11 -4.664128e+02 -2.574613e-07 1.524e-07 3.869e-01 + GE12 -4.664128e+02 -4.676155e-08 1.119e-08 3.192e-01 +E_delta_band = -6.89223640e-02 Ry = -9.37736871e-01 eV +E_delta_NN= -1.94089439e-01 Ry = -2.64072229e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2802 11 0.66 1e+02 % + Run_lcao lcao_line 7.2702 1 7.3 1e+02 % + Potential init_pot 0.29452 2 0.15 4 % + PW_Basis recip2real 0.27356 17 0.016 3.8 % + PW_Basis gathers_scatterp 0.12261 17 0.0072 1.7 % + Potential v_of_rho 1.0183 14 0.073 14 % + XC_Functional v_xc 0.3522 15 0.023 4.8 % + H_Hartree_pw v_hartree 0.62524 14 0.045 8.6 % + PW_Basis real2recip 0.73306 41 0.018 10 % + PW_Basis gatherp_scatters 0.3141 41 0.0077 4.3 % + ORB_control set_orb_tables 1.0895 1 1.1 15 % + ORB_gen_tables gen_tables 1.0895 1 1.1 15 % + ORB_table_phi init_Table 0.4712 1 0.47 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.46591 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18145 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.17991 56 0.0032 2.5 % + ORB_table_alpha init_Table_Alpha 0.24718 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24516 66 0.0037 3.4 % + LOOP_ions opt_ions 5.6083 1 5.6 77 % + ESolver_KS_LCAO Run 5.0942 1 5.1 70 % + HSolverLCAO solve 2.583 12 0.22 35 % + HamiltLCAO updateHk 1.3213 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.2916 12 0.11 18 % + Gint_Gamma distri_vl_value 0.87079 12 0.073 12 % + Gint_Gamma distri_vl 2.6518 6 0.44 36 % + LCAO_Deepks cal_projected_DM 5.2195 14 0.37 72 % + LCAO_gen_fixedH add_v_delta 2.5161 6 0.42 35 % + LCAO_DESCRIPTOR add_v_delta 2.5162 6 0.42 35 % + ElecStateLCAO psiToRho 1.2289 12 0.1 17 % + Charge mix_rho 0.8866 11 0.081 12 % + LOOP_ions force_stress 0.51391 1 0.51 7.1 % + Force_Stress_LCAO getForceStress 0.51388 1 0.51 7.1 % + Force_LCAO_gamma ftable_gamma 0.31395 1 0.31 4.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:43 2022 + FINISH Time : Wed Sep 28 11:08:50 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/49/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e14a4fc746df433013a171b76ee74df4502d231a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.629083 0.0816826 0.328946 +H 0.659581 0.0263009 0.310937 +H 0.650628 0.0937394 0.388941 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..fe2391bcd114fdbce0e719e867e76a72b9cff1bf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3059 2 + 2 -13.1063 2 + 3 -9.08654 2 + 4 -6.74823 2 + 5 1.33281 0 + 6 4.47107 0 + 7 11.0688 0 + 8 11.317 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..78c2a323ce45b63f9d1b0a24ee9908f74a6d8fde --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/running_scf.log @@ -0,0 +1,802 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.6143117056 2.28711407811 9.21047865046 0 0 0 0 + tauc_H1 18.4682724516 0.736424855524 8.70622348323 0 0 0 0 + tauc_H2 18.2175837765 2.62470268603 10.8903554136 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0867726247931 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0898444787213 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107884432073 (SEC) + + DONE : INIT CHARGE Time : 0.156110787479 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.436854 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000661 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000915 + + Density error is 0.214967182944 + + Energy Rydberg eV + E_KohnSham -34.1917371563 -465.202449844 + E_Harris -34.3834518485 -467.810862048 + E_Fermi -0.406843761667 -5.53539335442 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000973891471584 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011395357505 + + Density error is 0.0978631483487 + + Energy Rydberg eV + E_KohnSham -34.2809228967 -466.415884093 + E_Harris -34.2876208534 -466.507014469 + E_Fermi -0.215773948104 -2.93575517417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000935027646613 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109111924458 + + Density error is 0.0626709963111 + + Energy Rydberg eV + E_KohnSham -34.2811601148 -466.419111611 + E_Harris -34.2854812937 -466.477904267 + E_Fermi -0.203973484695 -2.77520163276 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000884493718243 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102903900405 + + Density error is 0.00200177727332 + + Energy Rydberg eV + E_KohnSham -34.281158341 -466.419087478 + E_Harris -34.2811595276 -466.419103623 + E_Fermi -0.168489582311 -2.29241837307 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000885937719439 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103151873885 + + Density error is 0.000859444914679 + + Energy Rydberg eV + E_KohnSham -34.2810999962 -466.418293656 + E_Harris -34.2811012102 -466.418310174 + E_Fermi -0.167684297371 -2.28146190937 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000885016206614 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010303350601 + + Density error is 0.000161100256733 + + Energy Rydberg eV + E_KohnSham -34.281138411 -466.418816316 + E_Harris -34.2811384663 -466.418817068 + E_Fermi -0.167727766561 -2.28205333804 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000885189319298 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103051492547 + + Density error is 3.76390685477e-05 + + Energy Rydberg eV + E_KohnSham -34.2811241167 -466.418621832 + E_Harris -34.281124124 -466.418621932 + E_Fermi -0.167593697735 -2.28022923809 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000885129757678 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103045514853 + + Density error is 1.61711569381e-05 + + Energy Rydberg eV + E_KohnSham -34.2811284292 -466.418680507 + E_Harris -34.2811284303 -466.418680522 + E_Fermi -0.167635597145 -2.28079930881 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000885132386075 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103045923783 + + Density error is 2.29977882344e-06 + + Energy Rydberg eV + E_KohnSham -34.2811270638 -466.418661929 + E_Harris -34.2811270638 -466.418661929 + E_Fermi -0.167619040848 -2.28057404883 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000885131793494 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103045705553 + + Density error is 3.1406206708e-07 + + Energy Rydberg eV + E_KohnSham -34.2811272774 -466.418664836 + E_Harris -34.2811272774 -466.418664836 + E_Fermi -0.167616689127 -2.28054205202 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000885132500501 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103045777807 + + Density error is 1.43930223404e-07 + + Energy Rydberg eV + E_KohnSham -34.2811273102 -466.418665282 + E_Harris -34.2811273102 -466.418665282 + E_Fermi -0.167616640656 -2.28054139254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000885132729274 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103045796788 + + Density error is 1.01113058932e-08 + + Energy Rydberg eV + E_KohnSham -34.2811273105 -466.418665286 + E_Harris -34.2811273105 -466.418665286 + E_band -7.97414832255 -108.493853884 + E_one_elec -69.3513280915 -943.573225912 + E_Hartree +36.0694454206 +490.749981421 + E_xc -8.21432257353 -111.76159221 + E_Ewald +7.33928883568 +99.856147433 + E_demet -2.98375750591e-79 -4.05961035307e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194897436115 -2.65171565675 + E_Fermi -0.167616506842 -2.2805395719 + + charge density convergence is achieved + final etot is -466.418665286 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3059 2.00000 + 2 -13.1063 2.00000 + 3 -9.08654 2.00000 + 4 -6.74823 2.00000 + 5 1.33281 0.00000 + 6 4.47107 0.00000 + 7 11.0688 0.00000 + 8 11.3170 0.00000 + + EFERMI = -2.280539571902854 eV + OUT.ABACUS/ final etot is -466.4186652862031 eV + correction force for each atom along direction 1 is 0.000129372 + correction force for each atom along direction 2 is -0.000105544 + correction force for each atom along direction 3 is 1.58423e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.28878563 -0.073932094 -0.68375459 + H1 +0.033274514 -0.039409885 +0.012457754 + H2 +0.25551111 +0.11334198 +0.67129683 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4186652862031 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0418 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0319 1 7.0 1.e+02% + Potential init_pot 0.29201 2 0.15 4.1% + PW_Basis recip2real 0.27978 17 0.016 4.0% + PW_Basis gathers_scatterp 0.12893 17 0.0076 1.8% + Charge atomic_rho 0.10008 1 0.10 1.4% + Potential v_of_rho 0.93010 14 0.066 13.% + XC_Functional v_xc 0.26040 15 0.017 3.7% + H_Hartree_pw v_hartree 0.63101 14 0.045 9.0% + PW_Basis real2recip 0.60836 41 0.015 8.6% + PW_Basis gatherp_scatters 0.24497 41 0.0060 3.5% + ORB_control set_orb_tables 1.1060 1 1.1 16.% + ORB_gen_tables gen_tables 1.1060 1 1.1 16.% + ORB_table_phi init_Table 0.48275 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47789 126 0.0038 6.8% + ORB_table_beta init_Table_Beta 0.18736 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18588 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.25501 1 0.26 3.6% + ORB_table_alpha S_PhiAlpha_R 0.25311 66 0.0038 3.6% + LOOP_ions opt_ions 5.4119 1 5.4 77.% + ESolver_KS_LCAO Run 4.8361 1 4.8 69.% + HSolverLCAO solve 2.7004 12 0.23 38.% + HamiltLCAO updateHk 1.3779 12 0.11 20.% + LCAO_Hamilt cal_Hgamma 1.3477 12 0.11 19.% + Gint_interface cal_gint 0.84628 25 0.034 12.% + Gint_Gamma distri_vl_value 0.65181 12 0.054 9.3% + Gint_Gamma distri_vl 2.5095 6 0.42 36.% + LCAO_Deepks cal_projected_DM 5.0594 14 0.36 72.% + LCAO_gen_fixedH add_v_delta 2.3782 6 0.40 34.% + LCAO_DESCRIPTOR add_v_delta 2.3782 6 0.40 34.% + ElecStateLCAO psiToRho 1.3015 12 0.11 18.% + Charge mix_rho 0.71482 11 0.065 10.% + LOOP_ions force_stress 0.57560 1 0.58 8.2% + Force_Stress_LCAO getForceStress 0.57557 1 0.58 8.2% + Force_LCAO_gamma ftable_gamma 0.36446 1 0.36 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.17938 1 0.18 2.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:48 2022 + Finish Time : Wed Sep 28 11:09:55 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b9aca5126f2b92b63789dca5f4ec169462cbb2c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123927 ima = 3.66994e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123054942395 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112114885529 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011262522829 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112867933112 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112816986219 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112848102994 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112840309298 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112843094125 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112842448669 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112842363398 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112842355214 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112842348324 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/STRU new file mode 100644 index 0000000000000000000000000000000000000000..426518e6c52d6b18ad106906b4d71d7c6664e2b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.385688294371 2.287114078091 9.210478650481 0 0 0 +H +0.0 +2 +-9.531727548378 0.736424855527 8.706223483226 0 0 0 +-9.782416223481 2.624702686053 10.890355413607 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/conv new file mode 100644 index 0000000000000000000000000000000000000000..610bd0e48c0d386007665636c587e7dfb006a570 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/conv @@ -0,0 +1 @@ +5 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..fe435c9d7a483bf828227bb0e52b6188925b9339 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748610949 0.01269731994 1.276234549 1.364830895 1.469393876 0.008411958305 0.01880936658 0.03900448661 +2.319967946e-19 0.001078600387 0.002585407219 0.01246778841 0.04508766944 -1.898999057e-19 1.997678946e-06 5.832828897e-06 +0.001665142866 0.005927139238 + +H atom_index 1 n_descriptor 18 +1.23916566 0.03453832543 0.1045991242 0.145171137 0.3177634181 0.02169616675 0.02770303722 0.03767459574 +1.898269858e-17 4.424318595e-05 0.09913309023 0.1145304862 0.1246129445 5.321441933e-18 4.729100547e-06 0.01324330845 +0.02590574135 0.03028427215 + +H atom_index 2 n_descriptor 18 +1.258292976 0.03387641019 0.1112047874 0.1540384885 0.3239307402 0.02257694628 0.02881557787 0.0370796593 +-2.894397073e-17 4.599904489e-05 0.1037389259 0.1154620859 0.1322703443 5.426399184e-18 3.712191618e-06 0.01309794348 +0.02661518476 0.03115087984 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c5caddcba2eedebc6db5598b585a8ff874c8ff63 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/e_base.npy 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diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..04752224477180418ebcae4816fa2d5dae385e7d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..2fc77ea0ee1ac987d506156674cec5641773813a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..517a9f5d766a191d893729ec2f595bd633a26179 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..e55009b39f1c5e7b567b7e001d6738b0fa15efb7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/log.scf @@ -0,0 +1,104 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0867954 SEC) : SETUP UNITCELL + DONE(0.089862 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107905 SEC) : INIT PLANEWAVE + DONE(0.15624 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.436923 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652024e+02 0.000000e+00 2.150e-01 5.182e-01 + GE2 -4.664159e+02 -1.213434e+00 9.786e-02 4.477e-01 + GE3 -4.664191e+02 -3.227518e-03 6.267e-02 4.966e-01 + GE4 -4.664191e+02 2.413286e-05 2.002e-03 3.894e-01 + GE5 -4.664183e+02 7.938225e-04 8.594e-04 3.905e-01 + GE6 -4.664188e+02 -5.226602e-04 1.611e-04 3.811e-01 + GE7 -4.664186e+02 1.944838e-04 3.764e-05 3.756e-01 + GE8 -4.664187e+02 -5.867513e-05 1.617e-05 3.641e-01 + GE9 -4.664187e+02 1.857817e-05 2.300e-06 3.675e-01 + GE10 -4.664187e+02 -2.906605e-06 3.141e-07 3.680e-01 + GE11 -4.664187e+02 -4.458362e-07 1.439e-07 3.645e-01 + GE12 -4.664187e+02 -4.679326e-09 1.011e-08 3.118e-01 +E_delta_band = -7.06865343e-02 Ry = -9.61739639e-01 eV +E_delta_NN= -1.94897436e-01 Ry = -2.65171566e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0418 11 0.64 1e+02 % + Run_lcao lcao_line 7.0319 1 7 1e+02 % + Potential init_pot 0.29201 2 0.15 4.1 % + PW_Basis recip2real 0.27978 17 0.016 4 % + PW_Basis gathers_scatterp 0.12893 17 0.0076 1.8 % + Charge atomic_rho 0.10008 1 0.1 1.4 % + Potential v_of_rho 0.9301 14 0.066 13 % + XC_Functional v_xc 0.2604 15 0.017 3.7 % + H_Hartree_pw v_hartree 0.63101 14 0.045 9 % + PW_Basis real2recip 0.60836 41 0.015 8.6 % + PW_Basis gatherp_scatters 0.24497 41 0.006 3.5 % + ORB_control set_orb_tables 1.106 1 1.1 16 % + ORB_gen_tables gen_tables 1.106 1 1.1 16 % + ORB_table_phi init_Table 0.48275 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47789 126 0.0038 6.8 % + ORB_table_beta init_Table_Beta 0.18736 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18588 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.25501 1 0.26 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.25311 66 0.0038 3.6 % + LOOP_ions opt_ions 5.4119 1 5.4 77 % + ESolver_KS_LCAO Run 4.8361 1 4.8 69 % + HSolverLCAO solve 2.7004 12 0.23 38 % + HamiltLCAO updateHk 1.3779 12 0.11 20 % + LCAO_Hamilt cal_Hgamma 1.3477 12 0.11 19 % + Gint_interface cal_gint 0.84628 25 0.034 12 % + Gint_Gamma distri_vl_value 0.65181 12 0.054 9.3 % + Gint_Gamma distri_vl 2.5095 6 0.42 36 % + LCAO_Deepks cal_projected_DM 5.0594 14 0.36 72 % + LCAO_gen_fixedH add_v_delta 2.3782 6 0.4 34 % + LCAO_DESCRIPTOR add_v_delta 2.3782 6 0.4 34 % + ElecStateLCAO psiToRho 1.3015 12 0.11 18 % + Charge mix_rho 0.71482 11 0.065 10 % + LOOP_ions force_stress 0.5756 1 0.58 8.2 % + Force_Stress_LCAO getForceStress 0.57557 1 0.58 8.2 % + Force_LCAO_gamma ftable_gamma 0.36446 1 0.36 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.17938 1 0.18 2.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:48 2022 + FINISH Time : Wed Sep 28 11:09:55 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/5/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4c81c838a33ab76d3bfb8641db172671ac30647e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.43111 0.840176 0.470664 +H 0.385105 0.840786 0.513069 +H 0.457391 0.78204 0.479002 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6e10af2b0f98e899f0f20f2a9c993d0b5dca2bac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6819 2 + 2 -13.2758 2 + 3 -9.2415 2 + 4 -6.83028 2 + 5 1.57073 0 + 6 4.92281 0 + 7 10.9848 0 + 8 11.2362 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..6fc2e2a713f0d79d246fc5e3f380d78aa1a4e9ab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/running_scf.log @@ -0,0 +1,798 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:03 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.0710877423 23.5249157492 13.1785957864 0 0 0 0 + tauc_H1 10.7829508163 23.5420197679 14.3659441102 0 0 0 0 + tauc_H2 12.8069571987 21.897112597 13.4120451755 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0873265382272 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0986053400339 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116955610955 (SEC) + + DONE : INIT CHARGE Time : 0.165525765084 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447564 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + No atoms on this sub-FFT-mesh. + Atom number in sub-FFT-grid = 0 + Local orbitals number in sub-FFT-grid = 0 + lgd_last = 0 + lgd_now = 0 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 0 + nCol_in_proc = 0 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 0 + nCol_in_proc = 0 +receiver_size is 0 ; receiver_size of each process is: +0 0 0 0 +sender_size is 288 ; sender_size of each process is: +0 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00155 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63e-322 + + Density error is 0.218562848714 + + Energy Rydberg eV + E_KohnSham -34.1840207258 -465.097462422 + E_Harris -34.3840483498 -467.818977864 + E_Fermi -0.427834643749 -5.82098895679 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00145390285486 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0970809142233 + + Energy Rydberg eV + E_KohnSham -34.2753112375 -466.339533553 + E_Harris -34.2819261404 -466.429533924 + E_Fermi -0.234652703633 -3.19261382051 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00133507758511 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.0617606449339 + + Energy Rydberg eV + E_KohnSham -34.275516271 -466.342323178 + E_Harris -34.2797050901 -466.399314986 + E_Fermi -0.21871159314 -2.97572388536 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00113886821567 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.00208935130318 + + Energy Rydberg eV + E_KohnSham -34.2755908163 -466.343337418 + E_Harris -34.2755937347 -466.343377125 + E_Fermi -0.182825310052 -2.48746595533 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00113582878791 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000937732775156 + + Energy Rydberg eV + E_KohnSham -34.2755068135 -466.342194501 + E_Harris -34.2755105172 -466.342244893 + E_Fermi -0.181326352668 -2.46707159385 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00113462761165 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 0.000126067586244 + + Energy Rydberg eV + E_KohnSham -34.2755684202 -466.343032703 + E_Harris -34.27556847 -466.343033381 + E_Fermi -0.181814614148 -2.47371473208 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0011344348037 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 4.81580918131e-05 + + Energy Rydberg eV + E_KohnSham -34.2755472544 -466.342744729 + E_Harris -34.2755472659 -466.342744885 + E_Fermi -0.181650251696 -2.4714784662 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00113446492373 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.58309552309e-05 + + Energy Rydberg eV + E_KohnSham -34.2755508553 -466.34279372 + E_Harris -34.2755508561 -466.342793731 + E_Fermi -0.181708135066 -2.47226600985 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00113442317367 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 2.11938715151e-06 + + Energy Rydberg eV + E_KohnSham -34.2755494841 -466.342775064 + E_Harris -34.2755494841 -466.342775065 + E_Fermi -0.181690783137 -2.47202992475 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00113442068671 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 3.97554626349e-07 + + Energy Rydberg eV + E_KohnSham -34.2755496324 -466.342777082 + E_Harris -34.2755496324 -466.342777082 + E_Fermi -0.181689275141 -2.47200940741 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00113442004685 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 1.36736460539e-07 + + Energy Rydberg eV + E_KohnSham -34.2755496613 -466.342777476 + E_Harris -34.2755496613 -466.342777476 + E_Fermi -0.181689040042 -2.47200620872 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00113441977254 + number of non-zero elements in receiver_buffer = 0 + receiver_size = 0 + last receiver_buffer = 1.63041663128e-322 + + Density error is 9.90490986434e-09 + + Energy Rydberg eV + E_KohnSham -34.2755496641 -466.342777514 + E_Harris -34.2755496641 -466.342777514 + E_band -8.08918396763 -110.05899413 + E_one_elec -70.0225294942 -952.705389494 + E_Hartree +36.380953612 +494.988267797 + E_xc -8.2649834161 -112.450868335 + E_Ewald +7.75382958027 +105.496263613 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196228044196 -2.66981950846 + E_Fermi -0.181688884607 -2.47200409392 + + charge density convergence is achieved + final etot is -466.342777514 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6819 2.00000 + 2 -13.2758 2.00000 + 3 -9.24150 2.00000 + 4 -6.83028 2.00000 + 5 1.57073 0.00000 + 6 4.92281 0.00000 + 7 10.9848 0.00000 + 8 11.2362 0.00000 + + EFERMI = -2.472004093919246 eV + OUT.ABACUS/ final etot is -466.3427775135893 eV + correction force for each atom along direction 1 is -9.44284e-05 + correction force for each atom along direction 2 is -8.78994e-05 + correction force for each atom along direction 3 is -2.46242e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.5340085 +0.79109494 -1.8793447 + H1 -2.1769895 +0.24677790 +1.8881673 + H2 +0.64298095 -1.0378728 -0.0088226941 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3427775135893 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0821 11 0.55 1.0e+02% + Run_lcao lcao_line 6.0727 1 6.1 1.e+02% + Potential init_pot 0.28653 2 0.14 4.7% + PW_Basis recip2real 0.27148 17 0.016 4.5% + PW_Basis gathers_scatterp 0.12438 17 0.0073 2.0% + Potential v_of_rho 0.93358 14 0.067 15.% + XC_Functional v_xc 0.27896 15 0.019 4.6% + H_Hartree_pw v_hartree 0.61612 14 0.044 10.% + PW_Basis real2recip 0.60382 41 0.015 9.9% + PW_Basis gatherp_scatters 0.27912 41 0.0068 4.6% + ORB_control set_orb_tables 1.1028 1 1.1 18.% + ORB_gen_tables gen_tables 1.1028 1 1.1 18.% + ORB_table_phi init_Table 0.48103 1 0.48 7.9% + ORB_table_phi cal_ST_Phi12_R 0.47616 126 0.0038 7.8% + ORB_table_beta init_Table_Beta 0.18969 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18816 56 0.0034 3.1% + ORB_table_alpha init_Table_Alpha 0.25224 1 0.25 4.1% + ORB_table_alpha S_PhiAlpha_R 0.25040 66 0.0038 4.1% + LOOP_ions opt_ions 4.4459 1 4.4 73.% + ESolver_KS_LCAO Run 3.9575 1 4.0 65.% + HSolverLCAO solve 1.8290 12 0.15 30.% + HamiltLCAO updateHk 0.92356 12 0.077 15.% + LCAO_Hamilt cal_Hgamma 0.89333 12 0.074 15.% + Gint_Gamma distri_vl_value 0.60294 12 0.050 9.9% + Gint_Gamma distri_vl 2.0752 6 0.35 34.% + LCAO_Deepks cal_projected_DM 4.1109 14 0.29 68.% + LCAO_gen_fixedH add_v_delta 1.9572 6 0.33 32.% + LCAO_DESCRIPTOR add_v_delta 1.9572 6 0.33 32.% + ElecStateLCAO psiToRho 0.82661 12 0.069 14.% + Charge mix_rho 0.69975 11 0.064 12.% + LOOP_ions force_stress 0.48829 1 0.49 8.0% + Force_Stress_LCAO getForceStress 0.48827 1 0.49 8.0% + Force_LCAO_gamma ftable_gamma 0.27879 1 0.28 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1028. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:03 2022 + Finish Time : Wed Sep 28 11:07:09 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..09ce3cb49a861e0d13145adba5347d557802514a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/OUT.ABACUS/warning.log @@ -0,0 +1,79 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124278 ima = 3.72041e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 0 + 2 3 + 3 3 + 4 0 + Grid_Technique::init_atoms_on_grid2 warning : no atom on this sub FFT grid. + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122635542635 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111919730808 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112272913645 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011258043716 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112493614084 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112543182392 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112537441333 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112540357712 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112539878143 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112539797306 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112539784522 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112539777866 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3b3ae3fc5eccda509ee71b847aa6e6f8ff9dbdd4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.928912257664 23.524915749220 13.178595786420 0 0 0 +H +0.0 +2 +-17.217049183695 23.542019767898 14.365944110260 0 0 0 +-15.193042801338 21.897112597035 13.412045175492 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/conv new file mode 100644 index 0000000000000000000000000000000000000000..59c8f9607786e36f9ba997912e04dff4d66461ba --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/conv @@ -0,0 +1 @@ +50 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..2be0e664161a3b79fb0f9dc9ce6f211e98f97145 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750543236 0.0128800589 1.300705074 1.384846869 1.471178532 0.00903574807 0.01888269331 0.03906679021 +-2.620949942e-18 0.001191467353 0.002889542584 0.01357846822 0.04942085926 3.193359202e-19 2.689739695e-06 7.142706841e-06 +0.001629203257 0.005995828631 + +H atom_index 1 n_descriptor 18 +1.310263549 0.03248818878 0.132765421 0.1800853024 0.3373887171 0.02558675938 0.03170471712 0.03653041708 +2.503666778e-17 5.976094988e-05 0.1082241111 0.1290190668 0.1545540678 -2.979389877e-18 7.800065205e-07 0.01413537198 +0.0292059795 0.0331167905 + +H atom_index 2 n_descriptor 18 +1.271268124 0.03365042858 0.1173092418 0.1597619045 0.3265694068 0.02376526965 0.02949258392 0.03686751132 +2.782375633e-17 5.591536866e-05 0.1084153726 0.1176682247 0.1374206016 -1.509772638e-18 2.768606069e-06 0.0132801664 +0.02801152508 0.03171111349 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c7febc5523795d1f4f496347915b5685e3f09cc4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:03 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0873513 SEC) : SETUP UNITCELL + DONE(0.0986238 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116978 SEC) : INIT PLANEWAVE + DONE(0.165644 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44763 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650975e+02 0.000000e+00 2.186e-01 4.467e-01 + GE2 -4.663395e+02 -1.242071e+00 9.708e-02 3.689e-01 + GE3 -4.663423e+02 -2.789624e-03 6.176e-02 4.263e-01 + GE4 -4.663433e+02 -1.014240e-03 2.089e-03 3.164e-01 + GE5 -4.663422e+02 1.142917e-03 9.377e-04 3.148e-01 + GE6 -4.663430e+02 -8.382020e-04 1.261e-04 3.095e-01 + GE7 -4.663427e+02 2.879743e-04 4.816e-05 3.052e-01 + GE8 -4.663428e+02 -4.899184e-05 1.583e-05 2.894e-01 + GE9 -4.663428e+02 1.865614e-05 2.119e-06 2.934e-01 + GE10 -4.663428e+02 -2.017855e-06 3.976e-07 2.976e-01 + GE11 -4.663428e+02 -3.939657e-07 1.367e-07 2.968e-01 + GE12 -4.663428e+02 -3.743287e-08 9.905e-09 2.310e-01 +E_delta_band = -7.34080981e-02 Ry = -9.98768414e-01 eV +E_delta_NN= -1.96228044e-01 Ry = -2.66981951e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0821 11 0.55 1e+02 % + Run_lcao lcao_line 6.0727 1 6.1 1e+02 % + Potential init_pot 0.28653 2 0.14 4.7 % + PW_Basis recip2real 0.27148 17 0.016 4.5 % + PW_Basis gathers_scatterp 0.12438 17 0.0073 2 % + Potential v_of_rho 0.93358 14 0.067 15 % + XC_Functional v_xc 0.27896 15 0.019 4.6 % + H_Hartree_pw v_hartree 0.61612 14 0.044 10 % + PW_Basis real2recip 0.60382 41 0.015 9.9 % + PW_Basis gatherp_scatters 0.27912 41 0.0068 4.6 % + ORB_control set_orb_tables 1.1028 1 1.1 18 % + ORB_gen_tables gen_tables 1.1028 1 1.1 18 % + ORB_table_phi init_Table 0.48103 1 0.48 7.9 % + ORB_table_phi cal_ST_Phi12_R 0.47616 126 0.0038 7.8 % + ORB_table_beta init_Table_Beta 0.18969 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18816 56 0.0034 3.1 % + ORB_table_alpha init_Table_Alpha 0.25224 1 0.25 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.2504 66 0.0038 4.1 % + LOOP_ions opt_ions 4.4459 1 4.4 73 % + ESolver_KS_LCAO Run 3.9575 1 4 65 % + HSolverLCAO solve 1.829 12 0.15 30 % + HamiltLCAO updateHk 0.92356 12 0.077 15 % + LCAO_Hamilt cal_Hgamma 0.89333 12 0.074 15 % + Gint_Gamma distri_vl_value 0.60294 12 0.05 9.9 % + Gint_Gamma distri_vl 2.0752 6 0.35 34 % + LCAO_Deepks cal_projected_DM 4.1109 14 0.29 68 % + LCAO_gen_fixedH add_v_delta 1.9572 6 0.33 32 % + LCAO_DESCRIPTOR add_v_delta 1.9572 6 0.33 32 % + ElecStateLCAO psiToRho 0.82661 12 0.069 14 % + Charge mix_rho 0.69975 11 0.064 12 % + LOOP_ions force_stress 0.48829 1 0.49 8 % + Force_Stress_LCAO getForceStress 0.48827 1 0.49 8 % + Force_LCAO_gamma ftable_gamma 0.27879 1 0.28 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:03 2022 + FINISH Time : Wed Sep 28 11:07:09 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/50/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c06f2167280c902eba0b6bdb07c88e4b4549c26e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.428677 0.830851 0.460031 +H 0.381395 0.839644 0.51079 +H 0.478886 0.805559 0.49514 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3071fc225547ed784f43c23bcf456e42f249ab2e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.954 2 + 2 -12.4969 2 + 3 -9.26077 2 + 4 -6.67328 2 + 5 0.872865 0 + 6 3.78914 0 + 7 11.1651 0 + 8 11.4217 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f302d7b690fc36932faec8360f95bfb8035fe01c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:30 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.0029485028 23.2638275437 12.8808603686 0 0 0 0 + tauc_H1 10.679068415 23.510037793 14.3021208818 0 0 0 0 + tauc_H2 13.4087978512 22.5556644948 13.8639279531 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0872727696308 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.088346429533 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106641409427 (SEC) + + DONE : INIT CHARGE Time : 0.150070949509 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.432613 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 1 + Local orbitals number in sub-FFT-grid = 13 + lgd_last = 0 + lgd_now = 13 + allocate DM , the dimension is 13 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 7 + nCol_in_proc = 7 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 7 + nCol_in_proc = 6 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 6 + nCol_in_proc = 7 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 6 + nCol_in_proc = 6 +receiver_size is 169 ; receiver_size of each process is: +49 42 42 36 +sender_size is 337 ; sender_size of each process is: +49 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000966 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000129 + + Density error is 0.210590171762 + + Energy Rydberg eV + E_KohnSham -34.1860079273 -465.124499685 + E_Harris -34.3693754919 -467.619343392 + E_Fermi -0.381593519516 -5.1918461853 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00129622983087 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000163726827594 + + Density error is 0.0992221361366 + + Energy Rydberg eV + E_KohnSham -34.2749570702 -466.33471486 + E_Harris -34.2824553067 -466.436733602 + E_Fermi -0.19289975749 -2.62453584468 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00123547524688 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.0001792393489 + + Density error is 0.0642076190637 + + Energy Rydberg eV + E_KohnSham -34.2755799476 -466.343189542 + E_Harris -34.2802966449 -466.407363501 + E_Fermi -0.188677143495 -2.56708423389 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115686957374 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000216672310971 + + Density error is 0.00192770123646 + + Energy Rydberg eV + E_KohnSham -34.2754404444 -466.341291504 + E_Harris -34.2754420429 -466.341313252 + E_Fermi -0.153458517629 -2.08791024638 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115806471991 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000216441460762 + + Density error is 0.00104772517875 + + Energy Rydberg eV + E_KohnSham -34.2754057004 -466.340818788 + E_Harris -34.2754063002 -466.340826948 + E_Fermi -0.153667960284 -2.09075985991 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115685232949 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000217123377545 + + Density error is 0.000186786141514 + + Energy Rydberg eV + E_KohnSham -34.2754161046 -466.340960343 + E_Harris -34.2754161161 -466.3409605 + E_Fermi -0.153100759932 -2.0830427032 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115708648635 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000217062151939 + + Density error is 3.09855149806e-05 + + Energy Rydberg eV + E_KohnSham -34.2754135362 -466.340925399 + E_Harris -34.2754135383 -466.340925427 + E_Fermi -0.15310964077 -2.0831635332 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115701897123 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000217077587439 + + Density error is 1.11431336939e-05 + + Energy Rydberg eV + E_KohnSham -34.2754157086 -466.340954956 + E_Harris -34.2754157091 -466.340954962 + E_Fermi -0.153118370554 -2.08328230801 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115701618252 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000217078715734 + + Density error is 2.22288114904e-06 + + Energy Rydberg eV + E_KohnSham -34.2754148325 -466.340943036 + E_Harris -34.2754148325 -466.340943036 + E_Fermi -0.153107806916 -2.08313858235 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115701069457 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000217077087491 + + Density error is 5.68622611235e-07 + + Energy Rydberg eV + E_KohnSham -34.2754149853 -466.340945114 + E_Harris -34.2754149853 -466.340945114 + E_Fermi -0.153106021162 -2.08311428591 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115701148741 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000217077255024 + + Density error is 1.95854759046e-07 + + Energy Rydberg eV + E_KohnSham -34.2754149944 -466.340945239 + E_Harris -34.2754149944 -466.340945239 + E_Fermi -0.153105733432 -2.08311037114 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115701172179 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000217077353511 + + Density error is 1.19785901801e-08 + + Energy Rydberg eV + E_KohnSham -34.2754149988 -466.340945299 + E_Harris -34.2754149988 -466.340945299 + E_band -7.8474382176 -106.769874462 + E_one_elec -68.4391252999 -931.162070215 + E_Hartree +35.6305488351 +484.778487024 + E_xc -8.14436322519 -110.809746444 + E_Ewald +6.80352447202 +92.5666993019 + E_demet -6.36314177267e-54 -8.65749852901e-53 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193414655804 -2.63154139565 + E_Fermi -0.153105549573 -2.08310786961 + + charge density convergence is achieved + final etot is -466.340945299 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9540 2.00000 + 2 -12.4969 2.00000 + 3 -9.26077 2.00000 + 4 -6.67328 2.00000 + 5 0.872865 0.00000 + 6 3.78914 0.00000 + 7 11.1651 0.00000 + 8 11.4217 0.00000 + + EFERMI = -2.083107869614143 eV + OUT.ABACUS/ final etot is -466.3409452985831 eV + correction force for each atom along direction 1 is 4.36437e-05 + correction force for each atom along direction 2 is -0.000158763 + correction force for each atom along direction 3 is 0.000131707 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.4291090 +0.16087663 +2.0869506 + H1 +1.4484896 -0.21822636 -1.8227878 + H2 -0.019380604 +0.057349729 -0.26416280 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3409452985831 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1556 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1466 1 7.1 1.e+02% + Potential init_pot 0.28277 2 0.14 4.0% + PW_Basis recip2real 0.26627 17 0.016 3.7% + PW_Basis gathers_scatterp 0.11967 17 0.0070 1.7% + Potential v_of_rho 1.0260 14 0.073 14.% + XC_Functional v_xc 0.35325 15 0.024 4.9% + H_Hartree_pw v_hartree 0.63197 14 0.045 8.8% + PW_Basis real2recip 0.73982 41 0.018 10.% + PW_Basis gatherp_scatters 0.32354 41 0.0079 4.5% + ORB_control set_orb_tables 1.0924 1 1.1 15.% + ORB_gen_tables gen_tables 1.0924 1 1.1 15.% + ORB_table_phi init_Table 0.47418 1 0.47 6.6% + ORB_table_phi cal_ST_Phi12_R 0.46903 126 0.0037 6.6% + ORB_table_beta init_Table_Beta 0.18140 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.17990 56 0.0032 2.5% + ORB_table_alpha init_Table_Alpha 0.24775 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24571 66 0.0037 3.4% + LOOP_ions opt_ions 5.5455 1 5.5 77.% + ESolver_KS_LCAO Run 5.0311 1 5.0 70.% + HSolverLCAO solve 2.4855 12 0.21 35.% + HamiltLCAO updateHk 1.2816 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2519 12 0.10 17.% + Gint_Gamma distri_vl_value 0.82814 12 0.069 12.% + Gint_Gamma distri_vl 2.6251 6 0.44 37.% + LCAO_Deepks cal_projected_DM 5.1570 14 0.37 72.% + LCAO_gen_fixedH add_v_delta 2.4826 6 0.41 35.% + LCAO_DESCRIPTOR add_v_delta 2.4827 6 0.41 35.% + ElecStateLCAO psiToRho 1.1743 12 0.098 16.% + Charge mix_rho 0.90080 11 0.082 13.% + LOOP_ions force_stress 0.51429 1 0.51 7.2% + Force_Stress_LCAO getForceStress 0.51427 1 0.51 7.2% + Force_LCAO_gamma ftable_gamma 0.31484 1 0.31 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:30 2022 + Finish Time : Wed Sep 28 11:05:37 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..441b0acf42668746595dcdf07a74d1b57d142d67 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123425 ima = 3.69916e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 1 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123564441627 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111744675388 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112670479692 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112881280216 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112869500443 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112877642465 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112874222708 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112875988901 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112875528199 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112875486706 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011287546476 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112875454476 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/STRU new file mode 100644 index 0000000000000000000000000000000000000000..86385c3e64f4276d7a35bd24087e407c721618f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.997051497140 23.263827543702 12.880860368589 0 0 0 +H +0.0 +2 +-17.320931585026 23.510037792956 14.302120881854 0 0 0 +-14.591202148853 22.555664494790 13.863927953067 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/conv new file mode 100644 index 0000000000000000000000000000000000000000..26962b961d9456ba0c89ae461027b644d4af4c96 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/conv @@ -0,0 +1 @@ +51 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..19bbb9cce9fef440e0b637c720bcd41808044541 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753389018 0.01237102472 1.232693025 1.329270546 1.468038927 0.009004935452 0.01674923377 0.03923135638 +-1.959332504e-18 0.0007863853271 0.002469906362 0.01153137573 0.04161741362 5.332071247e-19 1.783508178e-06 5.449429675e-06 +0.001547205272 0.005899135076 + +H atom_index 1 n_descriptor 18 +1.151624572 0.03757783206 0.07857924871 0.109475383 0.2837360699 0.01771986441 0.02251836135 0.04166390949 +-1.418248145e-17 3.318801833e-05 0.07384757429 0.0928240529 0.1106479323 -4.919315895e-18 6.721864216e-06 0.01591432422 +0.02165462125 0.02550705483 + +H atom_index 2 n_descriptor 18 +1.231178666 0.03529208146 0.1021246683 0.1413084809 0.3146367836 0.02146350644 0.02717767301 0.03853892712 +-1.363441401e-17 3.973811836e-05 0.09368138313 0.1150228685 0.1209101633 -1.292551259e-18 4.308731774e-06 0.01352177714 +0.02498793513 0.02981886627 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a5c700c42eec29df46895291f6f6a0d0328eae96 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:30 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872961 SEC) : SETUP UNITCELL + DONE(0.0883634 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106664 SEC) : INIT PLANEWAVE + DONE(0.150212 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.432681 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651245e+02 0.000000e+00 2.106e-01 5.162e-01 + GE2 -4.663347e+02 -1.210215e+00 9.922e-02 4.721e-01 + GE3 -4.663432e+02 -8.474682e-03 6.421e-02 5.462e-01 + GE4 -4.663413e+02 1.898039e-03 1.928e-03 4.030e-01 + GE5 -4.663408e+02 4.727159e-04 1.048e-03 4.036e-01 + GE6 -4.663410e+02 -1.415552e-04 1.868e-04 4.026e-01 + GE7 -4.663409e+02 3.494434e-05 3.099e-05 3.834e-01 + GE8 -4.663410e+02 -2.955732e-05 1.114e-05 3.840e-01 + GE9 -4.663409e+02 1.191989e-05 2.223e-06 3.844e-01 + GE10 -4.663409e+02 -2.078476e-06 5.686e-07 3.755e-01 + GE11 -4.663409e+02 -1.241849e-07 1.959e-07 3.791e-01 + GE12 -4.663409e+02 -5.991525e-08 1.198e-08 3.105e-01 +E_delta_band = -6.74148750e-02 Ry = -9.17226430e-01 eV +E_delta_NN= -1.93414656e-01 Ry = -2.63154140e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1556 11 0.65 1e+02 % + Run_lcao lcao_line 7.1466 1 7.1 1e+02 % + Potential init_pot 0.28277 2 0.14 4 % + PW_Basis recip2real 0.26627 17 0.016 3.7 % + PW_Basis gathers_scatterp 0.11967 17 0.007 1.7 % + Potential v_of_rho 1.026 14 0.073 14 % + XC_Functional v_xc 0.35325 15 0.024 4.9 % + H_Hartree_pw v_hartree 0.63197 14 0.045 8.8 % + PW_Basis real2recip 0.73982 41 0.018 10 % + PW_Basis gatherp_scatters 0.32354 41 0.0079 4.5 % + ORB_control set_orb_tables 1.0924 1 1.1 15 % + ORB_gen_tables gen_tables 1.0924 1 1.1 15 % + ORB_table_phi init_Table 0.47418 1 0.47 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.46903 126 0.0037 6.6 % + ORB_table_beta init_Table_Beta 0.1814 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.1799 56 0.0032 2.5 % + ORB_table_alpha init_Table_Alpha 0.24775 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24571 66 0.0037 3.4 % + LOOP_ions opt_ions 5.5455 1 5.5 77 % + ESolver_KS_LCAO Run 5.0311 1 5 70 % + HSolverLCAO solve 2.4855 12 0.21 35 % + HamiltLCAO updateHk 1.2816 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.2519 12 0.1 17 % + Gint_Gamma distri_vl_value 0.82814 12 0.069 12 % + Gint_Gamma distri_vl 2.6251 6 0.44 37 % + LCAO_Deepks cal_projected_DM 5.157 14 0.37 72 % + LCAO_gen_fixedH add_v_delta 2.4826 6 0.41 35 % + LCAO_DESCRIPTOR add_v_delta 2.4827 6 0.41 35 % + ElecStateLCAO psiToRho 1.1743 12 0.098 16 % + Charge mix_rho 0.9008 11 0.082 13 % + LOOP_ions force_stress 0.51429 1 0.51 7.2 % + Force_Stress_LCAO getForceStress 0.51427 1 0.51 7.2 % + Force_LCAO_gamma ftable_gamma 0.31484 1 0.31 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:30 2022 + FINISH Time : Wed Sep 28 11:05:37 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/51/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..1b0d6a4275e51327b5114d3d9de9b0e0a988ad81 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.425086 0.819133 0.462504 +H 0.373567 0.820408 0.502007 +H 0.482804 0.822665 0.493533 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ea7f7bc6bbc4ce0130ea561cd3c441c2c7a3a6e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1277 2 + 2 -13.5312 2 + 3 -8.6182 2 + 4 -6.70148 2 + 5 1.3358 0 + 6 4.53842 0 + 7 11.0864 0 + 8 11.2881 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3fc0be19a3884f8717a86c52773a5b90fbb53aa1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/running_scf.log @@ -0,0 +1,777 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:44 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.9023998317 22.9357150488 12.9501159963 0 0 0 0 + tauc_H1 10.4598680097 22.9714333674 14.0561822227 0 0 0 0 + tauc_H2 13.5185175386 23.0346163139 13.8189309632 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101353569933 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101731985339 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119717352744 (SEC) + + DONE : INIT CHARGE Time : 0.162974026984 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447035 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 1 + Local orbitals number in sub-FFT-grid = 13 + lgd_last = 0 + lgd_now = 13 + allocate DM , the dimension is 13 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 7 + nCol_in_proc = 7 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 7 + nCol_in_proc = 6 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 6 + nCol_in_proc = 7 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 6 + nCol_in_proc = 6 +receiver_size is 169 ; receiver_size of each process is: +49 42 42 36 +sender_size is 337 ; sender_size of each process is: +49 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00081 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000235 + + Density error is 0.218370614496 + + Energy Rydberg eV + E_KohnSham -34.1841330135 -465.098990173 + E_Harris -34.3824161741 -467.796770976 + E_Fermi -0.405727579219 -5.52020691313 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00124733992364 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000243500137775 + + Density error is 0.0985638924195 + + Energy Rydberg eV + E_KohnSham -34.2765816855 -466.356818885 + E_Harris -34.2832415205 -466.447430589 + E_Fermi -0.211144129539 -2.87276326098 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00120702030817 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000269985202506 + + Density error is 0.0632387686399 + + Energy Rydberg eV + E_KohnSham -34.2769812016 -466.362254581 + E_Harris -34.281240532 -466.420205744 + E_Fermi -0.200174975191 -2.72352025961 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115751437641 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000325326028182 + + Density error is 0.00220594624339 + + Energy Rydberg eV + E_KohnSham -34.2769752226 -466.362173232 + E_Harris -34.2769812797 -466.362255644 + E_Fermi -0.165078852314 -2.24601301077 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115801347103 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000327145191917 + + Density error is 0.000945310954923 + + Energy Rydberg eV + E_KohnSham -34.2769137437 -466.361336769 + E_Harris -34.2769145776 -466.361348115 + E_Fermi -0.164198908137 -2.23404075604 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115714066425 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000328131801378 + + Density error is 0.000225871230313 + + Energy Rydberg eV + E_KohnSham -34.2769490236 -466.361816777 + E_Harris -34.2769491168 -466.361818044 + E_Fermi -0.164178463941 -2.23376259848 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.0011575593516 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000328229377346 + + Density error is 4.23839656863e-05 + + Energy Rydberg eV + E_KohnSham -34.2769353028 -466.361630095 + E_Harris -34.2769353127 -466.36163023 + E_Fermi -0.164006652329 -2.23142498158 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115744471738 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000328218552747 + + Density error is 2.02237350508e-05 + + Energy Rydberg eV + E_KohnSham -34.2769410347 -466.361708082 + E_Harris -34.2769410365 -466.361708107 + E_Fermi -0.16405602686 -2.23209675654 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115744625775 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.00032821738819 + + Density error is 1.75257667679e-06 + + Energy Rydberg eV + E_KohnSham -34.2769394259 -466.361686193 + E_Harris -34.2769394259 -466.361686193 + E_Fermi -0.164034641751 -2.23180579721 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115744812304 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000328217665048 + + Density error is 3.11154979114e-07 + + Energy Rydberg eV + E_KohnSham -34.2769397244 -466.361690255 + E_Harris -34.2769397244 -466.361690255 + E_Fermi -0.164033037557 -2.23178397103 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115744882033 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000328217698741 + + Density error is 6.24526685367e-08 + + Energy Rydberg eV + E_KohnSham -34.2769397439 -466.361690519 + E_Harris -34.2769397439 -466.361690519 + E_band -7.93470131344 -107.957149791 + E_one_elec -69.3174326719 -943.112055069 + E_Hartree +36.071947147 +490.784019154 + E_xc -8.21388816241 -111.755681743 + E_Ewald +7.30680356919 +99.4141627078 + E_demet -2.52463257218e-77 -3.43493883381e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194542795787 -2.64689052755 + E_Fermi -0.164032881431 -2.23178184682 + + charge density convergence is achieved + final etot is -466.361690519 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1277 2.00000 + 2 -13.5312 2.00000 + 3 -8.61820 2.00000 + 4 -6.70148 2.00000 + 5 1.33580 0.00000 + 6 4.53842 0.00000 + 7 11.0864 0.00000 + 8 11.2881 0.00000 + + EFERMI = -2.231781846820616 eV + OUT.ABACUS/ final etot is -466.3616905192211 eV + correction force for each atom along direction 1 is -1.35535e-05 + correction force for each atom along direction 2 is 0.000134481 + correction force for each atom along direction 3 is 1.85759e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.35172386 -0.073569951 -1.3562014 + H1 +0.057127033 +0.051633866 +0.81236640 + H2 -0.40885089 +0.021936085 +0.54383501 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3616905192211 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7471 11 0.61 1.0e+02% + Run_lcao lcao_line 6.7376 1 6.7 1.e+02% + Potential init_pot 0.28477 2 0.14 4.2% + PW_Basis recip2real 0.25161 16 0.016 3.7% + PW_Basis gathers_scatterp 0.11393 16 0.0071 1.7% + Potential v_of_rho 0.97964 13 0.075 15.% + XC_Functional v_xc 0.35814 14 0.026 5.3% + H_Hartree_pw v_hartree 0.58222 13 0.045 8.6% + PW_Basis real2recip 0.67890 38 0.018 10.% + PW_Basis gatherp_scatters 0.29499 38 0.0078 4.4% + ORB_control set_orb_tables 1.0913 1 1.1 16.% + ORB_gen_tables gen_tables 1.0913 1 1.1 16.% + ORB_table_phi init_Table 0.47235 1 0.47 7.0% + ORB_table_phi cal_ST_Phi12_R 0.46715 126 0.0037 6.9% + ORB_table_beta init_Table_Beta 0.18452 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18305 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24519 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24325 66 0.0037 3.6% + LOOP_ions opt_ions 5.1217 1 5.1 76.% + ESolver_KS_LCAO Run 4.6144 1 4.6 68.% + HSolverLCAO solve 2.2626 11 0.21 34.% + HamiltLCAO updateHk 1.1883 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1608 11 0.11 17.% + Gint_Gamma distri_vl_value 0.75089 11 0.068 11.% + Gint_Gamma distri_vl 2.2248 6 0.37 33.% + LCAO_Deepks cal_projected_DM 4.7433 13 0.36 70.% + LCAO_gen_fixedH add_v_delta 2.0873 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.0875 6 0.35 31.% + ElecStateLCAO psiToRho 1.0464 11 0.095 16.% + Charge mix_rho 0.81475 10 0.081 12.% + LOOP_ions force_stress 0.50711 1 0.51 7.5% + Force_Stress_LCAO getForceStress 0.50708 1 0.51 7.5% + Force_LCAO_gamma ftable_gamma 0.30715 1 0.31 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:44 2022 + Finish Time : Wed Sep 28 11:13:51 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6beb068bc1fee177c5aa15a23cd7f4b99c7a26a3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123595 ima = 3.68758e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 1 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124253716248 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113212779604 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113723598302 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113956294428 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113909916823 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113937679209 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113927421263 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113930633551 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113929794412 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113929734345 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113929718881 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8b45e090b99b7e00f6080559aaa698d19fd03a9c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.097600168364 22.935715048838 12.950115996276 0 0 0 +H +0.0 +2 +-17.540131990308 22.971433367409 14.056182222716 0 0 0 +-14.481482461380 23.034616313896 13.818930963196 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/conv new file mode 100644 index 0000000000000000000000000000000000000000..64f8bd4eeac5a7c7d2363624f2a82fb9ac424186 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/conv @@ -0,0 +1 @@ +52 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4d1a784768dd2370a7dbfed80b9db1cd72d000ac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.739916076 0.01254368961 1.282130877 1.37762432 1.468677365 0.007154414675 0.02161670692 0.03874922161 +1.210058417e-20 0.001171978965 0.002195209902 0.01255549859 0.04034349306 -3.966667793e-19 1.226314994e-06 4.079118462e-06 +0.001907007539 0.005345018613 + +H atom_index 1 n_descriptor 18 +1.247319031 0.03331281732 0.1091487641 0.1516992676 0.3241367861 0.02165031584 0.02853651337 0.03654763829 +-1.798565031e-17 3.256518665e-05 0.1022106585 0.114734233 0.1302059751 -5.339862035e-18 3.880420054e-06 0.01267849355 +0.0259968247 0.0308899141 + +H atom_index 2 n_descriptor 18 +1.231682495 0.03387982885 0.1038924197 0.1446176179 0.3192921925 0.02099779803 0.02764036207 0.03705490764 +-4.667858779e-18 3.147725122e-05 0.09819646109 0.1142678523 0.1240766678 9.375327946e-18 4.461726138e-06 0.01282642888 +0.02541003478 0.03018737305 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3092e28f093c83cbf7b755d05dec2fc17009b231 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/log.scf @@ -0,0 +1,100 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:44 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101377 SEC) : SETUP UNITCELL + DONE(0.101748 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119738 SEC) : INIT PLANEWAVE + DONE(0.163113 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.4471 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650990e+02 0.000000e+00 2.184e-01 5.099e-01 + GE2 -4.663568e+02 -1.257829e+00 9.856e-02 4.710e-01 + GE3 -4.663623e+02 -5.435696e-03 6.324e-02 5.400e-01 + GE4 -4.663622e+02 8.134937e-05 2.206e-03 3.998e-01 + GE5 -4.663613e+02 8.364629e-04 9.453e-04 3.997e-01 + GE6 -4.663618e+02 -4.800083e-04 2.259e-04 3.971e-01 + GE7 -4.663616e+02 1.866823e-04 4.238e-05 3.863e-01 + GE8 -4.663617e+02 -7.798759e-05 2.022e-05 3.774e-01 + GE9 -4.663617e+02 2.188979e-05 1.753e-06 3.774e-01 + GE10 -4.663617e+02 -4.062000e-06 3.112e-07 3.782e-01 + GE11 -4.663617e+02 -2.645284e-07 6.245e-08 3.081e-01 +E_delta_band = -7.01731701e-02 Ry = -9.54754960e-01 eV +E_delta_NN= -1.94542796e-01 Ry = -2.64689053e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7471 11 0.61 1e+02 % + Run_lcao lcao_line 6.7376 1 6.7 1e+02 % + Potential init_pot 0.28477 2 0.14 4.2 % + PW_Basis recip2real 0.25161 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.11393 16 0.0071 1.7 % + Potential v_of_rho 0.97964 13 0.075 15 % + XC_Functional v_xc 0.35814 14 0.026 5.3 % + H_Hartree_pw v_hartree 0.58222 13 0.045 8.6 % + PW_Basis real2recip 0.6789 38 0.018 10 % + PW_Basis gatherp_scatters 0.29499 38 0.0078 4.4 % + ORB_control set_orb_tables 1.0913 1 1.1 16 % + ORB_gen_tables gen_tables 1.0913 1 1.1 16 % + ORB_table_phi init_Table 0.47235 1 0.47 7 % + ORB_table_phi cal_ST_Phi12_R 0.46715 126 0.0037 6.9 % + ORB_table_beta init_Table_Beta 0.18452 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18305 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24519 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24325 66 0.0037 3.6 % + LOOP_ions opt_ions 5.1217 1 5.1 76 % + ESolver_KS_LCAO Run 4.6144 1 4.6 68 % + HSolverLCAO solve 2.2626 11 0.21 34 % + HamiltLCAO updateHk 1.1883 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1608 11 0.11 17 % + Gint_Gamma distri_vl_value 0.75089 11 0.068 11 % + Gint_Gamma distri_vl 2.2248 6 0.37 33 % + LCAO_Deepks cal_projected_DM 4.7433 13 0.36 70 % + LCAO_gen_fixedH add_v_delta 2.0873 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.0875 6 0.35 31 % + ElecStateLCAO psiToRho 1.0464 11 0.095 16 % + Charge mix_rho 0.81475 10 0.081 12 % + LOOP_ions force_stress 0.50711 1 0.51 7.5 % + Force_Stress_LCAO getForceStress 0.50708 1 0.51 7.5 % + Force_LCAO_gamma ftable_gamma 0.30715 1 0.31 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:44 2022 + FINISH Time : Wed Sep 28 11:13:51 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/52/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..dc26d1663af3b5c6e0a7f30ed9e9d1451eb6e0fb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.41437 0.806377 0.458056 +H 0.380509 0.756049 0.481195 +H 0.447728 0.821857 0.510694 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2dfbc06604c4221af2d5970f5f90e116ec574701 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.549 2 + 2 -12.9442 2 + 3 -9.37919 2 + 4 -6.80233 2 + 5 1.4042 0 + 6 4.63257 0 + 7 11.0284 0 + 8 11.3042 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3a95186a5ca30526e062c1432ad12c6fd5c8bddf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:00 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.6023553678 22.5785630304 12.8255590601 0 0 0 0 + tauc_H1 10.6542440769 21.1693796477 13.4734676452 0 0 0 0 + tauc_H2 12.5363721583 23.0120009574 14.2994379766 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0875234177391 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0888961362373 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107258523537 (SEC) + + DONE : INIT CHARGE Time : 0.157206178379 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.442702 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 1 + Local orbitals number in sub-FFT-grid = 13 + lgd_last = 0 + lgd_now = 13 + allocate DM , the dimension is 13 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 7 + nCol_in_proc = 7 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 7 + nCol_in_proc = 6 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 6 + nCol_in_proc = 7 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 6 + nCol_in_proc = 6 +receiver_size is 169 ; receiver_size of each process is: +49 42 42 36 +sender_size is 337 ; sender_size of each process is: +49 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000744 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000312 + + Density error is 0.215645402794 + + Energy Rydberg eV + E_KohnSham -34.188433428 -465.157500315 + E_Harris -34.3823261576 -467.795546237 + E_Fermi -0.415888792836 -5.65845731691 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00109339719501 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000349335564104 + + Density error is 0.097320235572 + + Energy Rydberg eV + E_KohnSham -34.2784459586 -466.382183622 + E_Harris -34.285166625 -466.473622979 + E_Fermi -0.224714086323 -3.05739199485 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00104509698789 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000355083786924 + + Density error is 0.0622282184228 + + Energy Rydberg eV + E_KohnSham -34.2787011354 -466.385655481 + E_Harris -34.2830372653 -466.444651555 + E_Fermi -0.211686552892 -2.88014330931 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000981253620742 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000367817896142 + + Density error is 0.00198970765268 + + Energy Rydberg eV + E_KohnSham -34.278721074 -466.385926759 + E_Harris -34.2787225563 -466.385946927 + E_Fermi -0.175770979915 -2.39148686989 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000985244104226 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000367897891003 + + Density error is 0.000911645631078 + + Energy Rydberg eV + E_KohnSham -34.2786487329 -466.384942508 + E_Harris -34.2786511472 -466.384975356 + E_Fermi -0.174792275799 -2.37817091725 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000983577708822 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000367948014866 + + Density error is 9.84748237109e-05 + + Energy Rydberg eV + E_KohnSham -34.278700135 -466.385641869 + E_Harris -34.2787001446 -466.385642 + E_Fermi -0.174982324032 -2.38075665612 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000983308013747 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000367995061334 + + Density error is 4.26918827197e-05 + + Energy Rydberg eV + E_KohnSham -34.2786842376 -466.385425574 + E_Harris -34.2786842475 -466.385425709 + E_Fermi -0.174867652202 -2.37919646583 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000983276696781 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000367971241455 + + Density error is 1.57537290737e-05 + + Energy Rydberg eV + E_KohnSham -34.2786861879 -466.385452109 + E_Harris -34.278686189 -466.385452124 + E_Fermi -0.174922903712 -2.37994820118 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000983290373275 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000367975328732 + + Density error is 2.19150221162e-06 + + Energy Rydberg eV + E_KohnSham -34.2786847604 -466.385432687 + E_Harris -34.2786847604 -466.385432687 + E_Fermi -0.17490642114 -2.3797239443 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000983292990869 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000367978087242 + + Density error is 4.09444940575e-07 + + Energy Rydberg eV + E_KohnSham -34.2786849874 -466.385435776 + E_Harris -34.2786849874 -466.385435776 + E_Fermi -0.174904786007 -2.37970169717 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000983293806585 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000367977633736 + + Density error is 1.26401583257e-07 + + Energy Rydberg eV + E_KohnSham -34.2786850185 -466.385436199 + E_Harris -34.2786850185 -466.385436199 + E_Fermi -0.174904559423 -2.37969861433 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000983293873261 + number of non-zero elements in receiver_buffer = 169 + receiver_size = 169 + last receiver_buffer = 0.000367977562263 + + Density error is 1.03543650562e-08 + + Energy Rydberg eV + E_KohnSham -34.2786850228 -466.385436257 + E_Harris -34.2786850228 -466.385436257 + E_band -8.03702638962 -109.349353875 + E_one_elec -69.6399534121 -947.500174859 + E_Hartree +36.1957872734 +492.468950515 + E_xc -8.23474376226 -112.039436737 + E_Ewald +7.52379735967 +102.366514689 + E_demet -1.20074138588e-86 -1.63369246723e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195494731851 -2.65984228216 + E_Fermi -0.174904417093 -2.37969667783 + + charge density convergence is achieved + final etot is -466.385436257 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5490 2.00000 + 2 -12.9442 2.00000 + 3 -9.37919 2.00000 + 4 -6.80233 2.00000 + 5 1.40420 0.00000 + 6 4.63257 0.00000 + 7 11.0284 0.00000 + 8 11.3042 0.00000 + + EFERMI = -2.379696677829578 eV + OUT.ABACUS/ final etot is -466.3854362567408 eV + correction force for each atom along direction 1 is -1.99516e-05 + correction force for each atom along direction 2 is -0.000128825 + correction force for each atom along direction 3 is 0.000191732 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.31401070 +0.011367574 -0.84513892 + H1 -0.62618817 -0.69134767 -0.10090094 + H2 +0.94019888 +0.67998010 +0.94603986 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3854362567408 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9616 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9522 1 7.0 1.e+02% + Potential init_pot 0.28713 2 0.14 4.1% + PW_Basis recip2real 0.29063 17 0.017 4.2% + PW_Basis gathers_scatterp 0.13776 17 0.0081 2.0% + Potential v_of_rho 1.0691 14 0.076 15.% + XC_Functional v_xc 0.33555 15 0.022 4.8% + H_Hartree_pw v_hartree 0.69451 14 0.050 10.% + PW_Basis real2recip 0.70851 41 0.017 10.% + PW_Basis gatherp_scatters 0.31350 41 0.0076 4.5% + ORB_control set_orb_tables 1.1047 1 1.1 16.% + ORB_gen_tables gen_tables 1.1047 1 1.1 16.% + ORB_table_phi init_Table 0.48118 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47593 126 0.0038 6.8% + ORB_table_beta init_Table_Beta 0.18736 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18580 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24959 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24761 66 0.0038 3.6% + LOOP_ions opt_ions 5.3195 1 5.3 76.% + ESolver_KS_LCAO Run 4.7678 1 4.8 68.% + HSolverLCAO solve 2.2923 12 0.19 33.% + HamiltLCAO updateHk 1.2023 12 0.10 17.% + LCAO_Hamilt cal_Hgamma 1.1725 12 0.098 17.% + Gint_Gamma distri_vl_value 0.76725 12 0.064 11.% + Gint_Gamma distri_vl 2.5007 6 0.42 36.% + LCAO_Deepks cal_projected_DM 4.9172 14 0.35 71.% + LCAO_gen_fixedH add_v_delta 2.3639 6 0.39 34.% + LCAO_DESCRIPTOR add_v_delta 2.3640 6 0.39 34.% + ElecStateLCAO psiToRho 1.0564 12 0.088 15.% + Charge mix_rho 0.81215 11 0.074 12.% + LOOP_ions force_stress 0.55148 1 0.55 7.9% + Force_Stress_LCAO getForceStress 0.55145 1 0.55 7.9% + Force_LCAO_gamma ftable_gamma 0.33404 1 0.33 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:00 2022 + Finish Time : Wed Sep 28 11:04:07 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..928ba75fb5ed6c2d78e1a038bcc9e0e953903e27 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123877 ima = 3.69264e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 1 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122511305691 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111509936722 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011200187591 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112282751604 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011220886186 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112249409325 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112247551226 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112250438481 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112249749238 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112249659279 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112249642655 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112249636333 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b1e5255f842a6212a12e290c06e6f49eaf8baf40 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.397644632153 22.578563030384 12.825559060075 0 0 0 +H +0.0 +2 +-17.345755923128 21.169379647744 13.473467645185 0 0 0 +-15.463627841746 23.012000957352 14.299437976636 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/conv new file mode 100644 index 0000000000000000000000000000000000000000..47c80f00c10a7dd4718fc005c3a6e3f5a5490d15 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/conv @@ -0,0 +1 @@ +53 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..479647960aaa3445f15882693dd538442602f5d5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752913471 0.01286790314 1.284713985 1.366327452 1.470375048 0.009345556428 0.01750461725 0.03912210144 +3.178963657e-19 0.001018215017 0.002901438433 0.01350313879 0.0483424823 -1.534756676e-19 2.879387565e-06 7.508505768e-06 +0.001601787572 0.006136624595 + +H atom_index 1 n_descriptor 18 +1.260772714 0.03437072341 0.1144706632 0.154573537 0.3230435136 0.02361097395 0.02886477357 0.03750265332 +9.512422223e-19 5.36052627e-05 0.1062963362 0.1161695729 0.1327439933 1.034943993e-18 2.829359259e-06 0.01333178559 +0.02758981313 0.03123974387 + +H atom_index 2 n_descriptor 18 +1.276404915 0.03385860105 0.1203210472 0.1622380461 0.3278738 0.02437701819 0.02977174955 0.03713793564 +1.758556343e-17 5.512913411e-05 0.1080990456 0.1188874058 0.139293174 -4.51322096e-18 1.947676955e-06 0.01339238874 +0.02812802554 0.03189521488 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..97613c43edc71841b3f4e495f6e7fee0552e8f40 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:00 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0875481 SEC) : SETUP UNITCELL + DONE(0.0889133 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107282 SEC) : INIT PLANEWAVE + DONE(0.157337 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44276 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651575e+02 0.000000e+00 2.156e-01 5.080e-01 + GE2 -4.663822e+02 -1.224683e+00 9.732e-02 4.506e-01 + GE3 -4.663857e+02 -3.471859e-03 6.223e-02 5.199e-01 + GE4 -4.663859e+02 -2.712780e-04 1.990e-03 3.808e-01 + GE5 -4.663849e+02 9.842509e-04 9.116e-04 3.811e-01 + GE6 -4.663856e+02 -6.993615e-04 9.847e-05 3.723e-01 + GE7 -4.663854e+02 2.162958e-04 4.269e-05 3.678e-01 + GE8 -4.663855e+02 -2.653556e-05 1.575e-05 3.555e-01 + GE9 -4.663854e+02 1.942227e-05 2.192e-06 3.610e-01 + GE10 -4.663854e+02 -3.089017e-06 4.094e-07 3.604e-01 + GE11 -4.663854e+02 -4.226581e-07 1.264e-07 3.587e-01 + GE12 -4.663854e+02 -5.821514e-08 1.035e-08 2.871e-01 +E_delta_band = -7.19222503e-02 Ry = -9.78552418e-01 eV +E_delta_NN= -1.95494732e-01 Ry = -2.65984228e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9616 11 0.63 1e+02 % + Run_lcao lcao_line 6.9522 1 7 1e+02 % + Potential init_pot 0.28713 2 0.14 4.1 % + PW_Basis recip2real 0.29063 17 0.017 4.2 % + PW_Basis gathers_scatterp 0.13776 17 0.0081 2 % + Potential v_of_rho 1.0691 14 0.076 15 % + XC_Functional v_xc 0.33555 15 0.022 4.8 % + H_Hartree_pw v_hartree 0.69451 14 0.05 10 % + PW_Basis real2recip 0.70851 41 0.017 10 % + PW_Basis gatherp_scatters 0.3135 41 0.0076 4.5 % + ORB_control set_orb_tables 1.1047 1 1.1 16 % + ORB_gen_tables gen_tables 1.1047 1 1.1 16 % + ORB_table_phi init_Table 0.48118 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47593 126 0.0038 6.8 % + ORB_table_beta init_Table_Beta 0.18736 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.1858 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24959 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24761 66 0.0038 3.6 % + LOOP_ions opt_ions 5.3195 1 5.3 76 % + ESolver_KS_LCAO Run 4.7678 1 4.8 68 % + HSolverLCAO solve 2.2923 12 0.19 33 % + HamiltLCAO updateHk 1.2023 12 0.1 17 % + LCAO_Hamilt cal_Hgamma 1.1725 12 0.098 17 % + Gint_Gamma distri_vl_value 0.76725 12 0.064 11 % + Gint_Gamma distri_vl 2.5007 6 0.42 36 % + LCAO_Deepks cal_projected_DM 4.9172 14 0.35 71 % + LCAO_gen_fixedH add_v_delta 2.3639 6 0.39 34 % + LCAO_DESCRIPTOR add_v_delta 2.364 6 0.39 34 % + ElecStateLCAO psiToRho 1.0564 12 0.088 15 % + Charge mix_rho 0.81215 11 0.074 12 % + LOOP_ions force_stress 0.55148 1 0.55 7.9 % + Force_Stress_LCAO getForceStress 0.55145 1 0.55 7.9 % + Force_LCAO_gamma ftable_gamma 0.33404 1 0.33 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:00 2022 + FINISH Time : Wed Sep 28 11:04:07 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/53/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..307225b8de88b4ea2549bed955b2d76f6460704c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.40158 0.794186 0.450618 +H 0.399866 0.727534 0.44545 +H 0.392747 0.803365 0.517373 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..26edcbe7a8bf099ff07f530a36301b56bf5a5960 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0141 2 + 2 -12.675 2 + 3 -9.18144 2 + 4 -6.68593 2 + 5 1.01886 0 + 6 3.93638 0 + 7 11.1465 0 + 8 11.4047 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0619a7d206226723c7d8b8da4d3a9b1242dffc0a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/running_scf.log @@ -0,0 +1,799 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:44 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.2442442011 22.2372013699 12.6173150784 0 0 0 0 + tauc_H1 11.1962589857 20.3709528237 12.4726096757 0 0 0 0 + tauc_H2 10.9969110589 22.4942328424 14.486436399 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.126034699333 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.126598926312 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.14516697292 (SEC) + + DONE : INIT CHARGE Time : 0.221541315368 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.560595 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 +receiver_size is 324 ; receiver_size of each process is: +81 81 81 81 +sender_size is 369 ; sender_size of each process is: +81 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000512 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00161 + + Density error is 0.210147516352 + + Energy Rydberg eV + E_KohnSham -34.1929783934 -465.219337741 + E_Harris -34.3748877418 -467.694341399 + E_Fermi -0.385705974079 -5.24779900011 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000770914518328 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00141221566327 + + Density error is 0.098548805454 + + Energy Rydberg eV + E_KohnSham -34.2792469635 -466.393081853 + E_Harris -34.2863097226 -466.48917562 + E_Fermi -0.1985931904 -2.70199897344 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000743022447178 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00129799655407 + + Density error is 0.0634878484185 + + Energy Rydberg eV + E_KohnSham -34.2795398752 -466.397067121 + E_Harris -34.2840785809 -466.45881938 + E_Fermi -0.191231144185 -2.60183319598 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000715411852037 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107763330591 + + Density error is 0.00195237005289 + + Energy Rydberg eV + E_KohnSham -34.2794475633 -466.395811154 + E_Harris -34.2794492504 -466.395834108 + E_Fermi -0.15605852695 -2.123285188 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000714929888261 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107559750748 + + Density error is 0.000817509065181 + + Energy Rydberg eV + E_KohnSham -34.2794259921 -466.395517662 + E_Harris -34.2794261454 -466.395519747 + E_Fermi -0.155992019908 -2.12238031328 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000714748779075 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107274048003 + + Density error is 0.000164472710238 + + Energy Rydberg eV + E_KohnSham -34.2794347191 -466.395636399 + E_Harris -34.2794347117 -466.395636298 + E_Fermi -0.155568911899 -2.11662363348 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000714860194901 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107269106032 + + Density error is 2.24574577201e-05 + + Energy Rydberg eV + E_KohnSham -34.2794334276 -466.395618827 + E_Harris -34.2794334284 -466.395618839 + E_Fermi -0.155546346464 -2.11631661499 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000714821555809 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107263675091 + + Density error is 9.09105701103e-06 + + Energy Rydberg eV + E_KohnSham -34.2794349606 -466.395639684 + E_Harris -34.279434961 -466.395639689 + E_Fermi -0.155553412225 -2.11641274961 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00071482642921 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107262437346 + + Density error is 1.77386825762e-06 + + Energy Rydberg eV + E_KohnSham -34.2794342479 -466.395629987 + E_Harris -34.2794342479 -466.395629987 + E_Fermi -0.155545034663 -2.11629876702 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000714826419891 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107261898298 + + Density error is 4.20013430115e-07 + + Energy Rydberg eV + E_KohnSham -34.2794344098 -466.395632191 + E_Harris -34.2794344098 -466.395632191 + E_Fermi -0.155543810465 -2.11628211096 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000714827057397 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107261874129 + + Density error is 1.43191750898e-07 + + Energy Rydberg eV + E_KohnSham -34.2794344138 -466.395632245 + E_Harris -34.2794344138 -466.395632245 + E_Fermi -0.155543603125 -2.11627928995 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000714827295948 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00107261836422 + + Density error is 1.1276851101e-08 + + Energy Rydberg eV + E_KohnSham -34.2794344177 -466.395632297 + E_Harris -34.2794344177 -466.395632297 + E_band -7.87264806453 -107.112872026 + E_one_elec -68.6476498402 -933.999192135 + E_Hartree +35.7327267632 +486.168689056 + E_xc -8.16031534558 -111.026786177 + E_Ewald +6.92142626974 +94.1708355553 + E_demet -2.52983461253e-60 -3.44201657281e-59 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193693852911 -2.63534006717 + E_Fermi -0.155543474329 -2.11627753759 + + charge density convergence is achieved + final etot is -466.395632297 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0141 2.00000 + 2 -12.6750 2.00000 + 3 -9.18144 2.00000 + 4 -6.68593 2.00000 + 5 1.01886 0.00000 + 6 3.93638 0.00000 + 7 11.1465 0.00000 + 8 11.4047 0.00000 + + EFERMI = -2.116277537587969 eV + OUT.ABACUS/ final etot is -466.3956322974655 eV + correction force for each atom along direction 1 is -0.000115814 + correction force for each atom along direction 2 is -5.08668e-05 + correction force for each atom along direction 3 is 0.000136775 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.21215385 -0.55672094 +1.3631855 + H1 +0.032035299 +0.64487111 -0.045045556 + H2 +0.18011855 -0.088150171 -1.3181399 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3956322974655 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9166 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9054 1 6.9 1.e+02% + Potential init_pot 0.30074 2 0.15 4.3% + PW_Basis recip2real 0.29645 17 0.017 4.3% + PW_Basis gathers_scatterp 0.13418 17 0.0079 1.9% + Potential v_of_rho 0.95055 14 0.068 14.% + XC_Functional v_xc 0.24564 15 0.016 3.6% + H_Hartree_pw v_hartree 0.66499 14 0.047 9.6% + PW_Basis real2recip 0.61524 41 0.015 8.9% + PW_Basis gatherp_scatters 0.24897 41 0.0061 3.6% + ORB_control set_orb_tables 1.1989 1 1.2 17.% + ORB_gen_tables gen_tables 1.1989 1 1.2 17.% + ORB_table_phi init_Table 0.48797 1 0.49 7.1% + ORB_table_phi cal_ST_Phi12_R 0.47950 126 0.0038 6.9% + ORB_table_beta init_Table_Beta 0.19176 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.19026 56 0.0034 2.8% + ORB_table_alpha init_Table_Alpha 0.26221 1 0.26 3.8% + ORB_table_alpha S_PhiAlpha_R 0.26028 66 0.0039 3.8% + LOOP_ions opt_ions 5.0449 1 5.0 73.% + ESolver_KS_LCAO Run 4.5154 1 4.5 65.% + HSolverLCAO solve 2.2735 12 0.19 33.% + HamiltLCAO updateHk 1.1981 12 0.10 17.% + LCAO_Hamilt cal_Hgamma 1.1643 12 0.097 17.% + Gint_Gamma distri_vl_value 0.70778 12 0.059 10.% + Gint_Gamma distri_vl 2.4478 6 0.41 35.% + LCAO_Deepks cal_projected_DM 4.6429 14 0.33 67.% + LCAO_gen_fixedH add_v_delta 2.2498 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2499 6 0.37 33.% + ElecStateLCAO psiToRho 1.0039 12 0.084 15.% + Charge mix_rho 0.80342 11 0.073 12.% + LOOP_ions force_stress 0.52931 1 0.53 7.7% + Force_Stress_LCAO getForceStress 0.52928 1 0.53 7.7% + Force_LCAO_gamma ftable_gamma 0.31980 1 0.32 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:44 2022 + Finish Time : Wed Sep 28 11:01:51 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..498b00b695c3f9e746a83fd8c810b010cf3010fd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123741 ima = 3.69499e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123237136153 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112037583535 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112763716692 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112942245702 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112935285553 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112939982576 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011293787563 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112939228273 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112938772399 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112938749194 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112938732057 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112938725201 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/STRU new file mode 100644 index 0000000000000000000000000000000000000000..884d0be6255396dcaf48ab11eae323a9c93f1d5d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.755755798865 22.237201369919 12.617315078425 0 0 0 +H +0.0 +2 +-16.803741014358 20.370952823646 12.472609675736 0 0 0 +-17.003088941145 22.494232842350 14.486436399014 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/conv new file mode 100644 index 0000000000000000000000000000000000000000..a172cd11a929677ef774a9d27f645358ed2ffa0c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/conv @@ -0,0 +1 @@ +54 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..01fd813d5975d28333f96df3e4b2e295f43f8900 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751478386 0.01246860729 1.246100083 1.335907235 1.468155555 0.00868000566 0.01738454159 0.0391328251 +-3.265196303e-19 0.0008668053681 0.002469373097 0.0116987645 0.04221175514 5.033228591e-20 1.807092959e-06 5.413114129e-06 +0.001590853921 0.005934587396 + +H atom_index 1 n_descriptor 18 +1.216747359 0.03560395377 0.09709702561 0.1351674606 0.3098041389 0.02064907203 0.02635658889 0.03889919382 +-1.19439755e-17 3.91047629e-05 0.09063691677 0.1143337989 0.1156313486 2.652970245e-18 5.255151142e-06 0.01375576058 +0.02450023825 0.02912012702 + +H atom_index 2 n_descriptor 18 +1.192867024 0.03635625148 0.08981260555 0.1253027822 0.3008897323 0.01953049522 0.02495491261 0.03986496279 +1.672189934e-17 3.707617132e-05 0.08448072297 0.1069552573 0.113329142 1.431997114e-17 6.103135471e-06 0.01441328959 +0.02351325154 0.02786205777 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..8882172ab40645e1710832a649c489e8a9eab39c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:44 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.126056 SEC) : SETUP UNITCELL + DONE(0.126614 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.14519 SEC) : INIT PLANEWAVE + DONE(0.22167 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.560662 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652193e+02 0.000000e+00 2.101e-01 6.975e-01 + GE2 -4.663931e+02 -1.173744e+00 9.855e-02 4.075e-01 + GE3 -4.663971e+02 -3.985268e-03 6.349e-02 4.576e-01 + GE4 -4.663958e+02 1.255967e-03 1.952e-03 3.418e-01 + GE5 -4.663955e+02 2.934914e-04 8.175e-04 3.468e-01 + GE6 -4.663956e+02 -1.187366e-04 1.645e-04 3.333e-01 + GE7 -4.663956e+02 1.757229e-05 2.246e-05 3.183e-01 + GE8 -4.663956e+02 -2.085752e-05 9.091e-06 3.183e-01 + GE9 -4.663956e+02 9.696931e-06 1.774e-06 3.214e-01 + GE10 -4.663956e+02 -2.203454e-06 4.200e-07 3.191e-01 + GE11 -4.663956e+02 -5.428494e-08 1.432e-07 3.211e-01 + GE12 -4.663956e+02 -5.255457e-08 1.128e-08 2.649e-01 +E_delta_band = -6.80715881e-02 Ry = -9.26161470e-01 eV +E_delta_NN= -1.93693853e-01 Ry = -2.63534007e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9166 11 0.63 1e+02 % + Run_lcao lcao_line 6.9054 1 6.9 1e+02 % + Potential init_pot 0.30074 2 0.15 4.3 % + PW_Basis recip2real 0.29645 17 0.017 4.3 % + PW_Basis gathers_scatterp 0.13418 17 0.0079 1.9 % + Potential v_of_rho 0.95055 14 0.068 14 % + XC_Functional v_xc 0.24564 15 0.016 3.6 % + H_Hartree_pw v_hartree 0.66499 14 0.047 9.6 % + PW_Basis real2recip 0.61524 41 0.015 8.9 % + PW_Basis gatherp_scatters 0.24897 41 0.0061 3.6 % + ORB_control set_orb_tables 1.1989 1 1.2 17 % + ORB_gen_tables gen_tables 1.1989 1 1.2 17 % + ORB_table_phi init_Table 0.48797 1 0.49 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.4795 126 0.0038 6.9 % + ORB_table_beta init_Table_Beta 0.19176 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.19026 56 0.0034 2.8 % + ORB_table_alpha init_Table_Alpha 0.26221 1 0.26 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.26028 66 0.0039 3.8 % + LOOP_ions opt_ions 5.0449 1 5 73 % + ESolver_KS_LCAO Run 4.5154 1 4.5 65 % + HSolverLCAO solve 2.2735 12 0.19 33 % + HamiltLCAO updateHk 1.1981 12 0.1 17 % + LCAO_Hamilt cal_Hgamma 1.1643 12 0.097 17 % + Gint_Gamma distri_vl_value 0.70778 12 0.059 10 % + Gint_Gamma distri_vl 2.4478 6 0.41 35 % + LCAO_Deepks cal_projected_DM 4.6429 14 0.33 67 % + LCAO_gen_fixedH add_v_delta 2.2498 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2499 6 0.37 33 % + ElecStateLCAO psiToRho 1.0039 12 0.084 15 % + Charge mix_rho 0.80342 11 0.073 12 % + LOOP_ions force_stress 0.52931 1 0.53 7.7 % + Force_Stress_LCAO getForceStress 0.52928 1 0.53 7.7 % + Force_LCAO_gamma ftable_gamma 0.3198 1 0.32 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:44 2022 + FINISH Time : Wed Sep 28 11:01:51 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/54/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b73a7c04a949b291e48318afbc7add4966594226 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.383815 0.780552 0.435 +H 0.388495 0.726022 0.399345 +H 0.360034 0.758688 0.488144 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f26eaf3f403afa05adfc54ed49cdb6312b8cbc2c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6627 2 + 2 -13.1668 2 + 3 -9.29556 2 + 4 -6.82464 2 + 5 1.50207 0 + 6 4.8574 0 + 7 10.9945 0 + 8 11.2487 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..2f1b91a206a179aac9db14c2bfc3d84849d984dc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:00 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 10.7468180415 21.8554607777 12.1799975037 0 0 0 0 + tauc_H1 10.8778498731 20.328610344 11.1816484501 0 0 0 0 + tauc_H2 10.0809446962 21.2432556588 13.668032479 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0878341478013 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0882643338983 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106669308158 (SEC) + + DONE : INIT CHARGE Time : 0.15798422447 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.439456 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 18 + lgd_last = 0 + lgd_now = 18 + allocate DM , the dimension is 18 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 9 + nCol_in_proc = 9 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 9 + nCol_in_proc = 9 +receiver_size is 324 ; receiver_size of each process is: +81 81 81 81 +sender_size is 369 ; sender_size of each process is: +81 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000707 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00131 + + Density error is 0.217669264167 + + Energy Rydberg eV + E_KohnSham -34.1838789645 -465.09553366 + E_Harris -34.3822125231 -467.794000162 + E_Fermi -0.425136895074 -5.78428420303 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000938607618052 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00124493345878 + + Density error is 0.0971148201617 + + Energy Rydberg eV + E_KohnSham -34.2745338706 -466.328956934 + E_Harris -34.281183044 -466.419423579 + E_Fermi -0.233000907914 -3.1701399868 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000894471631847 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.00114754831385 + + Density error is 0.0618338371241 + + Energy Rydberg eV + E_KohnSham -34.2747188952 -466.331474322 + E_Harris -34.278947127 -466.389002368 + E_Fermi -0.217592533777 -2.96049830162 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0008373813348 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000990623052188 + + Density error is 0.00206246704266 + + Energy Rydberg eV + E_KohnSham -34.2747822924 -466.332336886 + E_Harris -34.2747851606 -466.33237591 + E_Fermi -0.18166164676 -2.471633504 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000841277620262 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000988640344296 + + Density error is 0.000905032313903 + + Energy Rydberg eV + E_KohnSham -34.2747047578 -466.331281974 + E_Harris -34.2747077018 -466.331322029 + E_Fermi -0.180320067665 -2.45338038399 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000839929914171 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000987511883525 + + Density error is 0.000142249673841 + + Energy Rydberg eV + E_KohnSham -34.2747617621 -466.332057557 + E_Harris -34.2747618391 -466.332058605 + E_Fermi -0.180724325545 -2.45888059462 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000839903330355 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000987512610727 + + Density error is 4.64649015445e-05 + + Energy Rydberg eV + E_KohnSham -34.274741225 -466.331778135 + E_Harris -34.2747412355 -466.331778278 + E_Fermi -0.18055303162 -2.4565500212 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000839882586255 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000987514022266 + + Density error is 1.69926184104e-05 + + Energy Rydberg eV + E_KohnSham -34.2747454668 -466.331835848 + E_Harris -34.2747454676 -466.33183586 + E_Fermi -0.180606839101 -2.45728210954 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000839879906388 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000987481217617 + + Density error is 2.38042871786e-06 + + Energy Rydberg eV + E_KohnSham -34.2747440967 -466.331817207 + E_Harris -34.2747440967 -466.331817207 + E_Fermi -0.180588550503 -2.45703328041 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000839880938863 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000987479531667 + + Density error is 4.62831652982e-07 + + Energy Rydberg eV + E_KohnSham -34.2747442294 -466.331819012 + E_Harris -34.2747442294 -466.331819012 + E_Fermi -0.180586813759 -2.45700965079 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000839881376346 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000987478980635 + + Density error is 1.49725019472e-07 + + Energy Rydberg eV + E_KohnSham -34.2747442631 -466.331819471 + E_Harris -34.2747442631 -466.331819471 + E_Fermi -0.180586512762 -2.45700555552 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000839881425233 + number of non-zero elements in receiver_buffer = 324 + receiver_size = 324 + last receiver_buffer = 0.000987478785066 + + Density error is 1.03731599033e-08 + + Energy Rydberg eV + E_KohnSham -34.2747442668 -466.331819521 + E_Harris -34.2747442668 -466.331819521 + E_band -8.07745419119 -109.899402334 + E_one_elec -69.9267943938 -951.40284663 + E_Hartree +36.3340057197 +494.349508952 + E_xc -8.25748630334 -112.348864882 + E_Ewald +7.69855180545 +104.744170902 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196073494165 -2.66771674742 + E_Fermi -0.18058634462 -2.45700326782 + + charge density convergence is achieved + final etot is -466.331819521 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6627 2.00000 + 2 -13.1668 2.00000 + 3 -9.29556 2.00000 + 4 -6.82464 2.00000 + 5 1.50207 0.00000 + 6 4.85740 0.00000 + 7 10.9945 0.00000 + 8 11.2487 0.00000 + + EFERMI = -2.457003267820913 eV + OUT.ABACUS/ final etot is -466.3318195208436 eV + correction force for each atom along direction 1 is -0.000118991 + correction force for each atom along direction 2 is -4.09996e-05 + correction force for each atom along direction 3 is 9.26126e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.1163284 +1.0692365 -2.4865886 + H1 +0.15028729 -0.20101095 -0.47588315 + H2 -1.2666157 -0.86822553 +2.9624718 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3318195208436 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6076 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5983 1 7.6 1.e+02% + Potential init_pot 0.28382 2 0.14 3.7% + PW_Basis recip2real 0.28341 17 0.017 3.7% + PW_Basis gathers_scatterp 0.13408 17 0.0079 1.8% + Potential v_of_rho 1.1137 14 0.080 15.% + XC_Functional v_xc 0.38372 15 0.026 5.0% + H_Hartree_pw v_hartree 0.68844 14 0.049 9.0% + PW_Basis real2recip 0.71120 41 0.017 9.3% + PW_Basis gatherp_scatters 0.31455 41 0.0077 4.1% + ORB_control set_orb_tables 1.1038 1 1.1 15.% + ORB_gen_tables gen_tables 1.1038 1 1.1 15.% + ORB_table_phi init_Table 0.48379 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47843 126 0.0038 6.3% + ORB_table_beta init_Table_Beta 0.18621 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18460 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24854 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24656 66 0.0037 3.2% + LOOP_ions opt_ions 5.9688 1 6.0 78.% + ESolver_KS_LCAO Run 5.3820 1 5.4 71.% + HSolverLCAO solve 2.8907 12 0.24 38.% + HamiltLCAO updateHk 1.4467 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4170 12 0.12 19.% + Gint_interface cal_gint 0.16328 25 0.0065 2.1% + Gint_Gamma distri_vl_value 0.94245 12 0.079 12.% + Gint_Gamma distri_vl 2.8105 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.5281 14 0.39 73.% + LCAO_gen_fixedH add_v_delta 2.6828 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.6829 6 0.45 35.% + ElecStateLCAO psiToRho 1.3966 12 0.12 18.% + Charge mix_rho 0.78193 11 0.071 10.% + LOOP_ions force_stress 0.58666 1 0.59 7.7% + Force_Stress_LCAO getForceStress 0.58664 1 0.59 7.7% + Force_LCAO_gamma ftable_gamma 0.36941 1 0.37 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:00 2022 + Finish Time : Wed Sep 28 11:06:08 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..897a5a1e6747dbd5a1488f3158eb4586518cfa60 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123991 ima = 3.7006e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 2 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122582835341 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111844443576 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112223933149 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112523134763 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112442683635 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112489552924 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112482239952 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112485166629 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112484709424 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112484612548 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112484596715 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112484589114 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ae5dea0f7725dda197a45e0f6516674a1c3de328 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-17.253181958511 21.855460777672 12.179997503661 0 0 0 +H +0.0 +2 +-17.122150126888 20.328610343967 11.181648450078 0 0 0 +-17.919055303826 21.243255658830 13.668032478998 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/conv new file mode 100644 index 0000000000000000000000000000000000000000..0ee4fdb2fc7577a9c19234372fffb003ba4f1d27 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/conv @@ -0,0 +1 @@ +55 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b4ba8c874cd8923a6d0ffd91bfa05c217eb40efc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75155667 0.01285645372 1.293199273 1.382644966 1.471049441 0.009197339173 0.01845410969 0.03910267423 +9.678930153e-19 0.001135026795 0.002916502527 0.01353901269 0.04936617555 -8.413251598e-19 2.769303714e-06 7.300336567e-06 +0.001608117541 0.006024269135 + +H atom_index 1 n_descriptor 18 +1.250519195 0.03448902509 0.1100722871 0.14976795 0.3199270532 0.02289556649 0.0282781559 0.03756237949 +3.40144225e-17 5.391983367e-05 0.1050634547 0.1148566741 0.1287747528 -5.456029603e-18 3.842180877e-06 0.01332715015 +0.02728120453 0.030805676 + +H atom_index 2 n_descriptor 18 +1.319298 0.03242193391 0.1369746878 0.1850873089 0.3395896215 0.02616273901 0.03219808386 0.03675086113 +8.195282936e-19 6.06672744e-05 0.1076714522 0.1319896848 0.1586322618 -1.944572391e-18 3.77095966e-07 0.01454260956 +0.02944991647 0.03338227518 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..86a56ab56a0aea8b9207a64e1a0d7aad6473e8dc Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:00 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0878564 SEC) : SETUP UNITCELL + DONE(0.0882818 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106689 SEC) : INIT PLANEWAVE + DONE(0.158105 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.439532 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650955e+02 0.000000e+00 2.177e-01 5.628e-01 + GE2 -4.663290e+02 -1.233423e+00 9.711e-02 5.052e-01 + GE3 -4.663315e+02 -2.517388e-03 6.183e-02 5.712e-01 + GE4 -4.663323e+02 -8.625635e-04 2.062e-03 4.380e-01 + GE5 -4.663313e+02 1.054912e-03 9.050e-04 4.358e-01 + GE6 -4.663321e+02 -7.755830e-04 1.422e-04 4.230e-01 + GE7 -4.663318e+02 2.794213e-04 4.646e-05 4.184e-01 + GE8 -4.663318e+02 -5.771284e-05 1.699e-05 4.035e-01 + GE9 -4.663318e+02 1.864101e-05 2.380e-06 4.077e-01 + GE10 -4.663318e+02 -1.804694e-06 4.628e-07 4.087e-01 + GE11 -4.663318e+02 -4.595452e-07 1.497e-07 4.064e-01 + GE12 -4.663318e+02 -4.942532e-08 1.037e-08 3.338e-01 +E_delta_band = -7.30523994e-02 Ry = -9.93928884e-01 eV +E_delta_NN= -1.96073494e-01 Ry = -2.66771675e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6076 11 0.69 1e+02 % + Run_lcao lcao_line 7.5983 1 7.6 1e+02 % + Potential init_pot 0.28382 2 0.14 3.7 % + PW_Basis recip2real 0.28341 17 0.017 3.7 % + PW_Basis gathers_scatterp 0.13408 17 0.0079 1.8 % + Potential v_of_rho 1.1137 14 0.08 15 % + XC_Functional v_xc 0.38372 15 0.026 5 % + H_Hartree_pw v_hartree 0.68844 14 0.049 9 % + PW_Basis real2recip 0.7112 41 0.017 9.3 % + PW_Basis gatherp_scatters 0.31455 41 0.0077 4.1 % + ORB_control set_orb_tables 1.1038 1 1.1 15 % + ORB_gen_tables gen_tables 1.1038 1 1.1 15 % + ORB_table_phi init_Table 0.48379 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47843 126 0.0038 6.3 % + ORB_table_beta init_Table_Beta 0.18621 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.1846 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24854 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24656 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9688 1 6 78 % + ESolver_KS_LCAO Run 5.382 1 5.4 71 % + HSolverLCAO solve 2.8907 12 0.24 38 % + HamiltLCAO updateHk 1.4467 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.417 12 0.12 19 % + Gint_interface cal_gint 0.16328 25 0.0065 2.1 % + Gint_Gamma distri_vl_value 0.94245 12 0.079 12 % + Gint_Gamma distri_vl 2.8105 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.5281 14 0.39 73 % + LCAO_gen_fixedH add_v_delta 2.6828 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.6829 6 0.45 35 % + ElecStateLCAO psiToRho 1.3966 12 0.12 18 % + Charge mix_rho 0.78193 11 0.071 10 % + LOOP_ions force_stress 0.58666 1 0.59 7.7 % + Force_Stress_LCAO getForceStress 0.58664 1 0.59 7.7 % + Force_LCAO_gamma ftable_gamma 0.36941 1 0.37 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:00 2022 + FINISH Time : Wed Sep 28 11:06:08 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/55/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..28b56d73c60313c78486c3d003da671b97bb47f3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.375826 0.786446 0.412259 +H 0.397568 0.75401 0.360844 +H 0.351876 0.736946 0.450756 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..dcca6a710dcdcd328dce7c05ff51b9ef9a0032a9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2813 2 + 2 -12.8873 2 + 3 -9.22204 2 + 4 -6.74342 2 + 5 1.22625 0 + 6 4.33645 0 + 7 11.0838 0 + 8 11.3433 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..da646043760a90a15327ddafc4c5ecacf84cf934 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:52 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 10.5231326613 22.0204872261 11.5432654413 0 0 0 0 + tauc_H1 11.1318944836 21.1122684111 10.1036438408 0 0 0 0 + tauc_H2 9.85254059731 20.6344993314 12.6211695484 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0858121126407 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0982205956994 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116633193296 (SEC) + + DONE : INIT CHARGE Time : 0.165353436361 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445966 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954 + + Density error is 0.213510505261 + + Energy Rydberg eV + E_KohnSham -34.1913099429 -465.196637307 + E_Harris -34.3801904294 -467.766488165 + E_Fermi -0.401967244902 -5.46904494003 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107292516097 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122318176039 + + Density error is 0.0979593371234 + + Energy Rydberg eV + E_KohnSham -34.2797477964 -466.399896034 + E_Harris -34.2865639435 -466.492634473 + E_Fermi -0.21256331523 -2.8920722729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100071870983 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117236201765 + + Density error is 0.0628313407744 + + Energy Rydberg eV + E_KohnSham -34.2800221596 -466.403628937 + E_Harris -34.2844326393 -466.463636591 + E_Fermi -0.202032003706 -2.74878642876 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000884317008418 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011055670994 + + Density error is 0.00195163652737 + + Energy Rydberg eV + E_KohnSham -34.27999395 -466.403245125 + E_Harris -34.2799946972 -466.403255292 + E_Fermi -0.166454316155 -2.2647271564 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883684664784 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110594994179 + + Density error is 0.000843578977414 + + Energy Rydberg eV + E_KohnSham -34.2799439431 -466.402564746 + E_Harris -34.2799448569 -466.40257718 + E_Fermi -0.165911154822 -2.25733706734 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882383428066 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110493854319 + + Density error is 0.000151566823996 + + Energy Rydberg eV + E_KohnSham -34.2799760124 -466.403001072 + E_Harris -34.279976053 -466.403001625 + E_Fermi -0.165807291812 -2.25592393859 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882548060089 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110520976804 + + Density error is 3.59338956539e-05 + + Energy Rydberg eV + E_KohnSham -34.2799641135 -466.402839179 + E_Harris -34.2799641196 -466.402839262 + E_Fermi -0.16571396662 -2.25465418422 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882499487743 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110509931179 + + Density error is 1.58167861878e-05 + + Energy Rydberg eV + E_KohnSham -34.2799679641 -466.402891569 + E_Harris -34.2799679651 -466.402891583 + E_Fermi -0.165747445582 -2.25510968886 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00088249126987 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110510172769 + + Density error is 2.93976958447e-06 + + Energy Rydberg eV + E_KohnSham -34.2799666274 -466.402873383 + E_Harris -34.2799666275 -466.402873383 + E_Fermi -0.165732688888 -2.25490891374 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882489086245 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110510322184 + + Density error is 3.91148034766e-07 + + Energy Rydberg eV + E_KohnSham -34.2799668291 -466.402876126 + E_Harris -34.2799668291 -466.402876126 + E_Fermi -0.165729626051 -2.2548672417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000882489090919 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110510385587 + + Density error is 1.42908999737e-07 + + Energy Rydberg eV + E_KohnSham -34.2799668719 -466.402876709 + E_Harris -34.2799668719 -466.402876709 + E_Fermi -0.165729481616 -2.25486527657 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00088248897619 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110510403277 + + Density error is 1.08092467676e-08 + + Energy Rydberg eV + E_KohnSham -34.2799668747 -466.402876747 + E_Harris -34.2799668747 -466.402876747 + E_band -7.95756773662 -108.268263439 + E_one_elec -69.1856382906 -941.318900519 + E_Hartree +35.9861547185 +489.616753281 + E_xc -8.20108432072 -111.58147654 + E_Ewald +7.24513587016 +98.5751306184 + E_demet -9.4828201245e-74 -1.29020386802e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194660306827 -2.64848934728 + E_Fermi -0.165729353061 -2.25486352748 + + charge density convergence is achieved + final etot is -466.402876747 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2813 2.00000 + 2 -12.8873 2.00000 + 3 -9.22204 2.00000 + 4 -6.74342 2.00000 + 5 1.22625 0.00000 + 6 4.33645 0.00000 + 7 11.0838 0.00000 + 8 11.3433 0.00000 + + EFERMI = -2.254863527479192 eV + OUT.ABACUS/ final etot is -466.4028767465018 eV + correction force for each atom along direction 1 is -7.38924e-05 + correction force for each atom along direction 2 is -7.51594e-05 + correction force for each atom along direction 3 is 4.08082e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.66975086 -0.33652071 +1.2947258 + H1 +0.41655999 -0.39028740 -0.93341811 + H2 +0.25319087 +0.72680811 -0.36130770 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4028767465018 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9018 11 0.63 1.0e+02% + Run_lcao lcao_line 6.8926 1 6.9 1.e+02% + Potential init_pot 0.28627 2 0.14 4.1% + PW_Basis recip2real 0.27636 17 0.016 4.0% + PW_Basis gathers_scatterp 0.12411 17 0.0073 1.8% + Potential v_of_rho 0.92123 14 0.066 13.% + XC_Functional v_xc 0.25655 15 0.017 3.7% + H_Hartree_pw v_hartree 0.62671 14 0.045 9.1% + PW_Basis real2recip 0.60818 41 0.015 8.8% + PW_Basis gatherp_scatters 0.25437 41 0.0062 3.7% + ORB_control set_orb_tables 1.1054 1 1.1 16.% + ORB_gen_tables gen_tables 1.1054 1 1.1 16.% + ORB_table_phi init_Table 0.48084 1 0.48 7.0% + ORB_table_phi cal_ST_Phi12_R 0.47598 126 0.0038 6.9% + ORB_table_beta init_Table_Beta 0.18844 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18694 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25672 1 0.26 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25478 66 0.0039 3.7% + LOOP_ions opt_ions 5.2646 1 5.3 76.% + ESolver_KS_LCAO Run 4.6982 1 4.7 68.% + HSolverLCAO solve 2.5676 12 0.21 37.% + HamiltLCAO updateHk 1.3242 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2935 12 0.11 19.% + Gint_interface cal_gint 0.26840 25 0.011 3.9% + Gint_Gamma distri_vl_value 0.80985 12 0.067 12.% + Gint_Gamma distri_vl 2.4370 6 0.41 35.% + LCAO_Deepks cal_projected_DM 4.8504 14 0.35 70.% + LCAO_gen_fixedH add_v_delta 2.3056 6 0.38 33.% + LCAO_DESCRIPTOR add_v_delta 2.3056 6 0.38 33.% + ElecStateLCAO psiToRho 1.2254 12 0.10 18.% + Charge mix_rho 0.71273 11 0.065 10.% + LOOP_ions force_stress 0.56631 1 0.57 8.2% + Force_Stress_LCAO getForceStress 0.56628 1 0.57 8.2% + Force_LCAO_gamma ftable_gamma 0.35800 1 0.36 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.10486 1 0.10 1.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:52 2022 + Finish Time : Wed Sep 28 11:10:59 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2315aeddfb51346c76c57e3a55fa5bf6d8afffaa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123703 ima = 3.70882e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122972787004 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111944389304 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112527277998 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112761037473 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112719594841 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112745582661 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112738786666 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112741494067 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112740837981 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112740721483 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112740707124 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112740700233 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/STRU new file mode 100644 index 0000000000000000000000000000000000000000..38409a2c988f401ac84d42e494ecc3188e6987e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-17.476867338677 22.020487226087 11.543265441231 0 0 0 +H +0.0 +2 +-16.868105516451 21.112268411137 10.103643840793 0 0 0 +-18.147459402691 20.634499331361 12.621169548455 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/conv new file mode 100644 index 0000000000000000000000000000000000000000..7d4f3a3c61887f688ce4f14d06f271dd8c5379e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/conv @@ -0,0 +1 @@ +56 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..966f0bca1f8cf60d34167ed14a64116ac8f143cd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75116893 0.01267091203 1.265531463 1.356775526 1.469275625 0.008823945913 0.01782042801 0.03909670814 +-1.959230891e-19 0.0009787170958 0.002651201089 0.01244704048 0.04522588135 -5.037778085e-20 2.183405872e-06 6.229023682e-06 +0.001610059515 0.006011583464 + +H atom_index 1 n_descriptor 18 +1.267509589 0.03387382906 0.1150475639 0.1581366942 0.3262018077 0.02328959698 0.02930007256 0.0371425478 +2.19347595e-17 4.818394461e-05 0.1050787851 0.1165497295 0.1356882367 -1.57688626e-17 2.876237083e-06 0.01320618395 +0.02698656074 0.03151385268 + +H atom_index 2 n_descriptor 18 +1.210903348 0.0357800562 0.09588716343 0.1325180312 0.3070980917 0.02060719985 0.02599013225 0.03905038352 +1.286908147e-17 4.29382942e-05 0.09135223103 0.1134771753 0.1137170001 -1.234228906e-17 5.777744326e-06 0.01392832174 +0.02482492785 0.02883635335 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..7ad6bc62dfb1c712176bb0e9dfb37c400974be74 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:52 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0858368 SEC) : SETUP UNITCELL + DONE(0.0982382 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116654 SEC) : INIT PLANEWAVE + DONE(0.165489 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446033 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651966e+02 0.000000e+00 2.135e-01 5.109e-01 + GE2 -4.663999e+02 -1.203259e+00 9.796e-02 4.313e-01 + GE3 -4.664036e+02 -3.732902e-03 6.283e-02 4.891e-01 + GE4 -4.664032e+02 3.838116e-04 1.952e-03 3.803e-01 + GE5 -4.664026e+02 6.803787e-04 8.436e-04 3.757e-01 + GE6 -4.664030e+02 -4.363255e-04 1.516e-04 3.699e-01 + GE7 -4.664028e+02 1.618932e-04 3.593e-05 3.621e-01 + GE8 -4.664029e+02 -5.239066e-05 1.582e-05 3.612e-01 + GE9 -4.664029e+02 1.818646e-05 2.940e-06 3.546e-01 + GE10 -4.664029e+02 -2.743479e-06 3.911e-07 3.527e-01 + GE11 -4.664029e+02 -5.823642e-07 1.429e-07 3.510e-01 + GE12 -4.664029e+02 -3.778583e-08 1.081e-08 2.978e-01 +E_delta_band = -7.01254548e-02 Ry = -9.54105761e-01 eV +E_delta_NN= -1.94660307e-01 Ry = -2.64848935e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9018 11 0.63 1e+02 % + Run_lcao lcao_line 6.8926 1 6.9 1e+02 % + Potential init_pot 0.28627 2 0.14 4.1 % + PW_Basis recip2real 0.27636 17 0.016 4 % + PW_Basis gathers_scatterp 0.12411 17 0.0073 1.8 % + Potential v_of_rho 0.92123 14 0.066 13 % + XC_Functional v_xc 0.25655 15 0.017 3.7 % + H_Hartree_pw v_hartree 0.62671 14 0.045 9.1 % + PW_Basis real2recip 0.60818 41 0.015 8.8 % + PW_Basis gatherp_scatters 0.25437 41 0.0062 3.7 % + ORB_control set_orb_tables 1.1054 1 1.1 16 % + ORB_gen_tables gen_tables 1.1054 1 1.1 16 % + ORB_table_phi init_Table 0.48084 1 0.48 7 % + ORB_table_phi cal_ST_Phi12_R 0.47598 126 0.0038 6.9 % + ORB_table_beta init_Table_Beta 0.18844 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18694 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.25672 1 0.26 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25478 66 0.0039 3.7 % + LOOP_ions opt_ions 5.2646 1 5.3 76 % + ESolver_KS_LCAO Run 4.6982 1 4.7 68 % + HSolverLCAO solve 2.5676 12 0.21 37 % + HamiltLCAO updateHk 1.3242 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.2935 12 0.11 19 % + Gint_interface cal_gint 0.2684 25 0.011 3.9 % + Gint_Gamma distri_vl_value 0.80985 12 0.067 12 % + Gint_Gamma distri_vl 2.437 6 0.41 35 % + LCAO_Deepks cal_projected_DM 4.8504 14 0.35 70 % + LCAO_gen_fixedH add_v_delta 2.3056 6 0.38 33 % + LCAO_DESCRIPTOR add_v_delta 2.3056 6 0.38 33 % + ElecStateLCAO psiToRho 1.2254 12 0.1 18 % + Charge mix_rho 0.71273 11 0.065 10 % + LOOP_ions force_stress 0.56631 1 0.57 8.2 % + Force_Stress_LCAO getForceStress 0.56628 1 0.57 8.2 % + Force_LCAO_gamma ftable_gamma 0.358 1 0.36 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.10486 1 0.1 1.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:52 2022 + FINISH Time : Wed Sep 28 11:10:59 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/56/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..02eef9bfda3dcee27d1ea55c98b522c0b8797759 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.359391 0.787749 0.388427 +H 0.414955 0.808308 0.36423 +H 0.378793 0.730398 0.412685 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8f1559e380efc9e92f6c3fa5cca22aa4c343c87d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5438 2 + 2 -12.9356 2 + 3 -9.38059 2 + 4 -6.80085 2 + 5 1.39485 0 + 6 4.62381 0 + 7 11.0301 0 + 8 11.3049 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..08afdde02f912847cd1bbc98401ac689a5ce3de3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:46 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 10.0629545728 22.0569857296 10.8759539115 0 0 0 0 + tauc_H1 11.6187455415 22.6326123273 10.1984454425 0 0 0 0 + tauc_H2 10.6062115814 20.4511320965 11.5551714122 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0869705355979 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0873230907139 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105354380507 (SEC) + + DONE : INIT CHARGE Time : 0.148286891861 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.430081 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00152 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000671 + + Density error is 0.215353802818 + + Energy Rydberg eV + E_KohnSham -34.1886192082 -465.160027984 + E_Harris -34.3820329768 -467.791557309 + E_Fermi -0.416078742559 -5.66104171548 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00145659699458 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000858481863487 + + Density error is 0.097306989672 + + Energy Rydberg eV + E_KohnSham -34.2783128794 -466.380372986 + E_Harris -34.2850312235 -466.471780748 + E_Fermi -0.224586876262 -3.05566121318 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00134184694374 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00082441695073 + + Density error is 0.0622234774645 + + Energy Rydberg eV + E_KohnSham -34.2785419197 -466.383489239 + E_Harris -34.2828720549 -466.442403752 + E_Fermi -0.211488429757 -2.87744770577 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114438157377 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785862346936 + + Density error is 0.00198981475314 + + Energy Rydberg eV + E_KohnSham -34.2785623299 -466.383766935 + E_Harris -34.2785636892 -466.383785429 + E_Fermi -0.175592766868 -2.38906215699 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114271008222 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787897502383 + + Density error is 0.000890073013099 + + Energy Rydberg eV + E_KohnSham -34.2784926348 -466.382818684 + E_Harris -34.2784949849 -466.382850659 + E_Fermi -0.174634469829 -2.37602385688 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011408753648 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000786976281422 + + Density error is 0.000102992574937 + + Energy Rydberg eV + E_KohnSham -34.2785418899 -466.383488834 + E_Harris -34.278541902 -466.383488999 + E_Fermi -0.174809463154 -2.37840476321 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114058513314 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787070953693 + + Density error is 4.1188051028e-05 + + Energy Rydberg eV + E_KohnSham -34.2785265689 -466.383280382 + E_Harris -34.2785265784 -466.38328051 + E_Fermi -0.174697307333 -2.37687880499 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114059843827 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000786994254032 + + Density error is 1.92447015053e-05 + + Energy Rydberg eV + E_KohnSham -34.2785288182 -466.383310985 + E_Harris -34.2785288199 -466.383311008 + E_Fermi -0.174750489774 -2.37760238922 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114056417582 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787007137322 + + Density error is 2.10686514974e-06 + + Energy Rydberg eV + E_KohnSham -34.2785272267 -466.383289331 + E_Harris -34.2785272267 -466.383289331 + E_Fermi -0.174729349506 -2.37731476112 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114056345346 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787009690767 + + Density error is 5.2873437921e-07 + + Energy Rydberg eV + E_KohnSham -34.2785275283 -466.383293435 + E_Harris -34.2785275283 -466.383293435 + E_Fermi -0.174728198051 -2.37729909477 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114056292484 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787009958294 + + Density error is 1.37853018094e-07 + + Energy Rydberg eV + E_KohnSham -34.2785275516 -466.383293752 + E_Harris -34.2785275516 -466.383293752 + E_Fermi -0.174727840005 -2.37729422331 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114056264947 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00078701007046 + + Density error is 1.06036970941e-08 + + Energy Rydberg eV + E_KohnSham -34.2785275581 -466.38329384 + E_Harris -34.2785275581 -466.38329384 + E_band -8.03499448708 -109.321708423 + E_one_elec -69.6260342295 -947.310794665 + E_Hartree +36.1891420619 +492.378537774 + E_xc -8.23368244438 -112.024996766 + E_Ewald +7.51565078851 +102.255674902 + E_demet -3.95798381161e-86 -5.38511324296e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195472649113 -2.65954183109 + E_Fermi -0.174727684503 -2.37729210759 + + charge density convergence is achieved + final etot is -466.38329384 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5438 2.00000 + 2 -12.9356 2.00000 + 3 -9.38059 2.00000 + 4 -6.80085 2.00000 + 5 1.39485 0.00000 + 6 4.62381 0.00000 + 7 11.0301 0.00000 + 8 11.3049 0.00000 + + EFERMI = -2.377292107589948 eV + OUT.ABACUS/ final etot is -466.3832938404202 eV + correction force for each atom along direction 1 is 7.30305e-05 + correction force for each atom along direction 2 is 1.61561e-05 + correction force for each atom along direction 3 is 0.000127146 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.97309605 -0.29739228 +0.39979078 + H1 +1.2079474 +0.89671905 -0.75803692 + H2 -0.23485132 -0.59932677 +0.35824614 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3832938404202 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2283 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2200 1 7.2 1.e+02% + Potential init_pot 0.28414 2 0.14 3.9% + PW_Basis recip2real 0.26827 17 0.016 3.7% + PW_Basis gathers_scatterp 0.11998 17 0.0071 1.7% + Potential v_of_rho 0.84944 14 0.061 12.% + XC_Functional v_xc 0.21133 15 0.014 2.9% + H_Hartree_pw v_hartree 0.59892 14 0.043 8.3% + PW_Basis real2recip 0.69852 41 0.017 9.7% + PW_Basis gatherp_scatters 0.28344 41 0.0069 3.9% + ORB_control set_orb_tables 1.0969 1 1.1 15.% + ORB_gen_tables gen_tables 1.0969 1 1.1 15.% + ORB_table_phi init_Table 0.47370 1 0.47 6.6% + ORB_table_phi cal_ST_Phi12_R 0.46848 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18641 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18484 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.24770 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24569 66 0.0037 3.4% + LOOP_ions opt_ions 5.6153 1 5.6 78.% + ESolver_KS_LCAO Run 5.0976 1 5.1 71.% + HSolverLCAO solve 2.7554 12 0.23 38.% + HamiltLCAO updateHk 1.4141 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3847 12 0.12 19.% + Gint_interface cal_gint 0.37704 25 0.015 5.2% + Gint_Gamma distri_vl_value 0.81450 12 0.068 11.% + Gint_Gamma distri_vl 2.6494 6 0.44 37.% + LCAO_Deepks cal_projected_DM 5.2563 14 0.38 73.% + LCAO_gen_fixedH add_v_delta 2.5107 6 0.42 35.% + LCAO_DESCRIPTOR add_v_delta 2.5109 6 0.42 35.% + ElecStateLCAO psiToRho 1.3192 12 0.11 18.% + Charge mix_rho 0.89025 11 0.081 12.% + LOOP_ions force_stress 0.51761 1 0.52 7.2% + Force_Stress_LCAO getForceStress 0.51759 1 0.52 7.2% + Force_LCAO_gamma ftable_gamma 0.32568 1 0.33 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.11617 1 0.12 1.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:46 2022 + Finish Time : Wed Sep 28 11:14:54 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..f139b304394b3d9e22fd3829483c833c748efaee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123819 ima = 3.66635e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122501207247 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111543796885 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112031110488 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112310085394 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112239061401 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112277785627 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112275494103 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112278585256 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011227772044 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112277642906 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112277620631 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112277613751 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e8df3deaa78b85bd07f502ac29f6df0182225cbb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-17.937045427179 22.056985729615 10.875953911534 0 0 0 +H +0.0 +2 +-16.381254458462 22.632612327311 10.198445442534 0 0 0 +-17.393788418624 20.451132096533 11.555171412180 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/conv new file mode 100644 index 0000000000000000000000000000000000000000..6d2c257b607dbd767fb587e7b7269b99452115f1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/conv @@ -0,0 +1 @@ +57 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..fe04a85fa93a08b41893fa61815b8b388902b9b3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752963508 0.01286042872 1.283681759 1.366217533 1.470344849 0.009350285957 0.01748486961 0.03912298572 +2.576963818e-18 0.001013616968 0.002898999021 0.01348247883 0.04828357326 6.058466211e-20 2.870295906e-06 7.497474062e-06 +0.001600321041 0.006134031262 + +H atom_index 1 n_descriptor 18 +1.281178436 0.03371211662 0.1221666023 0.1646558747 0.3293102437 0.02461043295 0.03004761456 0.03705881807 +-9.482235545e-18 5.546185941e-05 0.1083248582 0.1199776886 0.1413375744 9.763783945e-19 1.68903284e-06 0.01344552062 +0.02827083677 0.03208375057 + +H atom_index 2 n_descriptor 18 +1.254168776 0.03459689383 0.1120795799 0.1514406052 0.3209328031 0.02328620728 0.02847973628 0.03769728649 +1.224110359e-17 5.28368496e-05 0.1050269806 0.115459349 0.1300412436 -2.418512514e-18 3.206985882e-06 0.01335479914 +0.02733788295 0.03094635804 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..366c2b2af8b8b57d7336bd9e69b3186dba3fd7da Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:46 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0869935 SEC) : SETUP UNITCELL + DONE(0.0873383 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105376 SEC) : INIT PLANEWAVE + DONE(0.148417 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.430147 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651600e+02 0.000000e+00 2.154e-01 5.186e-01 + GE2 -4.663804e+02 -1.220345e+00 9.731e-02 4.755e-01 + GE3 -4.663835e+02 -3.116253e-03 6.222e-02 5.406e-01 + GE4 -4.663838e+02 -2.776955e-04 1.990e-03 4.061e-01 + GE5 -4.663828e+02 9.482504e-04 8.901e-04 4.071e-01 + GE6 -4.663835e+02 -6.701503e-04 1.030e-04 4.007e-01 + GE7 -4.663833e+02 2.084528e-04 4.119e-05 3.948e-01 + GE8 -4.663833e+02 -3.060337e-05 1.924e-05 3.918e-01 + GE9 -4.663833e+02 2.165374e-05 2.107e-06 3.888e-01 + GE10 -4.663833e+02 -4.104013e-06 5.287e-07 3.868e-01 + GE11 -4.663833e+02 -3.169522e-07 1.379e-07 3.890e-01 + GE12 -4.663833e+02 -8.812007e-08 1.060e-08 3.360e-01 +E_delta_band = -7.18689145e-02 Ry = -9.77826746e-01 eV +E_delta_NN= -1.95472649e-01 Ry = -2.65954183e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2283 11 0.66 1e+02 % + Run_lcao lcao_line 7.22 1 7.2 1e+02 % + Potential init_pot 0.28414 2 0.14 3.9 % + PW_Basis recip2real 0.26827 17 0.016 3.7 % + PW_Basis gathers_scatterp 0.11998 17 0.0071 1.7 % + Potential v_of_rho 0.84944 14 0.061 12 % + XC_Functional v_xc 0.21133 15 0.014 2.9 % + H_Hartree_pw v_hartree 0.59892 14 0.043 8.3 % + PW_Basis real2recip 0.69852 41 0.017 9.7 % + PW_Basis gatherp_scatters 0.28344 41 0.0069 3.9 % + ORB_control set_orb_tables 1.0969 1 1.1 15 % + ORB_gen_tables gen_tables 1.0969 1 1.1 15 % + ORB_table_phi init_Table 0.4737 1 0.47 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.46848 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.18641 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18484 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.2477 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24569 66 0.0037 3.4 % + LOOP_ions opt_ions 5.6153 1 5.6 78 % + ESolver_KS_LCAO Run 5.0976 1 5.1 71 % + HSolverLCAO solve 2.7554 12 0.23 38 % + HamiltLCAO updateHk 1.4141 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3847 12 0.12 19 % + Gint_interface cal_gint 0.37704 25 0.015 5.2 % + Gint_Gamma distri_vl_value 0.8145 12 0.068 11 % + Gint_Gamma distri_vl 2.6494 6 0.44 37 % + LCAO_Deepks cal_projected_DM 5.2563 14 0.38 73 % + LCAO_gen_fixedH add_v_delta 2.5107 6 0.42 35 % + LCAO_DESCRIPTOR add_v_delta 2.5109 6 0.42 35 % + ElecStateLCAO psiToRho 1.3192 12 0.11 18 % + Charge mix_rho 0.89025 11 0.081 12 % + LOOP_ions force_stress 0.51761 1 0.52 7.2 % + Force_Stress_LCAO getForceStress 0.51759 1 0.52 7.2 % + Force_LCAO_gamma ftable_gamma 0.32568 1 0.33 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.11617 1 0.12 1.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:46 2022 + FINISH Time : Wed Sep 28 11:14:54 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/57/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..23cf74edc1eea321ac3a6686fe3f99d6dd12d934 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.340835 0.788579 0.382896 +H 0.374418 0.838093 0.355532 +H 0.342832 0.733129 0.345248 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..aa39a4a483da12b81fa73d47dffeb131a413afdd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9841 2 + 2 -13.2646 2 + 3 -8.69591 2 + 4 -6.66821 2 + 5 1.16408 0 + 6 4.25744 0 + 7 11.1287 0 + 8 11.3432 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7fa6f493bec11cffc277ea00ae4ea7a91a58f6df --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:40 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.54337233603 22.0802135774 10.7210761292 0 0 0 0 + tauc_H1 10.4836917095 23.4665946557 9.95488478055 0 0 0 0 + tauc_H2 9.59928723751 20.5276122103 9.6669364758 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0875127377805 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0878684443489 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105811203315 (SEC) + + DONE : INIT CHARGE Time : 0.154058545539 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.433828 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00131 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000757 + + Density error is 0.213975863021 + + Energy Rydberg eV + E_KohnSham -34.1902017477 -465.181559538 + E_Harris -34.3792040091 -467.753067229 + E_Fermi -0.393617206182 -5.35543683492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012475723672 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104312457609 + + Density error is 0.0985875878528 + + Energy Rydberg eV + E_KohnSham -34.2778085858 -466.37351172 + E_Harris -34.2845561321 -466.465316798 + E_Fermi -0.203512304142 -2.76892694944 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115751926575 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010131411034 + + Density error is 0.0633067222052 + + Energy Rydberg eV + E_KohnSham -34.2779658369 -466.375651232 + E_Harris -34.2822910131 -466.434498272 + E_Fermi -0.193301545109 -2.63000244569 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000990721387464 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000981194706695 + + Density error is 0.00215849602491 + + Energy Rydberg eV + E_KohnSham -34.2779348058 -466.375229031 + E_Harris -34.2779401615 -466.3753019 + E_Fermi -0.158450088866 -2.15582405719 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00098578751423 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980162433679 + + Density error is 0.000797601257941 + + Energy Rydberg eV + E_KohnSham -34.2779016335 -466.374777699 + E_Harris -34.2779020536 -466.374783415 + E_Fermi -0.157800599536 -2.1469873015 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983770146737 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000979778117142 + + Density error is 0.000199066726523 + + Energy Rydberg eV + E_KohnSham -34.277924013 -466.375082187 + E_Harris -34.277924093 -466.375083277 + E_Fermi -0.157617702151 -2.14449885492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983798881762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980094221324 + + Density error is 3.17888557841e-05 + + Energy Rydberg eV + E_KohnSham -34.2779149889 -466.374959409 + E_Harris -34.2779149935 -466.374959471 + E_Fermi -0.15753049187 -2.14331229818 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983774590013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098000473464 + + Density error is 1.53035257249e-05 + + Energy Rydberg eV + E_KohnSham -34.2779195019 -466.375020811 + E_Harris -34.2779195029 -466.375020824 + E_Fermi -0.15756071782 -2.14372354332 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983744827546 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980008383122 + + Density error is 1.77311268968e-06 + + Energy Rydberg eV + E_KohnSham -34.2779183078 -466.375004565 + E_Harris -34.2779183078 -466.375004565 + E_Fermi -0.157544518558 -2.14350314106 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983741790453 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980010189051 + + Density error is 4.84524021127e-07 + + Energy Rydberg eV + E_KohnSham -34.2779185386 -466.375007704 + E_Harris -34.2779185386 -466.375007704 + E_Fermi -0.157543145104 -2.14348445426 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983741842402 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980010792324 + + Density error is 1.57685488113e-07 + + Energy Rydberg eV + E_KohnSham -34.2779185478 -466.375007829 + E_Harris -34.2779185478 -466.375007829 + E_Fermi -0.157542911716 -2.14348127885 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000983741640052 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098001095362 + + Density error is 9.65717145682e-09 + + Energy Rydberg eV + E_KohnSham -34.2779185513 -466.375007878 + E_Harris -34.2779185513 -466.375007878 + E_band -7.88094759536 -107.225792936 + E_one_elec -68.9362601533 -937.925936895 + E_Hartree +35.8889510705 +488.294229802 + E_xc -8.18465752992 -111.357978585 + E_Ewald +7.07918185788 +96.3172104454 + E_demet -7.72082558797e-67 -1.05047221261e-65 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193929265201 -2.63854301569 + E_Fermi -0.157542757498 -2.1434791806 + + charge density convergence is achieved + final etot is -466.375007878 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9841 2.00000 + 2 -13.2646 2.00000 + 3 -8.69591 2.00000 + 4 -6.66821 2.00000 + 5 1.16408 0.00000 + 6 4.25744 0.00000 + 7 11.1287 0.00000 + 8 11.3432 0.00000 + + EFERMI = -2.143479180598939 eV + OUT.ABACUS/ final etot is -466.3750078775276 eV + correction force for each atom along direction 1 is 0.000177005 + correction force for each atom along direction 2 is 1.04658e-05 + correction force for each atom along direction 3 is -6.44318e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.34948216 -0.68047109 +0.19411964 + H1 +0.065091278 -0.44220943 -0.39015326 + H2 +0.28439088 +1.1226805 +0.19603362 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3750078775276 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1796 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1695 1 7.2 1.e+02% + Potential init_pot 0.28287 2 0.14 3.9% + PW_Basis recip2real 0.27734 17 0.016 3.9% + PW_Basis gathers_scatterp 0.12448 17 0.0073 1.7% + Potential v_of_rho 0.92190 14 0.066 13.% + XC_Functional v_xc 0.26320 15 0.018 3.7% + H_Hartree_pw v_hartree 0.62175 14 0.044 8.7% + PW_Basis real2recip 0.61317 41 0.015 8.5% + PW_Basis gatherp_scatters 0.25583 41 0.0062 3.6% + ORB_control set_orb_tables 1.1135 1 1.1 16.% + ORB_gen_tables gen_tables 1.1135 1 1.1 16.% + ORB_table_phi init_Table 0.48726 1 0.49 6.8% + ORB_table_phi cal_ST_Phi12_R 0.48231 126 0.0038 6.7% + ORB_table_beta init_Table_Beta 0.18987 1 0.19 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18834 56 0.0034 2.6% + ORB_table_alpha init_Table_Alpha 0.25675 1 0.26 3.6% + ORB_table_alpha S_PhiAlpha_R 0.25477 66 0.0039 3.5% + LOOP_ions opt_ions 5.5474 1 5.5 77.% + ESolver_KS_LCAO Run 4.9657 1 5.0 69.% + HSolverLCAO solve 2.8368 12 0.24 40.% + HamiltLCAO updateHk 1.4343 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.4034 12 0.12 20.% + Gint_interface cal_gint 0.61312 25 0.025 8.5% + Gint_Gamma distri_vl_value 0.78523 12 0.065 11.% + Gint_Gamma distri_vl 2.5770 6 0.43 36.% + LCAO_Deepks cal_projected_DM 5.1495 14 0.37 72.% + LCAO_gen_fixedH add_v_delta 2.4446 6 0.41 34.% + LCAO_DESCRIPTOR add_v_delta 2.4446 6 0.41 34.% + ElecStateLCAO psiToRho 1.3826 12 0.12 19.% + Charge mix_rho 0.71069 11 0.065 9.9% + LOOP_ions force_stress 0.58157 1 0.58 8.1% + Force_Stress_LCAO getForceStress 0.58154 1 0.58 8.1% + Force_LCAO_gamma ftable_gamma 0.37182 1 0.37 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.14397 1 0.14 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:40 2022 + Finish Time : Wed Sep 28 11:09:47 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c7df80ef104b142760eea87867b7e44b593bf5ed --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123262 ima = 3.65086e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123932833222 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113137195906 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113667477073 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113842503151 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113817959928 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113836017396 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113827424252 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113829790414 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113829149633 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113829111946 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113829094723 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011382908669 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/STRU new file mode 100644 index 0000000000000000000000000000000000000000..37465506212b89bcbb93f5b27c857a644c20e944 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.456627663954 22.080213577388 10.721076129179 0 0 0 +H +0.0 +2 +-17.516308290535 23.466594655712 9.954884780547 0 0 0 +-18.400712762500 20.527612210312 9.666936475791 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/conv new file mode 100644 index 0000000000000000000000000000000000000000..24e6839043171c70b1b37e9a8de1402c143d04c9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/conv @@ -0,0 +1 @@ +58 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..848d82f3567827b8095ae077f5a89ca3be61e26a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742240298 0.01242935577 1.263557629 1.362771817 1.467925547 0.007319540099 0.02060163271 0.03881705269 +-4.331388589e-18 0.001069946632 0.002187733734 0.01184025157 0.03974733864 -6.403039686e-19 1.202491491e-06 4.015440348e-06 +0.001825007317 0.005468044411 + +H atom_index 1 n_descriptor 18 +1.230962084 0.0341801844 0.1022878426 0.1436997299 0.318402152 0.02082012832 0.02752329815 0.03740547989 +7.67675032e-17 3.182767799e-05 0.09614187892 0.1144501444 0.1231655851 -3.329258195e-19 4.567139154e-06 0.0129617269 +0.02501405727 0.03007374302 + +H atom_index 2 n_descriptor 18 +1.20258908 0.03516961889 0.09340748337 0.1316010373 0.3087723232 0.01959279792 0.0258828096 0.038516899 +-3.528973898e-18 2.983273293e-05 0.08853819893 0.1125855616 0.113795524 -3.53787212e-18 5.420386932e-06 0.01355566441 +0.02388419946 0.02867796358 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0723bb95c347ea55a69bbf6ebf36db3e812bae24 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:40 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0875373 SEC) : SETUP UNITCELL + DONE(0.0878846 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105831 SEC) : INIT PLANEWAVE + DONE(0.155087 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.433895 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651816e+02 0.000000e+00 2.140e-01 5.358e-01 + GE2 -4.663735e+02 -1.191952e+00 9.859e-02 4.552e-01 + GE3 -4.663757e+02 -2.139511e-03 6.331e-02 5.130e-01 + GE4 -4.663752e+02 4.222008e-04 2.158e-03 3.972e-01 + GE5 -4.663748e+02 4.513322e-04 7.976e-04 3.973e-01 + GE6 -4.663751e+02 -3.044883e-04 1.991e-04 3.958e-01 + GE7 -4.663750e+02 1.227785e-04 3.179e-05 3.846e-01 + GE8 -4.663750e+02 -6.140271e-05 1.530e-05 3.756e-01 + GE9 -4.663750e+02 1.624633e-05 1.773e-06 3.772e-01 + GE10 -4.663750e+02 -3.139426e-06 4.845e-07 3.750e-01 + GE11 -4.663750e+02 -1.250327e-07 1.577e-07 3.778e-01 + GE12 -4.663750e+02 -4.805554e-08 9.657e-09 3.208e-01 +E_delta_band = -6.87954687e-02 Ry = -9.36010371e-01 eV +E_delta_NN= -1.93929265e-01 Ry = -2.63854302e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1796 11 0.65 1e+02 % + Run_lcao lcao_line 7.1695 1 7.2 1e+02 % + Potential init_pot 0.28287 2 0.14 3.9 % + PW_Basis recip2real 0.27734 17 0.016 3.9 % + PW_Basis gathers_scatterp 0.12448 17 0.0073 1.7 % + Potential v_of_rho 0.9219 14 0.066 13 % + XC_Functional v_xc 0.2632 15 0.018 3.7 % + H_Hartree_pw v_hartree 0.62175 14 0.044 8.7 % + PW_Basis real2recip 0.61317 41 0.015 8.5 % + PW_Basis gatherp_scatters 0.25583 41 0.0062 3.6 % + ORB_control set_orb_tables 1.1135 1 1.1 16 % + ORB_gen_tables gen_tables 1.1135 1 1.1 16 % + ORB_table_phi init_Table 0.48726 1 0.49 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.48231 126 0.0038 6.7 % + ORB_table_beta init_Table_Beta 0.18987 1 0.19 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18834 56 0.0034 2.6 % + ORB_table_alpha init_Table_Alpha 0.25675 1 0.26 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.25477 66 0.0039 3.5 % + LOOP_ions opt_ions 5.5474 1 5.5 77 % + ESolver_KS_LCAO Run 4.9657 1 5 69 % + HSolverLCAO solve 2.8368 12 0.24 40 % + HamiltLCAO updateHk 1.4343 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.4034 12 0.12 20 % + Gint_interface cal_gint 0.61312 25 0.025 8.5 % + Gint_Gamma distri_vl_value 0.78523 12 0.065 11 % + Gint_Gamma distri_vl 2.577 6 0.43 36 % + LCAO_Deepks cal_projected_DM 5.1495 14 0.37 72 % + LCAO_gen_fixedH add_v_delta 2.4446 6 0.41 34 % + LCAO_DESCRIPTOR add_v_delta 2.4446 6 0.41 34 % + ElecStateLCAO psiToRho 1.3826 12 0.12 19 % + Charge mix_rho 0.71069 11 0.065 9.9 % + LOOP_ions force_stress 0.58157 1 0.58 8.1 % + Force_Stress_LCAO getForceStress 0.58154 1 0.58 8.1 % + Force_LCAO_gamma ftable_gamma 0.37182 1 0.37 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.14397 1 0.14 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:40 2022 + FINISH Time : Wed Sep 28 11:09:47 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/58/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9bbc343474388d59dcec186cbbfc9bcf1058f0a8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.328787 0.773285 0.380088 +H 0.370896 0.815067 0.352531 +H 0.293466 0.759282 0.32956 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bfe31f58d7e59005116cf6c8ec4f2863661a1006 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6019 2 + 2 -12.9761 2 + 3 -9.38889 2 + 4 -6.81261 2 + 5 1.42456 0 + 6 4.70461 0 + 7 11.0165 0 + 8 11.2886 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..bc3086bd9c4efd5abb99b85ff47b56ef8f6228e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:32 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 9.20604568987 21.6519858378 10.6424666263 0 0 0 0 + tauc_H1 10.3850890111 22.821872222 9.87087754614 0 0 0 0 + tauc_H2 8.21705600624 21.2599000069 9.22766901302 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0880009673241 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0937364396451 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.112070568427 (SEC) + + DONE : INIT CHARGE Time : 0.161637376077 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443895 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000823 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122 + + Density error is 0.216575090559 + + Energy Rydberg eV + E_KohnSham -34.185616398 -465.119172655 + E_Harris -34.3817475459 -467.787673821 + E_Fermi -0.419414825236 -5.70643144889 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121184149463 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131277246731 + + Density error is 0.0973719990769 + + Energy Rydberg eV + E_KohnSham -34.276673814 -466.358072357 + E_Harris -34.2833996918 -466.44958262 + E_Fermi -0.227327943015 -3.09295533962 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115707298322 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123089360353 + + Density error is 0.0622531604102 + + Energy Rydberg eV + E_KohnSham -34.2769645539 -466.362028077 + E_Harris -34.2812975361 -466.420981324 + E_Fermi -0.214022886487 -2.91193075862 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010836735927 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011036911338 + + Density error is 0.0020138618771 + + Energy Rydberg eV + E_KohnSham -34.2769913989 -466.362393322 + E_Harris -34.276993163 -466.362417324 + E_Fermi -0.177970855935 -2.42141771865 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108863844636 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110640092515 + + Density error is 0.000934882048306 + + Energy Rydberg eV + E_KohnSham -34.2769158111 -466.361364897 + E_Harris -34.2769183722 -466.361399742 + E_Fermi -0.176981890818 -2.40796215794 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108677198302 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110437439352 + + Density error is 0.00011011046988 + + Energy Rydberg eV + E_KohnSham -34.2769674232 -466.362067116 + E_Harris -34.276967448 -466.362067454 + E_Fermi -0.177173568088 -2.41057006099 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108654262817 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110406179031 + + Density error is 4.44010698588e-05 + + Energy Rydberg eV + E_KohnSham -34.2769506399 -466.361838768 + E_Harris -34.2769506507 -466.361838914 + E_Fermi -0.177046932881 -2.4088471006 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108649413521 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110404634055 + + Density error is 1.98584753355e-05 + + Energy Rydberg eV + E_KohnSham -34.2769535311 -466.361878104 + E_Harris -34.2769535326 -466.361878125 + E_Fermi -0.177103306585 -2.4096141042 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108649428413 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110402839624 + + Density error is 2.05592436019e-06 + + Energy Rydberg eV + E_KohnSham -34.2769519432 -466.3618565 + E_Harris -34.2769519432 -466.3618565 + E_Fermi -0.177081231975 -2.40931376372 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108649664377 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110402973402 + + Density error is 4.75450968015e-07 + + Energy Rydberg eV + E_KohnSham -34.2769522037 -466.361860043 + E_Harris -34.2769522037 -466.361860043 + E_Fermi -0.177079980678 -2.40929673896 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108649743126 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110403009995 + + Density error is 1.54593968989e-07 + + Energy Rydberg eV + E_KohnSham -34.2769522303 -466.361860405 + E_Harris -34.2769522303 -466.361860405 + E_Fermi -0.177079709133 -2.4092930444 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108649753229 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110403004458 + + Density error is 1.06938696212e-08 + + Energy Rydberg eV + E_KohnSham -34.2769522339 -466.361860455 + E_Harris -34.2769522339 -466.361860455 + E_band -8.05243542034 -109.559004494 + E_one_elec -69.7340685698 -948.780677272 + E_Hartree +36.2399247508 +493.069471702 + E_xc -8.2419949952 -112.138094822 + E_Ewald +7.58257728295 +103.166256574 + E_demet -1.79017075463e-88 -2.43565226559e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195690922218 -2.66251158904 + E_Fermi -0.177079535063 -2.40929067605 + + charge density convergence is achieved + final etot is -466.361860455 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6019 2.00000 + 2 -12.9761 2.00000 + 3 -9.38889 2.00000 + 4 -6.81261 2.00000 + 5 1.42456 0.00000 + 6 4.70461 0.00000 + 7 11.0165 0.00000 + 8 11.2886 0.00000 + + EFERMI = -2.409290676045462 eV + OUT.ABACUS/ final etot is -466.3618604551434 eV + correction force for each atom along direction 1 is -3.45244e-05 + correction force for each atom along direction 2 is 3.41256e-05 + correction force for each atom along direction 3 is -7.19330e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.0761161 +0.47111669 +1.3915765 + H1 +0.49633147 +0.33694199 +0.21586237 + H2 -1.5724476 -0.80805868 -1.6074389 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3618604551434 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.2816 11 0.75 1.0e+02% + Run_lcao lcao_line 8.2714 1 8.3 1.e+02% + Potential init_pot 0.28607 2 0.14 3.5% + PW_Basis recip2real 0.28697 17 0.017 3.5% + PW_Basis gathers_scatterp 0.13817 17 0.0081 1.7% + Potential v_of_rho 1.1122 14 0.079 13.% + XC_Functional v_xc 0.38655 15 0.026 4.7% + H_Hartree_pw v_hartree 0.68650 14 0.049 8.3% + PW_Basis real2recip 0.70395 41 0.017 8.5% + PW_Basis gatherp_scatters 0.31095 41 0.0076 3.8% + ORB_control set_orb_tables 1.0954 1 1.1 13.% + ORB_gen_tables gen_tables 1.0954 1 1.1 13.% + ORB_table_phi init_Table 0.47626 1 0.48 5.8% + ORB_table_phi cal_ST_Phi12_R 0.47109 126 0.0037 5.7% + ORB_table_beta init_Table_Beta 0.18385 1 0.18 2.2% + ORB_table_beta VNL_PhiBeta_R 0.18229 56 0.0033 2.2% + ORB_table_alpha init_Table_Alpha 0.24941 1 0.25 3.0% + ORB_table_alpha S_PhiAlpha_R 0.24744 66 0.0037 3.0% + LOOP_ions opt_ions 6.6547 1 6.7 80.% + ESolver_KS_LCAO Run 6.0327 1 6.0 73.% + HSolverLCAO solve 3.5474 12 0.30 43.% + HamiltLCAO updateHk 1.7641 12 0.15 21.% + LCAO_Hamilt cal_Hgamma 1.7343 12 0.14 21.% + Gint_interface cal_gint 0.84954 25 0.034 10.% + Gint_Gamma distri_vl_value 0.98492 12 0.082 12.% + Gint_Gamma distri_vl 3.1381 6 0.52 38.% + LCAO_Deepks cal_projected_DM 6.2378 14 0.45 75.% + LCAO_gen_fixedH add_v_delta 3.0084 6 0.50 36.% + LCAO_DESCRIPTOR add_v_delta 3.0086 6 0.50 36.% + ElecStateLCAO psiToRho 1.7469 12 0.15 21.% + Charge mix_rho 0.77871 11 0.071 9.4% + LOOP_ions force_stress 0.62192 1 0.62 7.5% + Force_Stress_LCAO getForceStress 0.62190 1 0.62 7.5% + Force_LCAO_gamma ftable_gamma 0.40455 1 0.40 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.17100 1 0.17 2.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:32 2022 + Finish Time : Wed Sep 28 11:06:41 2022 + Total Time : 0 h 0 mins 9 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..7ac7ddcca35492c25c91eb69330e95cfc4289c4e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123906 ima = 3.6451e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122580665754 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111555852722 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112044280721 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112340745214 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112265791842 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112307114083 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112303362383 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112306529696 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112305767795 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112305688342 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112305672135 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112305664205 + charge after normalized = 7.99999999999997 + charge before normalized = 7.99999999999997 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/STRU new file mode 100644 index 0000000000000000000000000000000000000000..846e80c468fb4272944a740444f9b2f630b1b2c8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-18.793954310144 21.651985837750 10.642466626272 0 0 0 +H +0.0 +2 +-17.614910988881 22.821872221980 9.870877546141 0 0 0 +-19.782943993752 21.259900006920 9.227669013015 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/conv new file mode 100644 index 0000000000000000000000000000000000000000..3fdf418b18b7377a14bfd36abb05fc4d7a2dc0ec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/conv @@ -0,0 +1 @@ +59 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..90b12209e13d73d953afa29bde45f53e9fefa066 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753048368 0.01287346035 1.286427685 1.371227526 1.470635169 0.00941612187 0.01760062194 0.0391311823 +2.680624337e-18 0.001035307776 0.002939698458 0.01362203276 0.04890129097 -4.074162302e-19 2.950798612e-06 7.63732184e-06 +0.001597017392 0.006120704443 + +H atom_index 1 n_descriptor 18 +1.250026443 0.03474317352 0.1107407188 0.1494809358 0.3194780278 0.02313455069 0.02823498977 0.03782224003 +5.029897576e-17 5.345661246e-05 0.1046822841 0.115060118 0.1283956558 5.380067521e-18 3.448575837e-06 0.01339419059 +0.02731503121 0.03076602646 + +H atom_index 2 n_descriptor 18 +1.298118918 0.03321355895 0.1290739518 0.173444309 0.3340155231 0.02549014374 0.03101185827 0.03687440973 +5.043455179e-17 5.813582687e-05 0.1086015043 0.1250212646 0.1487964029 -1.357990312e-18 8.792428369e-07 0.01379520131 +0.02892350286 0.0327151326 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e1554b127d455e4fe3c36f18ba4be051b938ea97 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:32 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0880262 SEC) : SETUP UNITCELL + DONE(0.0937541 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.112091 SEC) : INIT PLANEWAVE + DONE(0.161769 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443959 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651192e+02 0.000000e+00 2.166e-01 6.048e-01 + GE2 -4.663581e+02 -1.238900e+00 9.737e-02 5.559e-01 + GE3 -4.663620e+02 -3.955719e-03 6.225e-02 6.227e-01 + GE4 -4.663624e+02 -3.652454e-04 2.014e-03 4.851e-01 + GE5 -4.663614e+02 1.028425e-03 9.349e-04 4.883e-01 + GE6 -4.663621e+02 -7.022191e-04 1.101e-04 4.774e-01 + GE7 -4.663618e+02 2.283488e-04 4.440e-05 4.763e-01 + GE8 -4.663619e+02 -3.933662e-05 1.986e-05 4.629e-01 + GE9 -4.663619e+02 2.160413e-05 2.056e-06 4.688e-01 + GE10 -4.663619e+02 -3.543291e-06 4.755e-07 4.662e-01 + GE11 -4.663619e+02 -3.618573e-07 1.546e-07 4.651e-01 + GE12 -4.663619e+02 -4.988403e-08 1.069e-08 3.924e-01 +E_delta_band = -7.23002196e-02 Ry = -9.83694953e-01 eV +E_delta_NN= -1.95690922e-01 Ry = -2.66251159e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.2816 11 0.75 1e+02 % + Run_lcao lcao_line 8.2714 1 8.3 1e+02 % + Potential init_pot 0.28607 2 0.14 3.5 % + PW_Basis recip2real 0.28697 17 0.017 3.5 % + PW_Basis gathers_scatterp 0.13817 17 0.0081 1.7 % + Potential v_of_rho 1.1122 14 0.079 13 % + XC_Functional v_xc 0.38655 15 0.026 4.7 % + H_Hartree_pw v_hartree 0.6865 14 0.049 8.3 % + PW_Basis real2recip 0.70395 41 0.017 8.5 % + PW_Basis gatherp_scatters 0.31095 41 0.0076 3.8 % + ORB_control set_orb_tables 1.0954 1 1.1 13 % + ORB_gen_tables gen_tables 1.0954 1 1.1 13 % + ORB_table_phi init_Table 0.47626 1 0.48 5.8 % + ORB_table_phi cal_ST_Phi12_R 0.47109 126 0.0037 5.7 % + ORB_table_beta init_Table_Beta 0.18385 1 0.18 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.18229 56 0.0033 2.2 % + ORB_table_alpha init_Table_Alpha 0.24941 1 0.25 3 % + ORB_table_alpha S_PhiAlpha_R 0.24744 66 0.0037 3 % + LOOP_ions opt_ions 6.6547 1 6.7 80 % + ESolver_KS_LCAO Run 6.0327 1 6 73 % + HSolverLCAO solve 3.5474 12 0.3 43 % + HamiltLCAO updateHk 1.7641 12 0.15 21 % + LCAO_Hamilt cal_Hgamma 1.7343 12 0.14 21 % + Gint_interface cal_gint 0.84954 25 0.034 10 % + Gint_Gamma distri_vl_value 0.98492 12 0.082 12 % + Gint_Gamma distri_vl 3.1381 6 0.52 38 % + LCAO_Deepks cal_projected_DM 6.2378 14 0.45 75 % + LCAO_gen_fixedH add_v_delta 3.0084 6 0.5 36 % + LCAO_DESCRIPTOR add_v_delta 3.0086 6 0.5 36 % + ElecStateLCAO psiToRho 1.7469 12 0.15 21 % + Charge mix_rho 0.77871 11 0.071 9.4 % + LOOP_ions force_stress 0.62192 1 0.62 7.5 % + Force_Stress_LCAO getForceStress 0.6219 1 0.62 7.5 % + Force_LCAO_gamma ftable_gamma 0.40455 1 0.4 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.171 1 0.17 2.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:32 2022 + FINISH Time : Wed Sep 28 11:06:41 2022 + TOTAL Time : 9 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/59/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..349b45f27f2dd308f65c0603b13bff459f69996c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.623975 0.0986114 0.348822 +H 0.601479 0.0387792 0.360796 +H 0.600245 0.130717 0.400842 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..a321bd2a58b46f6a5352c77c78586a5cc08ea76e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4008 2 + 2 -12.8821 2 + 3 -9.31906 2 + 4 -6.77084 2 + 5 1.31074 0 + 6 4.44934 0 + 7 11.0606 0 + 8 11.3327 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0071395263653eb6a22e1f42a3c84bb91759d64e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:11 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.4712917232 2.76111930438 9.76700643232 0 0 0 0 + tauc_H1 16.8414032847 1.08581653961 10.1022940223 0 0 0 0 + tauc_H2 16.8068561974 3.66006632002 11.2235690883 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0725313724033 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0881244737084 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104385962445 (SEC) + + DONE : INIT CHARGE Time : 0.145521127071 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.391729 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000854 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000966 + + Density error is 0.213578403396 + + Energy Rydberg eV + E_KohnSham -34.1921738798 -465.208391772 + E_Harris -34.3816209375 -467.785951227 + E_Fermi -0.407445775123 -5.54358416769 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103173465456 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121306397374 + + Density error is 0.0974831200124 + + Energy Rydberg eV + E_KohnSham -34.2802488797 -466.406713622 + E_Harris -34.2869887605 -466.498414405 + E_Fermi -0.21797264452 -2.9656699736 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000973758802033 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011593899934 + + Density error is 0.0624543574298 + + Energy Rydberg eV + E_KohnSham -34.2804333387 -466.409223316 + E_Harris -34.2847912816 -466.46851617 + E_Fermi -0.205962828052 -2.8022680377 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883924585412 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108964873809 + + Density error is 0.00194953000651 + + Energy Rydberg eV + E_KohnSham -34.280430789 -466.409188626 + E_Harris -34.2804311173 -466.409193092 + E_Fermi -0.17030107041 -2.31706493307 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000884411476979 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109275830561 + + Density error is 0.000820706815092 + + Energy Rydberg eV + E_KohnSham -34.2803731867 -466.408404906 + E_Harris -34.2803746752 -466.408425158 + E_Fermi -0.169520778535 -2.30644851748 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883181459294 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109131554062 + + Density error is 9.69355385626e-05 + + Energy Rydberg eV + E_KohnSham -34.2804144649 -466.408966525 + E_Harris -34.2804144675 -466.408966559 + E_Fermi -0.169586395883 -2.30734128729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883042369895 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109121572109 + + Density error is 3.49665847607e-05 + + Energy Rydberg eV + E_KohnSham -34.280401595 -466.40879142 + E_Harris -34.2804016019 -466.408791514 + E_Fermi -0.169480250908 -2.30589711081 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883017278683 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109116751072 + + Density error is 1.08423877605e-05 + + Energy Rydberg eV + E_KohnSham -34.2804036251 -466.408819041 + E_Harris -34.2804036256 -466.408819049 + E_Fermi -0.169522822344 -2.30647632491 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883020096849 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109118033589 + + Density error is 1.72479792233e-06 + + Energy Rydberg eV + E_KohnSham -34.2804024415 -466.408802937 + E_Harris -34.2804024415 -466.408802938 + E_Fermi -0.169512579853 -2.30633696868 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883020581387 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109118000941 + + Density error is 1.02541585036e-07 + + Energy Rydberg eV + E_KohnSham -34.2804026112 -466.408805246 + E_Harris -34.2804026112 -466.408805246 + E_Fermi -0.169510793382 -2.30631266249 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000883020772983 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109118031568 + + Density error is 4.16595817253e-08 + + Energy Rydberg eV + E_KohnSham -34.2804026435 -466.408805685 + E_Harris -34.2804026435 -466.408805685 + E_band -7.99266033117 -108.745722683 + E_one_elec -69.3762663097 -943.912527778 + E_Hartree +36.073043489 +490.798935652 + E_xc -8.21491253542 -111.769619053 + E_Ewald +7.36185671404 +100.16319917 + E_demet -2.0779683938e-79 -2.82722104196e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194998084692 -2.6530850509 + E_Fermi -0.169510822264 -2.30631305546 + + charge density convergence is achieved + final etot is -466.408805685 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4008 2.00000 + 2 -12.8821 2.00000 + 3 -9.31906 2.00000 + 4 -6.77084 2.00000 + 5 1.31074 0.00000 + 6 4.44934 0.00000 + 7 11.0606 0.00000 + 8 11.3327 0.00000 + + EFERMI = -2.306313055456454 eV + OUT.ABACUS/ final etot is -466.4088056853377 eV + correction force for each atom along direction 1 is 4.83360e-05 + correction force for each atom along direction 2 is -7.45960e-06 + correction force for each atom along direction 3 is 0.000172250 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.082009712 +0.35043354 +0.023653682 + H1 -0.10908604 -0.77827383 -0.15028443 + H2 +0.027076328 +0.42784029 +0.12663075 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4088056853377 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7910 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7840 1 6.8 1.e+02% + Potential init_pot 0.24756 2 0.12 3.6% + PW_Basis recip2real 0.22874 16 0.014 3.4% + PW_Basis gathers_scatterp 0.10833 16 0.0068 1.6% + Potential v_of_rho 0.89669 13 0.069 13.% + XC_Functional v_xc 0.30205 14 0.022 4.4% + H_Hartree_pw v_hartree 0.56614 13 0.044 8.3% + PW_Basis real2recip 0.60136 38 0.016 8.9% + PW_Basis gatherp_scatters 0.26981 38 0.0071 4.0% + ORB_control set_orb_tables 0.90166 1 0.90 13.% + ORB_gen_tables gen_tables 0.90166 1 0.90 13.% + ORB_table_phi init_Table 0.37773 1 0.38 5.6% + ORB_table_phi cal_ST_Phi12_R 0.37348 126 0.0030 5.5% + ORB_table_beta init_Table_Beta 0.15700 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15568 56 0.0028 2.3% + ORB_table_alpha init_Table_Alpha 0.20928 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20759 66 0.0031 3.1% + LOOP_ions opt_ions 5.4196 1 5.4 80.% + ESolver_KS_LCAO Run 4.8536 1 4.9 71.% + HSolverLCAO solve 2.6959 11 0.25 40.% + HamiltLCAO updateHk 1.3704 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3468 11 0.12 20.% + Gint_interface cal_gint 0.57245 23 0.025 8.4% + Gint_Gamma distri_vl_value 0.74949 11 0.068 11.% + Gint_Gamma distri_vl 2.3304 6 0.39 34.% + LCAO_Deepks cal_projected_DM 5.0405 13 0.39 74.% + LCAO_gen_fixedH add_v_delta 2.2028 6 0.37 32.% + LCAO_DESCRIPTOR add_v_delta 2.2031 6 0.37 32.% + ElecStateLCAO psiToRho 1.3088 11 0.12 19.% + Charge mix_rho 0.72477 10 0.072 11.% + LOOP_ions force_stress 0.56586 1 0.57 8.3% + Force_Stress_LCAO getForceStress 0.56585 1 0.57 8.3% + Force_LCAO_gamma ftable_gamma 0.37063 1 0.37 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.13762 1 0.14 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:11 2022 + Finish Time : Wed Sep 28 11:04:18 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b314199a67e0a8b6556afad57a184f51d7b236d4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123903 ima = 3.70283e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122608795731 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111701621717 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112221209631 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011246843846 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011241167841 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112443556212 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112440857607 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112443324354 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112442815159 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112442736747 + charge after normalized = 8.00000000000004 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112442733376 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/STRU new file mode 100644 index 0000000000000000000000000000000000000000..445a6d7c87384515688c47251d3eee40ff1942b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.528708276786 2.761119304363 9.767006432334 0 0 0 +H +0.0 +2 +-11.158596715331 1.085816539607 10.102294022273 0 0 0 +-11.193143802626 3.660066320000 11.223569088273 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/conv new file mode 100644 index 0000000000000000000000000000000000000000..611599133f51f24f34360308a8d915ce0038219b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/conv @@ -0,0 +1 @@ +6 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f638db6008238f26f3cc816e829301d380c7062a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752304698 0.01278128614 1.274830882 1.358412966 1.46973408 0.009110636344 0.01749174897 0.03911238563 +-8.650806272e-18 0.0009827896676 0.002776063242 0.01298622393 0.04668042013 -1.400568978e-18 2.550959346e-06 6.915012057e-06 +0.001604603689 0.006104537465 + +H atom_index 1 n_descriptor 18 +1.258037725 0.03436453081 0.1126545353 0.1533670171 0.3226229554 0.02320165073 0.02872012918 0.03751579217 +1.508775749e-17 5.031806005e-05 0.1044150116 0.1157926017 0.1316297657 -1.663932628e-18 3.149217941e-06 0.01328271773 +0.02706496763 0.03110623647 + +H atom_index 2 n_descriptor 18 +1.246120915 0.03476757876 0.1084344275 0.1477852773 0.3187315894 0.02262432423 0.02802360505 0.03787912245 +-3.772424223e-17 4.917479998e-05 0.1017797989 0.1149567155 0.126817601 4.282891791e-18 3.82663277e-06 0.01336229659 +0.02662634389 0.03056623911 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..7eb779ddeee9b30e25fbc25d66118a11ff883058 Binary files /dev/null and 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0000000000000000000000000000000000000000..ac543483a4081e7dbee67fcee9e38dd81cc46184 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:11 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0725473 SEC) : SETUP UNITCELL + DONE(0.0881369 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104398 SEC) : INIT PLANEWAVE + DONE(0.145621 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.391774 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652084e+02 0.000000e+00 2.136e-01 5.195e-01 + GE2 -4.664067e+02 -1.198322e+00 9.748e-02 4.883e-01 + GE3 -4.664092e+02 -2.509694e-03 6.245e-02 5.519e-01 + GE4 -4.664092e+02 3.468995e-05 1.950e-03 4.287e-01 + GE5 -4.664084e+02 7.837197e-04 8.207e-04 4.272e-01 + GE6 -4.664090e+02 -5.616189e-04 9.694e-05 4.071e-01 + GE7 -4.664088e+02 1.751051e-04 3.497e-05 4.109e-01 + GE8 -4.664088e+02 -2.762162e-05 1.084e-05 4.084e-01 + GE9 -4.664088e+02 1.610387e-05 1.725e-06 4.089e-01 + GE10 -4.664088e+02 -2.308711e-06 1.025e-07 4.115e-01 + GE11 -4.664088e+02 -4.391394e-07 4.166e-08 3.382e-01 +E_delta_band = -7.08740833e-02 Ry = -9.64291374e-01 eV +E_delta_NN= -1.94998085e-01 Ry = -2.65308505e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.791 11 0.62 1e+02 % + Run_lcao lcao_line 6.784 1 6.8 1e+02 % + Potential init_pot 0.24756 2 0.12 3.6 % + PW_Basis recip2real 0.22874 16 0.014 3.4 % + PW_Basis gathers_scatterp 0.10833 16 0.0068 1.6 % + Potential v_of_rho 0.89669 13 0.069 13 % + XC_Functional v_xc 0.30205 14 0.022 4.4 % + H_Hartree_pw v_hartree 0.56614 13 0.044 8.3 % + PW_Basis real2recip 0.60136 38 0.016 8.9 % + PW_Basis gatherp_scatters 0.26981 38 0.0071 4 % + ORB_control set_orb_tables 0.90166 1 0.9 13 % + ORB_gen_tables gen_tables 0.90166 1 0.9 13 % + ORB_table_phi init_Table 0.37773 1 0.38 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.37348 126 0.003 5.5 % + ORB_table_beta init_Table_Beta 0.157 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15568 56 0.0028 2.3 % + ORB_table_alpha init_Table_Alpha 0.20928 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20759 66 0.0031 3.1 % + LOOP_ions opt_ions 5.4196 1 5.4 80 % + ESolver_KS_LCAO Run 4.8536 1 4.9 71 % + HSolverLCAO solve 2.6959 11 0.25 40 % + HamiltLCAO updateHk 1.3704 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3468 11 0.12 20 % + Gint_interface cal_gint 0.57245 23 0.025 8.4 % + Gint_Gamma distri_vl_value 0.74949 11 0.068 11 % + Gint_Gamma distri_vl 2.3304 6 0.39 34 % + LCAO_Deepks cal_projected_DM 5.0405 13 0.39 74 % + LCAO_gen_fixedH add_v_delta 2.2028 6 0.37 32 % + LCAO_DESCRIPTOR add_v_delta 2.2031 6 0.37 32 % + ElecStateLCAO psiToRho 1.3088 11 0.12 19 % + Charge mix_rho 0.72477 10 0.072 11 % + LOOP_ions force_stress 0.56586 1 0.57 8.3 % + Force_Stress_LCAO getForceStress 0.56585 1 0.57 8.3 % + Force_LCAO_gamma ftable_gamma 0.37063 1 0.37 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.13762 1 0.14 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:11 2022 + FINISH Time : Wed Sep 28 11:04:18 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/6/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..08310f23c4c40d46002cef80653c1bc559c98848 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.319124 0.769261 0.367455 +H 0.310375 0.827384 0.394658 +H 0.288186 0.774219 0.307653 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f127a0cb79cd94ad0f8b9d715fb57f5293ff4c8c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.187 2 + 2 -12.9542 2 + 3 -9.0995 2 + 4 -6.72106 2 + 5 1.19026 0 + 6 4.27904 0 + 7 11.0997 0 + 8 11.3477 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..8bb1a7cf4058f74f58b5e164f75467031f674006 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:31 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 8.9354706612 21.5392981899 10.2887448306 0 0 0 0 + tauc_H1 8.69049037801 23.1667562724 11.0504251682 0 0 0 0 + tauc_H2 8.06919988698 21.6781212818 8.61428652224 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0733486506664 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0766941784887 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0923128738913 (SEC) + + DONE : INIT CHARGE Time : 0.133640232552 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375817 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000488 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101 + + Density error is 0.21343726023 + + Energy Rydberg eV + E_KohnSham -34.1912993131 -465.196492681 + E_Harris -34.3798970496 -467.762496528 + E_Fermi -0.398655158003 -5.42398168594 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000778399890912 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120539997215 + + Density error is 0.098182967773 + + Energy Rydberg eV + E_KohnSham -34.2797682718 -466.400174616 + E_Harris -34.2866047874 -466.493190183 + E_Fermi -0.209017520126 -2.84382925555 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000753506816544 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115001694675 + + Density error is 0.0630905447004 + + Energy Rydberg eV + E_KohnSham -34.2800412663 -466.403888896 + E_Harris -34.2844538207 -466.46392478 + E_Fermi -0.199078727234 -2.70860504097 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000732127641234 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107532884546 + + Density error is 0.00198392900944 + + Energy Rydberg eV + E_KohnSham -34.2800026832 -466.403363947 + E_Harris -34.2800043894 -466.40338716 + E_Fermi -0.163660155266 -2.22671064719 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00073270431846 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107598555365 + + Density error is 0.00084817303009 + + Energy Rydberg eV + E_KohnSham -34.2799580655 -466.402756891 + E_Harris -34.2799585713 -466.402763773 + E_Fermi -0.163185299092 -2.22024989749 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00073235820647 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107495129311 + + Density error is 0.00015881033565 + + Energy Rydberg eV + E_KohnSham -34.2799835185 -466.403103197 + E_Harris -34.2799835396 -466.403103484 + E_Fermi -0.163003848909 -2.2177811411 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000732567009466 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107514517131 + + Density error is 3.43470623936e-05 + + Energy Rydberg eV + E_KohnSham -34.2799748323 -466.402985016 + E_Harris -34.2799748378 -466.402985091 + E_Fermi -0.162914520934 -2.21656577164 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000732498123303 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107505713542 + + Density error is 1.45948992208e-05 + + Energy Rydberg eV + E_KohnSham -34.279978362 -466.40303304 + E_Harris -34.2799783629 -466.403033053 + E_Fermi -0.16294484837 -2.21697839757 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000732505190965 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107505589109 + + Density error is 1.69900541505e-06 + + Energy Rydberg eV + E_KohnSham -34.2799770917 -466.403015756 + E_Harris -34.2799770917 -466.403015756 + E_Fermi -0.162929514274 -2.2167697665 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000732508117214 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107505787621 + + Density error is 2.26922456803e-07 + + Energy Rydberg eV + E_KohnSham -34.2799773063 -466.403018676 + E_Harris -34.2799773063 -466.403018676 + E_Fermi -0.162928144275 -2.21675112671 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000732508487737 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107505827603 + + Density error is 6.29225441388e-08 + + Energy Rydberg eV + E_KohnSham -34.2799773339 -466.403019052 + E_Harris -34.2799773339 -466.403019052 + E_band -7.93222840545 -107.923504152 + E_one_elec -69.0730790276 -939.78745318 + E_Hartree +35.9373608528 +488.95287868 + E_xc -8.19322022264 -111.474479997 + E_Ewald +7.17373848207 +97.603719318 + E_demet -9.35320349129e-71 -1.27256862035e-69 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194426458759 -2.64530768108 + E_Fermi -0.162928094289 -2.21675044661 + + charge density convergence is achieved + final etot is -466.403019052 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1870 2.00000 + 2 -12.9542 2.00000 + 3 -9.09950 2.00000 + 4 -6.72106 2.00000 + 5 1.19026 0.00000 + 6 4.27904 0.00000 + 7 11.0997 0.00000 + 8 11.3477 0.00000 + + EFERMI = -2.216750446607745 eV + OUT.ABACUS/ final etot is -466.4030190518759 eV + correction force for each atom along direction 1 is 6.54566e-05 + correction force for each atom along direction 2 is 0.000107092 + correction force for each atom along direction 3 is -4.73650e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.38949098 -0.69890199 -1.3580910 + H1 -0.12579159 +0.76942581 +0.34576463 + H2 +0.51528257 -0.070523821 +1.0123264 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4030190518759 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2843 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2776 1 7.3 1.e+02% + Potential init_pot 0.24079 2 0.12 3.3% + PW_Basis recip2real 0.21992 16 0.014 3.0% + PW_Basis gathers_scatterp 0.10642 16 0.0067 1.5% + Potential v_of_rho 0.95814 13 0.074 13.% + XC_Functional v_xc 0.37173 14 0.027 5.1% + H_Hartree_pw v_hartree 0.55780 13 0.043 7.7% + PW_Basis real2recip 0.60226 38 0.016 8.3% + PW_Basis gatherp_scatters 0.27113 38 0.0071 3.7% + ORB_control set_orb_tables 0.88854 1 0.89 12.% + ORB_gen_tables gen_tables 0.88854 1 0.89 12.% + ORB_table_phi init_Table 0.36915 1 0.37 5.1% + ORB_table_phi cal_ST_Phi12_R 0.36502 126 0.0029 5.0% + ORB_table_beta init_Table_Beta 0.15349 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15216 56 0.0027 2.1% + ORB_table_alpha init_Table_Alpha 0.20812 1 0.21 2.9% + ORB_table_alpha S_PhiAlpha_R 0.20651 66 0.0031 2.8% + LOOP_ions opt_ions 5.9424 1 5.9 82.% + ESolver_KS_LCAO Run 5.3736 1 5.4 74.% + HSolverLCAO solve 3.2009 11 0.29 44.% + HamiltLCAO updateHk 1.5826 11 0.14 22.% + LCAO_Hamilt cal_Hgamma 1.5590 11 0.14 21.% + Gint_interface cal_gint 0.82240 23 0.036 11.% + Gint_Gamma distri_vl_value 0.86395 11 0.079 12.% + Gint_Gamma distri_vl 2.5648 6 0.43 35.% + LCAO_Deepks cal_projected_DM 5.5601 13 0.43 76.% + LCAO_gen_fixedH add_v_delta 2.4502 6 0.41 34.% + LCAO_DESCRIPTOR add_v_delta 2.4504 6 0.41 34.% + ElecStateLCAO psiToRho 1.5893 11 0.14 22.% + Charge mix_rho 0.66905 10 0.067 9.2% + LOOP_ions force_stress 0.56872 1 0.57 7.8% + Force_Stress_LCAO getForceStress 0.56870 1 0.57 7.8% + Force_LCAO_gamma ftable_gamma 0.37374 1 0.37 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.16031 1 0.16 2.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:31 2022 + Finish Time : Wed Sep 28 11:09:38 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..dc17be44a2612beb45d161bec681aa6033e98b1c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123623 ima = 3.64853e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123230233909 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112184105404 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112782368049 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113001950023 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112969170002 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112988670028 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112982683123 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112985251882 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011298461505 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112984541839 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011298453342 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ffc4e7652f0c08e166cdc94e956b841d7ddf3d96 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-19.064529338784 21.539298189890 10.288744830554 0 0 0 +H +0.0 +2 +-19.309509621995 23.166756272415 11.050425168222 0 0 0 +-19.930800112997 21.678121281822 8.614286522231 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/conv new file mode 100644 index 0000000000000000000000000000000000000000..88982ba8520d4328e6650df4f95d2d39a177c78f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/conv @@ -0,0 +1 @@ +60 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..acf7a69303c207a030ff8cb338f646b112ea2930 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749376907 0.01259019962 1.261946613 1.356772891 1.468885792 0.008456397286 0.01838819976 0.03904714071 +3.742017049e-18 0.001000370924 0.002528664286 0.01206511794 0.04390273856 4.51564894e-19 1.866819338e-06 5.584807926e-06 +0.001638030176 0.005907084626 + +H atom_index 1 n_descriptor 18 +1.261415897 0.03385378266 0.1120173571 0.1555387943 0.3250365814 0.02265432204 0.02899603587 0.03711367742 +-7.858295303e-18 4.453215942e-05 0.1032984973 0.115775 0.1334557149 -1.243086592e-18 3.44566981e-06 0.01310266478 +0.02646332047 0.03127069556 + +H atom_index 2 n_descriptor 18 +1.200576399 0.0359082447 0.09207294796 0.1286208335 0.3042422667 0.01984224301 0.0254451939 0.03928195973 +-1.069199088e-17 3.914464234e-05 0.08781667704 0.1100353351 0.113454661 4.226049165e-18 6.227639817e-06 0.01408898997 +0.02409472961 0.02833059123 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d1d4f4879ad49bbb3fe507fd8a8f972c494eb6cf Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..e0d7fd85f30a1affa6f9f74d97b96bb28bafa681 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..db7e4b03254b712805bfdc71719b2ad16f37cb13 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..9d4bf28df2a24e092a212fdd65e1ffddddd085a4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..c2d5c184a7e14a1244e653d8fc1916f561add455 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:31 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733644 SEC) : SETUP UNITCELL + DONE(0.0767037 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0923252 SEC) : INIT PLANEWAVE + DONE(0.133742 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.37586 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651965e+02 0.000000e+00 2.134e-01 5.625e-01 + GE2 -4.664002e+02 -1.203682e+00 9.818e-02 5.323e-01 + GE3 -4.664039e+02 -3.714281e-03 6.309e-02 5.983e-01 + GE4 -4.664034e+02 5.249491e-04 1.984e-03 4.762e-01 + GE5 -4.664028e+02 6.070559e-04 8.482e-04 4.746e-01 + GE6 -4.664031e+02 -3.463059e-04 1.588e-04 4.728e-01 + GE7 -4.664030e+02 1.181809e-04 3.435e-05 4.586e-01 + GE8 -4.664030e+02 -4.802342e-05 1.459e-05 4.525e-01 + GE9 -4.664030e+02 1.728370e-05 1.699e-06 4.509e-01 + GE10 -4.664030e+02 -2.919648e-06 2.269e-07 4.557e-01 + GE11 -4.664030e+02 -3.760529e-07 6.292e-08 3.792e-01 +E_delta_band = -6.96490403e-02 Ry = -9.47623808e-01 eV +E_delta_NN= -1.94426459e-01 Ry = -2.64530768e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2843 11 0.66 1e+02 % + Run_lcao lcao_line 7.2776 1 7.3 1e+02 % + Potential init_pot 0.24079 2 0.12 3.3 % + PW_Basis recip2real 0.21992 16 0.014 3 % + PW_Basis gathers_scatterp 0.10642 16 0.0067 1.5 % + Potential v_of_rho 0.95814 13 0.074 13 % + XC_Functional v_xc 0.37173 14 0.027 5.1 % + H_Hartree_pw v_hartree 0.5578 13 0.043 7.7 % + PW_Basis real2recip 0.60226 38 0.016 8.3 % + PW_Basis gatherp_scatters 0.27113 38 0.0071 3.7 % + ORB_control set_orb_tables 0.88854 1 0.89 12 % + ORB_gen_tables gen_tables 0.88854 1 0.89 12 % + ORB_table_phi init_Table 0.36915 1 0.37 5.1 % + ORB_table_phi cal_ST_Phi12_R 0.36502 126 0.0029 5 % + ORB_table_beta init_Table_Beta 0.15349 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15216 56 0.0027 2.1 % + ORB_table_alpha init_Table_Alpha 0.20812 1 0.21 2.9 % + ORB_table_alpha S_PhiAlpha_R 0.20651 66 0.0031 2.8 % + LOOP_ions opt_ions 5.9424 1 5.9 82 % + ESolver_KS_LCAO Run 5.3736 1 5.4 74 % + HSolverLCAO solve 3.2009 11 0.29 44 % + HamiltLCAO updateHk 1.5826 11 0.14 22 % + LCAO_Hamilt cal_Hgamma 1.559 11 0.14 21 % + Gint_interface cal_gint 0.8224 23 0.036 11 % + Gint_Gamma distri_vl_value 0.86395 11 0.079 12 % + Gint_Gamma distri_vl 2.5648 6 0.43 35 % + LCAO_Deepks cal_projected_DM 5.5601 13 0.43 76 % + LCAO_gen_fixedH add_v_delta 2.4502 6 0.41 34 % + LCAO_DESCRIPTOR add_v_delta 2.4504 6 0.41 34 % + ElecStateLCAO psiToRho 1.5893 11 0.14 22 % + Charge mix_rho 0.66905 10 0.067 9.2 % + LOOP_ions force_stress 0.56872 1 0.57 7.8 % + Force_Stress_LCAO getForceStress 0.5687 1 0.57 7.8 % + Force_LCAO_gamma ftable_gamma 0.37374 1 0.37 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.16031 1 0.16 2.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:31 2022 + FINISH Time : Wed Sep 28 11:09:38 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/60/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..95e8204717602a7ff0e140889da1a5ca0137cc4c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.298478 0.779524 0.356448 +H 0.234483 0.794526 0.375282 +H 0.286017 0.76455 0.29345 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..99dd0cf7e6bbbf97cab0988c4bc368cce668858d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1449 2 + 2 -12.5051 2 + 3 -9.40395 2 + 4 -6.71728 2 + 5 1.01723 0 + 6 3.9877 0 + 7 11.1278 0 + 8 11.4042 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..587af4ed6f8b19cb34af0e7b1f733d13deaa2d89 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/running_scf.log @@ -0,0 +1,780 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:32 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 8.35739194052 21.826683878 9.9805323531 0 0 0 0 + tauc_H1 6.56552806634 22.2467237861 10.5079012593 0 0 0 0 + tauc_H2 8.00848296472 21.4073973057 8.21658823241 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0890372214323 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0954330454443 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.113705744295 (SEC) + + DONE : INIT CHARGE Time : 0.163545668704 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445034 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00088 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000657 + + Density error is 0.211484624962 + + Energy Rydberg eV + E_KohnSham -34.1878928245 -465.150145027 + E_Harris -34.37330249 -467.672772941 + E_Fermi -0.391006198804 -5.31991225705 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00129216976306 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000853724852763 + + Density error is 0.0985792771803 + + Energy Rydberg eV + E_KohnSham -34.2773013513 -466.36661044 + E_Harris -34.2845709575 -466.465518507 + E_Fermi -0.20125907197 -2.73827015298 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00123582327466 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000818657113798 + + Density error is 0.0636953997853 + + Energy Rydberg eV + E_KohnSham -34.2778557405 -466.374153293 + E_Harris -34.2824988476 -466.437326006 + E_Fermi -0.195121653622 -2.65476629244 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117159600141 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000786305201674 + + Density error is 0.0018882037563 + + Energy Rydberg eV + E_KohnSham -34.2777514367 -466.372734167 + E_Harris -34.2777512055 -466.372731022 + E_Fermi -0.159584220288 -2.17125470681 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117393808928 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787855214635 + + Density error is 0.00107341773568 + + Energy Rydberg eV + E_KohnSham -34.2777033521 -466.372079943 + E_Harris -34.2777043299 -466.372093247 + E_Fermi -0.159646706979 -2.17210488185 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117278488902 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787373884219 + + Density error is 0.000121156896851 + + Energy Rydberg eV + E_KohnSham -34.2777251007 -466.372375846 + E_Harris -34.2777251036 -466.372375887 + E_Fermi -0.159218763836 -2.16628241669 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011728950072 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787503883042 + + Density error is 3.14756718596e-05 + + Energy Rydberg eV + E_KohnSham -34.2777188855 -466.372291284 + E_Harris -34.2777188893 -466.372291336 + E_Fermi -0.159162581525 -2.16551801713 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117281139625 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787456469745 + + Density error is 1.22545459197e-05 + + Energy Rydberg eV + E_KohnSham -34.2777210655 -466.372320946 + E_Harris -34.2777210662 -466.372320954 + E_Fermi -0.159184689744 -2.16581881488 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117281198676 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787461758582 + + Density error is 1.34271219335e-06 + + Energy Rydberg eV + E_KohnSham -34.2777199702 -466.372306044 + E_Harris -34.2777199702 -466.372306044 + E_Fermi -0.159171060944 -2.16563338554 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117281235207 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787462272474 + + Density error is 3.17936027483e-07 + + Energy Rydberg eV + E_KohnSham -34.2777201661 -466.372308708 + E_Harris -34.2777201661 -466.372308708 + E_Fermi -0.159170670688 -2.16562807584 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117281327075 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787462868184 + + Density error is 7.57819391213e-08 + + Energy Rydberg eV + E_KohnSham -34.2777201781 -466.372308872 + E_Harris -34.2777201781 -466.372308872 + E_band -7.90422076106 -107.5424406 + E_one_elec -68.7596045917 -935.522414674 + E_Hartree +35.7776970052 +486.780540588 + E_xc -8.16756630403 -111.125440528 + E_Ewald +6.99711554957 +95.2006410385 + E_demet -4.31249741782e-62 -5.86745374927e-61 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193940301155 -2.63869316754 + E_Fermi -0.159170533484 -2.16562620908 + + charge density convergence is achieved + final etot is -466.372308872 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1449 2.00000 + 2 -12.5051 2.00000 + 3 -9.40395 2.00000 + 4 -6.71728 2.00000 + 5 1.01723 0.00000 + 6 3.98770 0.00000 + 7 11.1278 0.00000 + 8 11.4042 0.00000 + + EFERMI = -2.165626209079054 eV + OUT.ABACUS/ final etot is -466.3723088717170 eV + correction force for each atom along direction 1 is -0.000146153 + correction force for each atom along direction 2 is 0.000146337 + correction force for each atom along direction 3 is -3.05043e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.9081034 +0.35366598 +0.18840178 + H1 +1.5006554 -0.23832321 -0.0069813065 + H2 +0.40744797 -0.11534276 -0.18142047 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3723088717170 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9618 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9519 1 7.0 1.e+02% + Potential init_pot 0.28857 2 0.14 4.1% + PW_Basis recip2real 0.25920 16 0.016 3.7% + PW_Basis gathers_scatterp 0.11601 16 0.0073 1.7% + Charge atomic_rho 0.10026 1 0.10 1.4% + Potential v_of_rho 0.87009 13 0.067 12.% + XC_Functional v_xc 0.25821 14 0.018 3.7% + H_Hartree_pw v_hartree 0.57697 13 0.044 8.3% + PW_Basis real2recip 0.56153 38 0.015 8.1% + PW_Basis gatherp_scatters 0.23014 38 0.0061 3.3% + ORB_control set_orb_tables 1.1153 1 1.1 16.% + ORB_gen_tables gen_tables 1.1153 1 1.1 16.% + ORB_table_phi init_Table 0.48995 1 0.49 7.0% + ORB_table_phi cal_ST_Phi12_R 0.48499 126 0.0038 7.0% + ORB_table_beta init_Table_Beta 0.18920 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18773 56 0.0034 2.7% + ORB_table_alpha init_Table_Alpha 0.25570 1 0.26 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25379 66 0.0038 3.6% + LOOP_ions opt_ions 5.3070 1 5.3 76.% + ESolver_KS_LCAO Run 4.7213 1 4.7 68.% + HSolverLCAO solve 2.7529 11 0.25 40.% + HamiltLCAO updateHk 1.3930 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3649 11 0.12 20.% + Gint_interface cal_gint 0.82326 23 0.036 12.% + Gint_Gamma distri_vl_value 0.67188 11 0.061 9.7% + Gint_Gamma distri_vl 2.2622 6 0.38 32.% + LCAO_Deepks cal_projected_DM 4.9301 13 0.38 71.% + LCAO_gen_fixedH add_v_delta 2.1280 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.1279 6 0.35 31.% + ElecStateLCAO psiToRho 1.3413 11 0.12 19.% + Charge mix_rho 0.65112 10 0.065 9.4% + LOOP_ions force_stress 0.58550 1 0.59 8.4% + Force_Stress_LCAO getForceStress 0.58548 1 0.59 8.4% + Force_LCAO_gamma ftable_gamma 0.37683 1 0.38 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.17717 1 0.18 2.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:32 2022 + Finish Time : Wed Sep 28 11:04:39 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..f18665ea93733b7deedadb5f7ecbad0c0b5a4a43 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123666 ima = 3.67816e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123145819513 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111467578691 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011230422888 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011254239524 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112511904595 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112528899677 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112525515402 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011252775166 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112527195972 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112527155839 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112527140319 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c67e08e7d02ce9268c728439f8af634596effff4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-19.642608059460 21.826683878014 9.980532353081 0 0 0 +H +0.0 +2 +-21.434471933665 22.246723786032 10.507901259264 0 0 0 +-19.991517035301 21.407397305725 8.216588232401 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/conv new file mode 100644 index 0000000000000000000000000000000000000000..92850c2ebb60767825ececdb0dd1d56d1eecfdf4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/conv @@ -0,0 +1 @@ +61 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..73cfd20911b0411e5125325f39719e5bbb9c50f6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754697326 0.01258107237 1.247355379 1.334240527 1.468710505 0.009395521579 0.01628097839 0.0392336021 +-1.452968816e-18 0.00079668871 0.002657427111 0.01243571586 0.04381540115 -3.930100526e-19 2.290698871e-06 6.510772936e-06 +0.001563760967 0.006053868398 + +H atom_index 1 n_descriptor 18 +1.186554803 0.03689357693 0.08985190601 0.1224043967 0.296942778 0.01984234457 0.02450663551 0.0404577202 +-5.32149025e-17 3.940867237e-05 0.08438653876 0.1043494689 0.1127342442 -1.389660232e-18 5.825687233e-06 0.01480223301 +0.0237823789 0.02747011773 + +H atom_index 2 n_descriptor 18 +1.239838643 0.03522125157 0.1068646705 0.1449670298 0.3167154054 0.02244605012 0.02764758937 0.03838742484 +9.883451577e-18 4.407770451e-05 0.09791000257 0.1152360315 0.1241163539 -9.504560979e-18 3.524360253e-06 0.01348369758 +0.0259587472 0.03023608029 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..43603297d1ac24c5d5bbcf53f2674a1327f0c2fb Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..7b9256c291d2d5956e0e071c180023086f3b421a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:32 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0890595 SEC) : SETUP UNITCELL + DONE(0.0954503 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.113728 SEC) : INIT PLANEWAVE + DONE(0.163673 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445107 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651501e+02 0.000000e+00 2.115e-01 5.489e-01 + GE2 -4.663666e+02 -1.216465e+00 9.858e-02 4.683e-01 + GE3 -4.663742e+02 -7.542853e-03 6.370e-02 5.294e-01 + GE4 -4.663727e+02 1.419125e-03 1.888e-03 4.126e-01 + GE5 -4.663721e+02 6.542246e-04 1.073e-03 4.105e-01 + GE6 -4.663724e+02 -2.959038e-04 1.212e-04 4.037e-01 + GE7 -4.663723e+02 8.456216e-05 3.148e-05 3.895e-01 + GE8 -4.663723e+02 -2.966140e-05 1.225e-05 3.867e-01 + GE9 -4.663723e+02 1.490212e-05 1.343e-06 3.899e-01 + GE10 -4.663723e+02 -2.664607e-06 3.179e-07 3.906e-01 + GE11 -4.663723e+02 -1.634996e-07 7.578e-08 3.298e-01 +E_delta_band = -6.85784640e-02 Ry = -9.33057870e-01 eV +E_delta_NN= -1.93940301e-01 Ry = -2.63869317e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9618 11 0.63 1e+02 % + Run_lcao lcao_line 6.9519 1 7 1e+02 % + Potential init_pot 0.28857 2 0.14 4.1 % + PW_Basis recip2real 0.2592 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.11601 16 0.0073 1.7 % + Charge atomic_rho 0.10026 1 0.1 1.4 % + Potential v_of_rho 0.87009 13 0.067 12 % + XC_Functional v_xc 0.25821 14 0.018 3.7 % + H_Hartree_pw v_hartree 0.57697 13 0.044 8.3 % + PW_Basis real2recip 0.56153 38 0.015 8.1 % + PW_Basis gatherp_scatters 0.23014 38 0.0061 3.3 % + ORB_control set_orb_tables 1.1153 1 1.1 16 % + ORB_gen_tables gen_tables 1.1153 1 1.1 16 % + ORB_table_phi init_Table 0.48995 1 0.49 7 % + ORB_table_phi cal_ST_Phi12_R 0.48499 126 0.0038 7 % + ORB_table_beta init_Table_Beta 0.1892 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18773 56 0.0034 2.7 % + ORB_table_alpha init_Table_Alpha 0.2557 1 0.26 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25379 66 0.0038 3.6 % + LOOP_ions opt_ions 5.307 1 5.3 76 % + ESolver_KS_LCAO Run 4.7213 1 4.7 68 % + HSolverLCAO solve 2.7529 11 0.25 40 % + HamiltLCAO updateHk 1.393 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3649 11 0.12 20 % + Gint_interface cal_gint 0.82326 23 0.036 12 % + Gint_Gamma distri_vl_value 0.67188 11 0.061 9.7 % + Gint_Gamma distri_vl 2.2622 6 0.38 32 % + LCAO_Deepks cal_projected_DM 4.9301 13 0.38 71 % + LCAO_gen_fixedH add_v_delta 2.128 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.1279 6 0.35 31 % + ElecStateLCAO psiToRho 1.3413 11 0.12 19 % + Charge mix_rho 0.65112 10 0.065 9.4 % + LOOP_ions force_stress 0.5855 1 0.59 8.4 % + Force_Stress_LCAO getForceStress 0.58548 1 0.59 8.4 % + Force_LCAO_gamma ftable_gamma 0.37683 1 0.38 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.17717 1 0.18 2.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:32 2022 + FINISH Time : Wed Sep 28 11:04:39 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/61/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9821b2cc94110ca248a553cc24f7b0e4880dd376 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.274198 0.7869 0.35219 +H 0.217475 0.758299 0.361495 +H 0.305918 0.755715 0.306027 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2fdc415a4d589b6a102a7c5360847e6e4089b750 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4199 2 + 2 -13.4754 2 + 3 -8.90938 2 + 4 -6.77296 2 + 5 1.51034 0 + 6 4.76981 0 + 7 11.0274 0 + 8 11.2513 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3a5a6b1b9ca28ab2b136c5a99b3f2d90f27b00b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:24 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.67755485709 22.0331980607 9.86131688007 0 0 0 0 + tauc_H1 6.08929631823 21.2323681418 10.1218711673 0 0 0 0 + tauc_H2 8.56570272951 21.1600241878 8.56875124956 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0733393985615 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0858027404422 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.101468917764 (SEC) + + DONE : INIT CHARGE Time : 0.142959899704 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.387089 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00091 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000999 + + Density error is 0.218682905819 + + Energy Rydberg eV + E_KohnSham -34.1863322159 -465.128911857 + E_Harris -34.3858855171 -467.843973808 + E_Fermi -0.418399248891 -5.69261382384 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112278277476 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108100102525 + + Density error is 0.0976753926401 + + Energy Rydberg eV + E_KohnSham -34.2782254298 -466.379183173 + E_Harris -34.2847790353 -466.468349551 + E_Fermi -0.224381873124 -3.05287200239 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001069320822 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102061864224 + + Density error is 0.0623963263819 + + Energy Rydberg eV + E_KohnSham -34.2785303701 -466.3833321 + E_Harris -34.2827154754 -466.440273378 + E_Fermi -0.210397176701 -2.86260044625 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992064387378 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092243741747 + + Density error is 0.00210982482147 + + Energy Rydberg eV + E_KohnSham -34.2785722846 -466.383902376 + E_Harris -34.2785752774 -466.383943094 + E_Fermi -0.174885615014 -2.37944086243 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000993304434635 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092139627321 + + Density error is 0.000916690206468 + + Energy Rydberg eV + E_KohnSham -34.2784967 -466.382873994 + E_Harris -34.2784987069 -466.382901299 + E_Fermi -0.17367194588 -2.36292804671 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992176474392 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920283636535 + + Density error is 0.000192941932645 + + Energy Rydberg eV + E_KohnSham -34.2785460725 -466.383545742 + E_Harris -34.2785461815 -466.383547225 + E_Fermi -0.173946624205 -2.36666523705 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00099237868795 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920335411643 + + Density error is 4.59826315572e-05 + + Energy Rydberg eV + E_KohnSham -34.2785272292 -466.383289365 + E_Harris -34.2785272406 -466.38328952 + E_Fermi -0.173744008989 -2.36390851562 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992324334283 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920296415386 + + Density error is 1.78474154233e-05 + + Energy Rydberg eV + E_KohnSham -34.278532719 -466.383364058 + E_Harris -34.2785327203 -466.383364075 + E_Fermi -0.173799640903 -2.36466542664 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992315722918 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920278101271 + + Density error is 1.64354845175e-06 + + Energy Rydberg eV + E_KohnSham -34.2785311982 -466.383343367 + E_Harris -34.2785311982 -466.383343367 + E_Fermi -0.173780283608 -2.36440205712 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992315777625 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920278649722 + + Density error is 1.3623782919e-07 + + Energy Rydberg eV + E_KohnSham -34.2785314297 -466.383346516 + E_Harris -34.2785314297 -466.383346516 + E_Fermi -0.17377860417 -2.3643792072 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000992316084586 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000920279084892 + + Density error is 3.42302597631e-08 + + Energy Rydberg eV + E_KohnSham -34.2785314588 -466.383346911 + E_Harris -34.2785314588 -466.383346911 + E_band -8.02277253695 -109.15542026 + E_one_elec -69.7362094172 -948.809804996 + E_Hartree +36.2575860352 +493.309765804 + E_xc -8.24464568329 -112.174159284 + E_Ewald +7.56818064112 +102.970380213 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195537106817 -2.66041882314 + E_Fermi -0.173778672887 -2.36438014214 + + charge density convergence is achieved + final etot is -466.383346911 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4199 2.00000 + 2 -13.4754 2.00000 + 3 -8.90938 2.00000 + 4 -6.77296 2.00000 + 5 1.51034 0.00000 + 6 4.76981 0.00000 + 7 11.0274 0.00000 + 8 11.2513 0.00000 + + EFERMI = -2.364380142140608 eV + OUT.ABACUS/ final etot is -466.3833469113621 eV + correction force for each atom along direction 1 is -6.59388e-05 + correction force for each atom along direction 2 is 1.36842e-05 + correction force for each atom along direction 3 is -8.44777e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.56250325 +1.5018824 +0.95827530 + H1 -0.96223921 -0.71008989 -0.033769425 + H2 +0.39973596 -0.79179249 -0.92450588 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3833469113621 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3899 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3827 1 7.4 1.e+02% + Potential init_pot 0.24187 2 0.12 3.3% + PW_Basis recip2real 0.22709 16 0.014 3.1% + PW_Basis gathers_scatterp 0.10865 16 0.0068 1.5% + Potential v_of_rho 0.94811 13 0.073 13.% + XC_Functional v_xc 0.35621 14 0.025 4.8% + H_Hartree_pw v_hartree 0.56298 13 0.043 7.6% + PW_Basis real2recip 0.60740 38 0.016 8.2% + PW_Basis gatherp_scatters 0.27144 38 0.0071 3.7% + ORB_control set_orb_tables 0.89847 1 0.90 12.% + ORB_gen_tables gen_tables 0.89847 1 0.90 12.% + ORB_table_phi init_Table 0.37690 1 0.38 5.1% + ORB_table_phi cal_ST_Phi12_R 0.37269 126 0.0030 5.0% + ORB_table_beta init_Table_Beta 0.15473 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15345 56 0.0027 2.1% + ORB_table_alpha init_Table_Alpha 0.20878 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20712 66 0.0031 2.8% + LOOP_ions opt_ions 6.0283 1 6.0 82.% + ESolver_KS_LCAO Run 5.4540 1 5.5 74.% + HSolverLCAO solve 3.2696 11 0.30 44.% + HamiltLCAO updateHk 1.6176 11 0.15 22.% + LCAO_Hamilt cal_Hgamma 1.5943 11 0.14 22.% + Gint_interface cal_gint 1.0094 23 0.044 14.% + Gint_Gamma distri_vl_value 0.82214 11 0.075 11.% + Gint_Gamma distri_vl 2.6071 6 0.43 35.% + LCAO_Deepks cal_projected_DM 5.6662 13 0.44 77.% + LCAO_gen_fixedH add_v_delta 2.4827 6 0.41 34.% + LCAO_DESCRIPTOR add_v_delta 2.4826 6 0.41 34.% + ElecStateLCAO psiToRho 1.6315 11 0.15 22.% + Charge mix_rho 0.68967 10 0.069 9.3% + LOOP_ions force_stress 0.57421 1 0.57 7.8% + Force_Stress_LCAO getForceStress 0.57418 1 0.57 7.8% + Force_LCAO_gamma ftable_gamma 0.37702 1 0.38 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.18514 1 0.19 2.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:24 2022 + Finish Time : Wed Sep 28 11:08:31 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3d2ee75d59bea11d35a698bdf4e514be235e889b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123674 ima = 3.68407e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123393036836 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112577458228 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112980703962 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113252701062 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113186048628 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113225791122 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113215709992 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113218845619 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113218182116 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113218113602 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113218110926 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0e90cead4f6d92d96bd2e96dbf9468ea8d7f8c5f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.322445142910 22.033198060683 9.861316880082 0 0 0 +H +0.0 +2 +-21.910703681744 21.232368141792 10.121871167294 0 0 0 +-19.434297270513 21.160024187800 8.568751249542 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/conv new file mode 100644 index 0000000000000000000000000000000000000000..ac85e6276c778fa632464adc3820305e311d510a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/conv @@ -0,0 +1 @@ +62 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..16ec976bac44084ab205c11df076c7a7e0305eab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745009836 0.01274617214 1.295526289 1.382853402 1.470090431 0.007992938314 0.02042864693 0.03890498074 +2.809972246e-18 0.001239408201 0.002525078263 0.01290951512 0.04523263249 2.933509481e-19 1.79435988e-06 5.445997179e-06 +0.0017615523 0.005708593473 + +H atom_index 1 n_descriptor 18 +1.269339705 0.03302758118 0.1156759471 0.1600947719 0.3281173074 0.02288646457 0.02954081067 0.03635005829 +-6.43666492e-17 4.497055028e-05 0.1069533481 0.116660619 0.1376302772 -5.142273341e-18 3.300628239e-06 0.01297374629 +0.02718315623 0.03168545741 + +H atom_index 2 n_descriptor 18 +1.271514923 0.03295371466 0.1164752448 0.161164269 0.3287468353 0.0229806756 0.02966508736 0.03630690585 +-2.412111471e-17 4.516369396e-05 0.1072138401 0.117020653 0.1385431227 7.08596415e-18 3.184756664e-06 0.01299044882 +0.02725697357 0.03177247159 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d19fb1eea1fe889a59eafdf8c1075bc9a378af72 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..bfd06e14464c1ba47d8d8aa8a890ae5b6084b629 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..ee80d3b88a700bd0e02da917b82c61e5ebaab43c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..c252a9292e116a9237861360c8f6cda8a45253d4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:24 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733552 SEC) : SETUP UNITCELL + DONE(0.0858153 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.101481 SEC) : INIT PLANEWAVE + DONE(0.143068 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.387138 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651289e+02 0.000000e+00 2.187e-01 5.643e-01 + GE2 -4.663792e+02 -1.250271e+00 9.768e-02 5.463e-01 + GE3 -4.663833e+02 -4.148926e-03 6.240e-02 6.040e-01 + GE4 -4.663839e+02 -5.702761e-04 2.110e-03 4.789e-01 + GE5 -4.663829e+02 1.028382e-03 9.167e-04 4.805e-01 + GE6 -4.663835e+02 -6.717484e-04 1.929e-04 4.710e-01 + GE7 -4.663833e+02 2.563767e-04 4.598e-05 4.735e-01 + GE8 -4.663834e+02 -7.469278e-05 1.785e-05 4.629e-01 + GE9 -4.663833e+02 2.069166e-05 1.644e-06 4.661e-01 + GE10 -4.663833e+02 -3.149716e-06 1.362e-07 4.613e-01 + GE11 -4.663833e+02 -3.951191e-07 3.423e-08 3.882e-01 +E_delta_band = -7.20940723e-02 Ry = -9.80890175e-01 eV +E_delta_NN= -1.95537107e-01 Ry = -2.66041882e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3899 11 0.67 1e+02 % + Run_lcao lcao_line 7.3827 1 7.4 1e+02 % + Potential init_pot 0.24187 2 0.12 3.3 % + PW_Basis recip2real 0.22709 16 0.014 3.1 % + PW_Basis gathers_scatterp 0.10865 16 0.0068 1.5 % + Potential v_of_rho 0.94811 13 0.073 13 % + XC_Functional v_xc 0.35621 14 0.025 4.8 % + H_Hartree_pw v_hartree 0.56298 13 0.043 7.6 % + PW_Basis real2recip 0.6074 38 0.016 8.2 % + PW_Basis gatherp_scatters 0.27144 38 0.0071 3.7 % + ORB_control set_orb_tables 0.89847 1 0.9 12 % + ORB_gen_tables gen_tables 0.89847 1 0.9 12 % + ORB_table_phi init_Table 0.3769 1 0.38 5.1 % + ORB_table_phi cal_ST_Phi12_R 0.37269 126 0.003 5 % + ORB_table_beta init_Table_Beta 0.15473 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15345 56 0.0027 2.1 % + ORB_table_alpha init_Table_Alpha 0.20878 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20712 66 0.0031 2.8 % + LOOP_ions opt_ions 6.0283 1 6 82 % + ESolver_KS_LCAO Run 5.454 1 5.5 74 % + HSolverLCAO solve 3.2696 11 0.3 44 % + HamiltLCAO updateHk 1.6176 11 0.15 22 % + LCAO_Hamilt cal_Hgamma 1.5943 11 0.14 22 % + Gint_interface cal_gint 1.0094 23 0.044 14 % + Gint_Gamma distri_vl_value 0.82214 11 0.075 11 % + Gint_Gamma distri_vl 2.6071 6 0.43 35 % + LCAO_Deepks cal_projected_DM 5.6662 13 0.44 77 % + LCAO_gen_fixedH add_v_delta 2.4827 6 0.41 34 % + LCAO_DESCRIPTOR add_v_delta 2.4826 6 0.41 34 % + ElecStateLCAO psiToRho 1.6315 11 0.15 22 % + Charge mix_rho 0.68967 10 0.069 9.3 % + LOOP_ions force_stress 0.57421 1 0.57 7.8 % + Force_Stress_LCAO getForceStress 0.57418 1 0.57 7.8 % + Force_LCAO_gamma ftable_gamma 0.37702 1 0.38 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.18514 1 0.19 2.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:24 2022 + FINISH Time : Wed Sep 28 11:08:31 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/62/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..522f001791cbd0fd485a87948e88300137d26dc6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.252774 0.795619 0.351411 +H 0.209934 0.749089 0.349676 +H 0.307871 0.761011 0.359243 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f4a8e19788f08bb8671b79b783562f6d36bb0fea --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5603 2 + 2 -13.024 2 + 3 -9.32714 2 + 4 -6.80391 2 + 5 1.42098 0 + 6 4.68593 0 + 7 11.0222 0 + 8 11.2876 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f6a389c404eb6d3097612b6403d33e02693f322a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:39 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 7.07767521874 22.2773373761 9.83950741784 0 0 0 0 + tauc_H1 5.87816597496 20.974492459 9.79091517412 0 0 0 0 + tauc_H2 8.62038866738 21.3083069813 10.0587957092 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.110999762449 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.122618921564 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.140891642513 (SEC) + + DONE : INIT CHARGE Time : 0.186997670304 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.468225 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000797 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00153 + + Density error is 0.216495680116 + + Energy Rydberg eV + E_KohnSham -34.186833871 -465.135737225 + E_Harris -34.382418128 -467.796797559 + E_Fermi -0.41785906733 -5.68526427666 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000937797214394 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133371014327 + + Density error is 0.0973637107994 + + Energy Rydberg eV + E_KohnSham -34.2774406422 -466.368505591 + E_Harris -34.2841466087 -466.459744946 + E_Fermi -0.22619987026 -3.0776071224 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000885659664686 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122901520576 + + Density error is 0.0622690090311 + + Energy Rydberg eV + E_KohnSham -34.2777166568 -466.372260962 + E_Harris -34.2820364174 -466.43103432 + E_Fermi -0.212848275394 -2.89594935483 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813205768246 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104769819737 + + Density error is 0.00200360594724 + + Energy Rydberg eV + E_KohnSham -34.2777445027 -466.372639825 + E_Harris -34.2777458097 -466.372657608 + E_Fermi -0.17688126452 -2.40659306692 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000814915369395 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104585524696 + + Density error is 0.000922821480806 + + Energy Rydberg eV + E_KohnSham -34.2776702192 -466.371629146 + E_Harris -34.2776725769 -466.371661225 + E_Fermi -0.175866630947 -2.39278826894 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813744164617 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104402529418 + + Density error is 9.90220388302e-05 + + Energy Rydberg eV + E_KohnSham -34.2777214992 -466.372326846 + E_Harris -34.2777215145 -466.372327054 + E_Fermi -0.176065480929 -2.39549376174 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813772470746 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104369021795 + + Density error is 4.97476670642e-05 + + Energy Rydberg eV + E_KohnSham -34.2777049465 -466.372101635 + E_Harris -34.2777049602 -466.372101822 + E_Fermi -0.175934395784 -2.39371025685 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00081372829754 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104372190887 + + Density error is 1.31510855391e-05 + + Energy Rydberg eV + E_KohnSham -34.2777077454 -466.372139716 + E_Harris -34.277707746 -466.372139725 + E_Fermi -0.17599315396 -2.39450970285 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813727965731 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104370724931 + + Density error is 2.53271756932e-06 + + Energy Rydberg eV + E_KohnSham -34.2777062696 -466.372119637 + E_Harris -34.2777062696 -466.372119637 + E_Fermi -0.175980698415 -2.39434023647 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813729519342 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104370455013 + + Density error is 1.8379536203e-07 + + Energy Rydberg eV + E_KohnSham -34.2777064149 -466.372121613 + E_Harris -34.2777064149 -466.372121613 + E_Fermi -0.175978132492 -2.3943053253 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000813729427716 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104370445658 + + Density error is 9.54884558663e-08 + + Energy Rydberg eV + E_KohnSham -34.2777064652 -466.372122298 + E_Harris -34.2777064652 -466.372122298 + E_band -8.04300605339 -109.430711375 + E_one_elec -69.6963141587 -948.267002157 + E_Hartree +36.224113298 +492.85434585 + E_xc -8.23949144266 -112.104032242 + E_Ewald +7.55746216554 +102.824547871 + E_demet -5.83777679229e-88 -7.94270280273e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19561633606 -2.66149679229 + E_Fermi -0.175978101499 -2.39430490361 + + charge density convergence is achieved + final etot is -466.372122298 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5603 2.00000 + 2 -13.0240 2.00000 + 3 -9.32714 2.00000 + 4 -6.80391 2.00000 + 5 1.42098 0.00000 + 6 4.68593 0.00000 + 7 11.0222 0.00000 + 8 11.2876 0.00000 + + EFERMI = -2.394304903611131 eV + OUT.ABACUS/ final etot is -466.3721222977630 eV + correction force for each atom along direction 1 is -2.41760e-05 + correction force for each atom along direction 2 is -3.27328e-05 + correction force for each atom along direction 3 is 2.33382e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.3460311 +1.2801704 +0.066545475 + H1 -1.7962847 -1.4151775 -0.10515010 + H2 +0.45025362 +0.13500707 +0.038604623 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3721222977630 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4085 11 0.67 1.0e+02% + Run_lcao lcao_line 7.4002 1 7.4 1.e+02% + Potential init_pot 0.28261 2 0.14 3.8% + PW_Basis recip2real 0.26637 16 0.017 3.6% + PW_Basis gathers_scatterp 0.12261 16 0.0077 1.7% + Potential v_of_rho 1.0927 13 0.084 15.% + XC_Functional v_xc 0.40079 14 0.029 5.4% + H_Hartree_pw v_hartree 0.65606 13 0.050 8.9% + PW_Basis real2recip 0.72271 38 0.019 9.8% + PW_Basis gatherp_scatters 0.32908 38 0.0087 4.4% + ORB_control set_orb_tables 1.0989 1 1.1 15.% + ORB_gen_tables gen_tables 1.0989 1 1.1 15.% + ORB_table_phi init_Table 0.47542 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47018 126 0.0037 6.3% + ORB_table_beta init_Table_Beta 0.18442 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18291 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24963 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24764 66 0.0038 3.3% + LOOP_ions opt_ions 5.7564 1 5.8 78.% + ESolver_KS_LCAO Run 5.1939 1 5.2 70.% + HSolverLCAO solve 2.7064 11 0.25 37.% + HamiltLCAO updateHk 1.3800 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.3513 11 0.12 18.% + Gint_interface cal_gint 0.63724 23 0.028 8.6% + Gint_Gamma distri_vl_value 0.69514 11 0.063 9.4% + Gint_Gamma distri_vl 2.5004 6 0.42 34.% + LCAO_Deepks cal_projected_DM 5.4028 13 0.42 73.% + LCAO_gen_fixedH add_v_delta 2.3608 6 0.39 32.% + LCAO_DESCRIPTOR add_v_delta 2.3609 6 0.39 32.% + ElecStateLCAO psiToRho 1.2908 11 0.12 17.% + Charge mix_rho 0.81733 10 0.082 11.% + LOOP_ions force_stress 0.56232 1 0.56 7.6% + Force_Stress_LCAO getForceStress 0.56230 1 0.56 7.6% + Force_LCAO_gamma ftable_gamma 0.34530 1 0.35 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.15223 1 0.15 2.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:39 2022 + Finish Time : Wed Sep 28 11:07:47 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..df19df5b9116537e316501a80101f523509d35d1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123939 ima = 3.65958e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122657115402 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111672129104 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112147206102 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112433844195 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112360447797 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112401095868 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112397357932 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112400568305 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112400053739 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112399929596 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112399925514 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7bf25c80c66dc4ec7391e431c0a266bc14ce3572 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-20.922324781242 22.277337376084 9.839507417841 0 0 0 +H +0.0 +2 +-22.121834025029 20.974492458969 9.790915174129 0 0 0 +-19.379611332602 21.308306981316 10.058795709184 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/conv new file mode 100644 index 0000000000000000000000000000000000000000..8f1f88e847a3df7e1fa01b9024f0fd4e2fb9eb23 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/conv @@ -0,0 +1 @@ +63 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4c60b9f727ac188457ca4234169865c0916008fc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752146913 0.01284426879 1.285481894 1.371779703 1.470505448 0.00921210577 0.017906653 0.0391119827 +-5.053000752e-19 0.001058745871 0.002876970134 0.01337615014 0.04838667245 4.320970111e-20 2.750881401e-06 7.276793854e-06 +0.001605313374 0.006085942617 + +H atom_index 1 n_descriptor 18 +1.296409414 0.03311988266 0.1275834351 0.17256868 0.3337544282 0.02515385953 0.03092150111 0.03676837755 +-3.814401949e-18 5.690069619e-05 0.1085268221 0.1239499742 0.1480830259 -8.992717646e-18 1.137525478e-06 0.01370871386 +0.02867017281 0.03264941618 + +H atom_index 2 n_descriptor 18 +1.246590857 0.03472610431 0.1088490719 0.1479382406 0.3186293316 0.0227488131 0.02804427091 0.03780767131 +1.867578572e-17 5.203216351e-05 0.1033475765 0.1147613364 0.1270800372 -5.503753543e-18 3.891237275e-06 0.01337519007 +0.0269823369 0.03060741101 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e716c2ebfe97f6b0c58a127d6f3f506800fafd06 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..457a9528246410f5b82285555ffca1ac2fc361e6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..03fae8efe0c4c5dc2247d004cfc6666f9a806396 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..0d10c71b578998a4cd80ce887b79d27a80aa54bf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:39 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.111025 SEC) : SETUP UNITCELL + DONE(0.122639 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.140913 SEC) : INIT PLANEWAVE + DONE(0.187136 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.468296 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651357e+02 0.000000e+00 2.165e-01 5.587e-01 + GE2 -4.663685e+02 -1.232768e+00 9.736e-02 5.282e-01 + GE3 -4.663723e+02 -3.755371e-03 6.227e-02 5.993e-01 + GE4 -4.663726e+02 -3.788633e-04 2.004e-03 4.578e-01 + GE5 -4.663716e+02 1.010679e-03 9.228e-04 4.599e-01 + GE6 -4.663723e+02 -6.977002e-04 9.902e-05 4.428e-01 + GE7 -4.663721e+02 2.252109e-04 4.975e-05 4.364e-01 + GE8 -4.663721e+02 -3.808068e-05 1.315e-05 4.301e-01 + GE9 -4.663721e+02 2.007902e-05 2.533e-06 4.314e-01 + GE10 -4.663721e+02 -1.976726e-06 1.838e-07 4.303e-01 + GE11 -4.663721e+02 -6.843407e-07 9.549e-08 3.494e-01 +E_delta_band = -7.21400088e-02 Ry = -9.81515173e-01 eV +E_delta_NN= -1.95616336e-01 Ry = -2.66149679e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4085 11 0.67 1e+02 % + Run_lcao lcao_line 7.4002 1 7.4 1e+02 % + Potential init_pot 0.28261 2 0.14 3.8 % + PW_Basis recip2real 0.26637 16 0.017 3.6 % + PW_Basis gathers_scatterp 0.12261 16 0.0077 1.7 % + Potential v_of_rho 1.0927 13 0.084 15 % + XC_Functional v_xc 0.40079 14 0.029 5.4 % + H_Hartree_pw v_hartree 0.65606 13 0.05 8.9 % + PW_Basis real2recip 0.72271 38 0.019 9.8 % + PW_Basis gatherp_scatters 0.32908 38 0.0087 4.4 % + ORB_control set_orb_tables 1.0989 1 1.1 15 % + ORB_gen_tables gen_tables 1.0989 1 1.1 15 % + ORB_table_phi init_Table 0.47542 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47018 126 0.0037 6.3 % + ORB_table_beta init_Table_Beta 0.18442 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18291 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24963 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24764 66 0.0038 3.3 % + LOOP_ions opt_ions 5.7564 1 5.8 78 % + ESolver_KS_LCAO Run 5.1939 1 5.2 70 % + HSolverLCAO solve 2.7064 11 0.25 37 % + HamiltLCAO updateHk 1.38 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.3513 11 0.12 18 % + Gint_interface cal_gint 0.63724 23 0.028 8.6 % + Gint_Gamma distri_vl_value 0.69514 11 0.063 9.4 % + Gint_Gamma distri_vl 2.5004 6 0.42 34 % + LCAO_Deepks cal_projected_DM 5.4028 13 0.42 73 % + LCAO_gen_fixedH add_v_delta 2.3608 6 0.39 32 % + LCAO_DESCRIPTOR add_v_delta 2.3609 6 0.39 32 % + ElecStateLCAO psiToRho 1.2908 11 0.12 17 % + Charge mix_rho 0.81733 10 0.082 11 % + LOOP_ions force_stress 0.56232 1 0.56 7.6 % + Force_Stress_LCAO getForceStress 0.5623 1 0.56 7.6 % + Force_LCAO_gamma ftable_gamma 0.3453 1 0.35 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.15223 1 0.15 2.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:39 2022 + FINISH Time : Wed Sep 28 11:07:47 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/63/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..766e3835e256005a74ce81d1feb047aeaf9ab2a3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.243332 0.804137 0.356279 +H 0.21325 0.780196 0.301339 +H 0.261832 0.751259 0.395087 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..99304e5c0d8d812b4cd8995f1c6a1031ce20ea44 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.8671 2 + 2 -12.9311 2 + 3 -8.85777 2 + 4 -6.64556 2 + 5 0.995342 0 + 6 3.94343 0 + 7 11.1661 0 + 8 11.3969 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..cf28b133e364f5d5c6b5671bdaff1f701d8dac86 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:51 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.81330195641 22.5158416055 9.97582139546 0 0 0 0 + tauc_H1 5.97100580608 21.8455005398 8.43750238512 0 0 0 0 + tauc_H2 7.33130714799 21.03525227 11.0624455186 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0877525149136 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101732843999 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.120156275528 (SEC) + + DONE : INIT CHARGE Time : 0.169878497877 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450572 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000857 + + Density error is 0.211759733165 + + Energy Rydberg eV + E_KohnSham -34.1905045129 -465.18567887 + E_Harris -34.37481971 -467.693415778 + E_Fermi -0.383068087549 -5.21190871263 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107589951184 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111759458669 + + Density error is 0.0989894683745 + + Energy Rydberg eV + E_KohnSham -34.2776597739 -466.371487031 + E_Harris -34.2847305938 -466.46769047 + E_Fermi -0.194328246513 -2.64397143492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100822881994 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107745640683 + + Density error is 0.0638629180783 + + Energy Rydberg eV + E_KohnSham -34.2779887187 -466.375962554 + E_Harris -34.2824991564 -466.437330208 + E_Fermi -0.187360522113 -2.54917068099 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000893013946897 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103005229571 + + Density error is 0.00210335069252 + + Energy Rydberg eV + E_KohnSham -34.2778979315 -466.374727331 + E_Harris -34.2779030967 -466.374797607 + E_Fermi -0.152503434665 -2.07491567602 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000891700194179 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102784178105 + + Density error is 0.000849141803425 + + Energy Rydberg eV + E_KohnSham -34.2778773086 -466.374446742 + E_Harris -34.2778773828 -466.374447751 + E_Fermi -0.152293421634 -2.07205830214 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000890246827082 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102741062561 + + Density error is 0.000198222702647 + + Energy Rydberg eV + E_KohnSham -34.2778864232 -466.374570753 + E_Harris -34.2778864164 -466.37457066 + E_Fermi -0.15186767637 -2.06626574065 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000890331985969 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102759544826 + + Density error is 2.33629434461e-05 + + Energy Rydberg eV + E_KohnSham -34.2778845678 -466.374545508 + E_Harris -34.2778845689 -466.374545523 + E_Fermi -0.151852044908 -2.0660530637 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000890285523925 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102751565023 + + Density error is 9.94668318719e-06 + + Energy Rydberg eV + E_KohnSham -34.2778865876 -466.374572989 + E_Harris -34.2778865881 -466.374572995 + E_Fermi -0.151861570274 -2.06618266295 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000890282510598 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102752008532 + + Density error is 2.00189873663e-06 + + Energy Rydberg eV + E_KohnSham -34.2778858325 -466.374562715 + E_Harris -34.2778858325 -466.374562716 + E_Fermi -0.151852012048 -2.06605261661 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000890280122585 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102751973475 + + Density error is 5.41502192996e-07 + + Energy Rydberg eV + E_KohnSham -34.2778860152 -466.374565201 + E_Harris -34.2778860152 -466.374565201 + E_Fermi -0.151850819165 -2.06603638661 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000890279919575 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010275202893 + + Density error is 1.91426408721e-07 + + Energy Rydberg eV + E_KohnSham -34.2778860065 -466.374565083 + E_Harris -34.2778860065 -466.374565083 + E_Fermi -0.151850545481 -2.06603266295 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000890279715189 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102752045305 + + Density error is 1.04243452741e-08 + + Energy Rydberg eV + E_KohnSham -34.2778860102 -466.374565133 + E_Harris -34.2778860102 -466.374565133 + E_band -7.83518688295 -106.603186503 + E_one_elec -68.5563399043 -932.756856723 + E_Hartree +35.7024228684 +485.756383416 + E_xc -8.1551814426 -110.956935843 + E_Ewald +6.85706453161 +93.2951491836 + E_demet -1.21294802437e-57 -1.65030045093e-56 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193394473244 -2.63126679782 + E_Fermi -0.151850359366 -2.06603013073 + + charge density convergence is achieved + final etot is -466.374565133 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.8671 2.00000 + 2 -12.9311 2.00000 + 3 -8.85777 2.00000 + 4 -6.64556 2.00000 + 5 0.995342 0.00000 + 6 3.94343 0.00000 + 7 11.1661 0.00000 + 8 11.3969 0.00000 + + EFERMI = -2.066030130729040 eV + OUT.ABACUS/ final etot is -466.3745651328628 eV + correction force for each atom along direction 1 is -0.000110702 + correction force for each atom along direction 2 is -5.09863e-05 + correction force for each atom along direction 3 is 5.39958e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.10673619 -0.99426971 +0.28573985 + H1 +0.45980771 -0.015483917 +0.86278734 + H2 -0.56654390 +1.0097536 -1.1485272 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3745651328628 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.4503 11 0.77 1.0e+02% + Run_lcao lcao_line 8.4412 1 8.4 1.e+02% + Potential init_pot 0.28348 2 0.14 3.4% + PW_Basis recip2real 0.28098 17 0.017 3.3% + PW_Basis gathers_scatterp 0.13210 17 0.0078 1.6% + Potential v_of_rho 1.0988 14 0.078 13.% + XC_Functional v_xc 0.37391 15 0.025 4.4% + H_Hartree_pw v_hartree 0.68423 14 0.049 8.1% + PW_Basis real2recip 0.70250 41 0.017 8.3% + PW_Basis gatherp_scatters 0.30803 41 0.0075 3.6% + ORB_control set_orb_tables 1.0920 1 1.1 13.% + ORB_gen_tables gen_tables 1.0920 1 1.1 13.% + ORB_table_phi init_Table 0.47452 1 0.47 5.6% + ORB_table_phi cal_ST_Phi12_R 0.46935 126 0.0037 5.6% + ORB_table_beta init_Table_Beta 0.18232 1 0.18 2.2% + ORB_table_beta VNL_PhiBeta_R 0.18073 56 0.0032 2.1% + ORB_table_alpha init_Table_Alpha 0.24932 1 0.25 3.0% + ORB_table_alpha S_PhiAlpha_R 0.24740 66 0.0037 2.9% + LOOP_ions opt_ions 6.8207 1 6.8 81.% + ESolver_KS_LCAO Run 6.2001 1 6.2 73.% + HSolverLCAO solve 3.7233 12 0.31 44.% + HamiltLCAO updateHk 1.8325 12 0.15 22.% + LCAO_Hamilt cal_Hgamma 1.8031 12 0.15 21.% + Gint_interface cal_gint 0.98883 25 0.040 12.% + Gint_Gamma distri_vl_value 0.99885 12 0.083 12.% + Gint_Gamma distri_vl 3.2093 6 0.53 38.% + LCAO_Deepks cal_projected_DM 6.4160 14 0.46 76.% + LCAO_gen_fixedH add_v_delta 3.0790 6 0.51 36.% + LCAO_DESCRIPTOR add_v_delta 3.0791 6 0.51 36.% + ElecStateLCAO psiToRho 1.8548 12 0.15 22.% + Charge mix_rho 0.77938 11 0.071 9.2% + LOOP_ions force_stress 0.62041 1 0.62 7.3% + Force_Stress_LCAO getForceStress 0.62039 1 0.62 7.3% + Force_LCAO_gamma ftable_gamma 0.40353 1 0.40 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.18739 1 0.19 2.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:51 2022 + Finish Time : Wed Sep 28 11:11:59 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..16bd1af83b45975a8779575576611d462c3071fd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123288 ima = 3.66038e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123937256966 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112768058625 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113479565661 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113641527397 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113635674548 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113641132162 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113638245934 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113639675185 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113639193429 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113639197976 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011363917839 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113639168503 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8450e8b81464f63936bec2c4fb32b68431479abb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.186698043569 22.515841605472 9.975821395487 0 0 0 +H +0.0 +2 +-22.028994193898 21.845500539795 8.437502385141 0 0 0 +-20.668692852031 21.035252269930 11.062445518624 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/conv new file mode 100644 index 0000000000000000000000000000000000000000..e00faa53578e4680f3466b33acad3dabfee1e7ef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/conv @@ -0,0 +1 @@ +64 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..1faf9974c52462deb1a1d1bd51baf4b4eedc7900 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746204861 0.01232069542 1.245090662 1.343757848 1.467477945 0.007753986056 0.01914643626 0.03896658265 +6.514655373e-19 0.0009463616941 0.002224002066 0.01122267692 0.03958994969 2.786783427e-19 1.267353788e-06 4.157160828e-06 +0.001700660109 0.00563578924 + +H atom_index 1 n_descriptor 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:51 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087773 SEC) : SETUP UNITCELL + DONE(0.101754 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.120176 SEC) : INIT PLANEWAVE + DONE(0.170004 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450634 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651857e+02 0.000000e+00 2.118e-01 6.127e-01 + GE2 -4.663715e+02 -1.185808e+00 9.899e-02 5.722e-01 + GE3 -4.663760e+02 -4.475524e-03 6.386e-02 6.369e-01 + GE4 -4.663747e+02 1.235224e-03 2.103e-03 5.016e-01 + GE5 -4.663744e+02 2.805890e-04 8.491e-04 5.000e-01 + GE6 -4.663746e+02 -1.240107e-04 1.982e-04 4.949e-01 + GE7 -4.663745e+02 2.524476e-05 2.336e-05 4.770e-01 + GE8 -4.663746e+02 -2.748143e-05 9.947e-06 4.835e-01 + GE9 -4.663746e+02 1.027374e-05 2.002e-06 4.835e-01 + GE10 -4.663746e+02 -2.485770e-06 5.415e-07 4.795e-01 + GE11 -4.663746e+02 1.177689e-07 1.914e-07 4.798e-01 + GE12 -4.663746e+02 -4.937060e-08 1.042e-08 4.094e-01 +E_delta_band = -6.75424099e-02 Ry = -9.18961632e-01 eV +E_delta_NN= -1.93394473e-01 Ry = -2.63126680e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.4503 11 0.77 1e+02 % + Run_lcao lcao_line 8.4412 1 8.4 1e+02 % + Potential init_pot 0.28348 2 0.14 3.4 % + PW_Basis recip2real 0.28098 17 0.017 3.3 % + PW_Basis gathers_scatterp 0.1321 17 0.0078 1.6 % + Potential v_of_rho 1.0988 14 0.078 13 % + XC_Functional v_xc 0.37391 15 0.025 4.4 % + H_Hartree_pw v_hartree 0.68423 14 0.049 8.1 % + PW_Basis real2recip 0.7025 41 0.017 8.3 % + PW_Basis gatherp_scatters 0.30803 41 0.0075 3.6 % + ORB_control set_orb_tables 1.092 1 1.1 13 % + ORB_gen_tables gen_tables 1.092 1 1.1 13 % + ORB_table_phi init_Table 0.47452 1 0.47 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.46935 126 0.0037 5.6 % + ORB_table_beta init_Table_Beta 0.18232 1 0.18 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.18073 56 0.0032 2.1 % + ORB_table_alpha init_Table_Alpha 0.24932 1 0.25 3 % + ORB_table_alpha S_PhiAlpha_R 0.2474 66 0.0037 2.9 % + LOOP_ions opt_ions 6.8207 1 6.8 81 % + ESolver_KS_LCAO Run 6.2001 1 6.2 73 % + HSolverLCAO solve 3.7233 12 0.31 44 % + HamiltLCAO updateHk 1.8325 12 0.15 22 % + LCAO_Hamilt cal_Hgamma 1.8031 12 0.15 21 % + Gint_interface cal_gint 0.98883 25 0.04 12 % + Gint_Gamma distri_vl_value 0.99885 12 0.083 12 % + Gint_Gamma distri_vl 3.2093 6 0.53 38 % + LCAO_Deepks cal_projected_DM 6.416 14 0.46 76 % + LCAO_gen_fixedH add_v_delta 3.079 6 0.51 36 % + LCAO_DESCRIPTOR add_v_delta 3.0791 6 0.51 36 % + ElecStateLCAO psiToRho 1.8548 12 0.15 22 % + Charge mix_rho 0.77938 11 0.071 9.2 % + LOOP_ions force_stress 0.62041 1 0.62 7.3 % + Force_Stress_LCAO getForceStress 0.62039 1 0.62 7.3 % + Force_LCAO_gamma ftable_gamma 0.40353 1 0.4 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.18739 1 0.19 2.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:51 2022 + FINISH Time : Wed Sep 28 11:11:59 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/64/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c06b814312ec46fd836679cb8a640668fc760a6f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.222788 0.802513 0.357018 +H 0.232244 0.772521 0.298332 +H 0.217063 0.75153 0.393923 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..36fa0e81fe096a667ec453e88abd2431c42066b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5071 2 + 2 -12.8946 2 + 3 -9.37428 2 + 4 -6.79111 2 + 5 1.32672 0 + 6 4.57399 0 + 7 11.0398 0 + 8 11.3067 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..89cf79ee513b6db3ba2b87c634eb3e9b18960905 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:19 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 6.23805299557 22.4703549857 9.99649665108 0 0 0 0 + tauc_H1 6.50282996403 21.6305765137 8.35330659859 0 0 0 0 + tauc_H2 6.07777448063 21.0428505597 11.0298461717 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.087715218106 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0880980028744 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106206191389 (SEC) + + DONE : INIT CHARGE Time : 0.155478129676 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437605 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00134 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102 + + Density error is 0.214935894445 + + Energy Rydberg eV + E_KohnSham -34.1873303785 -465.142492557 + E_Harris -34.3798922876 -467.762431738 + E_Fermi -0.412932536456 -5.61823538539 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127167351006 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00137154068175 + + Density error is 0.0974331346616 + + Energy Rydberg eV + E_KohnSham -34.2766590562 -466.357871568 + E_Harris -34.2834080645 -466.449696536 + E_Fermi -0.223040502133 -3.03462171379 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117498880239 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131532936575 + + Density error is 0.0622883248259 + + Energy Rydberg eV + E_KohnSham -34.2768835647 -466.360926162 + E_Harris -34.2812433097 -466.420243536 + E_Fermi -0.210383878869 -2.86241951997 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101696060472 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124363116795 + + Density error is 0.00197165586306 + + Energy Rydberg eV + E_KohnSham -34.2768936951 -466.361063994 + E_Harris -34.2768948742 -466.361080036 + E_Fermi -0.174456768817 -2.37360611058 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101714909786 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124842392336 + + Density error is 0.000854462566279 + + Energy Rydberg eV + E_KohnSham -34.2768307296 -466.360207304 + E_Harris -34.2768323967 -466.360229986 + E_Fermi -0.17362516951 -2.36229162155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101542844006 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124669289021 + + Density error is 0.000103379501292 + + Energy Rydberg eV + E_KohnSham -34.2768745917 -466.360804079 + E_Harris -34.2768746115 -466.360804348 + E_Fermi -0.173720015581 -2.36358206854 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101527822075 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124658545431 + + Density error is 4.49914184722e-05 + + Energy Rydberg eV + E_KohnSham -34.2768600616 -466.360606387 + E_Harris -34.276860073 -466.360606541 + E_Fermi -0.17360118222 -2.36196525773 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101529081565 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124651356208 + + Density error is 1.35194105575e-05 + + Energy Rydberg eV + E_KohnSham -34.2768630981 -466.3606477 + E_Harris -34.2768630988 -466.360647709 + E_Fermi -0.173650293783 -2.36263345482 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101527657445 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124652266574 + + Density error is 2.5851342924e-06 + + Energy Rydberg eV + E_KohnSham -34.2768616652 -466.360628204 + E_Harris -34.2768616652 -466.360628205 + E_Fermi -0.17363710195 -2.36245397073 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101527209084 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124652411136 + + Density error is 2.03290911535e-07 + + Energy Rydberg eV + E_KohnSham -34.2768617989 -466.360630024 + E_Harris -34.2768617989 -466.360630024 + E_Fermi -0.173634670908 -2.3624208947 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101527221068 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012465244074 + + Density error is 1.09560617372e-07 + + Energy Rydberg eV + E_KohnSham -34.2768618513 -466.360630736 + E_Harris -34.2768618513 -466.360630736 + E_Fermi -0.1736346164 -2.36242015308 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010152720798 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124652451559 + + Density error is 1.06203361349e-08 + + Energy Rydberg eV + E_KohnSham -34.2768618508 -466.36063073 + E_Harris -34.2768618508 -466.36063073 + E_band -8.0212171899 -109.134258678 + E_one_elec -69.5360416415 -946.086382689 + E_Hartree +36.1466326897 +491.800168093 + E_xc -8.22700805078 -111.934186983 + E_Ewald +7.46336386796 +101.544274852 + E_demet -1.6920639348e-82 -2.30217108935e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195344402447 -2.65779694568 + E_Fermi -0.173634497323 -2.36241853296 + + charge density convergence is achieved + final etot is -466.36063073 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5071 2.00000 + 2 -12.8946 2.00000 + 3 -9.37428 2.00000 + 4 -6.79111 2.00000 + 5 1.32672 0.00000 + 6 4.57399 0.00000 + 7 11.0398 0.00000 + 8 11.3067 0.00000 + + EFERMI = -2.362418532961586 eV + OUT.ABACUS/ final etot is -466.3606307299602 eV + correction force for each atom along direction 1 is 2.31050e-05 + correction force for each atom along direction 2 is -6.11127e-05 + correction force for each atom along direction 3 is 1.01797e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.30169178 +1.0974908 -1.9057639 + H1 -0.029478616 +0.55588822 +0.17074933 + H2 -0.27221317 -1.6533791 +1.7350146 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3606307299602 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.3298 11 0.76 1.0e+02% + Run_lcao lcao_line 8.3205 1 8.3 1.e+02% + Potential init_pot 0.28586 2 0.14 3.4% + PW_Basis recip2real 0.28595 17 0.017 3.4% + PW_Basis gathers_scatterp 0.13781 17 0.0081 1.7% + Potential v_of_rho 1.0850 14 0.078 13.% + XC_Functional v_xc 0.36508 15 0.024 4.4% + H_Hartree_pw v_hartree 0.67976 14 0.049 8.2% + PW_Basis real2recip 0.71317 41 0.017 8.6% + PW_Basis gatherp_scatters 0.31948 41 0.0078 3.8% + ORB_control set_orb_tables 1.0934 1 1.1 13.% + ORB_gen_tables gen_tables 1.0934 1 1.1 13.% + ORB_table_phi init_Table 0.47314 1 0.47 5.7% + ORB_table_phi cal_ST_Phi12_R 0.46796 126 0.0037 5.6% + ORB_table_beta init_Table_Beta 0.18581 1 0.19 2.2% + ORB_table_beta VNL_PhiBeta_R 0.18429 56 0.0033 2.2% + ORB_table_alpha init_Table_Alpha 0.24953 1 0.25 3.0% + ORB_table_alpha S_PhiAlpha_R 0.24757 66 0.0038 3.0% + LOOP_ions opt_ions 6.7109 1 6.7 81.% + ESolver_KS_LCAO Run 6.1052 1 6.1 73.% + HSolverLCAO solve 3.6590 12 0.30 44.% + HamiltLCAO updateHk 1.8084 12 0.15 22.% + LCAO_Hamilt cal_Hgamma 1.7789 12 0.15 21.% + Gint_interface cal_gint 0.98389 25 0.039 12.% + Gint_Gamma distri_vl_value 0.98416 12 0.082 12.% + Gint_Gamma distri_vl 3.1597 6 0.53 38.% + LCAO_Deepks cal_projected_DM 6.3211 14 0.45 76.% + LCAO_gen_fixedH add_v_delta 3.0343 6 0.51 36.% + LCAO_DESCRIPTOR add_v_delta 3.0344 6 0.51 36.% + ElecStateLCAO psiToRho 1.8100 12 0.15 22.% + Charge mix_rho 0.78646 11 0.071 9.4% + LOOP_ions force_stress 0.60557 1 0.61 7.3% + Force_Stress_LCAO getForceStress 0.60554 1 0.61 7.3% + Force_LCAO_gamma ftable_gamma 0.39298 1 0.39 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.18854 1 0.19 2.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:19 2022 + Finish Time : Wed Sep 28 11:11:27 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..27432253471fbfbf82fba02c08f074a14500e3a2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124182 ima = 3.69232e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122578099193 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011160380242 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112112903121 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112383164134 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112321041207 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112356107636 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112351647141 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112354763153 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112354269951 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112354140223 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112354135901 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011235413045 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1b540dad3e363a839eac1d8c6e52dc566cb7b1c3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-21.761947004443 22.470354985672 9.996496651100 0 0 0 +H +0.0 +2 +-21.497170035956 21.630576513678 8.353306598587 0 0 0 +-21.922225519371 21.042850559722 11.029846171668 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/conv new file mode 100644 index 0000000000000000000000000000000000000000..063f6c6db3db6e1aa21c5478dd6f508d0b3dbbde --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/conv @@ -0,0 +1 @@ +65 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..21401f7d9a1fd84928468125fc901c5e401530d1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75312908 0.01280081432 1.275928032 1.367003776 1.470210033 0.009357387467 0.0174428497 0.03914132565 +-1.626191797e-18 0.000991201942 0.002873384082 0.01327919627 0.04785392996 8.486376776e-20 2.749778013e-06 7.325307797e-06 +0.001589603799 0.006093870798 + +H atom_index 1 n_descriptor 18 +1.224331304 0.03559318909 0.1016466582 0.1379760759 0.3108882657 0.02176248291 0.02673210902 0.03873643076 +2.66527194e-17 4.893423892e-05 0.09724150954 0.1139080947 0.1183250935 -5.438206041e-18 4.886408626e-06 0.01375011537 +0.0260522486 0.02951929234 + +H atom_index 2 n_descriptor 18 +1.298725925 0.03318420445 0.1289458558 0.1738323902 0.334426785 0.02539586895 0.03105266852 0.03688416486 +-1.273199136e-17 5.60749517e-05 0.1082927242 0.1244580599 0.1490398617 -7.390914401e-19 8.90999412e-07 0.01378430969 +0.02867408342 0.03272547798 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f4b1e35d41c6d12f3b2af81d9ff0f43ea6acac60 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:19 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0877376 SEC) : SETUP UNITCELL + DONE(0.0881134 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106224 SEC) : INIT PLANEWAVE + DONE(0.15561 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.437686 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651425e+02 0.000000e+00 2.149e-01 6.046e-01 + GE2 -4.663579e+02 -1.215379e+00 9.743e-02 5.664e-01 + GE3 -4.663609e+02 -3.054594e-03 6.229e-02 6.321e-01 + GE4 -4.663611e+02 -1.378320e-04 1.972e-03 4.958e-01 + GE5 -4.663602e+02 8.566897e-04 8.545e-04 4.901e-01 + GE6 -4.663608e+02 -5.967746e-04 1.034e-04 4.858e-01 + GE7 -4.663606e+02 1.976920e-04 4.499e-05 4.761e-01 + GE8 -4.663606e+02 -4.131309e-05 1.352e-05 4.695e-01 + GE9 -4.663606e+02 1.949556e-05 2.585e-06 4.710e-01 + GE10 -4.663606e+02 -1.819347e-06 2.033e-07 4.733e-01 + GE11 -4.663606e+02 -7.121048e-07 1.096e-07 4.712e-01 + GE12 -4.663606e+02 5.954170e-09 1.062e-08 4.028e-01 +E_delta_band = -7.15356862e-02 Ry = -9.73292942e-01 eV +E_delta_NN= -1.95344402e-01 Ry = -2.65779695e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.3298 11 0.76 1e+02 % + Run_lcao lcao_line 8.3205 1 8.3 1e+02 % + Potential init_pot 0.28586 2 0.14 3.4 % + PW_Basis recip2real 0.28595 17 0.017 3.4 % + PW_Basis gathers_scatterp 0.13781 17 0.0081 1.7 % + Potential v_of_rho 1.085 14 0.078 13 % + XC_Functional v_xc 0.36508 15 0.024 4.4 % + H_Hartree_pw v_hartree 0.67976 14 0.049 8.2 % + PW_Basis real2recip 0.71317 41 0.017 8.6 % + PW_Basis gatherp_scatters 0.31948 41 0.0078 3.8 % + ORB_control set_orb_tables 1.0934 1 1.1 13 % + ORB_gen_tables gen_tables 1.0934 1 1.1 13 % + ORB_table_phi init_Table 0.47314 1 0.47 5.7 % + ORB_table_phi cal_ST_Phi12_R 0.46796 126 0.0037 5.6 % + ORB_table_beta init_Table_Beta 0.18581 1 0.19 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.18429 56 0.0033 2.2 % + ORB_table_alpha init_Table_Alpha 0.24953 1 0.25 3 % + ORB_table_alpha S_PhiAlpha_R 0.24757 66 0.0038 3 % + LOOP_ions opt_ions 6.7109 1 6.7 81 % + ESolver_KS_LCAO Run 6.1052 1 6.1 73 % + HSolverLCAO solve 3.659 12 0.3 44 % + HamiltLCAO updateHk 1.8084 12 0.15 22 % + LCAO_Hamilt cal_Hgamma 1.7789 12 0.15 21 % + Gint_interface cal_gint 0.98389 25 0.039 12 % + Gint_Gamma distri_vl_value 0.98416 12 0.082 12 % + Gint_Gamma distri_vl 3.1597 6 0.53 38 % + LCAO_Deepks cal_projected_DM 6.3211 14 0.45 76 % + LCAO_gen_fixedH add_v_delta 3.0343 6 0.51 36 % + LCAO_DESCRIPTOR add_v_delta 3.0344 6 0.51 36 % + ElecStateLCAO psiToRho 1.81 12 0.15 22 % + Charge mix_rho 0.78646 11 0.071 9.4 % + LOOP_ions force_stress 0.60557 1 0.61 7.3 % + Force_Stress_LCAO getForceStress 0.60554 1 0.61 7.3 % + Force_LCAO_gamma ftable_gamma 0.39298 1 0.39 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.18854 1 0.19 2.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:19 2022 + FINISH Time : Wed Sep 28 11:11:27 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/65/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ecae9b067d3a38a1baabad688947065309006ca6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.211213 0.795749 0.37152 +H 0.23683 0.777956 0.314296 +H 0.181476 0.74103 0.396294 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3f898959f131e70d71ccddf120017701dfe18278 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1516 2 + 2 -13.0493 2 + 3 -9.00387 2 + 4 -6.71251 2 + 5 1.21356 0 + 6 4.29246 0 + 7 11.1026 0 + 8 11.344 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1474c57249a52944a87129d6ced50c193b2cc2d9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:21 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.91396383606 22.2809723775 10.4025732031 0 0 0 0 + tauc_H1 6.63123657927 21.7827814865 8.8002843749 0 0 0 0 + tauc_H2 5.08132655633 20.7488357938 11.0962244081 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0882535131633 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0969420994912 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115300265198 (SEC) + + DONE : INIT CHARGE Time : 0.165089892495 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447729 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00124 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102 + + Density error is 0.213857894445 + + Energy Rydberg eV + E_KohnSham -34.1918773723 -465.204357581 + E_Harris -34.380997252 -467.777465549 + E_Fermi -0.398355259653 -5.41990135955 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118761361606 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122193755722 + + Density error is 0.0982534055632 + + Energy Rydberg eV + E_KohnSham -34.2803879692 -466.408606031 + E_Harris -34.2871870582 -466.501112383 + E_Fermi -0.208309156518 -2.83419147422 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110540707164 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116788569241 + + Density error is 0.0630898952326 + + Energy Rydberg eV + E_KohnSham -34.2806635325 -466.412355262 + E_Harris -34.2850456748 -466.471977367 + E_Fermi -0.198204106902 -2.69670522087 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000965985796363 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108997883272 + + Density error is 0.00201899322963 + + Energy Rydberg eV + E_KohnSham -34.2806303152 -466.411903318 + E_Harris -34.2806325764 -466.411934083 + E_Fermi -0.162913178457 -2.21654750631 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000964462280892 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108885668012 + + Density error is 0.000845079729714 + + Energy Rydberg eV + E_KohnSham -34.2805853311 -466.411291278 + E_Harris -34.2805860348 -466.411300852 + E_Fermi -0.162360105956 -2.20902256888 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000962875941103 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108789741557 + + Density error is 0.000184336383203 + + Energy Rydberg eV + E_KohnSham -34.2806119663 -466.411653669 + E_Harris -34.2806120146 -466.411654326 + E_Fermi -0.162208668368 -2.2069621548 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000962979667083 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108815681504 + + Density error is 3.36465591592e-05 + + Energy Rydberg eV + E_KohnSham -34.2806018453 -466.411515965 + E_Harris -34.2806018503 -466.411516034 + E_Fermi -0.162110991939 -2.20563319881 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000962933947101 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108805955503 + + Density error is 1.65658927902e-05 + + Energy Rydberg eV + E_KohnSham -34.2806060819 -466.411573608 + E_Harris -34.2806060831 -466.411573624 + E_Fermi -0.162142525938 -2.20606224087 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000962922295226 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108805988517 + + Density error is 2.59293646556e-06 + + Energy Rydberg eV + E_KohnSham -34.280604767 -466.411555717 + E_Harris -34.280604767 -466.411555718 + E_Fermi -0.162126608497 -2.20584567298 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000962918790699 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108805947341 + + Density error is 5.24856368069e-07 + + Energy Rydberg eV + E_KohnSham -34.2806050233 -466.411559205 + E_Harris -34.2806050233 -466.411559205 + E_Fermi -0.162124160743 -2.20581236958 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000962918574569 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108806004929 + + Density error is 1.79322838115e-07 + + Energy Rydberg eV + E_KohnSham -34.2806050439 -466.411559484 + E_Harris -34.2806050439 -466.411559484 + E_Fermi -0.1621239199 -2.20580909274 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000962918371895 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108806018125 + + Density error is 1.02969642524e-08 + + Energy Rydberg eV + E_KohnSham -34.2806050475 -466.411559534 + E_Harris -34.2806050475 -466.411559534 + E_band -7.92569227772 -107.834575572 + E_one_elec -69.0748316928 -939.811299413 + E_Hartree +35.941875413 +489.014302422 + E_xc -8.19377994459 -111.482095405 + E_Ewald +7.17092599915 +97.5654535248 + E_demet -2.99242145425e-71 -4.07139825952e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194373719561 -2.64459012749 + E_Fermi -0.162123743938 -2.20580669866 + + charge density convergence is achieved + final etot is -466.411559534 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1516 2.00000 + 2 -13.0493 2.00000 + 3 -9.00387 2.00000 + 4 -6.71251 2.00000 + 5 1.21356 0.00000 + 6 4.29246 0.00000 + 7 11.1026 0.00000 + 8 11.3440 0.00000 + + EFERMI = -2.205806698655177 eV + OUT.ABACUS/ final etot is -466.4115595338191 eV + correction force for each atom along direction 1 is -2.75965e-05 + correction force for each atom along direction 2 is -2.77282e-05 + correction force for each atom along direction 3 is -4.00625e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.56391268 -0.35812429 +0.84164877 + H1 +0.13253382 -0.27567865 -0.39592986 + H2 +0.43137885 +0.63380294 -0.44571890 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4115595338191 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.4495 11 0.77 1.0e+02% + Run_lcao lcao_line 8.4392 1 8.4 1.e+02% + Potential init_pot 0.28696 2 0.14 3.4% + PW_Basis recip2real 0.28498 17 0.017 3.4% + PW_Basis gathers_scatterp 0.13651 17 0.0080 1.6% + Potential v_of_rho 1.1150 14 0.080 13.% + XC_Functional v_xc 0.38395 15 0.026 4.5% + H_Hartree_pw v_hartree 0.69021 14 0.049 8.2% + PW_Basis real2recip 0.71157 41 0.017 8.4% + PW_Basis gatherp_scatters 0.31793 41 0.0078 3.8% + ORB_control set_orb_tables 1.1116 1 1.1 13.% + ORB_gen_tables gen_tables 1.1116 1 1.1 13.% + ORB_table_phi init_Table 0.48259 1 0.48 5.7% + ORB_table_phi cal_ST_Phi12_R 0.47732 126 0.0038 5.6% + ORB_table_beta init_Table_Beta 0.18991 1 0.19 2.2% + ORB_table_beta VNL_PhiBeta_R 0.18834 56 0.0034 2.2% + ORB_table_alpha init_Table_Alpha 0.25296 1 0.25 3.0% + ORB_table_alpha S_PhiAlpha_R 0.25100 66 0.0038 3.0% + LOOP_ions opt_ions 6.8022 1 6.8 81.% + ESolver_KS_LCAO Run 6.1763 1 6.2 73.% + HSolverLCAO solve 3.6805 12 0.31 44.% + HamiltLCAO updateHk 1.8166 12 0.15 21.% + LCAO_Hamilt cal_Hgamma 1.7871 12 0.15 21.% + Gint_interface cal_gint 0.83285 25 0.033 9.9% + Gint_Gamma distri_vl_value 1.0386 12 0.087 12.% + Gint_Gamma distri_vl 3.2012 6 0.53 38.% + LCAO_Deepks cal_projected_DM 6.3780 14 0.46 75.% + LCAO_gen_fixedH add_v_delta 3.0699 6 0.51 36.% + LCAO_DESCRIPTOR add_v_delta 3.0701 6 0.51 36.% + ElecStateLCAO psiToRho 1.8261 12 0.15 22.% + Charge mix_rho 0.78003 11 0.071 9.2% + LOOP_ions force_stress 0.62571 1 0.63 7.4% + Force_Stress_LCAO getForceStress 0.62568 1 0.63 7.4% + Force_LCAO_gamma ftable_gamma 0.40774 1 0.41 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.17091 1 0.17 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:21 2022 + Finish Time : Wed Sep 28 11:08:29 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..03715f574408f811a64b9a5539444bbcab9a3820 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123545 ima = 3.65742e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123381162994 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112382516744 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112959728497 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113173785628 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113140673916 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113161947417 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011315435214 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113156924166 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113156179708 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113156112225 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113156093514 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113156084322 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/STRU new file mode 100644 index 0000000000000000000000000000000000000000..019018b2c1ea59388fec9554c3b7f1871c4d4f18 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.086036163917 22.280972377479 10.402573203086 0 0 0 +H +0.0 +2 +-21.368763420747 21.782781486489 8.800284374876 0 0 0 +-22.918673443656 20.748835793800 11.096224408061 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/conv new file mode 100644 index 0000000000000000000000000000000000000000..b12adeb34400dcb73d876e4ae82f77245cd9386c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/conv @@ -0,0 +1 @@ +66 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c3a2feeb1ba9e6bb7e1a6bb3d7a4ed6da941802a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747685493 0.01257266002 1.264675702 1.358433511 1.468724353 0.008162064586 0.01893632382 0.03899036988 +-1.49056016e-18 0.001035065868 0.002454352043 0.01198990424 0.04317779835 2.796317148e-19 1.703711556e-06 5.215751544e-06 +0.001678096526 0.005833535512 + +H atom_index 1 n_descriptor 18 +1.250860254 0.03403035293 0.1081118471 0.1509086306 0.3222985769 0.02199487444 0.02843347736 0.03724225816 +-5.895642607e-17 4.159237017e-05 0.1009001869 0.1150845053 0.1294871546 1.086510057e-17 4.092274065e-06 0.01305723803 +0.02598272457 0.03083502912 + +H atom_index 2 n_descriptor 18 +1.209692242 0.03544482441 0.09470377455 0.1327472427 0.3083428578 0.02012423475 0.02603496854 0.0387359007 +-4.151635739e-17 3.806627695e-05 0.09014803167 0.1136759338 0.1138306237 2.437504553e-18 5.891263037e-06 0.01373961899 +0.02437782224 0.02884877157 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..18f4341a5565dd663d6da733d069fc3ba843da92 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:21 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0882768 SEC) : SETUP UNITCELL + DONE(0.0969615 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115319 SEC) : INIT PLANEWAVE + DONE(0.165218 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447791 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652044e+02 0.000000e+00 2.139e-01 6.151e-01 + GE2 -4.664086e+02 -1.204248e+00 9.825e-02 5.686e-01 + GE3 -4.664124e+02 -3.749231e-03 6.309e-02 6.352e-01 + GE4 -4.664119e+02 4.519439e-04 2.019e-03 4.973e-01 + GE5 -4.664113e+02 6.120409e-04 8.451e-04 4.974e-01 + GE6 -4.664117e+02 -3.623916e-04 1.843e-04 4.936e-01 + GE7 -4.664115e+02 1.377044e-04 3.365e-05 4.808e-01 + GE8 -4.664116e+02 -5.764283e-05 1.657e-05 4.754e-01 + GE9 -4.664116e+02 1.789013e-05 2.593e-06 4.770e-01 + GE10 -4.664116e+02 -3.487197e-06 5.249e-07 4.785e-01 + GE11 -4.664116e+02 -2.795633e-07 1.793e-07 4.807e-01 + GE12 -4.664116e+02 -4.958947e-08 1.030e-08 4.092e-01 +E_delta_band = -6.95788973e-02 Ry = -9.46669464e-01 eV +E_delta_NN= -1.94373720e-01 Ry = -2.64459013e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.4495 11 0.77 1e+02 % + Run_lcao lcao_line 8.4392 1 8.4 1e+02 % + Potential init_pot 0.28696 2 0.14 3.4 % + PW_Basis recip2real 0.28498 17 0.017 3.4 % + PW_Basis gathers_scatterp 0.13651 17 0.008 1.6 % + Potential v_of_rho 1.115 14 0.08 13 % + XC_Functional v_xc 0.38395 15 0.026 4.5 % + H_Hartree_pw v_hartree 0.69021 14 0.049 8.2 % + PW_Basis real2recip 0.71157 41 0.017 8.4 % + PW_Basis gatherp_scatters 0.31793 41 0.0078 3.8 % + ORB_control set_orb_tables 1.1116 1 1.1 13 % + ORB_gen_tables gen_tables 1.1116 1 1.1 13 % + ORB_table_phi init_Table 0.48259 1 0.48 5.7 % + ORB_table_phi cal_ST_Phi12_R 0.47732 126 0.0038 5.6 % + ORB_table_beta init_Table_Beta 0.18991 1 0.19 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.18834 56 0.0034 2.2 % + ORB_table_alpha init_Table_Alpha 0.25296 1 0.25 3 % + ORB_table_alpha S_PhiAlpha_R 0.251 66 0.0038 3 % + LOOP_ions opt_ions 6.8022 1 6.8 81 % + ESolver_KS_LCAO Run 6.1763 1 6.2 73 % + HSolverLCAO solve 3.6805 12 0.31 44 % + HamiltLCAO updateHk 1.8166 12 0.15 21 % + LCAO_Hamilt cal_Hgamma 1.7871 12 0.15 21 % + Gint_interface cal_gint 0.83285 25 0.033 9.9 % + Gint_Gamma distri_vl_value 1.0386 12 0.087 12 % + Gint_Gamma distri_vl 3.2012 6 0.53 38 % + LCAO_Deepks cal_projected_DM 6.378 14 0.46 75 % + LCAO_gen_fixedH add_v_delta 3.0699 6 0.51 36 % + LCAO_DESCRIPTOR add_v_delta 3.0701 6 0.51 36 % + ElecStateLCAO psiToRho 1.8261 12 0.15 22 % + Charge mix_rho 0.78003 11 0.071 9.2 % + LOOP_ions force_stress 0.62571 1 0.63 7.4 % + Force_Stress_LCAO getForceStress 0.62568 1 0.63 7.4 % + Force_LCAO_gamma ftable_gamma 0.40774 1 0.41 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.17091 1 0.17 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:21 2022 + FINISH Time : Wed Sep 28 11:08:29 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/66/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fb82be49444f8578082ced2f12e076b59ef00f64 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.194464 0.788265 0.379845 +H 0.230767 0.75412 0.33865 +H 0.13784 0.758698 0.370412 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2c9eb30f9debfe637c443bbab2cf932884349074 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5507 2 + 2 -12.9122 2 + 3 -9.40275 2 + 4 -6.80262 2 + 5 1.39473 0 + 6 4.61777 0 + 7 11.03 0 + 8 11.3089 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..2fdb90e982d0e298fd64685f4b6b4ad6eabc31d7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:14 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.44499188857 22.0714315063 10.6356646612 0 0 0 0 + tauc_H1 6.46146508185 21.1153684229 9.4822064646 0 0 0 0 + tauc_H2 3.85951032474 21.243533023 10.3715310833 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0858390896617 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.102193501605 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.121069056951 (SEC) + + DONE : INIT CHARGE Time : 0.169614744664 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451196 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000904 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00167 + + Density error is 0.215810329769 + + Energy Rydberg eV + E_KohnSham -34.187546375 -465.145431339 + E_Harris -34.3820557771 -467.791867523 + E_Fermi -0.415762081914 -5.65673332637 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115658986048 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00142749751547 + + Density error is 0.0974432554079 + + Energy Rydberg eV + E_KohnSham -34.2783234417 -466.380516694 + E_Harris -34.2850819491 -466.472470904 + E_Fermi -0.223984413401 -3.04746428544 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109786988487 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131093171666 + + Density error is 0.0623607768029 + + Energy Rydberg eV + E_KohnSham -34.278656512 -466.385048348 + E_Harris -34.2830272593 -466.444515415 + E_Fermi -0.211557494562 -2.87838738064 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101658033639 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110713138383 + + Density error is 0.00198241474382 + + Energy Rydberg eV + E_KohnSham -34.2786681169 -466.38520624 + E_Harris -34.2786697584 -466.385228574 + E_Fermi -0.175558625367 -2.38859763804 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102013784879 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110619438268 + + Density error is 0.000971952719017 + + Energy Rydberg eV + E_KohnSham -34.2785925669 -466.38417833 + E_Harris -34.278595066 -466.384212332 + E_Fermi -0.174675117394 -2.37657689537 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101841087792 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110393042512 + + Density error is 9.87156434531e-05 + + Energy Rydberg eV + E_KohnSham -34.2786442781 -466.384881897 + E_Harris -34.2786442885 -466.384882038 + E_Fermi -0.174811172755 -2.37842802353 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101819930936 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110346683513 + + Density error is 4.56700612106e-05 + + Energy Rydberg eV + E_KohnSham -34.2786284881 -466.384667063 + E_Harris -34.2786284994 -466.384667216 + E_Fermi -0.174693696556 -2.37682967785 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101818026791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110353404128 + + Density error is 1.62012906538e-05 + + Energy Rydberg eV + E_KohnSham -34.2786303232 -466.384692031 + E_Harris -34.2786303244 -466.384692047 + E_Fermi -0.174753259837 -2.37764007786 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101818948346 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110351323441 + + Density error is 2.31859518239e-06 + + Energy Rydberg eV + E_KohnSham -34.2786288646 -466.384672186 + E_Harris -34.2786288646 -466.384672187 + E_Fermi -0.174737110387 -2.37742035331 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101818898906 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110350869349 + + Density error is 2.56012299651e-07 + + Energy Rydberg eV + E_KohnSham -34.2786290932 -466.384675296 + E_Harris -34.2786290932 -466.384675296 + E_Fermi -0.174734765422 -2.37738844843 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101818993075 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110350929429 + + Density error is 6.26097240911e-08 + + Energy Rydberg eV + E_KohnSham -34.2786291324 -466.38467583 + E_Harris -34.2786291324 -466.38467583 + E_band -8.03608812595 -109.336588143 + E_one_elec -69.6250533379 -947.297448949 + E_Hartree +36.1879324986 +492.362080821 + E_xc -8.23342243179 -112.021459113 + E_Ewald +7.51551262481 +102.253795088 + E_demet -3.96539630272e-86 -5.39519845451e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195465472714 -2.65944419118 + E_Fermi -0.174734706527 -2.37738764713 + + charge density convergence is achieved + final etot is -466.38467583 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5507 2.00000 + 2 -12.9122 2.00000 + 3 -9.40275 2.00000 + 4 -6.80262 2.00000 + 5 1.39473 0.00000 + 6 4.61777 0.00000 + 7 11.0300 0.00000 + 8 11.3089 0.00000 + + EFERMI = -2.377387647130224 eV + OUT.ABACUS/ final etot is -466.3846758301108 eV + correction force for each atom along direction 1 is 7.73802e-06 + correction force for each atom along direction 2 is -4.35079e-06 + correction force for each atom along direction 3 is -2.00977e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.22257751 +0.52619981 +0.40151272 + H1 +0.98061459 -0.29831353 -0.55764775 + H2 -1.2031921 -0.22788628 +0.15613503 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3846758301108 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9523 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9436 1 6.9 1.e+02% + Potential init_pot 0.28669 2 0.14 4.1% + PW_Basis recip2real 0.25917 16 0.016 3.7% + PW_Basis gathers_scatterp 0.11798 16 0.0074 1.7% + Potential v_of_rho 0.85812 13 0.066 12.% + XC_Functional v_xc 0.24580 14 0.018 3.5% + H_Hartree_pw v_hartree 0.57785 13 0.044 8.3% + PW_Basis real2recip 0.56808 38 0.015 8.2% + PW_Basis gatherp_scatters 0.23718 38 0.0062 3.4% + ORB_control set_orb_tables 1.1085 1 1.1 16.% + ORB_gen_tables gen_tables 1.1085 1 1.1 16.% + ORB_table_phi init_Table 0.48601 1 0.49 7.0% + ORB_table_phi cal_ST_Phi12_R 0.48108 126 0.0038 6.9% + ORB_table_beta init_Table_Beta 0.18772 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18617 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25558 1 0.26 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25363 66 0.0038 3.6% + LOOP_ions opt_ions 5.3040 1 5.3 76.% + ESolver_KS_LCAO Run 4.7090 1 4.7 68.% + HSolverLCAO solve 2.7508 11 0.25 40.% + HamiltLCAO updateHk 1.3967 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3685 11 0.12 20.% + Gint_interface cal_gint 0.57866 23 0.025 8.3% + Gint_Gamma distri_vl_value 0.76581 11 0.070 11.% + Gint_Gamma distri_vl 2.2569 6 0.38 32.% + LCAO_Deepks cal_projected_DM 4.8907 13 0.38 70.% + LCAO_gen_fixedH add_v_delta 2.1264 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.1264 6 0.35 31.% + ElecStateLCAO psiToRho 1.3357 11 0.12 19.% + Charge mix_rho 0.65402 10 0.065 9.4% + LOOP_ions force_stress 0.59485 1 0.59 8.6% + Force_Stress_LCAO getForceStress 0.59482 1 0.59 8.6% + Force_LCAO_gamma ftable_gamma 0.38114 1 0.38 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.14492 1 0.14 2.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:14 2022 + Finish Time : Wed Sep 28 11:02:21 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..f41cfbfe201940652a744ebcf3718cf97f5c6e1f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123921 ima = 3.63352e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122599591841 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111483994093 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112010600009 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112299600873 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112224644637 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112265469789 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112263921717 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112266883633 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112266171392 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112266067151 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112266054299 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1fb13a5f325ae67362a9336c82780b4004c7286d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.555008111459 22.071431506270 10.635664661211 0 0 0 +H +0.0 +2 +-21.538534918170 21.115368422941 9.482206464591 0 0 0 +-24.140489675265 21.243533023004 10.371531083242 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/conv new file mode 100644 index 0000000000000000000000000000000000000000..eb8ebcea106b7d2356ca04e88bdd262839d39d7a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/conv @@ -0,0 +1 @@ +67 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0d9d473e1c0248d9ecedfd7c902906cc30b8b92f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753275954 0.0128732829 1.284107692 1.364863937 1.470354582 0.009414644559 0.01734733573 0.03912930591 +3.678074827e-18 0.001001868995 0.002916054428 0.01356884521 0.04837557608 -6.5377104e-19 2.939253057e-06 7.622100699e-06 +0.001599560763 0.006151488384 + +H atom_index 1 n_descriptor 18 +1.266843277 0.0342253951 0.1169981984 0.1575055046 0.3248802816 0.02399388574 0.02921543298 0.03739930097 +2.413370904e-17 5.428927541e-05 0.1072265379 0.1171404759 0.1352337542 5.062737743e-19 2.377492231e-06 0.01335075872 +0.02785357603 0.03150021624 + +H atom_index 2 n_descriptor 18 +1.268749356 0.03416275377 0.1177139658 0.15844151 0.3254759915 0.02408798642 0.02932649605 0.0373536093 +9.894535434e-18 5.447785658e-05 0.1074520535 0.1174685378 0.1360336271 4.851785108e-18 2.270647901e-06 0.01335679879 +0.02791937213 0.0315808527 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..beb62559f3ab09dd1de7889f662ccadc25a2ebb1 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..1e2251f9053fb4e5736b3d90a6295606083f3480 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..9ce2609c9843dcccba453a351a655223899328fb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..ccdbe3715dcc82f4e1c03ad27e143f47ddb51e10 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:14 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0858612 SEC) : SETUP UNITCELL + DONE(0.102211 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.121098 SEC) : INIT PLANEWAVE + DONE(0.169737 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451261 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651454e+02 0.000000e+00 2.158e-01 5.423e-01 + GE2 -4.663805e+02 -1.235085e+00 9.744e-02 4.694e-01 + GE3 -4.663850e+02 -4.531654e-03 6.236e-02 5.218e-01 + GE4 -4.663852e+02 -1.578924e-04 1.982e-03 4.122e-01 + GE5 -4.663842e+02 1.027910e-03 9.720e-04 4.104e-01 + GE6 -4.663849e+02 -7.035666e-04 9.872e-05 3.956e-01 + GE7 -4.663847e+02 2.148334e-04 4.567e-05 3.992e-01 + GE8 -4.663847e+02 -2.496780e-05 1.620e-05 3.865e-01 + GE9 -4.663847e+02 1.984502e-05 2.319e-06 3.903e-01 + GE10 -4.663847e+02 -3.109727e-06 2.560e-07 3.899e-01 + GE11 -4.663847e+02 -5.341614e-07 6.261e-08 3.303e-01 +E_delta_band = -7.18669865e-02 Ry = -9.77800514e-01 eV +E_delta_NN= -1.95465473e-01 Ry = -2.65944419e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9523 11 0.63 1e+02 % + Run_lcao lcao_line 6.9436 1 6.9 1e+02 % + Potential init_pot 0.28669 2 0.14 4.1 % + PW_Basis recip2real 0.25917 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.11798 16 0.0074 1.7 % + Potential v_of_rho 0.85812 13 0.066 12 % + XC_Functional v_xc 0.2458 14 0.018 3.5 % + H_Hartree_pw v_hartree 0.57785 13 0.044 8.3 % + PW_Basis real2recip 0.56808 38 0.015 8.2 % + PW_Basis gatherp_scatters 0.23718 38 0.0062 3.4 % + ORB_control set_orb_tables 1.1085 1 1.1 16 % + ORB_gen_tables gen_tables 1.1085 1 1.1 16 % + ORB_table_phi init_Table 0.48601 1 0.49 7 % + ORB_table_phi cal_ST_Phi12_R 0.48108 126 0.0038 6.9 % + ORB_table_beta init_Table_Beta 0.18772 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18617 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.25558 1 0.26 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25363 66 0.0038 3.6 % + LOOP_ions opt_ions 5.304 1 5.3 76 % + ESolver_KS_LCAO Run 4.709 1 4.7 68 % + HSolverLCAO solve 2.7508 11 0.25 40 % + HamiltLCAO updateHk 1.3967 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3685 11 0.12 20 % + Gint_interface cal_gint 0.57866 23 0.025 8.3 % + Gint_Gamma distri_vl_value 0.76581 11 0.07 11 % + Gint_Gamma distri_vl 2.2569 6 0.38 32 % + LCAO_Deepks cal_projected_DM 4.8907 13 0.38 70 % + LCAO_gen_fixedH add_v_delta 2.1264 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.1264 6 0.35 31 % + ElecStateLCAO psiToRho 1.3357 11 0.12 19 % + Charge mix_rho 0.65402 10 0.065 9.4 % + LOOP_ions force_stress 0.59485 1 0.59 8.6 % + Force_Stress_LCAO getForceStress 0.59482 1 0.59 8.6 % + Force_LCAO_gamma ftable_gamma 0.38114 1 0.38 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.14492 1 0.14 2.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:14 2022 + FINISH Time : Wed Sep 28 11:02:21 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/67/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ea8f3fef3eed9f0a47606dec40e7095b6ec68058 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.170001 0.789752 0.39909 +H 0.205914 0.745576 0.366421 +H 0.136508 0.822922 0.353959 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0fea41389984d39c32ca16dd7a1fab50c8b83f16 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2531 2 + 2 -13.1507 2 + 3 -9.01329 2 + 4 -6.73591 2 + 5 1.31827 0 + 6 4.44331 0 + 7 11.0773 0 + 8 11.3191 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..18e2aeb4811313131e27f2655b0f032941e6ae3b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/running_scf.log @@ -0,0 +1,780 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:50 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.76002317785 22.1130576193 11.1745118654 0 0 0 0 + tauc_H1 5.76558867712 20.8761167407 10.2597990096 0 0 0 0 + tauc_H2 3.82222958552 23.0418090845 9.91085700817 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0963262230818 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101112626132 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119401997022 (SEC) + + DONE : INIT CHARGE Time : 0.170559867481 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.465456 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000988 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113 + + Density error is 0.215083357418 + + Energy Rydberg eV + E_KohnSham -34.1916261466 -465.20093948 + E_Harris -34.3835015201 -467.811537864 + E_Fermi -0.404821928575 -5.50788490397 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119666777753 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012570291989 + + Density error is 0.0980011328267 + + Energy Rydberg eV + E_KohnSham -34.2810146501 -466.417132463 + E_Harris -34.2877190216 -466.508350117 + E_Fermi -0.213748702856 -2.90820029896 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113306156033 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119099964631 + + Density error is 0.0628489998867 + + Energy Rydberg eV + E_KohnSham -34.2812747064 -466.42067071 + E_Harris -34.2856000592 -466.479520155 + E_Fermi -0.202344839756 -2.75304278157 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103170137132 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108818156388 + + Density error is 0.00202201760708 + + Energy Rydberg eV + E_KohnSham -34.2812664326 -466.42055814 + E_Harris -34.281268654 -466.420588363 + E_Fermi -0.16693818786 -2.27131056869 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103128726722 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108807276111 + + Density error is 0.000871001414249 + + Energy Rydberg eV + E_KohnSham -34.2812094059 -466.419782251 + E_Harris -34.281210468 -466.419796702 + E_Fermi -0.166173697492 -2.26090914362 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010299523265 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108667957416 + + Density error is 0.000181348666383 + + Energy Rydberg eV + E_KohnSham -34.281245865 -466.420278302 + E_Harris -34.2812459467 -466.420279415 + E_Fermi -0.166177312676 -2.26095833072 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010301051964 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108685056982 + + Density error is 3.86100211596e-05 + + Energy Rydberg eV + E_KohnSham -34.28123158 -466.420083946 + E_Harris -34.2812315878 -466.420084052 + E_Fermi -0.166039778502 -2.25908708228 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103004956494 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010867901882 + + Density error is 1.62237973885e-05 + + Energy Rydberg eV + E_KohnSham -34.2812364825 -466.420150647 + E_Harris -34.2812364835 -466.420150661 + E_Fermi -0.16608175565 -2.25965821069 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103003455734 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108677548845 + + Density error is 1.71498900328e-06 + + Energy Rydberg eV + E_KohnSham -34.2812351031 -466.420131879 + E_Harris -34.2812351031 -466.42013188 + E_Fermi -0.166064248195 -2.25942000954 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103003416233 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108677487556 + + Density error is 2.49758790977e-07 + + Energy Rydberg eV + E_KohnSham -34.281235318 -466.420134803 + E_Harris -34.281235318 -466.420134803 + E_Fermi -0.166062745652 -2.2593995664 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103003483498 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108677558868 + + Density error is 7.06298925748e-08 + + Energy Rydberg eV + E_KohnSham -34.2812353422 -466.420135133 + E_Harris -34.2812353422 -466.420135133 + E_band -7.96034439332 -108.306041792 + E_one_elec -69.2949618461 -942.8063238 + E_Hartree +36.0456041598 +490.425604426 + E_xc -8.2104369963 -111.70872622 + E_Ewald +7.30289885998 +99.3610364135 + E_demet -9.5446272303e-78 -1.29861315618e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194761728422 -2.64986925887 + E_Fermi -0.166062665065 -2.25939846995 + + charge density convergence is achieved + final etot is -466.420135133 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2531 2.00000 + 2 -13.1507 2.00000 + 3 -9.01329 2.00000 + 4 -6.73591 2.00000 + 5 1.31827 0.00000 + 6 4.44331 0.00000 + 7 11.0773 0.00000 + 8 11.3191 0.00000 + + EFERMI = -2.259398469951106 eV + OUT.ABACUS/ final etot is -466.4201351332445 eV + correction force for each atom along direction 1 is 0.000108280 + correction force for each atom along direction 2 is -5.14511e-05 + correction force for each atom along direction 3 is -0.000118241 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.14749417 -0.10699162 +0.52663831 + H1 -0.0049259135 -0.013595648 -0.16203190 + H2 -0.14256825 +0.12058727 -0.36460642 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4201351332445 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8872 11 0.72 1.0e+02% + Run_lcao lcao_line 7.8730 1 7.9 1.e+02% + Potential init_pot 0.29862 2 0.15 3.8% + PW_Basis recip2real 0.27355 16 0.017 3.5% + PW_Basis gathers_scatterp 0.13461 16 0.0084 1.7% + Charge atomic_rho 0.10199 1 0.10 1.3% + Potential v_of_rho 1.0421 13 0.080 13.% + XC_Functional v_xc 0.36748 14 0.026 4.7% + H_Hartree_pw v_hartree 0.63760 13 0.049 8.1% + PW_Basis real2recip 0.66768 38 0.018 8.5% + PW_Basis gatherp_scatters 0.30269 38 0.0080 3.8% + ORB_control set_orb_tables 1.1198 1 1.1 14.% + ORB_gen_tables gen_tables 1.1198 1 1.1 14.% + ORB_table_phi init_Table 0.48458 1 0.48 6.1% + ORB_table_phi cal_ST_Phi12_R 0.47921 126 0.0038 6.1% + ORB_table_beta init_Table_Beta 0.19119 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18955 56 0.0034 2.4% + ORB_table_alpha init_Table_Alpha 0.25642 1 0.26 3.3% + ORB_table_alpha S_PhiAlpha_R 0.25440 66 0.0039 3.2% + LOOP_ions opt_ions 6.2032 1 6.2 79.% + ESolver_KS_LCAO Run 5.5789 1 5.6 71.% + HSolverLCAO solve 3.2936 11 0.30 42.% + HamiltLCAO updateHk 1.6338 11 0.15 21.% + LCAO_Hamilt cal_Hgamma 1.6063 11 0.15 20.% + Gint_interface cal_gint 0.58900 23 0.026 7.5% + Gint_Gamma distri_vl_value 0.95925 11 0.087 12.% + Gint_Gamma distri_vl 2.6714 6 0.45 34.% + LCAO_Deepks cal_projected_DM 5.7606 13 0.44 73.% + LCAO_gen_fixedH add_v_delta 2.5404 6 0.42 32.% + LCAO_DESCRIPTOR add_v_delta 2.5406 6 0.42 32.% + ElecStateLCAO psiToRho 1.6198 11 0.15 21.% + Charge mix_rho 0.71417 10 0.071 9.1% + LOOP_ions force_stress 0.62419 1 0.62 7.9% + Force_Stress_LCAO getForceStress 0.62416 1 0.62 7.9% + Force_LCAO_gamma ftable_gamma 0.40320 1 0.40 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.14571 1 0.15 1.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:50 2022 + Finish Time : Wed Sep 28 11:04:58 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1e22e3973947660517921d764f1787a4436a6986 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123388 ima = 3.68981e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123275327723 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112334953249 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112854547039 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113090444643 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113043065212 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113072954326 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011306381588 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113066647011 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113066022983 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113065956347 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113065945327 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4ab04e0d05961484e28aab2e62660b8b5c4064e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.239976822167 22.113057619311 11.174511865353 0 0 0 +H +0.0 +2 +-22.234411322899 20.876116740730 10.259799009600 0 0 0 +-24.177770414483 23.041809084525 9.910857008150 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/conv new file mode 100644 index 0000000000000000000000000000000000000000..7bbdf7d5ef190d8e4ef9ae3631ef4321d2489ddf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/conv @@ -0,0 +1 @@ +68 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..65fb768cf27dec6d0d7cab64660188206d4a6c00 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747422228 0.01265968708 1.275057502 1.364856558 1.469174045 0.008193002475 0.01916599495 0.03897083736 +-4.645065084e-18 0.001089909885 0.002512869236 0.0123227752 0.0442464082 1.977086982e-18 1.827389296e-06 5.477649532e-06 +0.001691522541 0.005858722665 + +H atom_index 1 n_descriptor 18 +1.240216364 0.03436886558 0.1047734535 0.1459424488 0.3186507554 0.02160065066 0.0278055305 0.03752006522 +4.80185789e-19 4.231257461e-05 0.09911743601 0.1145738175 0.1252702573 2.717032553e-18 4.697479605e-06 0.01315985768 +0.0258065161 0.03035572608 + +H atom_index 2 n_descriptor 18 +1.248672511 0.03407399057 0.1076485295 0.1498169257 0.321395891 0.02198459658 0.02829707205 0.03724547192 +-1.605248885e-17 4.306360184e-05 0.1012529374 0.1148882316 0.1286224131 3.634352419e-19 4.272926569e-06 0.0130777728 +0.02612421333 0.03074375173 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..7705460c106fbde6ee68795132b5436faddcc5f2 Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..2e996ab6953c4e9511ef60ca19dce84d75ffc8d9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:50 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0963577 SEC) : SETUP UNITCELL + DONE(0.101131 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119422 SEC) : INIT PLANEWAVE + DONE(0.170715 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.465523 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652009e+02 0.000000e+00 2.151e-01 6.065e-01 + GE2 -4.664171e+02 -1.216193e+00 9.800e-02 5.653e-01 + GE3 -4.664207e+02 -3.538247e-03 6.285e-02 6.287e-01 + GE4 -4.664206e+02 1.125702e-04 2.022e-03 4.866e-01 + GE5 -4.664198e+02 7.758892e-04 8.710e-04 4.859e-01 + GE6 -4.664203e+02 -4.960516e-04 1.813e-04 4.773e-01 + GE7 -4.664201e+02 1.943568e-04 3.861e-05 4.732e-01 + GE8 -4.664202e+02 -6.670115e-05 1.622e-05 4.637e-01 + GE9 -4.664201e+02 1.876743e-05 1.715e-06 4.669e-01 + GE10 -4.664201e+02 -2.923544e-06 2.498e-07 4.634e-01 + GE11 -4.664201e+02 -3.302416e-07 7.063e-08 3.936e-01 +E_delta_band = -7.04222088e-02 Ry = -9.58143306e-01 eV +E_delta_NN= -1.94761728e-01 Ry = -2.64986926e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8872 11 0.72 1e+02 % + Run_lcao lcao_line 7.873 1 7.9 1e+02 % + Potential init_pot 0.29862 2 0.15 3.8 % + PW_Basis recip2real 0.27355 16 0.017 3.5 % + PW_Basis gathers_scatterp 0.13461 16 0.0084 1.7 % + Charge atomic_rho 0.10199 1 0.1 1.3 % + Potential v_of_rho 1.0421 13 0.08 13 % + XC_Functional v_xc 0.36748 14 0.026 4.7 % + H_Hartree_pw v_hartree 0.6376 13 0.049 8.1 % + PW_Basis real2recip 0.66768 38 0.018 8.5 % + PW_Basis gatherp_scatters 0.30269 38 0.008 3.8 % + ORB_control set_orb_tables 1.1198 1 1.1 14 % + ORB_gen_tables gen_tables 1.1198 1 1.1 14 % + ORB_table_phi init_Table 0.48458 1 0.48 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.47921 126 0.0038 6.1 % + ORB_table_beta init_Table_Beta 0.19119 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18955 56 0.0034 2.4 % + ORB_table_alpha init_Table_Alpha 0.25642 1 0.26 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.2544 66 0.0039 3.2 % + LOOP_ions opt_ions 6.2032 1 6.2 79 % + ESolver_KS_LCAO Run 5.5789 1 5.6 71 % + HSolverLCAO solve 3.2936 11 0.3 42 % + HamiltLCAO updateHk 1.6338 11 0.15 21 % + LCAO_Hamilt cal_Hgamma 1.6063 11 0.15 20 % + Gint_interface cal_gint 0.589 23 0.026 7.5 % + Gint_Gamma distri_vl_value 0.95925 11 0.087 12 % + Gint_Gamma distri_vl 2.6714 6 0.45 34 % + LCAO_Deepks cal_projected_DM 5.7606 13 0.44 73 % + LCAO_gen_fixedH add_v_delta 2.5404 6 0.42 32 % + LCAO_DESCRIPTOR add_v_delta 2.5406 6 0.42 32 % + ElecStateLCAO psiToRho 1.6198 11 0.15 21 % + Charge mix_rho 0.71417 10 0.071 9.1 % + LOOP_ions force_stress 0.62419 1 0.62 7.9 % + Force_Stress_LCAO getForceStress 0.62416 1 0.62 7.9 % + Force_LCAO_gamma ftable_gamma 0.4032 1 0.4 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.14571 1 0.15 1.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:50 2022 + FINISH Time : Wed Sep 28 11:04:58 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/68/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..31a3880c4f064a7b2f58ab8e853bffe4d6824a9a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.157892 0.794211 0.420737 +H 0.185041 0.75484 0.374894 +H 0.191043 0.849953 0.409211 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..fabf62e5d476b7fb807bb2ce413a82d3a3f13e3d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2748 2 + 2 -12.7674 2 + 3 -9.31074 2 + 4 -6.74407 2 + 5 1.20519 0 + 6 4.25854 0 + 7 11.0908 0 + 8 11.3636 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e307eb7306c97a7d634b8d9a75bd203f5508ab44 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:57 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.42098249148 22.2379163274 11.7806315965 0 0 0 0 + tauc_H1 5.1811609107 21.1355270063 10.4970373919 0 0 0 0 + tauc_H2 5.34921112975 23.7986914818 11.4579159081 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0728167772849 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0860551289683 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.10181617271 (SEC) + + DONE : INIT CHARGE Time : 0.143146695098 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388131 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00142 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104 + + Density error is 0.212193828873 + + Energy Rydberg eV + E_KohnSham -34.1930933317 -465.220901557 + E_Harris -34.3795494802 -467.757767603 + E_Fermi -0.399858798337 -5.44035805281 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00135996890515 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117654340927 + + Density error is 0.0978027720269 + + Energy Rydberg eV + E_KohnSham -34.2805608234 -466.410957833 + E_Harris -34.2874026775 -466.504046034 + E_Fermi -0.211024862104 -2.87114054427 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125576642539 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111739496946 + + Density error is 0.0627772128311 + + Energy Rydberg eV + E_KohnSham -34.2807912995 -466.414093622 + E_Harris -34.2852231494 -466.474392033 + E_Fermi -0.200823926127 -2.73234969006 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106824475307 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103476344825 + + Density error is 0.00191928121433 + + Energy Rydberg eV + E_KohnSham -34.2807538132 -466.413583595 + E_Harris -34.2807540942 -466.413587418 + E_Fermi -0.165278203034 -2.24872531646 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106653291457 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010359743425 + + Density error is 0.000816814435935 + + Energy Rydberg eV + E_KohnSham -34.2807074389 -466.412952641 + E_Harris -34.2807086183 -466.412968686 + E_Fermi -0.164821452614 -2.24251090819 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106440967183 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103477766021 + + Density error is 0.000114727621964 + + Energy Rydberg eV + E_KohnSham -34.2807380182 -466.413368693 + E_Harris -34.2807378721 -466.413366705 + E_Fermi -0.164681018776 -2.24060020779 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106433748366 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103489598371 + + Density error is 3.06422692938e-05 + + Energy Rydberg eV + E_KohnSham -34.2807279377 -466.41323154 + E_Harris -34.2807279425 -466.413231606 + E_Fermi -0.164600645663 -2.2395066755 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106431781474 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103483662428 + + Density error is 1.25082786282e-05 + + Energy Rydberg eV + E_KohnSham -34.2807305768 -466.413267447 + E_Harris -34.2807305774 -466.413267456 + E_Fermi -0.164632252655 -2.23993671069 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106429142912 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103483282742 + + Density error is 1.41090034238e-06 + + Energy Rydberg eV + E_KohnSham -34.2807294269 -466.413251802 + E_Harris -34.2807294269 -466.413251802 + E_Fermi -0.164618605257 -2.2397510283 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106429055911 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010348338444 + + Density error is 1.68634996329e-07 + + Energy Rydberg eV + E_KohnSham -34.2807296202 -466.413254432 + E_Harris -34.2807296202 -466.413254432 + E_Fermi -0.164617567703 -2.23973691166 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106429098866 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103483426483 + + Density error is 3.9462108493e-08 + + Energy Rydberg eV + E_KohnSham -34.2807296428 -466.41325474 + E_Harris -34.2807296428 -466.41325474 + E_band -7.95210900798 -108.193993626 + E_one_elec -69.1157023734 -940.367373551 + E_Hartree +35.9499553653 +489.124235814 + E_xc -8.19508454222 -111.499845366 + E_Ewald +7.20476582293 +98.0258679475 + E_demet -2.79903264555e-72 -3.80827928674e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194526002553 -2.64666204389 + E_Fermi -0.164617530082 -2.2397363998 + + charge density convergence is achieved + final etot is -466.41325474 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2748 2.00000 + 2 -12.7674 2.00000 + 3 -9.31074 2.00000 + 4 -6.74407 2.00000 + 5 1.20519 0.00000 + 6 4.25854 0.00000 + 7 11.0908 0.00000 + 8 11.3636 0.00000 + + EFERMI = -2.239736399802681 eV + OUT.ABACUS/ final etot is -466.4132547399200 eV + correction force for each atom along direction 1 is -2.55093e-05 + correction force for each atom along direction 2 is 7.06203e-05 + correction force for each atom along direction 3 is 1.05950e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.35669111 -0.091864538 -0.42263585 + H1 -0.25032332 -0.12689176 +0.21405273 + H2 -0.10636779 +0.21875630 +0.20858313 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4132547399200 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3261 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3190 1 7.3 1.e+02% + Potential init_pot 0.24433 2 0.12 3.3% + PW_Basis recip2real 0.22405 16 0.014 3.1% + PW_Basis gathers_scatterp 0.10772 16 0.0067 1.5% + Potential v_of_rho 0.96945 13 0.075 13.% + XC_Functional v_xc 0.37831 14 0.027 5.2% + H_Hartree_pw v_hartree 0.56222 13 0.043 7.7% + PW_Basis real2recip 0.61308 38 0.016 8.4% + PW_Basis gatherp_scatters 0.27837 38 0.0073 3.8% + ORB_control set_orb_tables 0.89486 1 0.89 12.% + ORB_gen_tables gen_tables 0.89486 1 0.89 12.% + ORB_table_phi init_Table 0.37407 1 0.37 5.1% + ORB_table_phi cal_ST_Phi12_R 0.36985 126 0.0029 5.0% + ORB_table_beta init_Table_Beta 0.15440 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15306 56 0.0027 2.1% + ORB_table_alpha init_Table_Alpha 0.20847 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20681 66 0.0031 2.8% + LOOP_ions opt_ions 5.9625 1 6.0 81.% + ESolver_KS_LCAO Run 5.3904 1 5.4 74.% + HSolverLCAO solve 3.1983 11 0.29 44.% + HamiltLCAO updateHk 1.5792 11 0.14 22.% + LCAO_Hamilt cal_Hgamma 1.5558 11 0.14 21.% + Gint_interface cal_gint 0.34262 23 0.015 4.7% + Gint_Gamma distri_vl_value 1.0381 11 0.094 14.% + Gint_Gamma distri_vl 2.5701 6 0.43 35.% + LCAO_Deepks cal_projected_DM 5.5195 13 0.42 75.% + LCAO_gen_fixedH add_v_delta 2.4607 6 0.41 34.% + LCAO_DESCRIPTOR add_v_delta 2.4608 6 0.41 34.% + ElecStateLCAO psiToRho 1.5826 11 0.14 22.% + Charge mix_rho 0.68022 10 0.068 9.3% + LOOP_ions force_stress 0.57200 1 0.57 7.8% + Force_Stress_LCAO getForceStress 0.57198 1 0.57 7.8% + Force_LCAO_gamma ftable_gamma 0.37531 1 0.38 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.10003 1 0.10 1.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:57 2022 + Finish Time : Wed Sep 28 11:04:04 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..416a926661b9b4bcfd13065c02218a02f634d1fa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123666 ima = 3.69439e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012278585942 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111762315538 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112363777508 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112590007782 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112550468612 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112574093848 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112569679701 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112572015476 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112571461342 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112571400793 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112571391872 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e816feb62a13d090f8c04135498d061d486edf14 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.579017508534 22.237916327389 11.780631596478 0 0 0 +H +0.0 +2 +-22.818839089285 21.135527006266 10.497037391959 0 0 0 +-22.650788870256 23.798691481829 11.457915908092 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/conv new file mode 100644 index 0000000000000000000000000000000000000000..0a9433e632435a99fc3a53ca8fe4415c326dfcd3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/conv @@ -0,0 +1 @@ +69 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..80e56e6b0df336026f89b9ba7c465fc70802a494 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752563529 0.01269758779 1.264504045 1.348887783 1.469189084 0.009063747527 0.01720339689 0.03913171586 +6.503969421e-19 0.0009228115515 0.002694293771 0.01263218781 0.04528743272 -4.523701467e-19 2.363718473e-06 6.565039005e-06 +0.001595937526 0.006084235607 + +H atom_index 1 n_descriptor 18 +1.231564978 0.03527824131 0.1032385082 0.1412684429 0.314003383 0.02182695156 0.02717564419 0.03843360629 +-1.241104815e-17 4.556317796e-05 0.09694022044 0.1145213911 0.121068693 8.368820315e-18 4.520654596e-06 0.01355379269 +0.02578592208 0.02985802123 + +H atom_index 2 n_descriptor 18 +1.239864307 0.03499816895 0.1060344364 0.1449856579 0.3168577708 0.02222785866 0.02766285207 0.03813719944 +-3.082576774e-17 4.633181343e-05 0.09904797857 0.1148515823 0.124298431 1.884407699e-18 4.086125522e-06 0.01342436713 +0.02610740666 0.03025891512 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..37f962981e77f7821a9b7380141f250e3871a199 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..306fc991138517856715c6953cd32fbfcac3f87e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..41248516166566b1244eec8785d8f9a03d239370 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..13a962db719c1dc3221818af1261387e279adfe3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:57 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0728324 SEC) : SETUP UNITCELL + DONE(0.0860676 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.101829 SEC) : INIT PLANEWAVE + DONE(0.14325 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.388172 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652209e+02 0.000000e+00 2.122e-01 5.609e-01 + GE2 -4.664110e+02 -1.190056e+00 9.780e-02 5.422e-01 + GE3 -4.664141e+02 -3.135789e-03 6.278e-02 6.011e-01 + GE4 -4.664136e+02 5.100270e-04 1.919e-03 4.774e-01 + GE5 -4.664130e+02 6.309544e-04 8.168e-04 4.786e-01 + GE6 -4.664134e+02 -4.160522e-04 1.147e-04 4.733e-01 + GE7 -4.664132e+02 1.371523e-04 3.064e-05 4.499e-01 + GE8 -4.664133e+02 -3.590617e-05 1.251e-05 4.605e-01 + GE9 -4.664133e+02 1.564465e-05 1.411e-06 4.570e-01 + GE10 -4.664133e+02 -2.630423e-06 1.686e-07 4.542e-01 + GE11 -4.664133e+02 -3.075018e-07 3.946e-08 3.760e-01 +E_delta_band = -6.98620871e-02 Ry = -9.50522459e-01 eV +E_delta_NN= -1.94526003e-01 Ry = -2.64666204e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3261 11 0.67 1e+02 % + Run_lcao lcao_line 7.319 1 7.3 1e+02 % + Potential init_pot 0.24433 2 0.12 3.3 % + PW_Basis recip2real 0.22405 16 0.014 3.1 % + PW_Basis gathers_scatterp 0.10772 16 0.0067 1.5 % + Potential v_of_rho 0.96945 13 0.075 13 % + XC_Functional v_xc 0.37831 14 0.027 5.2 % + H_Hartree_pw v_hartree 0.56222 13 0.043 7.7 % + PW_Basis real2recip 0.61308 38 0.016 8.4 % + PW_Basis gatherp_scatters 0.27837 38 0.0073 3.8 % + ORB_control set_orb_tables 0.89486 1 0.89 12 % + ORB_gen_tables gen_tables 0.89486 1 0.89 12 % + ORB_table_phi init_Table 0.37407 1 0.37 5.1 % + ORB_table_phi cal_ST_Phi12_R 0.36985 126 0.0029 5 % + ORB_table_beta init_Table_Beta 0.1544 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15306 56 0.0027 2.1 % + ORB_table_alpha init_Table_Alpha 0.20847 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20681 66 0.0031 2.8 % + LOOP_ions opt_ions 5.9625 1 6 81 % + ESolver_KS_LCAO Run 5.3904 1 5.4 74 % + HSolverLCAO solve 3.1983 11 0.29 44 % + HamiltLCAO updateHk 1.5792 11 0.14 22 % + LCAO_Hamilt cal_Hgamma 1.5558 11 0.14 21 % + Gint_interface cal_gint 0.34262 23 0.015 4.7 % + Gint_Gamma distri_vl_value 1.0381 11 0.094 14 % + Gint_Gamma distri_vl 2.5701 6 0.43 35 % + LCAO_Deepks cal_projected_DM 5.5195 13 0.42 75 % + LCAO_gen_fixedH add_v_delta 2.4607 6 0.41 34 % + LCAO_DESCRIPTOR add_v_delta 2.4608 6 0.41 34 % + ElecStateLCAO psiToRho 1.5826 11 0.14 22 % + Charge mix_rho 0.68022 10 0.068 9.3 % + LOOP_ions force_stress 0.572 1 0.57 7.8 % + Force_Stress_LCAO getForceStress 0.57198 1 0.57 7.8 % + Force_LCAO_gamma ftable_gamma 0.37531 1 0.38 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.10003 1 0.1 1.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:57 2022 + FINISH Time : Wed Sep 28 11:04:04 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/69/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..cb8d26616220bc7b1aaddf42685a08ab5b8bbd81 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.626952 0.117329 0.35562 +H 0.59035 0.0641472 0.36103 +H 0.583601 0.165923 0.346128 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..00879912e999c148a3e6fcc228f277fd2a563d8a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.32 2 + 2 -13.0799 2 + 3 -9.11672 2 + 4 -6.75126 2 + 5 1.33095 0 + 6 4.47063 0 + 7 11.0677 0 + 8 11.3179 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fd88c0ebbcdc3f511ac5846ce03e9fb0207264b7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:19 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.5546513904 3.28521787677 9.95736626649 0 0 0 0 + tauc_H1 16.5298035803 1.79612211372 10.1088287162 0 0 0 0 + tauc_H2 16.3408291712 4.64585492924 9.69159555791 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0729166377332 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0854002072031 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.101042189147 (SEC) + + DONE : INIT CHARGE Time : 0.142299601122 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.38893 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107 + + Density error is 0.214474864291 + + Energy Rydberg eV + E_KohnSham -34.1924020074 -465.211495607 + E_Harris -34.3832664429 -467.808339476 + E_Fermi -0.407386789088 -5.54278162151 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120270685926 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102837807243 + + Density error is 0.0977736591013 + + Energy Rydberg eV + E_KohnSham -34.2809076471 -466.415676612 + E_Harris -34.2875926111 -466.506630214 + E_Fermi -0.21646241451 -2.94512224017 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111629426895 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000965227382222 + + Density error is 0.0626190861965 + + Energy Rydberg eV + E_KohnSham -34.281082521 -466.418055894 + E_Harris -34.2853976024 -466.476765588 + E_Fermi -0.20431296559 -2.7798205073 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000965848706691 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000868617526087 + + Density error is 0.00198864696147 + + Energy Rydberg eV + E_KohnSham -34.2810845291 -466.418083215 + E_Harris -34.2810858776 -466.418101563 + E_Fermi -0.168830918161 -2.29706248556 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000963423639711 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00086890567226 + + Density error is 0.000834895928602 + + Energy Rydberg eV + E_KohnSham -34.2810274105 -466.417306077 + E_Harris -34.2810286984 -466.417323599 + E_Fermi -0.167998587041 -2.28573803971 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000961897788585 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867740178518 + + Density error is 0.00015225043369 + + Energy Rydberg eV + E_KohnSham -34.2810669178 -466.417843602 + E_Harris -34.2810669787 -466.417844429 + E_Fermi -0.168068533367 -2.2866897083 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000961841082273 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867851959075 + + Density error is 3.76198053021e-05 + + Energy Rydberg eV + E_KohnSham -34.2810521049 -466.417642061 + E_Harris -34.2810521127 -466.417642168 + E_Fermi -0.16793486977 -2.28487112176 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000961831059278 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867825184497 + + Density error is 1.5840613283e-05 + + Energy Rydberg eV + E_KohnSham -34.2810564057 -466.417700577 + E_Harris -34.2810564067 -466.417700591 + E_Fermi -0.167979447087 -2.28547762727 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00096180074447 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867814190985 + + Density error is 1.2998425293e-06 + + Energy Rydberg eV + E_KohnSham -34.2810550124 -466.417681621 + E_Harris -34.2810550124 -466.417681621 + E_Fermi -0.167961292618 -2.28523062305 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000961801590716 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867814360491 + + Density error is 2.08668065212e-07 + + Energy Rydberg eV + E_KohnSham -34.2810552503 -466.417684856 + E_Harris -34.2810552503 -466.417684856 + E_Fermi -0.167960612597 -2.28522137089 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000961802002001 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000867814573019 + + Density error is 4.3659648015e-08 + + Energy Rydberg eV + E_KohnSham -34.2810552672 -466.417685087 + E_Harris -34.2810552672 -466.417685087 + E_band -7.97721988733 -108.535644667 + E_one_elec -69.3582507439 -943.66741343 + E_Hartree +36.0716194267 +490.779560291 + E_xc -8.21470072398 -111.766737211 + E_Ewald +7.34446882401 +99.9266247898 + E_demet -2.26605828116e-79 -3.08313046238e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194922228816 -2.65205297875 + E_Fermi -0.167960543186 -2.28522042651 + + charge density convergence is achieved + final etot is -466.417685087 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3200 2.00000 + 2 -13.0799 2.00000 + 3 -9.11672 2.00000 + 4 -6.75126 2.00000 + 5 1.33095 0.00000 + 6 4.47063 0.00000 + 7 11.0677 0.00000 + 8 11.3179 0.00000 + + EFERMI = -2.285220426506406 eV + OUT.ABACUS/ final etot is -466.4176850868088 eV + correction force for each atom along direction 1 is -0.000182327 + correction force for each atom along direction 2 is -1.06631e-05 + correction force for each atom along direction 3 is 1.04181e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.43646889 +0.66043614 -0.067223854 + H1 -0.44460274 -0.67958798 +0.070135894 + H2 +0.0081338523 +0.019151834 -0.0029120395 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4176850868088 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7152 11 0.61 1.0e+02% + Run_lcao lcao_line 6.7082 1 6.7 1.e+02% + Potential init_pot 0.24502 2 0.12 3.6% + PW_Basis recip2real 0.22826 16 0.014 3.4% + PW_Basis gathers_scatterp 0.11145 16 0.0070 1.7% + Potential v_of_rho 0.95115 13 0.073 14.% + XC_Functional v_xc 0.35528 14 0.025 5.3% + H_Hartree_pw v_hartree 0.56905 13 0.044 8.5% + PW_Basis real2recip 0.62383 38 0.016 9.3% + PW_Basis gatherp_scatters 0.29270 38 0.0077 4.4% + ORB_control set_orb_tables 0.89672 1 0.90 13.% + ORB_gen_tables gen_tables 0.89672 1 0.90 13.% + ORB_table_phi init_Table 0.37468 1 0.37 5.6% + ORB_table_phi cal_ST_Phi12_R 0.37049 126 0.0029 5.5% + ORB_table_beta init_Table_Beta 0.15609 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15473 56 0.0028 2.3% + ORB_table_alpha init_Table_Alpha 0.20834 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20674 66 0.0031 3.1% + LOOP_ions opt_ions 5.3491 1 5.3 80.% + ESolver_KS_LCAO Run 4.7959 1 4.8 71.% + HSolverLCAO solve 2.6149 11 0.24 39.% + HamiltLCAO updateHk 1.3245 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3010 11 0.12 19.% + Gint_interface cal_gint 0.66130 23 0.029 9.8% + Gint_Gamma distri_vl_value 0.67175 11 0.061 10.% + Gint_Gamma distri_vl 2.3010 6 0.38 34.% + LCAO_Deepks cal_projected_DM 4.9802 13 0.38 74.% + LCAO_gen_fixedH add_v_delta 2.1761 6 0.36 32.% + LCAO_DESCRIPTOR add_v_delta 2.1763 6 0.36 32.% + ElecStateLCAO psiToRho 1.2699 11 0.12 19.% + Charge mix_rho 0.69752 10 0.070 10.% + LOOP_ions force_stress 0.55305 1 0.55 8.2% + Force_Stress_LCAO getForceStress 0.55303 1 0.55 8.2% + Force_LCAO_gamma ftable_gamma 0.36266 1 0.36 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.14389 1 0.14 2.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:19 2022 + Finish Time : Wed Sep 28 11:02:25 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2146fc1ecca87c8a7715b9d1f79ecd3771e81012 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123744 ima = 3.6827e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122955903796 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112076084679 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112568958014 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112807244375 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755104239 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112787392214 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112779507373 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112782328185 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112781677422 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112781629075 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112781618363 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ef944489a967bdf1564e6ac2667e523979f0d484 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.445348609571 3.285217876782 9.957366266471 0 0 0 +H +0.0 +2 +-11.470196419735 1.796122113701 10.108828716187 0 0 0 +-11.659170828754 4.645854929251 9.691595557911 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/conv new file mode 100644 index 0000000000000000000000000000000000000000..63d901d384af02fb48239fcf6a1d6c3f5a2b0e56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/conv @@ -0,0 +1 @@ +7 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..6b830edd91f8b368b6a9c9d21d049c373e0934ee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749105825 0.01270784933 1.276022659 1.364292154 1.469439419 0.008501772542 0.01864590789 0.03901667211 +1.796015175e-18 0.001068799139 0.002611358717 0.01251546494 0.04534389407 5.738339649e-20 2.063305815e-06 5.969171181e-06 +0.001654523894 0.005952977785 + +H atom_index 1 n_descriptor 18 +1.260774663 0.0338514569 0.1121932692 0.1551202007 0.3245163942 0.02275824588 0.02894515976 0.03706549825 +2.795180626e-17 4.693581717e-05 0.1043184188 0.1156868261 0.1331924967 8.910243815e-18 3.532238334e-06 0.01311988214 +0.0267528762 0.03125101337 + +H atom_index 2 n_descriptor 18 +1.238096104 0.03463350497 0.1043391477 0.1445919493 0.3172080564 0.02170790808 0.02762615058 0.03776599111 +-3.315925822e-17 4.483541028e-05 0.09894053581 0.1145017399 0.1241035755 1.12086969e-18 4.754496936e-06 0.01328544988 +0.02591336414 0.03022525578 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..029d600050d0f7c13cb1907e5c04de1bf517fd91 Binary files /dev/null and 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0000000000000000000000000000000000000000..0f854455ba8086b108631d8a3bf055b9ceb5e68b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:19 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0729326 SEC) : SETUP UNITCELL + DONE(0.0854113 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.101054 SEC) : INIT PLANEWAVE + DONE(0.142401 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.388972 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652115e+02 0.000000e+00 2.145e-01 5.185e-01 + GE2 -4.664157e+02 -1.204181e+00 9.777e-02 4.789e-01 + GE3 -4.664181e+02 -2.379282e-03 6.262e-02 5.451e-01 + GE4 -4.664181e+02 -2.732089e-05 1.989e-03 4.204e-01 + GE5 -4.664173e+02 7.771375e-04 8.349e-04 4.205e-01 + GE6 -4.664178e+02 -5.375247e-04 1.523e-04 4.130e-01 + GE7 -4.664176e+02 2.015409e-04 3.762e-05 4.074e-01 + GE8 -4.664177e+02 -5.851626e-05 1.584e-05 3.992e-01 + GE9 -4.664177e+02 1.895668e-05 1.300e-06 4.020e-01 + GE10 -4.664177e+02 -3.235559e-06 2.087e-07 4.047e-01 + GE11 -4.664177e+02 -2.305659e-07 4.366e-08 3.303e-01 +E_delta_band = -7.07301788e-02 Ry = -9.62333452e-01 eV +E_delta_NN= -1.94922229e-01 Ry = -2.65205298e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7152 11 0.61 1e+02 % + Run_lcao lcao_line 6.7082 1 6.7 1e+02 % + Potential init_pot 0.24502 2 0.12 3.6 % + PW_Basis recip2real 0.22826 16 0.014 3.4 % + PW_Basis gathers_scatterp 0.11145 16 0.007 1.7 % + Potential v_of_rho 0.95115 13 0.073 14 % + XC_Functional v_xc 0.35528 14 0.025 5.3 % + H_Hartree_pw v_hartree 0.56905 13 0.044 8.5 % + PW_Basis real2recip 0.62383 38 0.016 9.3 % + PW_Basis gatherp_scatters 0.2927 38 0.0077 4.4 % + ORB_control set_orb_tables 0.89672 1 0.9 13 % + ORB_gen_tables gen_tables 0.89672 1 0.9 13 % + ORB_table_phi init_Table 0.37468 1 0.37 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.37049 126 0.0029 5.5 % + ORB_table_beta init_Table_Beta 0.15609 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15473 56 0.0028 2.3 % + ORB_table_alpha init_Table_Alpha 0.20834 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20674 66 0.0031 3.1 % + LOOP_ions opt_ions 5.3491 1 5.3 80 % + ESolver_KS_LCAO Run 4.7959 1 4.8 71 % + HSolverLCAO solve 2.6149 11 0.24 39 % + HamiltLCAO updateHk 1.3245 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.301 11 0.12 19 % + Gint_interface cal_gint 0.6613 23 0.029 9.8 % + Gint_Gamma distri_vl_value 0.67175 11 0.061 10 % + Gint_Gamma distri_vl 2.301 6 0.38 34 % + LCAO_Deepks cal_projected_DM 4.9802 13 0.38 74 % + LCAO_gen_fixedH add_v_delta 2.1761 6 0.36 32 % + LCAO_DESCRIPTOR add_v_delta 2.1763 6 0.36 32 % + ElecStateLCAO psiToRho 1.2699 11 0.12 19 % + Charge mix_rho 0.69752 10 0.07 10 % + LOOP_ions force_stress 0.55305 1 0.55 8.2 % + Force_Stress_LCAO getForceStress 0.55303 1 0.55 8.2 % + Force_LCAO_gamma ftable_gamma 0.36266 1 0.36 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.14389 1 0.14 2.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:19 2022 + FINISH Time : Wed Sep 28 11:02:25 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/7/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..7aff2669965b4b49144e7355e3daaf6d7e92afbe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.13993 0.793814 0.437255 +H 0.143706 0.77415 0.375497 +H 0.192937 0.829132 0.448016 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3c1a86fddb1c7686d258633692daa6f024615d3f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3743 2 + 2 -13.2454 2 + 3 -9.03937 2 + 4 -6.76312 2 + 5 1.41668 0 + 6 4.61005 0 + 7 11.0483 0 + 8 11.2891 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1d2d249b0641b045c9bd8bc0823bada5d17a00c0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:27 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.91804347521 22.2267931371 12.2431378304 0 0 0 0 + tauc_H1 4.02377706052 21.6762137458 10.5139210867 0 0 0 0 + tauc_H2 5.40224201034 23.2157080091 12.5444586003 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0877140194031 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0881792543527 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106194127986 (SEC) + + DONE : INIT CHARGE Time : 0.153991648261 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.436003 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00153 + + Density error is 0.216806072639 + + Energy Rydberg eV + E_KohnSham -34.1892841347 -465.169074773 + E_Harris -34.3849850431 -467.831722231 + E_Fermi -0.412848784426 -5.61709588057 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00135579794885 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00137493359733 + + Density error is 0.0977717400192 + + Energy Rydberg eV + E_KohnSham -34.2802253977 -466.406394133 + E_Harris -34.286874853 -466.496864614 + E_Fermi -0.21984322464 -2.9911205218 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00128337650959 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127602611576 + + Density error is 0.0626238148993 + + Energy Rydberg eV + E_KohnSham -34.2805250845 -466.410471582 + E_Harris -34.2848059152 -466.468715271 + E_Fermi -0.207319333419 -2.82072424005 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116950048759 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111182188425 + + Density error is 0.00204087965286 + + Energy Rydberg eV + E_KohnSham -34.2805399074 -466.410673257 + E_Harris -34.2805418672 -466.410699922 + E_Fermi -0.171736109577 -2.3365896426 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117037595102 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111107469708 + + Density error is 0.000921586363028 + + Energy Rydberg eV + E_KohnSham -34.2804696421 -466.409717249 + E_Harris -34.2804713747 -466.409740822 + E_Fermi -0.170767028296 -2.32340461535 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116876985135 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110925114036 + + Density error is 0.000160200223343 + + Energy Rydberg eV + E_KohnSham -34.2805150303 -466.410334786 + E_Harris -34.2805150901 -466.4103356 + E_Fermi -0.170907843594 -2.32532050577 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116885140201 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011091595104 + + Density error is 4.22158828388e-05 + + Energy Rydberg eV + E_KohnSham -34.2804984222 -466.410108822 + E_Harris -34.280498432 -466.410108955 + E_Fermi -0.170751264013 -2.32319013128 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116879652146 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110915734593 + + Density error is 1.67475863688e-05 + + Energy Rydberg eV + E_KohnSham -34.2805029624 -466.410170595 + E_Harris -34.2805029636 -466.41017061 + E_Fermi -0.170801709163 -2.32387647276 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116878117704 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110913032263 + + Density error is 1.48266599617e-06 + + Energy Rydberg eV + E_KohnSham -34.2805014869 -466.41015052 + E_Harris -34.2805014869 -466.41015052 + E_Fermi -0.170783193332 -2.32362455196 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116878055836 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110912722342 + + Density error is 1.56405315388e-07 + + Energy Rydberg eV + E_KohnSham -34.280501721 -466.410153704 + E_Harris -34.280501721 -466.410153704 + E_Fermi -0.170781928072 -2.3236073372 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011687812616 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110912774809 + + Density error is 4.05844468837e-08 + + Energy Rydberg eV + E_KohnSham -34.2805017447 -466.410154027 + E_Harris -34.2805017447 -466.410154027 + E_band -7.99990279058 -108.844261398 + E_one_elec -69.5364836034 -946.09239589 + E_Hartree +36.1586501565 +491.963674118 + E_xc -8.22872665483 -111.95756979 + E_Ewald +7.44989185455 +101.360978706 + E_demet -1.00002738302e-84 -1.36060705651e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195220052737 -2.65610508108 + E_Fermi -0.17078193884 -2.32360748371 + + charge density convergence is achieved + final etot is -466.410154027 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3743 2.00000 + 2 -13.2454 2.00000 + 3 -9.03937 2.00000 + 4 -6.76312 2.00000 + 5 1.41668 0.00000 + 6 4.61005 0.00000 + 7 11.0483 0.00000 + 8 11.2891 0.00000 + + EFERMI = -2.323607483708729 eV + OUT.ABACUS/ final etot is -466.4101540265377 eV + correction force for each atom along direction 1 is 9.67197e-05 + correction force for each atom along direction 2 is 0.000112429 + correction force for each atom along direction 3 is -4.29411e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.89678340 -0.33071191 +0.56054576 + H1 +0.11961027 -0.15147147 -0.62200628 + H2 +0.77717313 +0.48218338 +0.061460525 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4101540265377 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7046 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6950 1 6.7 1.e+02% + Potential init_pot 0.28941 2 0.14 4.3% + PW_Basis recip2real 0.26193 16 0.016 3.9% + PW_Basis gathers_scatterp 0.12006 16 0.0075 1.8% + Charge atomic_rho 0.10008 1 0.10 1.5% + Potential v_of_rho 0.86826 13 0.067 13.% + XC_Functional v_xc 0.25149 14 0.018 3.8% + H_Hartree_pw v_hartree 0.58223 13 0.045 8.7% + PW_Basis real2recip 0.57002 38 0.015 8.5% + PW_Basis gatherp_scatters 0.24189 38 0.0064 3.6% + ORB_control set_orb_tables 1.1116 1 1.1 17.% + ORB_gen_tables gen_tables 1.1116 1 1.1 17.% + ORB_table_phi init_Table 0.48781 1 0.49 7.3% + ORB_table_phi cal_ST_Phi12_R 0.48282 126 0.0038 7.2% + ORB_table_beta init_Table_Beta 0.18750 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18601 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25509 1 0.26 3.8% + ORB_table_alpha S_PhiAlpha_R 0.25322 66 0.0038 3.8% + LOOP_ions opt_ions 5.0701 1 5.1 76.% + ESolver_KS_LCAO Run 4.4968 1 4.5 67.% + HSolverLCAO solve 2.5294 11 0.23 38.% + HamiltLCAO updateHk 1.2960 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2676 11 0.12 19.% + Gint_interface cal_gint 0.18718 23 0.0081 2.8% + Gint_Gamma distri_vl_value 0.81478 11 0.074 12.% + Gint_Gamma distri_vl 2.1582 6 0.36 32.% + LCAO_Deepks cal_projected_DM 4.6375 13 0.36 69.% + LCAO_gen_fixedH add_v_delta 2.0269 6 0.34 30.% + LCAO_DESCRIPTOR add_v_delta 2.0268 6 0.34 30.% + ElecStateLCAO psiToRho 1.2167 11 0.11 18.% + Charge mix_rho 0.65277 10 0.065 9.7% + LOOP_ions force_stress 0.57323 1 0.57 8.5% + Force_Stress_LCAO getForceStress 0.57321 1 0.57 8.5% + Force_LCAO_gamma ftable_gamma 0.36394 1 0.36 5.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:27 2022 + Finish Time : Wed Sep 28 11:11:34 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e1400b86a11e4241660ed0be5aba885cd9c2ec23 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123723 ima = 3.69053e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123198537311 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112234932294 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112715179032 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112979624424 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112917966319 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112954458261 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112946411617 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112949435561 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112948776876 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112948717541 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112948711151 + charge after normalized = 7.99999999999997 + charge before normalized = 7.99999999999997 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/STRU new file mode 100644 index 0000000000000000000000000000000000000000..bb39e929761ebc821732a74d0ed3e14aa36eb7a0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.081956524818 22.226793137126 12.243137830400 0 0 0 +H +0.0 +2 +-23.976222939461 21.676213745784 10.513921086713 0 0 0 +-22.597757989635 23.215708009121 12.544458600285 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/conv new file mode 100644 index 0000000000000000000000000000000000000000..4b6b5a4989de547e681637a526b61711e1261860 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/conv @@ -0,0 +1 @@ +70 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..cca1c292bab722ced0ab42494194ccec26388123 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747542861 0.01273633722 1.284895263 1.372498443 1.469750141 0.008304360536 0.01934928561 0.03897109964 +-1.189214458e-19 0.001145447003 0.002591574776 0.01267117864 0.04556763388 -1.309366758e-19 1.982129172e-06 5.812042022e-06 +0.001692648321 0.005876647973 + +H atom_index 1 n_descriptor 18 +1.256149168 0.03381136214 0.1105592722 0.153167442 0.3234255222 0.02244328512 0.02871100983 0.03698779779 +-1.036351442e-17 4.599812772e-05 0.1039528721 0.1152144669 0.1316011895 -1.008365427e-18 3.930090649e-06 0.01306340121 +0.02665627644 0.03107964042 + +H atom_index 2 n_descriptor 18 +1.263363401 0.03356249805 0.1131258323 0.1566062958 0.3256358298 0.02276958731 0.02912729835 0.0367974691 +7.832717395e-18 4.666153685e-05 0.1054035661 0.1158306474 0.1345550789 -4.679654995e-18 3.53336469e-06 0.01305916231 +0.0269130858 0.03138875154 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0a340e4f8588618d5da4b5e83f3fad23041079ca Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:27 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0877364 SEC) : SETUP UNITCELL + DONE(0.088193 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106211 SEC) : INIT PLANEWAVE + DONE(0.154118 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.436072 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651691e+02 0.000000e+00 2.168e-01 5.202e-01 + GE2 -4.664064e+02 -1.237319e+00 9.777e-02 4.480e-01 + GE3 -4.664105e+02 -4.077448e-03 6.262e-02 5.062e-01 + GE4 -4.664107e+02 -2.016757e-04 2.041e-03 3.899e-01 + GE5 -4.664097e+02 9.560084e-04 9.216e-04 3.946e-01 + GE6 -4.664103e+02 -6.175374e-04 1.602e-04 3.809e-01 + GE7 -4.664101e+02 2.259646e-04 4.222e-05 3.802e-01 + GE8 -4.664102e+02 -6.177307e-05 1.675e-05 3.683e-01 + GE9 -4.664102e+02 2.007527e-05 1.483e-06 3.667e-01 + GE10 -4.664102e+02 -3.184922e-06 1.564e-07 3.693e-01 + GE11 -4.664102e+02 -3.221159e-07 4.058e-08 3.120e-01 +E_delta_band = -7.13865552e-02 Ry = -9.71263911e-01 eV +E_delta_NN= -1.95220053e-01 Ry = -2.65610508e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7046 11 0.61 1e+02 % + Run_lcao lcao_line 6.695 1 6.7 1e+02 % + Potential init_pot 0.28941 2 0.14 4.3 % + PW_Basis recip2real 0.26193 16 0.016 3.9 % + PW_Basis gathers_scatterp 0.12006 16 0.0075 1.8 % + Charge atomic_rho 0.10008 1 0.1 1.5 % + Potential v_of_rho 0.86826 13 0.067 13 % + XC_Functional v_xc 0.25149 14 0.018 3.8 % + H_Hartree_pw v_hartree 0.58223 13 0.045 8.7 % + PW_Basis real2recip 0.57002 38 0.015 8.5 % + PW_Basis gatherp_scatters 0.24189 38 0.0064 3.6 % + ORB_control set_orb_tables 1.1116 1 1.1 17 % + ORB_gen_tables gen_tables 1.1116 1 1.1 17 % + ORB_table_phi init_Table 0.48781 1 0.49 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.48282 126 0.0038 7.2 % + ORB_table_beta init_Table_Beta 0.1875 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18601 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25509 1 0.26 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.25322 66 0.0038 3.8 % + LOOP_ions opt_ions 5.0701 1 5.1 76 % + ESolver_KS_LCAO Run 4.4968 1 4.5 67 % + HSolverLCAO solve 2.5294 11 0.23 38 % + HamiltLCAO updateHk 1.296 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2676 11 0.12 19 % + Gint_interface cal_gint 0.18718 23 0.0081 2.8 % + Gint_Gamma distri_vl_value 0.81478 11 0.074 12 % + Gint_Gamma distri_vl 2.1582 6 0.36 32 % + LCAO_Deepks cal_projected_DM 4.6375 13 0.36 69 % + LCAO_gen_fixedH add_v_delta 2.0269 6 0.34 30 % + LCAO_DESCRIPTOR add_v_delta 2.0268 6 0.34 30 % + ElecStateLCAO psiToRho 1.2167 11 0.11 18 % + Charge mix_rho 0.65277 10 0.065 9.7 % + LOOP_ions force_stress 0.57323 1 0.57 8.5 % + Force_Stress_LCAO getForceStress 0.57321 1 0.57 8.5 % + Force_LCAO_gamma ftable_gamma 0.36394 1 0.36 5.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:27 2022 + FINISH Time : Wed Sep 28 11:11:34 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/70/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a370ae4d43b34d8084b200a6f2fcf09c05f73567 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.133976 0.790427 0.435519 +H 0.0995829 0.779895 0.382166 +H 0.181563 0.828797 0.410882 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..987c6f77964559392c48d9e059c9d7523f063c35 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4445 2 + 2 -12.883 2 + 3 -9.34727 2 + 4 -6.77983 2 + 5 1.32502 0 + 6 4.49679 0 + 7 11.052 0 + 8 11.3249 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9dbd81254bd60f2469db6d140b97526ab63d2a9f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:00 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.75132062889 22.131953118 12.1945289271 0 0 0 0 + tauc_H1 2.7883208523 21.837065696 10.7006403455 0 0 0 0 + tauc_H2 5.08377536057 23.2063261027 11.5047016704 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.106158236219 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.106532627336 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124518597601 (SEC) + + DONE : INIT CHARGE Time : 0.167644943822 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448184 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00136 + + Density error is 0.215109908227 + + Energy Rydberg eV + E_KohnSham -34.1887849362 -465.162282828 + E_Harris -34.3814582326 -467.783737512 + E_Fermi -0.410305165436 -5.58248816876 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00134649894266 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132830483172 + + Density error is 0.0977582495822 + + Energy Rydberg eV + E_KohnSham -34.2792088634 -466.392563474 + E_Harris -34.2860126346 -466.485133531 + E_Fermi -0.218992282479 -2.97954285974 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127221309526 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123947318867 + + Density error is 0.0626968048698 + + Energy Rydberg eV + E_KohnSham -34.2795580203 -466.397313998 + E_Harris -34.2839618471 -466.457231135 + E_Fermi -0.207710016481 -2.82603975581 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115739159769 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010909844865 + + Density error is 0.00196040871469 + + Energy Rydberg eV + E_KohnSham -34.2795483789 -466.39718282 + E_Harris -34.2795492017 -466.397194014 + E_Fermi -0.171832551924 -2.33790180805 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115894552739 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109104607516 + + Density error is 0.000964658854174 + + Energy Rydberg eV + E_KohnSham -34.2794792953 -466.396242889 + E_Harris -34.2794812069 -466.396268898 + E_Fermi -0.17112681598 -2.32829977792 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115711660109 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108905747103 + + Density error is 9.65928363499e-05 + + Energy Rydberg eV + E_KohnSham -34.2795244589 -466.396857372 + E_Harris -34.2795244646 -466.396857449 + E_Fermi -0.17115009878 -2.32861655666 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115702490825 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108884994185 + + Density error is 4.00067388684e-05 + + Energy Rydberg eV + E_KohnSham -34.2795104064 -466.396666177 + E_Harris -34.2795104154 -466.3966663 + E_Fermi -0.171039518804 -2.32711203892 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115696943542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108883289651 + + Density error is 1.35925938843e-05 + + Energy Rydberg eV + E_KohnSham -34.2795125841 -466.396695807 + E_Harris -34.2795125849 -466.396695817 + E_Fermi -0.171087897969 -2.32777027122 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115696353709 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010888213142 + + Density error is 2.4411282136e-06 + + Energy Rydberg eV + E_KohnSham -34.2795112413 -466.396677537 + E_Harris -34.2795112414 -466.396677538 + E_Fermi -0.171074738336 -2.32759122523 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115696444555 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010888204628 + + Density error is 1.37227071382e-07 + + Energy Rydberg eV + E_KohnSham -34.2795114113 -466.396679849 + E_Harris -34.2795114113 -466.396679849 + E_Fermi -0.171072268609 -2.32755762287 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115696452885 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108882053827 + + Density error is 5.29785520909e-08 + + Energy Rydberg eV + E_KohnSham -34.2795114624 -466.396680545 + E_Harris -34.2795114624 -466.396680545 + E_band -8.004681797 -108.909283116 + E_one_elec -69.4425360175 -944.814173408 + E_Hartree +36.1034287683 +491.212348586 + E_xc -8.21985680011 -111.836889226 + E_Ewald +7.40343939785 +100.728960608 + E_demet -6.34975454599e-81 -8.63928427268e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195131767839 -2.65490390342 + E_Fermi -0.171072289131 -2.32755790208 + + charge density convergence is achieved + final etot is -466.396680545 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4445 2.00000 + 2 -12.8830 2.00000 + 3 -9.34727 2.00000 + 4 -6.77983 2.00000 + 5 1.32502 0.00000 + 6 4.49679 0.00000 + 7 11.0520 0.00000 + 8 11.3249 0.00000 + + EFERMI = -2.327557902079588 eV + OUT.ABACUS/ final etot is -466.3966805447382 eV + correction force for each atom along direction 1 is -4.00339e-05 + correction force for each atom along direction 2 is -6.75356e-05 + correction force for each atom along direction 3 is -4.01094e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.74224361 +0.36589542 +0.56775480 + H1 -0.94637335 -0.42956296 -0.88536534 + H2 +0.20412974 +0.063667541 +0.31761054 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3966805447382 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4325 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4224 1 7.4 1.e+02% + Potential init_pot 0.28200 2 0.14 3.8% + PW_Basis recip2real 0.25968 16 0.016 3.5% + PW_Basis gathers_scatterp 0.11991 16 0.0075 1.6% + Potential v_of_rho 0.79988 13 0.062 11.% + XC_Functional v_xc 0.20358 14 0.015 2.7% + H_Hartree_pw v_hartree 0.56120 13 0.043 7.6% + PW_Basis real2recip 0.64859 38 0.017 8.7% + PW_Basis gatherp_scatters 0.26664 38 0.0070 3.6% + ORB_control set_orb_tables 1.0922 1 1.1 15.% + ORB_gen_tables gen_tables 1.0922 1 1.1 15.% + ORB_table_phi init_Table 0.47453 1 0.47 6.4% + ORB_table_phi cal_ST_Phi12_R 0.46921 126 0.0037 6.3% + ORB_table_beta init_Table_Beta 0.18245 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18092 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24782 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24583 66 0.0037 3.3% + LOOP_ions opt_ions 5.8069 1 5.8 78.% + ESolver_KS_LCAO Run 5.2361 1 5.2 70.% + HSolverLCAO solve 3.1120 11 0.28 42.% + HamiltLCAO updateHk 1.5396 11 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.5120 11 0.14 20.% + Gint_interface cal_gint 0.27283 23 0.012 3.7% + Gint_Gamma distri_vl_value 0.98934 11 0.090 13.% + Gint_Gamma distri_vl 2.5037 6 0.42 34.% + LCAO_Deepks cal_projected_DM 5.3672 13 0.41 72.% + LCAO_gen_fixedH add_v_delta 2.3840 6 0.40 32.% + LCAO_DESCRIPTOR add_v_delta 2.3842 6 0.40 32.% + ElecStateLCAO psiToRho 1.5328 11 0.14 21.% + Charge mix_rho 0.77388 10 0.077 10.% + LOOP_ions force_stress 0.57066 1 0.57 7.7% + Force_Stress_LCAO getForceStress 0.57064 1 0.57 7.7% + Force_LCAO_gamma ftable_gamma 0.37818 1 0.38 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.10487 1 0.10 1.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:00 2022 + Finish Time : Wed Sep 28 11:14:07 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..44caf4b9f01392a9d6f516fbe3b74ce7f3cdf025 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012378 ima = 3.66431e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122757571174 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111558857509 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112132320284 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112404572345 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112339958971 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112375614628 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112372934477 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112375756393 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112375180804 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112375057454 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112375054771 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7729900a509931180d348b0c77ecaa1c769f7bcc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.248679371115 22.131953118009 12.194528927051 0 0 0 +H +0.0 +2 +-25.211679147719 21.837065696026 10.700640345519 0 0 0 +-22.916224639412 23.206326102649 11.504701670383 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/conv new file mode 100644 index 0000000000000000000000000000000000000000..1a7ffd39191026460d4ec5fd1f2e73c46b4deb56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/conv @@ -0,0 +1 @@ +71 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..be2f527c021f4f654ddcbcd3d2caa31178321874 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752685912 0.0128014386 1.276291735 1.360841606 1.469921484 0.009219651381 0.01742554878 0.03912310637 +-3.340194734e-18 0.0009844824484 0.002819107752 0.0131398738 0.04717984458 8.925609682e-19 2.657170615e-06 7.121872209e-06 +0.001600100222 0.006113778709 + +H atom_index 1 n_descriptor 18 +1.273412033 0.03390752482 0.118665381 0.1608083724 0.3272547995 0.0240593042 0.02960719827 0.03717726832 +1.828104019e-17 5.267117514e-05 0.10714559 0.1179182517 0.1380109186 -3.180456351e-18 2.196163531e-06 0.01333425505 +0.02773289672 0.03176312539 + +H atom_index 2 n_descriptor 18 +1.23898248 0.03506012583 0.1062880569 0.1444929625 0.3161614504 0.02238260807 0.02759869132 0.03816267016 +4.967768826e-18 4.936294e-05 0.1004801483 0.1145783227 0.1239778346 1.575198339e-18 4.147379111e-06 0.0134716969 +0.02648670805 0.03023230608 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..61e145e5563c72ce14b45b919c306d83242f30fd Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..b27fba90fe1a3b6d1b363614747758b2942a02a7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..960e96a034be55723bdd8b1e60dd764156d71b41 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..79ae489b519f96a7697b887cf193159a71f47bed Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..ccd0636b4c26ea24a79af5cd9625d20903ebe508 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:00 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.106182 SEC) : SETUP UNITCELL + DONE(0.106547 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124539 SEC) : INIT PLANEWAVE + DONE(0.16778 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44826 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651623e+02 0.000000e+00 2.151e-01 5.635e-01 + GE2 -4.663926e+02 -1.230281e+00 9.776e-02 5.278e-01 + GE3 -4.663973e+02 -4.750524e-03 6.270e-02 5.869e-01 + GE4 -4.663972e+02 1.311777e-04 1.960e-03 4.544e-01 + GE5 -4.663962e+02 9.399312e-04 9.647e-04 4.539e-01 + GE6 -4.663969e+02 -6.144829e-04 9.659e-05 4.474e-01 + GE7 -4.663967e+02 1.911950e-04 4.001e-05 4.452e-01 + GE8 -4.663967e+02 -2.962973e-05 1.359e-05 4.365e-01 + GE9 -4.663967e+02 1.826931e-05 2.441e-06 4.374e-01 + GE10 -4.663967e+02 -2.311950e-06 1.372e-07 4.387e-01 + GE11 -4.663967e+02 -6.954283e-07 5.298e-08 3.836e-01 +E_delta_band = -7.11449569e-02 Ry = -9.67976797e-01 eV +E_delta_NN= -1.95131768e-01 Ry = -2.65490390e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4325 11 0.68 1e+02 % + Run_lcao lcao_line 7.4224 1 7.4 1e+02 % + Potential init_pot 0.282 2 0.14 3.8 % + PW_Basis recip2real 0.25968 16 0.016 3.5 % + PW_Basis gathers_scatterp 0.11991 16 0.0075 1.6 % + Potential v_of_rho 0.79988 13 0.062 11 % + XC_Functional v_xc 0.20358 14 0.015 2.7 % + H_Hartree_pw v_hartree 0.5612 13 0.043 7.6 % + PW_Basis real2recip 0.64859 38 0.017 8.7 % + PW_Basis gatherp_scatters 0.26664 38 0.007 3.6 % + ORB_control set_orb_tables 1.0922 1 1.1 15 % + ORB_gen_tables gen_tables 1.0922 1 1.1 15 % + ORB_table_phi init_Table 0.47453 1 0.47 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.46921 126 0.0037 6.3 % + ORB_table_beta init_Table_Beta 0.18245 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18092 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24782 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24583 66 0.0037 3.3 % + LOOP_ions opt_ions 5.8069 1 5.8 78 % + ESolver_KS_LCAO Run 5.2361 1 5.2 70 % + HSolverLCAO solve 3.112 11 0.28 42 % + HamiltLCAO updateHk 1.5396 11 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.512 11 0.14 20 % + Gint_interface cal_gint 0.27283 23 0.012 3.7 % + Gint_Gamma distri_vl_value 0.98934 11 0.09 13 % + Gint_Gamma distri_vl 2.5037 6 0.42 34 % + LCAO_Deepks cal_projected_DM 5.3672 13 0.41 72 % + LCAO_gen_fixedH add_v_delta 2.384 6 0.4 32 % + LCAO_DESCRIPTOR add_v_delta 2.3842 6 0.4 32 % + ElecStateLCAO psiToRho 1.5328 11 0.14 21 % + Charge mix_rho 0.77388 10 0.077 10 % + LOOP_ions force_stress 0.57066 1 0.57 7.7 % + Force_Stress_LCAO getForceStress 0.57064 1 0.57 7.7 % + Force_LCAO_gamma ftable_gamma 0.37818 1 0.38 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.10487 1 0.1 1.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:00 2022 + FINISH Time : Wed Sep 28 11:14:07 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/71/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..6c6f9e32208bc9d2d222229c310e8e38ac1da79f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.113791 0.781246 0.419665 +H 0.0490408 0.788572 0.40787 +H 0.143458 0.825796 0.380665 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f764368964096a4175eec40653f068754ce063d0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1472 2 + 2 -12.9831 2 + 3 -9.05382 2 + 4 -6.71296 2 + 5 1.20378 0 + 6 4.24653 0 + 7 11.1065 0 + 8 11.3546 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..5b518a897b12bb01ec68a5c3453e88ac0e9065a4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:56 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.18615887412 21.8748781987 11.7506296074 0 0 0 0 + tauc_H1 1.37314211643 22.0800230711 11.4203718097 0 0 0 0 + tauc_H2 4.01681545612 23.1222837636 10.6586077411 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0879696040173 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101436070655 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119555824213 (SEC) + + DONE : INIT CHARGE Time : 0.168796514476 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.452935 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000842 + + Density error is 0.214002957188 + + Energy Rydberg eV + E_KohnSham -34.1915041165 -465.199279174 + E_Harris -34.3810029067 -467.777542486 + E_Fermi -0.397624685611 -5.40996138976 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00127665689059 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000930800217847 + + Density error is 0.0984487062627 + + Energy Rydberg eV + E_KohnSham -34.2810525206 -466.417647718 + E_Harris -34.2879381859 -466.511332001 + E_Fermi -0.20669241254 -2.81219454392 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00120328481019 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000882633407959 + + Density error is 0.063341583249 + + Energy Rydberg eV + E_KohnSham -34.281435167 -466.422853889 + E_Harris -34.2858760096 -466.483274652 + E_Fermi -0.197606278008 -2.68857134148 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108431733081 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000805174939409 + + Density error is 0.00199719720052 + + Energy Rydberg eV + E_KohnSham -34.2813879296 -466.422211191 + E_Harris -34.2813899015 -466.42223802 + E_Fermi -0.162234768576 -2.20731726634 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108387347807 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803824910831 + + Density error is 0.000937338070917 + + Energy Rydberg eV + E_KohnSham -34.2813369089 -466.421517018 + E_Harris -34.2813375375 -466.421525571 + E_Fermi -0.161799137752 -2.20139020491 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108228760378 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802789076074 + + Density error is 0.000175300589037 + + Energy Rydberg eV + E_KohnSham -34.2813640821 -466.421886729 + E_Harris -34.281364108 -466.421887081 + E_Fermi -0.161592139336 -2.19857384698 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108243867002 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802904246276 + + Density error is 3.42574847813e-05 + + Energy Rydberg eV + E_KohnSham -34.2813546 -466.421757719 + E_Harris -34.2813546054 -466.421757792 + E_Fermi -0.161497806294 -2.1972903801 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108237163668 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802850474482 + + Density error is 1.61325607658e-05 + + Energy Rydberg eV + E_KohnSham -34.2813584159 -466.421809637 + E_Harris -34.2813584171 -466.421809652 + E_Fermi -0.161530125504 -2.19773010551 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108236196265 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802844246951 + + Density error is 2.28493975019e-06 + + Energy Rydberg eV + E_KohnSham -34.2813571048 -466.421791798 + E_Harris -34.2813571048 -466.421791798 + E_Fermi -0.161514184811 -2.19751322125 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108236010525 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802843845315 + + Density error is 4.33452592128e-07 + + Energy Rydberg eV + E_KohnSham -34.2813573451 -466.421795068 + E_Harris -34.2813573451 -466.421795068 + E_Fermi -0.161512002865 -2.19748353435 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108236033311 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802844387517 + + Density error is 1.52762723546e-07 + + Energy Rydberg eV + E_KohnSham -34.2813573684 -466.421795385 + E_Harris -34.2813573684 -466.421795385 + E_Fermi -0.161511830062 -2.19748118325 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108236023658 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000802844469342 + + Density error is 1.05162649137e-08 + + Energy Rydberg eV + E_KohnSham -34.2813573718 -466.42179543 + E_Harris -34.2813573718 -466.42179543 + E_band -7.92271100276 -107.794013245 + E_one_elec -69.0338923892 -939.254291611 + E_Hartree +35.9206126691 +488.725007951 + E_xc -8.19032045978 -111.435026699 + E_Ewald +7.14711426618 +97.2414782771 + E_demet -1.58679645418e-70 -2.1589473343e-69 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19430966118 -2.6437185685 + E_Fermi -0.161511684949 -2.19747920889 + + charge density convergence is achieved + final etot is -466.42179543 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1472 2.00000 + 2 -12.9831 2.00000 + 3 -9.05382 2.00000 + 4 -6.71296 2.00000 + 5 1.20378 0.00000 + 6 4.24653 0.00000 + 7 11.1065 0.00000 + 8 11.3546 0.00000 + + EFERMI = -2.197479208889801 eV + OUT.ABACUS/ final etot is -466.4217954301801 eV + correction force for each atom along direction 1 is -4.27469e-05 + correction force for each atom along direction 2 is 4.82234e-05 + correction force for each atom along direction 3 is 2.74783e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.097029047 +0.14621446 -0.13891118 + H1 +0.30251187 +0.027600579 -0.0041599474 + H2 -0.20548282 -0.17381504 +0.14307113 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4217954301801 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7850 11 0.71 1.0e+02% + Run_lcao lcao_line 7.7757 1 7.8 1.e+02% + Potential init_pot 0.29015 2 0.15 3.7% + PW_Basis recip2real 0.28719 17 0.017 3.7% + PW_Basis gathers_scatterp 0.13599 17 0.0080 1.7% + Potential v_of_rho 1.1159 14 0.080 14.% + XC_Functional v_xc 0.38492 15 0.026 4.9% + H_Hartree_pw v_hartree 0.69113 14 0.049 8.9% + PW_Basis real2recip 0.71088 41 0.017 9.1% + PW_Basis gatherp_scatters 0.31039 41 0.0076 4.0% + ORB_control set_orb_tables 1.0952 1 1.1 14.% + ORB_gen_tables gen_tables 1.0952 1 1.1 14.% + ORB_table_phi init_Table 0.47759 1 0.48 6.1% + ORB_table_phi cal_ST_Phi12_R 0.47236 126 0.0037 6.1% + ORB_table_beta init_Table_Beta 0.18347 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18194 56 0.0032 2.3% + ORB_table_alpha init_Table_Alpha 0.24833 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24638 66 0.0037 3.2% + LOOP_ions opt_ions 6.1405 1 6.1 79.% + ESolver_KS_LCAO Run 5.5315 1 5.5 71.% + HSolverLCAO solve 3.0425 12 0.25 39.% + HamiltLCAO updateHk 1.5240 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4931 12 0.12 19.% + Gint_interface cal_gint 0.32514 25 0.013 4.2% + Gint_Gamma distri_vl_value 0.93818 12 0.078 12.% + Gint_Gamma distri_vl 2.8793 6 0.48 37.% + LCAO_Deepks cal_projected_DM 5.6911 14 0.41 73.% + LCAO_gen_fixedH add_v_delta 2.7437 6 0.46 35.% + LCAO_DESCRIPTOR add_v_delta 2.7437 6 0.46 35.% + ElecStateLCAO psiToRho 1.4836 12 0.12 19.% + Charge mix_rho 0.77992 11 0.071 10.% + LOOP_ions force_stress 0.60888 1 0.61 7.8% + Force_Stress_LCAO getForceStress 0.60885 1 0.61 7.8% + Force_LCAO_gamma ftable_gamma 0.39228 1 0.39 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.11170 1 0.11 1.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:56 2022 + Finish Time : Wed Sep 28 11:10:04 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2007ec567358243f77b2708b6a9bdfef3d621171 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123645 ima = 3.68749e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123444544824 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112208295194 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112847210648 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113074813765 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113038813457 + charge after normalized = 8.00000000000005 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113060098092 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011305357476 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113056187194 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113055478603 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113055406624 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113055390231 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113055382732 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/STRU new file mode 100644 index 0000000000000000000000000000000000000000..71b4768e4691d58e1ade070da39c0475e6a96e66 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.813841125870 21.874878198695 11.750629607404 0 0 0 +H +0.0 +2 +-26.626857883587 22.080023071074 11.420371809650 0 0 0 +-23.983184543861 23.122283763557 10.658607741052 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/conv new file mode 100644 index 0000000000000000000000000000000000000000..28499cb348955b5fb5d816b80c77919df1ebfeb4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/conv @@ -0,0 +1 @@ +72 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f33f1a9dfd74aba055f001e8ad5a141a84fccb6a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748563831 0.01258425405 1.263631115 1.354197311 1.468684008 0.008285996669 0.01857983919 0.0390146221 +-5.214478111e-19 0.001008551641 0.0024797317 0.01201071327 0.04332676122 -4.71757647e-19 1.785322816e-06 5.370247976e-06 +0.001659366463 0.005889982548 + +H atom_index 1 n_descriptor 18 +1.228469531 0.03491084298 0.1006701628 0.1405785922 0.3145633824 0.02105064616 0.02710107598 0.03810558531 +2.065734532e-17 4.047743128e-05 0.09501760737 0.1144146467 0.1205095489 -4.938344295e-18 5.118595849e-06 0.01338316547 +0.02515317252 0.02976592697 + +H atom_index 2 n_descriptor 18 +1.228387829 0.03491382803 0.1006474389 0.1405469028 0.314543917 0.02104754064 0.02709686181 0.03810867947 +2.781538063e-17 4.047084034e-05 0.09499812392 0.1144147545 0.1204819552 5.795973546e-18 5.121676918e-06 0.01338449127 +0.02515005741 0.02976240253 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f7bc1cd48a3482bce1703e8ec4d5484c39600368 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:56 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0879943 SEC) : SETUP UNITCELL + DONE(0.101453 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119575 SEC) : INIT PLANEWAVE + DONE(0.168927 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.453005 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651993e+02 0.000000e+00 2.140e-01 5.687e-01 + GE2 -4.664176e+02 -1.218369e+00 9.845e-02 5.135e-01 + GE3 -4.664229e+02 -5.206171e-03 6.334e-02 5.844e-01 + GE4 -4.664222e+02 6.426986e-04 1.997e-03 4.442e-01 + GE5 -4.664215e+02 6.941727e-04 9.373e-04 4.439e-01 + GE6 -4.664219e+02 -3.697114e-04 1.753e-04 4.371e-01 + GE7 -4.664218e+02 1.290105e-04 3.426e-05 4.284e-01 + GE8 -4.664218e+02 -5.191767e-05 1.613e-05 4.219e-01 + GE9 -4.664218e+02 1.783878e-05 2.285e-06 4.226e-01 + GE10 -4.664218e+02 -3.270047e-06 4.335e-07 4.235e-01 + GE11 -4.664218e+02 -3.168418e-07 1.528e-07 4.252e-01 + GE12 -4.664218e+02 -4.542155e-08 1.052e-08 3.518e-01 +E_delta_band = -6.94382031e-02 Ry = -9.44755221e-01 eV +E_delta_NN= -1.94309661e-01 Ry = -2.64371857e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.785 11 0.71 1e+02 % + Run_lcao lcao_line 7.7757 1 7.8 1e+02 % + Potential init_pot 0.29015 2 0.15 3.7 % + PW_Basis recip2real 0.28719 17 0.017 3.7 % + PW_Basis gathers_scatterp 0.13599 17 0.008 1.7 % + Potential v_of_rho 1.1159 14 0.08 14 % + XC_Functional v_xc 0.38492 15 0.026 4.9 % + H_Hartree_pw v_hartree 0.69113 14 0.049 8.9 % + PW_Basis real2recip 0.71088 41 0.017 9.1 % + PW_Basis gatherp_scatters 0.31039 41 0.0076 4 % + ORB_control set_orb_tables 1.0952 1 1.1 14 % + ORB_gen_tables gen_tables 1.0952 1 1.1 14 % + ORB_table_phi init_Table 0.47759 1 0.48 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.47236 126 0.0037 6.1 % + ORB_table_beta init_Table_Beta 0.18347 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18194 56 0.0032 2.3 % + ORB_table_alpha init_Table_Alpha 0.24833 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24638 66 0.0037 3.2 % + LOOP_ions opt_ions 6.1405 1 6.1 79 % + ESolver_KS_LCAO Run 5.5315 1 5.5 71 % + HSolverLCAO solve 3.0425 12 0.25 39 % + HamiltLCAO updateHk 1.524 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4931 12 0.12 19 % + Gint_interface cal_gint 0.32514 25 0.013 4.2 % + Gint_Gamma distri_vl_value 0.93818 12 0.078 12 % + Gint_Gamma distri_vl 2.8793 6 0.48 37 % + LCAO_Deepks cal_projected_DM 5.6911 14 0.41 73 % + LCAO_gen_fixedH add_v_delta 2.7437 6 0.46 35 % + LCAO_DESCRIPTOR add_v_delta 2.7437 6 0.46 35 % + ElecStateLCAO psiToRho 1.4836 12 0.12 19 % + Charge mix_rho 0.77992 11 0.071 10 % + LOOP_ions force_stress 0.60888 1 0.61 7.8 % + Force_Stress_LCAO getForceStress 0.60885 1 0.61 7.8 % + Force_LCAO_gamma ftable_gamma 0.39228 1 0.39 5 % + Force_LCAO_gamma cal_fvl_dphi 0.1117 1 0.11 1.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:56 2022 + FINISH Time : Wed Sep 28 11:10:04 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/72/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..74b2f8bcfbd116fb8d03dafd4abc90f5cfe6579b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.101526 0.764241 0.415545 +H 0.0422783 0.794451 0.423591 +H 0.126021 0.788022 0.357849 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..53573a29b8fa1c3cfdba9c74b52e2b6c48ed8e7d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0087 2 + 2 -12.8936 2 + 3 -9.00985 2 + 4 -6.68144 2 + 5 1.08897 0 + 6 4.05774 0 + 7 11.1383 0 + 8 11.3831 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..889ecd8eec77d3f0e04bd1639c2500758fa52b56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:45 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 2.84272448455 21.3987392001 11.6352732957 0 0 0 0 + tauc_H1 1.18379256159 22.2446377378 11.8605341624 0 0 0 0 + tauc_H2 3.52859867758 22.0646119146 10.0197688332 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870425684212 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0988896649933 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116995283651 (SEC) + + DONE : INIT CHARGE Time : 0.165654488059 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447599 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000785 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000805 + + Density error is 0.21283437041 + + Energy Rydberg eV + E_KohnSham -34.1909987405 -465.192403182 + E_Harris -34.3779465034 -467.735957985 + E_Fermi -0.38976151145 -5.30297741681 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107426801943 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000947966463636 + + Density error is 0.0987992394113 + + Energy Rydberg eV + E_KohnSham -34.280001998 -466.403354625 + E_Harris -34.2870541373 -466.499303902 + E_Fermi -0.199475079199 -2.7139976861 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103077585513 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000905274244575 + + Density error is 0.0637589477936 + + Energy Rydberg eV + E_KohnSham -34.2804387093 -466.409296386 + E_Harris -34.2849563558 -466.470762121 + E_Fermi -0.192191141668 -2.61489463181 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000978940272488 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000842806700231 + + Density error is 0.0020067535964 + + Energy Rydberg eV + E_KohnSham -34.2803585681 -466.40820601 + E_Harris -34.2803616951 -466.408248554 + E_Fermi -0.157022946629 -2.13640679091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000979142811492 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000841523902823 + + Density error is 0.000946826337173 + + Energy Rydberg eV + E_KohnSham -34.2803174936 -466.407647162 + E_Harris -34.2803178705 -466.407652291 + E_Fermi -0.15678270324 -2.13313811191 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000978450079912 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000840662348194 + + Density error is 0.000192062957612 + + Energy Rydberg eV + E_KohnSham -34.2803368002 -466.407909842 + E_Harris -34.2803368222 -466.407910142 + E_Fermi -0.156432186518 -2.12836908725 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000978721365883 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000840842775518 + + Density error is 3.13654608878e-05 + + Energy Rydberg eV + E_KohnSham -34.2803302031 -466.407820084 + E_Harris -34.2803302069 -466.407820135 + E_Fermi -0.156381344393 -2.12767734464 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000978645461373 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000840780233758 + + Density error is 1.3961086108e-05 + + Energy Rydberg eV + E_KohnSham -34.2803336309 -466.407866721 + E_Harris -34.2803336317 -466.407866732 + E_Fermi -0.156404088496 -2.12798679404 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000978646152609 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000840775668753 + + Density error is 1.89765904294e-06 + + Energy Rydberg eV + E_KohnSham -34.2803325164 -466.407851557 + E_Harris -34.2803325164 -466.407851558 + E_Fermi -0.156390008807 -2.12779523005 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000978647171276 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000840776557364 + + Density error is 2.57321197163e-07 + + Energy Rydberg eV + E_KohnSham -34.2803327047 -466.40785412 + E_Harris -34.2803327047 -466.40785412 + E_Fermi -0.156388205918 -2.12777070048 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000978647578895 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000840777032307 + + Density error is 6.04044845931e-08 + + Energy Rydberg eV + E_KohnSham -34.2803327299 -466.407854462 + E_Harris -34.2803327299 -466.407854462 + E_band -7.87810641886 -107.187136747 + E_one_elec -68.7637276287 -935.57851147 + E_Hartree +35.7944866945 +487.008976031 + E_xc -8.17008676047 -111.159733097 + E_Ewald +6.98442210822 +95.027937909 + E_demet -2.30508318934e-63 -3.1362265739e-62 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19382116423 -2.63707222652 + E_Fermi -0.156388103421 -2.12776930594 + + charge density convergence is achieved + final etot is -466.407854462 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0087 2.00000 + 2 -12.8936 2.00000 + 3 -9.00985 2.00000 + 4 -6.68144 2.00000 + 5 1.08897 0.00000 + 6 4.05774 0.00000 + 7 11.1383 0.00000 + 8 11.3831 0.00000 + + EFERMI = -2.127769305941866 eV + OUT.ABACUS/ final etot is -466.4078544622543 eV + correction force for each atom along direction 1 is -3.17880e-05 + correction force for each atom along direction 2 is 0.000168397 + correction force for each atom along direction 3 is -0.000134503 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.30869312 +0.51580361 -0.49071930 + H1 +0.74148715 -0.29670427 -0.22482721 + H2 -0.43279403 -0.21909934 +0.71554652 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4078544622543 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4735 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4644 1 6.5 1.e+02% + Potential init_pot 0.28736 2 0.14 4.4% + PW_Basis recip2real 0.26717 16 0.017 4.1% + PW_Basis gathers_scatterp 0.12587 16 0.0079 1.9% + Potential v_of_rho 0.86780 13 0.067 13.% + XC_Functional v_xc 0.25192 14 0.018 3.9% + H_Hartree_pw v_hartree 0.58216 13 0.045 9.0% + PW_Basis real2recip 0.56753 38 0.015 8.8% + PW_Basis gatherp_scatters 0.23715 38 0.0062 3.7% + ORB_control set_orb_tables 1.1026 1 1.1 17.% + ORB_gen_tables gen_tables 1.1026 1 1.1 17.% + ORB_table_phi init_Table 0.48409 1 0.48 7.5% + ORB_table_phi cal_ST_Phi12_R 0.47910 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18647 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18492 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25131 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.24945 66 0.0038 3.9% + LOOP_ions opt_ions 4.8377 1 4.8 75.% + ESolver_KS_LCAO Run 4.2623 1 4.3 66.% + HSolverLCAO solve 2.2955 11 0.21 35.% + HamiltLCAO updateHk 1.1910 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1627 11 0.11 18.% + Gint_interface cal_gint 0.30309 23 0.013 4.7% + Gint_Gamma distri_vl_value 0.68009 11 0.062 11.% + Gint_Gamma distri_vl 2.0469 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.4266 13 0.34 68.% + LCAO_gen_fixedH add_v_delta 1.9174 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9174 6 0.32 30.% + ElecStateLCAO psiToRho 1.0858 11 0.099 17.% + Charge mix_rho 0.65220 10 0.065 10.% + LOOP_ions force_stress 0.57519 1 0.58 8.9% + Force_Stress_LCAO getForceStress 0.57516 1 0.58 8.9% + Force_LCAO_gamma ftable_gamma 0.36523 1 0.37 5.6% + Force_LCAO_gamma cal_fvl_dphi 0.11059 1 0.11 1.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:45 2022 + Finish Time : Wed Sep 28 11:12:52 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1a897b23dc92773f9c8d7739b77c266939b36c24 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123187 ima = 3.7025e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123702847587 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011233735084 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113058119462 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113262117266 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113238784612 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011325378609 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113247919832 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113250170025 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113249589698 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113249517543 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113249504894 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9b3029cf36a7a678057138442f45cd9d8fdb7f1e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-25.157275515428 21.398739200075 11.635273295680 0 0 0 +H +0.0 +2 +-26.816207438391 22.244637737772 11.860534162437 0 0 0 +-24.471401322416 22.064611914600 10.019768833170 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/conv new file mode 100644 index 0000000000000000000000000000000000000000..ea875d4a82159426096e3e4bc752035a6137297a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/conv @@ -0,0 +1 @@ +73 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..cccafb1a333342efc66a74fc5cf050e161713c33 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74835953 0.01246529708 1.25276966 1.345772068 1.468096444 0.008161603478 0.0185011439 0.03902327259 +6.220654736e-18 0.0009556457106 0.002379914348 0.01160072206 0.04171146443 1.205218827e-18 1.579679031e-06 4.90217875e-06 +0.001655467543 0.00582192889 + +H atom_index 1 n_descriptor 18 +1.211172852 0.03547235746 0.09485202278 0.1333724742 0.3089548347 0.02011061118 0.02612052759 0.03879503203 +-2.003875378e-17 3.647682565e-05 0.08939556351 0.1140771015 0.1141233938 -3.741467035e-18 5.651323404e-06 0.01372293993 +0.02417141937 0.02890467486 + +H atom_index 2 n_descriptor 18 +1.210053286 0.03550918602 0.09450699241 0.1329019861 0.30854852 0.02005947331 0.02605481994 0.03884010594 +2.933447143e-17 3.638411116e-05 0.08910110623 0.1137101032 0.1140386449 -8.17437577e-18 5.689971743e-06 0.0137511134 +0.02412574444 0.02884689498 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..12e799949078b43e53122e7df597de505acbd31e Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..98b5720292fcff265675fe2030a658098bd23015 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..d72d37270860ff493249872e87d5714753d40f70 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..b86384de6b83830a7f3b47485bfca4a94fe18096 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:45 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870676 SEC) : SETUP UNITCELL + DONE(0.0989066 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.117016 SEC) : INIT PLANEWAVE + DONE(0.165784 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447661 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651924e+02 0.000000e+00 2.128e-01 4.990e-01 + GE2 -4.664034e+02 -1.210951e+00 9.880e-02 4.249e-01 + GE3 -4.664093e+02 -5.941761e-03 6.376e-02 4.805e-01 + GE4 -4.664082e+02 1.090376e-03 2.007e-03 3.710e-01 + GE5 -4.664076e+02 5.588478e-04 9.468e-04 3.706e-01 + GE6 -4.664079e+02 -2.626801e-04 1.921e-04 3.660e-01 + GE7 -4.664078e+02 8.975784e-05 3.137e-05 3.531e-01 + GE8 -4.664079e+02 -4.663653e-05 1.396e-05 3.477e-01 + GE9 -4.664079e+02 1.516333e-05 1.898e-06 3.505e-01 + GE10 -4.664079e+02 -2.562510e-06 2.573e-07 3.481e-01 + GE11 -4.664079e+02 -3.423229e-07 6.040e-08 2.898e-01 +E_delta_band = -6.83940208e-02 Ry = -9.30548391e-01 eV +E_delta_NN= -1.93821164e-01 Ry = -2.63707223e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4735 11 0.59 1e+02 % + Run_lcao lcao_line 6.4644 1 6.5 1e+02 % + Potential init_pot 0.28736 2 0.14 4.4 % + PW_Basis recip2real 0.26717 16 0.017 4.1 % + PW_Basis gathers_scatterp 0.12587 16 0.0079 1.9 % + Potential v_of_rho 0.8678 13 0.067 13 % + XC_Functional v_xc 0.25192 14 0.018 3.9 % + H_Hartree_pw v_hartree 0.58216 13 0.045 9 % + PW_Basis real2recip 0.56753 38 0.015 8.8 % + PW_Basis gatherp_scatters 0.23715 38 0.0062 3.7 % + ORB_control set_orb_tables 1.1026 1 1.1 17 % + ORB_gen_tables gen_tables 1.1026 1 1.1 17 % + ORB_table_phi init_Table 0.48409 1 0.48 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.4791 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18647 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18492 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.25131 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.24945 66 0.0038 3.9 % + LOOP_ions opt_ions 4.8377 1 4.8 75 % + ESolver_KS_LCAO Run 4.2623 1 4.3 66 % + HSolverLCAO solve 2.2955 11 0.21 35 % + HamiltLCAO updateHk 1.191 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1627 11 0.11 18 % + Gint_interface cal_gint 0.30309 23 0.013 4.7 % + Gint_Gamma distri_vl_value 0.68009 11 0.062 11 % + Gint_Gamma distri_vl 2.0469 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.4266 13 0.34 68 % + LCAO_gen_fixedH add_v_delta 1.9174 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9174 6 0.32 30 % + ElecStateLCAO psiToRho 1.0858 11 0.099 17 % + Charge mix_rho 0.6522 10 0.065 10 % + LOOP_ions force_stress 0.57519 1 0.58 8.9 % + Force_Stress_LCAO getForceStress 0.57516 1 0.58 8.9 % + Force_LCAO_gamma ftable_gamma 0.36523 1 0.37 5.6 % + Force_LCAO_gamma cal_fvl_dphi 0.11059 1 0.11 1.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:45 2022 + FINISH Time : Wed Sep 28 11:12:52 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/73/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ece91f0e58b12d98e27284c44f937f4dfe20d377 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.0877363 0.741538 0.406294 +H 0.118555 0.79975 0.405838 +H 0.0816407 0.732173 0.343888 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0fc2a0886f7dc17af13f65ba00b0adaa06ef940d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.54 2 + 2 -12.9442 2 + 3 -9.36769 2 + 4 -6.79918 2 + 5 1.37982 0 + 6 4.62789 0 + 7 11.0304 0 + 8 11.3001 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..46d0e2bafa470338f1d2c4b30e35d17a113d11df --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:59 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 2.45661514295 20.763051888 11.3762444789 0 0 0 0 + tauc_H1 3.31953263408 22.392987503 11.3634688507 0 0 0 0 + tauc_H2 2.28593931408 20.5008408407 9.62886168274 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0863517780432 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0977014122509 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115905520884 (SEC) + + DONE : INIT CHARGE Time : 0.165357254666 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450779 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000665 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000936 + + Density error is 0.215413535541 + + Energy Rydberg eV + E_KohnSham -34.1879157168 -465.150456492 + E_Harris -34.3813514542 -467.782284718 + E_Fermi -0.415515778893 -5.65338220186 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100309824426 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127183350494 + + Density error is 0.0973218708972 + + Energy Rydberg eV + E_KohnSham -34.2774632336 -466.368812963 + E_Harris -34.2841797394 -466.460195712 + E_Fermi -0.224822364647 -3.05886519703 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000960088541548 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121838811035 + + Density error is 0.0621843355184 + + Energy Rydberg eV + E_KohnSham -34.2776752506 -466.371697602 + E_Harris -34.2820024302 -466.4305719 + E_Fermi -0.211614287397 -2.8791600868 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000905653690366 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115057747667 + + Density error is 0.00199025031083 + + Energy Rydberg eV + E_KohnSham -34.2776965608 -466.371987541 + E_Harris -34.2776980111 -466.372007275 + E_Fermi -0.175720063692 -2.39079411914 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000909698199937 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115609587402 + + Density error is 0.000864998522801 + + Energy Rydberg eV + E_KohnSham -34.2776293649 -466.371073295 + E_Harris -34.2776314447 -466.371101593 + E_Fermi -0.174756513287 -2.37768434331 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000908221275767 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001154172703 + + Density error is 0.000111753483471 + + Energy Rydberg eV + E_KohnSham -34.2776776797 -466.371730652 + E_Harris -34.2776777069 -466.371731021 + E_Fermi -0.174939575427 -2.38017503151 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000908104316408 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115399625727 + + Density error is 4.1227065854e-05 + + Energy Rydberg eV + E_KohnSham -34.277661373 -466.371508788 + E_Harris -34.2776613818 -466.371508907 + E_Fermi -0.174817258543 -2.37851082493 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000908055656777 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011539367306 + + Density error is 1.71319687135e-05 + + Energy Rydberg eV + E_KohnSham -34.2776644263 -466.37155033 + E_Harris -34.2776644274 -466.371550345 + E_Fermi -0.174865285232 -2.37916426155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000908061251732 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115394093564 + + Density error is 2.23655105264e-06 + + Energy Rydberg eV + E_KohnSham -34.2776629833 -466.371530696 + E_Harris -34.2776629833 -466.371530696 + E_Fermi -0.174846617784 -2.3789102779 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000908064631598 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011539440294 + + Density error is 3.22980405201e-07 + + Energy Rydberg eV + E_KohnSham -34.277663194 -466.371533563 + E_Harris -34.277663194 -466.371533563 + E_Fermi -0.174844960197 -2.37888772527 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000908064972188 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115394449841 + + Density error is 1.28853361181e-07 + + Energy Rydberg eV + E_KohnSham -34.2776632311 -466.371534068 + E_Harris -34.2776632311 -466.371534068 + E_Fermi -0.174844786147 -2.37888535719 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000908065034679 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115394454341 + + Density error is 1.04740500053e-08 + + Energy Rydberg eV + E_KohnSham -34.2776632326 -466.371534088 + E_Harris -34.2776632326 -466.371534088 + E_band -8.03355601105 -109.302136952 + E_one_elec -69.6203351491 -947.233254697 + E_Hartree +36.1868508308 +492.347363974 + E_xc -8.23343619793 -112.021646411 + E_Ewald +7.51288565372 +102.218053313 + E_demet -1.54983460095e-85 -2.10865815305e-84 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195479737642 -2.65963827548 + E_Fermi -0.174844642326 -2.3788834004 + + charge density convergence is achieved + final etot is -466.371534088 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5400 2.00000 + 2 -12.9442 2.00000 + 3 -9.36769 2.00000 + 4 -6.79918 2.00000 + 5 1.37982 0.00000 + 6 4.62789 0.00000 + 7 11.0304 0.00000 + 8 11.3001 0.00000 + + EFERMI = -2.378883400400424 eV + OUT.ABACUS/ final etot is -466.3715340883202 eV + correction force for each atom along direction 1 is -0.000111869 + correction force for each atom along direction 2 is 8.63155e-05 + correction force for each atom along direction 3 is -6.30426e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.34965576 +0.61877945 +1.6424650 + H1 +0.053237295 +0.078556330 +0.41499915 + H2 -0.40289305 -0.69733578 -2.0574641 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3715340883202 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7703 11 0.71 1.0e+02% + Run_lcao lcao_line 7.7617 1 7.8 1.e+02% + Potential init_pot 0.28786 2 0.14 3.7% + PW_Basis recip2real 0.29106 17 0.017 3.7% + PW_Basis gathers_scatterp 0.13729 17 0.0081 1.8% + Potential v_of_rho 1.1122 14 0.079 14.% + XC_Functional v_xc 0.37493 15 0.025 4.8% + H_Hartree_pw v_hartree 0.69816 14 0.050 9.0% + PW_Basis real2recip 0.72146 41 0.018 9.3% + PW_Basis gatherp_scatters 0.31960 41 0.0078 4.1% + ORB_control set_orb_tables 1.1140 1 1.1 14.% + ORB_gen_tables gen_tables 1.1140 1 1.1 14.% + ORB_table_phi init_Table 0.48256 1 0.48 6.2% + ORB_table_phi cal_ST_Phi12_R 0.47742 126 0.0038 6.1% + ORB_table_beta init_Table_Beta 0.18925 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18768 56 0.0034 2.4% + ORB_table_alpha init_Table_Alpha 0.25402 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.25203 66 0.0038 3.2% + LOOP_ions opt_ions 6.1178 1 6.1 79.% + ESolver_KS_LCAO Run 5.5105 1 5.5 71.% + HSolverLCAO solve 2.9998 12 0.25 39.% + HamiltLCAO updateHk 1.5160 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4862 12 0.12 19.% + Gint_interface cal_gint 0.45046 25 0.018 5.8% + Gint_Gamma distri_vl_value 0.88471 12 0.074 11.% + Gint_Gamma distri_vl 2.8765 6 0.48 37.% + LCAO_Deepks cal_projected_DM 5.6791 14 0.41 73.% + LCAO_gen_fixedH add_v_delta 2.7358 6 0.46 35.% + LCAO_DESCRIPTOR add_v_delta 2.7360 6 0.46 35.% + ElecStateLCAO psiToRho 1.4469 12 0.12 19.% + Charge mix_rho 0.79797 11 0.073 10.% + LOOP_ions force_stress 0.60709 1 0.61 7.8% + Force_Stress_LCAO getForceStress 0.60706 1 0.61 7.8% + Force_LCAO_gamma ftable_gamma 0.39120 1 0.39 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.12321 1 0.12 1.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:59 2022 + Finish Time : Wed Sep 28 11:13:07 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..9c0b80b088b287cf0c9f300cb07054ecd5934b96 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123771 ima = 3.72048e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122520377797 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111615072955 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112094770599 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112369669346 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112301378991 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112340408948 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112335902662 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011233882954 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112338173314 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112338075539 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112338065801 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112338059288 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/STRU new file mode 100644 index 0000000000000000000000000000000000000000..14e949f2456d71f982e3ec47fd12bc19c953be2f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-25.543384857031 20.763051888040 11.376244478922 0 0 0 +H +0.0 +2 +-24.680467365921 22.392987502993 11.363468850719 0 0 0 +-25.714060685915 20.500840840707 9.628861682727 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/conv new file mode 100644 index 0000000000000000000000000000000000000000..75fea200abd336629978861359d9a26604a54f1d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/conv @@ -0,0 +1 @@ +74 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..caf2de9289f4f755a96ca840c68f2468fa9b4189 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752848102 0.01283783964 1.281580736 1.368245053 1.470355794 0.009329474176 0.01757251235 0.03912681038 +1.362596299e-17 0.001017542421 0.002889322983 0.01340034808 0.04821943164 -4.752913625e-19 2.810368517e-06 7.403232024e-06 +0.001597070058 0.006109029435 + +H atom_index 1 n_descriptor 18 +1.239812294 0.03505311143 0.1068639017 0.144826938 0.3162379129 0.02252912308 0.0276416364 0.0381376051 +-3.2414513e-18 5.117757092e-05 0.1016134319 0.1144833458 0.1243287 1.993212208e-18 4.09576654e-06 0.01348169779 +0.02674698114 0.03028217181 + +H atom_index 2 n_descriptor 18 +1.294141931 0.0332896997 0.1270978787 0.1713757675 0.3330864403 0.02518029905 0.03079117327 0.03687874684 +2.141932263e-17 5.644944903e-05 0.1084813158 0.1233373256 0.1470192346 -4.244172804e-18 1.109219272e-06 0.01367154567 +0.02862394528 0.03256794488 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fe356a42608b1fd01880cf55ed18302df2bc8e96 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:59 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0863769 SEC) : SETUP UNITCELL + DONE(0.0977196 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115927 SEC) : INIT PLANEWAVE + DONE(0.16548 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450843 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651505e+02 0.000000e+00 2.154e-01 5.701e-01 + GE2 -4.663688e+02 -1.218356e+00 9.732e-02 5.151e-01 + GE3 -4.663717e+02 -2.884639e-03 6.218e-02 5.819e-01 + GE4 -4.663720e+02 -2.899394e-04 1.990e-03 4.384e-01 + GE5 -4.663711e+02 9.142466e-04 8.650e-04 4.510e-01 + GE6 -4.663717e+02 -6.573571e-04 1.118e-04 4.342e-01 + GE7 -4.663715e+02 2.218644e-04 4.123e-05 4.293e-01 + GE8 -4.663716e+02 -4.154200e-05 1.713e-05 4.151e-01 + GE9 -4.663715e+02 1.963349e-05 2.237e-06 4.215e-01 + GE10 -4.663715e+02 -2.867313e-06 3.230e-07 4.190e-01 + GE11 -4.663715e+02 -5.043910e-07 1.289e-07 4.204e-01 + GE12 -4.663715e+02 -2.052163e-08 1.047e-08 3.479e-01 +E_delta_band = -7.18513676e-02 Ry = -9.77588008e-01 eV +E_delta_NN= -1.95479738e-01 Ry = -2.65963828e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7703 11 0.71 1e+02 % + Run_lcao lcao_line 7.7617 1 7.8 1e+02 % + Potential init_pot 0.28786 2 0.14 3.7 % + PW_Basis recip2real 0.29106 17 0.017 3.7 % + PW_Basis gathers_scatterp 0.13729 17 0.0081 1.8 % + Potential v_of_rho 1.1122 14 0.079 14 % + XC_Functional v_xc 0.37493 15 0.025 4.8 % + H_Hartree_pw v_hartree 0.69816 14 0.05 9 % + PW_Basis real2recip 0.72146 41 0.018 9.3 % + PW_Basis gatherp_scatters 0.3196 41 0.0078 4.1 % + ORB_control set_orb_tables 1.114 1 1.1 14 % + ORB_gen_tables gen_tables 1.114 1 1.1 14 % + ORB_table_phi init_Table 0.48256 1 0.48 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.47742 126 0.0038 6.1 % + ORB_table_beta init_Table_Beta 0.18925 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18768 56 0.0034 2.4 % + ORB_table_alpha init_Table_Alpha 0.25402 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.25203 66 0.0038 3.2 % + LOOP_ions opt_ions 6.1178 1 6.1 79 % + ESolver_KS_LCAO Run 5.5105 1 5.5 71 % + HSolverLCAO solve 2.9998 12 0.25 39 % + HamiltLCAO updateHk 1.516 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4862 12 0.12 19 % + Gint_interface cal_gint 0.45046 25 0.018 5.8 % + Gint_Gamma distri_vl_value 0.88471 12 0.074 11 % + Gint_Gamma distri_vl 2.8765 6 0.48 37 % + LCAO_Deepks cal_projected_DM 5.6791 14 0.41 73 % + LCAO_gen_fixedH add_v_delta 2.7358 6 0.46 35 % + LCAO_DESCRIPTOR add_v_delta 2.736 6 0.46 35 % + ElecStateLCAO psiToRho 1.4469 12 0.12 19 % + Charge mix_rho 0.79797 11 0.073 10 % + LOOP_ions force_stress 0.60709 1 0.61 7.8 % + Force_Stress_LCAO getForceStress 0.60706 1 0.61 7.8 % + Force_LCAO_gamma ftable_gamma 0.3912 1 0.39 5 % + Force_LCAO_gamma cal_fvl_dphi 0.12321 1 0.12 1.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:59 2022 + FINISH Time : Wed Sep 28 11:13:07 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/74/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..f49039a278c6b1e5aa45ac107abb10c3705d1dd6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.0870249 0.707392 0.396163 +H 0.137878 0.671672 0.376128 +H 0.0401689 0.693624 0.354573 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c86568704108519b4a5d1089de89b5898ecda2f1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4124 2 + 2 -13.1826 2 + 3 -9.1123 2 + 4 -6.77178 2 + 5 1.41313 0 + 6 4.61474 0 + 7 11.0437 0 + 8 11.2914 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c6cd9dc0c25c320a89f8bd917307c5e9bdcd4b9c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:09 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 2.43669693052 19.8069720959 11.0925601458 0 0 0 0 + tauc_H1 3.86059678553 18.8068252006 10.531574254 0 0 0 0 + tauc_H2 1.12472833653 19.4214665489 9.92803232545 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0881548786796 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0885088900885 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106666366132 (SEC) + + DONE : INIT CHARGE Time : 0.156072848901 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438793 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000759 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00139 + + Density error is 0.216903331803 + + Energy Rydberg eV + E_KohnSham -34.1885441919 -465.159007335 + E_Harris -34.3845368819 -467.825624685 + E_Fermi -0.41351568368 -5.62616951042 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112063636417 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127430501116 + + Density error is 0.097818346768 + + Energy Rydberg eV + E_KohnSham -34.2798855476 -466.401770235 + E_Harris -34.2865668511 -466.492674033 + E_Fermi -0.220686985902 -3.00260048271 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107653085961 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118165348688 + + Density error is 0.0626309719789 + + Energy Rydberg eV + E_KohnSham -34.2802295845 -466.406451098 + E_Harris -34.2845380269 -466.465070464 + E_Fermi -0.208356677878 -2.83483803549 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102145258771 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102162454355 + + Density error is 0.00202437927948 + + Energy Rydberg eV + E_KohnSham -34.2802417762 -466.406616974 + E_Harris -34.2802436704 -466.406642746 + E_Fermi -0.172646066585 -2.34897024285 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102466326646 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102027597891 + + Density error is 0.000948219934835 + + Energy Rydberg eV + E_KohnSham -34.2801689617 -466.405626282 + E_Harris -34.2801708099 -466.405651427 + E_Fermi -0.171716572973 -2.33632383346 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102338858294 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101848695391 + + Density error is 0.000141115739156 + + Energy Rydberg eV + E_KohnSham -34.2802152615 -466.406256223 + E_Harris -34.2802153002 -466.40625675 + E_Fermi -0.171838946405 -2.33798880943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102352599679 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101833912171 + + Density error is 4.35235003658e-05 + + Energy Rydberg eV + E_KohnSham -34.2801990324 -466.406035415 + E_Harris -34.2801990429 -466.406035558 + E_Fermi -0.171694413376 -2.33602233668 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102345686244 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101832752586 + + Density error is 1.62103912935e-05 + + Energy Rydberg eV + E_KohnSham -34.2802030757 -466.406090426 + E_Harris -34.2802030767 -466.40609044 + E_Fermi -0.1717451546 -2.33671270646 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102346203029 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101830390527 + + Density error is 2.34494002613e-06 + + Energy Rydberg eV + E_KohnSham -34.280201597 -466.406070307 + E_Harris -34.280201597 -466.406070308 + E_Fermi -0.171728725274 -2.336489174 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102346151576 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101830044676 + + Density error is 2.08847249787e-07 + + Energy Rydberg eV + E_KohnSham -34.2802017921 -466.406072963 + E_Harris -34.2802017921 -466.406072963 + E_Fermi -0.171726203359 -2.33645486159 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102346216945 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101830101759 + + Density error is 9.65227342956e-08 + + Energy Rydberg eV + E_KohnSham -34.2802018338 -466.40607353 + E_Harris -34.2802018338 -466.40607353 + E_band -8.00827613538 -108.958186599 + E_one_elec -69.5587338955 -946.395126645 + E_Hartree +36.1664580286 +492.069905667 + E_xc -8.2300444213 -111.975498923 + E_Ewald +7.46589684873 +101.578737823 + E_demet -3.90377332034e-85 -5.3113560857e-84 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195294546768 -2.65711862437 + E_Fermi -0.171726220255 -2.33645509147 + + charge density convergence is achieved + final etot is -466.40607353 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4124 2.00000 + 2 -13.1826 2.00000 + 3 -9.11230 2.00000 + 4 -6.77178 2.00000 + 5 1.41313 0.00000 + 6 4.61474 0.00000 + 7 11.0437 0.00000 + 8 11.2914 0.00000 + + EFERMI = -2.336455091470272 eV + OUT.ABACUS/ final etot is -466.4060735297844 eV + correction force for each atom along direction 1 is -3.07554e-05 + correction force for each atom along direction 2 is -7.12730e-05 + correction force for each atom along direction 3 is -1.45341e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.68172318 +0.48167919 +0.97153283 + H1 +0.30697755 -0.20361380 -0.10734455 + H2 -0.98870073 -0.27806539 -0.86418828 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4060735297844 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2217 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2124 1 7.2 1.e+02% + Potential init_pot 0.28509 2 0.14 3.9% + PW_Basis recip2real 0.26941 16 0.017 3.7% + PW_Basis gathers_scatterp 0.12652 16 0.0079 1.8% + Potential v_of_rho 1.0135 13 0.078 14.% + XC_Functional v_xc 0.34203 14 0.024 4.7% + H_Hartree_pw v_hartree 0.63629 13 0.049 8.8% + PW_Basis real2recip 0.65010 38 0.017 9.0% + PW_Basis gatherp_scatters 0.28432 38 0.0075 3.9% + ORB_control set_orb_tables 1.0910 1 1.1 15.% + ORB_gen_tables gen_tables 1.0910 1 1.1 15.% + ORB_table_phi init_Table 0.47463 1 0.47 6.6% + ORB_table_phi cal_ST_Phi12_R 0.46953 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18421 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18265 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24573 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24379 66 0.0037 3.4% + LOOP_ions opt_ions 5.5872 1 5.6 77.% + ESolver_KS_LCAO Run 4.9739 1 5.0 69.% + HSolverLCAO solve 2.6861 11 0.24 37.% + HamiltLCAO updateHk 1.3754 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.3481 11 0.12 19.% + Gint_interface cal_gint 0.45109 23 0.020 6.2% + Gint_Gamma distri_vl_value 0.76161 11 0.069 11.% + Gint_Gamma distri_vl 2.3959 6 0.40 33.% + LCAO_Deepks cal_projected_DM 5.1578 13 0.40 71.% + LCAO_gen_fixedH add_v_delta 2.2572 6 0.38 31.% + LCAO_DESCRIPTOR add_v_delta 2.2573 6 0.38 31.% + ElecStateLCAO psiToRho 1.2823 11 0.12 18.% + Charge mix_rho 0.74138 10 0.074 10.% + LOOP_ions force_stress 0.61319 1 0.61 8.5% + Force_Stress_LCAO getForceStress 0.61316 1 0.61 8.5% + Force_LCAO_gamma ftable_gamma 0.39514 1 0.40 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.12818 1 0.13 1.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:09 2022 + Finish Time : Wed Sep 28 11:09:16 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6520be06f31f9e415d3927e47173e59062f5c89e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123969 ima = 3.69228e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123109704249 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112054229 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112555207411 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112828295404 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112764131192 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112801113486 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112794277958 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112797382849 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011279676663 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112796662834 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112796657112 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/STRU new file mode 100644 index 0000000000000000000000000000000000000000..928bc2861cd65e07dfef3ad000cddb723c50b7ba --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-25.563303069461 19.806972095940 11.092560145768 0 0 0 +H +0.0 +2 +-24.139403214458 18.806825200575 10.531574253946 0 0 0 +-26.875271663484 19.421466548857 9.928032325440 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/conv new file mode 100644 index 0000000000000000000000000000000000000000..e7557f9adf3ecef4705391264972791bf4b351be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/conv @@ -0,0 +1 @@ +75 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..981f3e63aaa83a76b8eb386965b5fc83634040ce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74878803 0.01275966305 1.284299258 1.37159021 1.469899263 0.008523957569 0.01894845616 0.03900813712 +-2.092682267e-18 0.001123634213 0.002658573162 0.01277135931 0.04626645719 5.281250426e-19 2.148607955e-06 6.144105032e-06 +0.001663984482 0.005941866983 + +H atom_index 1 n_descriptor 18 +1.24907073 0.03420518886 0.1082613168 0.1495823759 0.3207069456 0.0222673082 0.02826371295 0.03733121414 +-4.722977536e-17 4.721770882e-05 0.1025109296 0.1148261072 0.1285082514 6.96085343e-18 4.24582808e-06 0.01316704609 +0.02651532399 0.03074619308 + +H atom_index 2 n_descriptor 18 +1.274533757 0.03333897456 0.117412801 0.1618040857 0.3285389651 0.02343864991 0.02973518498 0.03668094895 +-9.469645337e-18 4.961681768e-05 0.1071724059 0.1174838108 0.138992222 -3.07019978e-19 2.811518802e-06 0.01317930971 +0.02741580725 0.03183233214 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..aa9d6b0c789fe00804c3cd50ff8eb4b97adaee66 Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..0ca797c0e44c206202e02c8108047c75a7332afe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:09 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0881755 SEC) : SETUP UNITCELL + DONE(0.088524 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106686 SEC) : INIT PLANEWAVE + DONE(0.156201 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438859 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651590e+02 0.000000e+00 2.169e-01 5.572e-01 + GE2 -4.664018e+02 -1.242763e+00 9.782e-02 5.027e-01 + GE3 -4.664065e+02 -4.680863e-03 6.263e-02 5.703e-01 + GE4 -4.664066e+02 -1.658763e-04 2.024e-03 4.317e-01 + GE5 -4.664056e+02 9.906923e-04 9.482e-04 4.314e-01 + GE6 -4.664063e+02 -6.299410e-04 1.411e-04 4.239e-01 + GE7 -4.664060e+02 2.208077e-04 4.352e-05 4.183e-01 + GE8 -4.664061e+02 -5.501088e-05 1.621e-05 4.088e-01 + GE9 -4.664061e+02 2.011869e-05 2.345e-06 4.117e-01 + GE10 -4.664061e+02 -2.655176e-06 2.088e-07 4.136e-01 + GE11 -4.664061e+02 -5.671927e-07 9.652e-08 3.403e-01 +E_delta_band = -7.15161525e-02 Ry = -9.73027172e-01 eV +E_delta_NN= -1.95294547e-01 Ry = -2.65711862e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2217 11 0.66 1e+02 % + Run_lcao lcao_line 7.2124 1 7.2 1e+02 % + Potential init_pot 0.28509 2 0.14 3.9 % + PW_Basis recip2real 0.26941 16 0.017 3.7 % + PW_Basis gathers_scatterp 0.12652 16 0.0079 1.8 % + Potential v_of_rho 1.0135 13 0.078 14 % + XC_Functional v_xc 0.34203 14 0.024 4.7 % + H_Hartree_pw v_hartree 0.63629 13 0.049 8.8 % + PW_Basis real2recip 0.6501 38 0.017 9 % + PW_Basis gatherp_scatters 0.28432 38 0.0075 3.9 % + ORB_control set_orb_tables 1.091 1 1.1 15 % + ORB_gen_tables gen_tables 1.091 1 1.1 15 % + ORB_table_phi init_Table 0.47463 1 0.47 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.46953 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.18421 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18265 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24573 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24379 66 0.0037 3.4 % + LOOP_ions opt_ions 5.5872 1 5.6 77 % + ESolver_KS_LCAO Run 4.9739 1 5 69 % + HSolverLCAO solve 2.6861 11 0.24 37 % + HamiltLCAO updateHk 1.3754 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.3481 11 0.12 19 % + Gint_interface cal_gint 0.45109 23 0.02 6.2 % + Gint_Gamma distri_vl_value 0.76161 11 0.069 11 % + Gint_Gamma distri_vl 2.3959 6 0.4 33 % + LCAO_Deepks cal_projected_DM 5.1578 13 0.4 71 % + LCAO_gen_fixedH add_v_delta 2.2572 6 0.38 31 % + LCAO_DESCRIPTOR add_v_delta 2.2573 6 0.38 31 % + ElecStateLCAO psiToRho 1.2823 11 0.12 18 % + Charge mix_rho 0.74138 10 0.074 10 % + LOOP_ions force_stress 0.61319 1 0.61 8.5 % + Force_Stress_LCAO getForceStress 0.61316 1 0.61 8.5 % + Force_LCAO_gamma ftable_gamma 0.39514 1 0.4 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.12818 1 0.13 1.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:09 2022 + FINISH Time : Wed Sep 28 11:09:16 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/75/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..65c99e63df81d734f3e5408933cfe8aac352a725 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.0917732 0.680438 0.378927 +H 0.0952878 0.632471 0.427922 +H 0.0257106 0.692074 0.369349 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3baba1c9de8a9a66f5137563681432a7f3821052 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.818 2 + 2 -12.7412 2 + 3 -8.96799 2 + 4 -6.63785 2 + 5 0.908817 0 + 6 3.77532 0 + 7 11.1831 0 + 8 11.4221 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..13d409829b46aea22f2af988bd0af3406a2fc713 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:38 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 2.56964921409 19.0522538976 10.609942244 0 0 0 0 + tauc_H1 2.66805836895 17.7091760512 11.9818087886 0 0 0 0 + tauc_H2 0.719895825801 19.3780607439 10.3417618366 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0878474972791 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0987784298177 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116976324642 (SEC) + + DONE : INIT CHARGE Time : 0.167067753127 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446312 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000672 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00171 + + Density error is 0.210937299873 + + Energy Rydberg eV + E_KohnSham -34.1889873218 -465.165036426 + E_Harris -34.371706367 -467.651056575 + E_Fermi -0.378808395342 -5.15395262689 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000994354213403 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133279524248 + + Density error is 0.0994087580669 + + Energy Rydberg eV + E_KohnSham -34.2766707673 -466.358030905 + E_Harris -34.2840011531 -466.45776592 + E_Fermi -0.189609084464 -2.57976394127 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000956379296985 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123277366521 + + Density error is 0.0642915260168 + + Energy Rydberg eV + E_KohnSham -34.277145169 -466.364485472 + E_Harris -34.2817741889 -466.427466519 + E_Fermi -0.184695010507 -2.51290453507 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000915017252924 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103462220923 + + Density error is 0.00205283465792 + + Energy Rydberg eV + E_KohnSham -34.2770191223 -466.362770519 + E_Harris -34.2770241159 -466.36283846 + E_Fermi -0.149842206895 -2.03870781467 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914453345774 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010337238692 + + Density error is 0.000943279312159 + + Energy Rydberg eV + E_KohnSham -34.2769971811 -466.362471993 + E_Harris -34.2769975126 -466.362476503 + E_Fermi -0.149869327129 -2.03907680437 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914014123487 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103055646511 + + Density error is 0.000205116469128 + + Energy Rydberg eV + E_KohnSham -34.2770033369 -466.362555747 + E_Harris -34.2770033276 -466.36255562 + E_Fermi -0.14934828763 -2.03198769831 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914155944077 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103050922872 + + Density error is 2.38184279963e-05 + + Energy Rydberg eV + E_KohnSham -34.2770027048 -466.362547147 + E_Harris -34.2770027057 -466.362547158 + E_Fermi -0.149343928017 -2.03192838274 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914119280785 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103048558594 + + Density error is 9.39426206878e-06 + + Energy Rydberg eV + E_KohnSham -34.2770043762 -466.362569887 + E_Harris -34.2770043766 -466.362569892 + E_Fermi -0.149351875753 -2.03203651723 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914120667622 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103047147486 + + Density error is 2.38248300531e-06 + + Energy Rydberg eV + E_KohnSham -34.277003692 -466.362560579 + E_Harris -34.277003692 -466.362560579 + E_Fermi -0.149343171737 -2.03191809302 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914115938616 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103046178349 + + Density error is 5.47712501921e-07 + + Energy Rydberg eV + E_KohnSham -34.2770038535 -466.362562775 + E_Harris -34.2770038535 -466.362562775 + E_Fermi -0.149341608103 -2.03189681868 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000914116701071 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103046150601 + + Density error is 2.15066094835e-07 + + Energy Rydberg eV + E_KohnSham -34.2770038458 -466.362562671 + E_Harris -34.2770038458 -466.362562671 + E_Fermi -0.149341339412 -2.03189316295 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00091411701366 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103046104981 + + Density error is 1.10705694664e-08 + + Energy Rydberg eV + E_KohnSham -34.2770038488 -466.362562711 + E_Harris -34.2770038488 -466.362562711 + E_band -7.81510599495 -106.329972005 + E_one_elec -68.3676220138 -930.189218098 + E_Hartree +35.6083289873 +484.476170486 + E_xc -8.14036404638 -110.755334825 + E_Ewald +6.74884491583 +91.8227457736 + E_demet -2.14596645511e-53 -2.91973715064e-52 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193145853774 -2.6278841564 + E_Fermi -0.149341138897 -2.03189043481 + + charge density convergence is achieved + final etot is -466.362562711 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.8180 2.00000 + 2 -12.7412 2.00000 + 3 -8.96799 2.00000 + 4 -6.63785 2.00000 + 5 0.908817 0.00000 + 6 3.77532 0.00000 + 7 11.1831 0.00000 + 8 11.4221 0.00000 + + EFERMI = -2.031890434808664 eV + OUT.ABACUS/ final etot is -466.3625627113366 eV + correction force for each atom along direction 1 is -3.47422e-05 + correction force for each atom along direction 2 is -7.85788e-05 + correction force for each atom along direction 3 is 8.47078e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.89775288 -0.89655760 +0.94971844 + H1 -0.30555486 +1.2618757 -1.2810710 + H2 +1.2033077 -0.36531809 +0.33135257 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3625627113366 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7171 11 0.61 1.0e+02% + Run_lcao lcao_line 6.7077 1 6.7 1.e+02% + Potential init_pot 0.28399 2 0.14 4.2% + PW_Basis recip2real 0.27842 17 0.016 4.1% + PW_Basis gathers_scatterp 0.12552 17 0.0074 1.9% + Potential v_of_rho 0.92280 14 0.066 14.% + XC_Functional v_xc 0.25920 15 0.017 3.9% + H_Hartree_pw v_hartree 0.62637 14 0.045 9.3% + PW_Basis real2recip 0.59774 41 0.015 8.9% + PW_Basis gatherp_scatters 0.24393 41 0.0059 3.6% + ORB_control set_orb_tables 1.1152 1 1.1 17.% + ORB_gen_tables gen_tables 1.1152 1 1.1 17.% + ORB_table_phi init_Table 0.49131 1 0.49 7.3% + ORB_table_phi cal_ST_Phi12_R 0.48640 126 0.0039 7.2% + ORB_table_beta init_Table_Beta 0.18746 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18599 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25633 1 0.26 3.8% + ORB_table_alpha S_PhiAlpha_R 0.25442 66 0.0039 3.8% + LOOP_ions opt_ions 5.0695 1 5.1 75.% + ESolver_KS_LCAO Run 4.5066 1 4.5 67.% + HSolverLCAO solve 2.3807 12 0.20 35.% + HamiltLCAO updateHk 1.2209 12 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1904 12 0.099 18.% + Gint_interface cal_gint 0.30532 25 0.012 4.5% + Gint_Gamma distri_vl_value 0.70302 12 0.059 10.% + Gint_Gamma distri_vl 2.3446 6 0.39 35.% + LCAO_Deepks cal_projected_DM 4.6753 14 0.33 70.% + LCAO_gen_fixedH add_v_delta 2.2108 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2108 6 0.37 33.% + ElecStateLCAO psiToRho 1.1348 12 0.095 17.% + Charge mix_rho 0.71481 11 0.065 11.% + LOOP_ions force_stress 0.56265 1 0.56 8.4% + Force_Stress_LCAO getForceStress 0.56262 1 0.56 8.4% + Force_LCAO_gamma ftable_gamma 0.35426 1 0.35 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.11171 1 0.11 1.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:38 2022 + Finish Time : Wed Sep 28 11:07:45 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1afd40e7d7b4199b7d92e04ff130f6fa18d08b92 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123452 ima = 3.65379e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123977705465 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112479601964 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011331730539 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113489638882 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113487305832 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001134908769 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113488746038 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113490048969 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113489617064 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113489619534 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113489600576 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113489589826 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7c79424c51e08affb1dab52d8d37704a8642c8ef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-25.430350785900 19.052253897654 10.609942243996 0 0 0 +H +0.0 +2 +-25.331941631036 17.709176051266 11.981808788547 0 0 0 +-27.280104174181 19.378060743909 10.341761836617 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/conv new file mode 100644 index 0000000000000000000000000000000000000000..0467b245d4858bd665752bb8b5fe6602e1ff0084 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/conv @@ -0,0 +1 @@ +76 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..16f53b346629045d113a6b5ac4eddb90f7fa79a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748653525 0.01226819545 1.236209181 1.332713535 1.467351254 0.008082909787 0.01828747691 0.03906476363 +-6.001942067e-19 0.0008727599736 0.002252473941 0.01102078365 0.03951522828 1.735912138e-19 1.331834667e-06 4.29951175e-06 +0.001633101268 0.00571098317 + +H atom_index 1 n_descriptor 18 +1.174385319 0.03661502501 0.08366217907 0.1188636182 0.2955677104 0.01827665413 0.0240068161 0.04038246673 +1.228716813e-17 3.067454281e-05 0.078606745 0.1012036161 0.1126807695 -6.009734213e-18 6.271096458e-06 0.01480783429 +0.0222636338 0.02693738649 + +H atom_index 2 n_descriptor 18 +1.194134323 0.03603399624 0.08928297775 0.1266030234 0.3031933065 0.01916570016 0.02515674907 0.03956613009 +-2.773017478e-17 3.215355639e-05 0.08356780104 0.1080528823 0.1136916976 -6.393802776e-18 5.856182477e-06 0.01417183646 +0.02309374711 0.02801435658 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5ddddbef3ba70d818061d70c65c68d75b89c5f93 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:38 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0878737 SEC) : SETUP UNITCELL + DONE(0.0987989 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116997 SEC) : INIT PLANEWAVE + DONE(0.167203 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44638 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651650e+02 0.000000e+00 2.109e-01 5.006e-01 + GE2 -4.663580e+02 -1.192994e+00 9.941e-02 4.189e-01 + GE3 -4.663645e+02 -6.454567e-03 6.429e-02 4.749e-01 + GE4 -4.663628e+02 1.714953e-03 2.053e-03 3.612e-01 + GE5 -4.663625e+02 2.985261e-04 9.433e-04 3.614e-01 + GE6 -4.663626e+02 -8.375470e-05 2.051e-04 3.574e-01 + GE7 -4.663625e+02 8.600743e-06 2.382e-05 3.382e-01 + GE8 -4.663626e+02 -2.274051e-05 9.394e-06 3.395e-01 + GE9 -4.663626e+02 9.308176e-06 2.382e-06 3.420e-01 + GE10 -4.663626e+02 -2.196181e-06 5.477e-07 3.365e-01 + GE11 -4.663626e+02 1.040817e-07 2.151e-07 3.351e-01 + GE12 -4.663626e+02 -4.034267e-08 1.107e-08 2.799e-01 +E_delta_band = -6.69541620e-02 Ry = -9.10958109e-01 eV +E_delta_NN= -1.93145854e-01 Ry = -2.62788416e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7171 11 0.61 1e+02 % + Run_lcao lcao_line 6.7077 1 6.7 1e+02 % + Potential init_pot 0.28399 2 0.14 4.2 % + PW_Basis recip2real 0.27842 17 0.016 4.1 % + PW_Basis gathers_scatterp 0.12552 17 0.0074 1.9 % + Potential v_of_rho 0.9228 14 0.066 14 % + XC_Functional v_xc 0.2592 15 0.017 3.9 % + H_Hartree_pw v_hartree 0.62637 14 0.045 9.3 % + PW_Basis real2recip 0.59774 41 0.015 8.9 % + PW_Basis gatherp_scatters 0.24393 41 0.0059 3.6 % + ORB_control set_orb_tables 1.1152 1 1.1 17 % + ORB_gen_tables gen_tables 1.1152 1 1.1 17 % + ORB_table_phi init_Table 0.49131 1 0.49 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.4864 126 0.0039 7.2 % + ORB_table_beta init_Table_Beta 0.18746 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18599 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25633 1 0.26 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.25442 66 0.0039 3.8 % + LOOP_ions opt_ions 5.0695 1 5.1 75 % + ESolver_KS_LCAO Run 4.5066 1 4.5 67 % + HSolverLCAO solve 2.3807 12 0.2 35 % + HamiltLCAO updateHk 1.2209 12 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1904 12 0.099 18 % + Gint_interface cal_gint 0.30532 25 0.012 4.5 % + Gint_Gamma distri_vl_value 0.70302 12 0.059 10 % + Gint_Gamma distri_vl 2.3446 6 0.39 35 % + LCAO_Deepks cal_projected_DM 4.6753 14 0.33 70 % + LCAO_gen_fixedH add_v_delta 2.2108 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2108 6 0.37 33 % + ElecStateLCAO psiToRho 1.1348 12 0.095 17 % + Charge mix_rho 0.71481 11 0.065 11 % + LOOP_ions force_stress 0.56265 1 0.56 8.4 % + Force_Stress_LCAO getForceStress 0.56262 1 0.56 8.4 % + Force_LCAO_gamma ftable_gamma 0.35426 1 0.35 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.11171 1 0.11 1.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:38 2022 + FINISH Time : Wed Sep 28 11:07:45 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/76/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..12d40b04ebfab2aebc682c2dee9b252b74c3e0ac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.0787106 0.654484 0.369772 +H 0.137778 0.68116 0.381238 +H 0.0485168 0.705581 0.342875 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b4755586139e9f33d2b6dbba938426326a24dc4f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3801 2 + 2 -12.8286 2 + 3 -9.34249 2 + 4 -6.76643 2 + 5 1.28084 0 + 6 4.40058 0 + 7 11.0675 0 + 8 11.342 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..da10bb56cf0828fcfd2fb2a6f9b24f8d64af554b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:33 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 2.20389596525 18.3255399495 10.3536204922 0 0 0 0 + tauc_H1 3.85777546452 19.072476804 10.6746563741 0 0 0 0 + tauc_H2 1.35847127224 19.7562691687 9.60049640077 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0866657954808 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0874956808267 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105608337456 (SEC) + + DONE : INIT CHARGE Time : 0.155090305108 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.43524 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00126 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000931 + + Density error is 0.213907177707 + + Energy Rydberg eV + E_KohnSham -34.1908503149 -465.190383747 + E_Harris -34.3809354892 -467.776625223 + E_Fermi -0.405919943508 -5.52282416355 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00123046985245 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105390076494 + + Density error is 0.0977034579642 + + Energy Rydberg eV + E_KohnSham -34.2800619926 -466.404170893 + E_Harris -34.2868837212 -466.496985272 + E_Fermi -0.215803668715 -2.93615954383 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114269511529 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000996491841692 + + Density error is 0.0627081335032 + + Energy Rydberg eV + E_KohnSham -34.280380261 -466.408501156 + E_Harris -34.2848012299 -466.468651523 + E_Fermi -0.204983726365 -2.78894667583 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000996889446871 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908456993111 + + Density error is 0.00193630963187 + + Energy Rydberg eV + E_KohnSham -34.2803602184 -466.408228463 + E_Harris -34.2803608477 -466.408237025 + E_Fermi -0.169224740862 -2.30242071829 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000996957396634 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909228898974 + + Density error is 0.000926159074803 + + Energy Rydberg eV + E_KohnSham -34.2802991008 -466.407396915 + E_Harris -34.2803006045 -466.407417374 + E_Fermi -0.168629282923 -2.29431909741 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000995224795642 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000907891719454 + + Density error is 9.88090194178e-05 + + Energy Rydberg eV + E_KohnSham -34.2803390454 -466.40794039 + E_Harris -34.2803390482 -466.407940428 + E_Fermi -0.168586675728 -2.29373939678 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000995158021717 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000907823650366 + + Density error is 3.64461083281e-05 + + Energy Rydberg eV + E_KohnSham -34.2803266948 -466.407772351 + E_Harris -34.2803267022 -466.407772452 + E_Fermi -0.168483700701 -2.29233834966 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000995140414418 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000907778853952 + + Density error is 1.19562083637e-05 + + Energy Rydberg eV + E_KohnSham -34.2803288101 -466.40780113 + E_Harris -34.2803288107 -466.407801139 + E_Fermi -0.168524960402 -2.29289971669 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000995129302671 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000907777929854 + + Density error is 2.12959853243e-06 + + Energy Rydberg eV + E_KohnSham -34.2803275581 -466.407784097 + E_Harris -34.2803275582 -466.407784097 + E_Fermi -0.168513958845 -2.29275003282 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000995126366357 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000907778613323 + + Density error is 1.24019312787e-07 + + Energy Rydberg eV + E_KohnSham -34.2803277318 -466.40778646 + E_Harris -34.2803277318 -466.40778646 + E_Fermi -0.168511651793 -2.29271864377 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000995126626457 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000907778914732 + + Density error is 4.59456181681e-08 + + Energy Rydberg eV + E_KohnSham -34.28032777 -466.40778698 + E_Harris -34.28032777 -466.40778698 + E_band -7.98453583764 -108.635183277 + E_one_elec -69.3144750962 -943.071815188 + E_Hartree +36.0430074327 +490.390274141 + E_xc -8.21006016757 -111.703599202 + E_Ewald +7.32544890932 +99.6678455747 + E_demet -1.41850625522e-77 -1.92997677197e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194888434487 -2.65159318332 + E_Fermi -0.168511657211 -2.2927187175 + + charge density convergence is achieved + final etot is -466.40778698 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3801 2.00000 + 2 -12.8286 2.00000 + 3 -9.34249 2.00000 + 4 -6.76643 2.00000 + 5 1.28084 0.00000 + 6 4.40058 0.00000 + 7 11.0675 0.00000 + 8 11.3420 0.00000 + + EFERMI = -2.292718717496184 eV + OUT.ABACUS/ final etot is -466.4077869801341 eV + correction force for each atom along direction 1 is 7.33660e-06 + correction force for each atom along direction 2 is 0.000171741 + correction force for each atom along direction 3 is -0.000156138 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.36486724 -0.034496770 +0.13051643 + H1 +0.23841239 -0.26375987 +0.16971970 + H2 -0.60327963 +0.29825664 -0.30023613 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4077869801341 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2092 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2007 1 7.2 1.e+02% + Potential init_pot 0.28413 2 0.14 3.9% + PW_Basis recip2real 0.26819 16 0.017 3.7% + PW_Basis gathers_scatterp 0.12444 16 0.0078 1.7% + Potential v_of_rho 0.99954 13 0.077 14.% + XC_Functional v_xc 0.32594 14 0.023 4.5% + H_Hartree_pw v_hartree 0.63865 13 0.049 8.9% + PW_Basis real2recip 0.65580 38 0.017 9.1% + PW_Basis gatherp_scatters 0.29142 38 0.0077 4.0% + ORB_control set_orb_tables 1.0912 1 1.1 15.% + ORB_gen_tables gen_tables 1.0912 1 1.1 15.% + ORB_table_phi init_Table 0.47438 1 0.47 6.6% + ORB_table_phi cal_ST_Phi12_R 0.46925 126 0.0037 6.5% + ORB_table_beta init_Table_Beta 0.18203 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18047 56 0.0032 2.5% + ORB_table_alpha init_Table_Alpha 0.24865 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24670 66 0.0037 3.4% + LOOP_ions opt_ions 5.5949 1 5.6 78.% + ESolver_KS_LCAO Run 4.9804 1 5.0 69.% + HSolverLCAO solve 2.6948 11 0.24 37.% + HamiltLCAO updateHk 1.3783 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.3508 11 0.12 19.% + Gint_interface cal_gint 0.56348 23 0.024 7.8% + Gint_Gamma distri_vl_value 0.72348 11 0.066 10.% + Gint_Gamma distri_vl 2.3987 6 0.40 33.% + LCAO_Deepks cal_projected_DM 5.1824 13 0.40 72.% + LCAO_gen_fixedH add_v_delta 2.2585 6 0.38 31.% + LCAO_DESCRIPTOR add_v_delta 2.2587 6 0.38 31.% + ElecStateLCAO psiToRho 1.2869 11 0.12 18.% + Charge mix_rho 0.74906 10 0.075 10.% + LOOP_ions force_stress 0.61437 1 0.61 8.5% + Force_Stress_LCAO getForceStress 0.61435 1 0.61 8.5% + Force_LCAO_gamma ftable_gamma 0.39508 1 0.40 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.14489 1 0.14 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:33 2022 + Finish Time : Wed Sep 28 11:04:40 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1f3c4b64da5de69a2b8c86e45ddcf8f33e896505 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123689 ima = 3.65918e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012274459721 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111587419554 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112174519204 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112430972883 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112375042603 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112406183943 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112403355525 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240599938 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112405453521 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112405357395 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112405351906 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/STRU new file mode 100644 index 0000000000000000000000000000000000000000..484e32f2a0dad1398bd29a1271d275b2b1d849ee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-25.796104034729 18.325539949539 10.353620492225 0 0 0 +H +0.0 +2 +-24.142224535499 19.072476804043 10.674656374146 0 0 0 +-26.641528727758 19.756269168743 9.600496400757 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/conv new file mode 100644 index 0000000000000000000000000000000000000000..c91d008a2acd80ad1cdc948bd5c72b258064bc82 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/conv @@ -0,0 +1 @@ +77 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..467bb5fb4e1a66b7cefec3eb1d9894c9bcd3de50 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75274387 0.01277126436 1.272094802 1.355434882 1.469622712 0.009179280292 0.01727853683 0.03912526026 +5.722386488e-19 0.0009559066979 0.00277679322 0.01297720037 0.04647678907 -1.138841213e-19 2.567656815e-06 6.95618626e-06 +0.00159906135 0.006114597275 + +H atom_index 1 n_descriptor 18 +1.241104477 0.03499392046 0.1068992724 0.1454803169 0.3169880928 0.02243991036 0.02772583124 0.0381072631 +2.444497894e-17 4.844612436e-05 0.1004097833 0.1147759784 0.1247845655 -2.384583064e-18 3.992445118e-06 0.01343582516 +0.02642912142 0.03032571065 + +H atom_index 2 n_descriptor 18 +1.25556926 0.03450458087 0.1119739462 0.1521865687 0.3217767036 0.02314420346 0.02857276714 0.03764569811 +5.904734948e-18 4.982200358e-05 0.1037464372 0.1156591697 0.1305772724 1.233892562e-18 3.180311288e-06 0.01330673136 +0.02696815984 0.03099223001 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/dm_eig.npy new file mode 100644 index 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..4ffe5ca12f9975a7372d0f9f402cc5e61bab7cfd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:33 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0866879 SEC) : SETUP UNITCELL + DONE(0.0875121 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105628 SEC) : INIT PLANEWAVE + DONE(0.155224 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.435304 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651904e+02 0.000000e+00 2.139e-01 5.632e-01 + GE2 -4.664042e+02 -1.213787e+00 9.770e-02 5.009e-01 + GE3 -4.664085e+02 -4.330263e-03 6.271e-02 5.691e-01 + GE4 -4.664082e+02 2.726931e-04 1.936e-03 4.320e-01 + GE5 -4.664074e+02 8.315475e-04 9.262e-04 4.351e-01 + GE6 -4.664079e+02 -5.434743e-04 9.881e-05 4.243e-01 + GE7 -4.664078e+02 1.680384e-04 3.645e-05 4.102e-01 + GE8 -4.664078e+02 -2.877928e-05 1.196e-05 4.142e-01 + GE9 -4.664078e+02 1.703339e-05 2.130e-06 4.132e-01 + GE10 -4.664078e+02 -2.362520e-06 1.240e-07 4.129e-01 + GE11 -4.664078e+02 -5.205097e-07 4.595e-08 3.420e-01 +E_delta_band = -7.06395863e-02 Ry = -9.61100877e-01 eV +E_delta_NN= -1.94888434e-01 Ry = -2.65159318e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.2092 11 0.66 1e+02 % + Run_lcao lcao_line 7.2007 1 7.2 1e+02 % + Potential init_pot 0.28413 2 0.14 3.9 % + PW_Basis recip2real 0.26819 16 0.017 3.7 % + PW_Basis gathers_scatterp 0.12444 16 0.0078 1.7 % + Potential v_of_rho 0.99954 13 0.077 14 % + XC_Functional v_xc 0.32594 14 0.023 4.5 % + H_Hartree_pw v_hartree 0.63865 13 0.049 8.9 % + PW_Basis real2recip 0.6558 38 0.017 9.1 % + PW_Basis gatherp_scatters 0.29142 38 0.0077 4 % + ORB_control set_orb_tables 1.0912 1 1.1 15 % + ORB_gen_tables gen_tables 1.0912 1 1.1 15 % + ORB_table_phi init_Table 0.47438 1 0.47 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.46925 126 0.0037 6.5 % + ORB_table_beta init_Table_Beta 0.18203 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18047 56 0.0032 2.5 % + ORB_table_alpha init_Table_Alpha 0.24865 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.2467 66 0.0037 3.4 % + LOOP_ions opt_ions 5.5949 1 5.6 78 % + ESolver_KS_LCAO Run 4.9804 1 5 69 % + HSolverLCAO solve 2.6948 11 0.24 37 % + HamiltLCAO updateHk 1.3783 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.3508 11 0.12 19 % + Gint_interface cal_gint 0.56348 23 0.024 7.8 % + Gint_Gamma distri_vl_value 0.72348 11 0.066 10 % + Gint_Gamma distri_vl 2.3987 6 0.4 33 % + LCAO_Deepks cal_projected_DM 5.1824 13 0.4 72 % + LCAO_gen_fixedH add_v_delta 2.2585 6 0.38 31 % + LCAO_DESCRIPTOR add_v_delta 2.2587 6 0.38 31 % + ElecStateLCAO psiToRho 1.2869 11 0.12 18 % + Charge mix_rho 0.74906 10 0.075 10 % + LOOP_ions force_stress 0.61437 1 0.61 8.5 % + Force_Stress_LCAO getForceStress 0.61435 1 0.61 8.5 % + Force_LCAO_gamma ftable_gamma 0.39508 1 0.4 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.14489 1 0.14 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:33 2022 + FINISH Time : Wed Sep 28 11:04:40 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/77/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..f85359bf747a42579334b6fbb8590d5468b10c9b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.09099 0.645885 0.366553 +H 0.125312 0.607279 0.324513 +H 0.0347655 0.65876 0.334876 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ca2b0d5e47eb61f7df2da8591a3c0b68454e0ee0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1618 2 + 2 -12.9612 2 + 3 -9.08125 2 + 4 -6.71641 2 + 5 1.20351 0 + 6 4.24961 0 + 7 11.1045 0 + 8 11.3548 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0a2073085fbda73329cb6b36df6dd42367677489 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:44 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 2.54772033815 18.0847727506 10.2634756985 0 0 0 0 + tauc_H1 3.50873358121 17.0038241735 9.0863598762 0 0 0 0 + tauc_H2 0.973432873201 18.4452749455 9.37652170033 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0876606096307 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0880610645821 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106224734229 (SEC) + + DONE : INIT CHARGE Time : 0.154988258687 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.432629 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00161 + + Density error is 0.213987402193 + + Energy Rydberg eV + E_KohnSham -34.1913162721 -465.196723421 + E_Harris -34.3808825567 -467.77590504 + E_Fermi -0.398005887968 -5.41514791391 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113501299686 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138072194727 + + Density error is 0.0984253993265 + + Energy Rydberg eV + E_KohnSham -34.2809745783 -466.416587258 + E_Harris -34.2878698039 -466.510401615 + E_Fermi -0.207082290276 -2.81749910264 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108973596773 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127828626929 + + Density error is 0.0633291633024 + + Energy Rydberg eV + E_KohnSham -34.2813631625 -466.421874217 + E_Harris -34.2858103959 -466.482381932 + E_Fermi -0.19803038282 -2.69434158348 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103374196939 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010910322756 + + Density error is 0.00198747766901 + + Energy Rydberg eV + E_KohnSham -34.2813150995 -466.421220287 + E_Harris -34.281316829 -466.421243818 + E_Fermi -0.162620940979 -2.21257141144 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103512015733 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108947233218 + + Density error is 0.000943951394094 + + Energy Rydberg eV + E_KohnSham -34.2812627374 -466.420507864 + E_Harris -34.2812634507 -466.420517568 + E_Fermi -0.162190586233 -2.20671613473 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103416911669 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010869097009 + + Density error is 0.000171970431621 + + Energy Rydberg eV + E_KohnSham -34.2812910673 -466.420893312 + E_Harris -34.2812911008 -466.420893768 + E_Fermi -0.161986131814 -2.20393438965 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103440163591 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010868681191 + + Density error is 3.48906788343e-05 + + Energy Rydberg eV + E_KohnSham -34.2812809594 -466.420755787 + E_Harris -34.281280965 -466.420755864 + E_Fermi -0.161894979869 -2.20269420382 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103432463808 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108683821466 + + Density error is 1.60726338171e-05 + + Energy Rydberg eV + E_KohnSham -34.2812848682 -466.420808968 + E_Harris -34.2812848693 -466.420808983 + E_Fermi -0.161927776015 -2.20314041827 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103432825325 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108681286266 + + Density error is 2.38745874908e-06 + + Energy Rydberg eV + E_KohnSham -34.2812835549 -466.420791101 + E_Harris -34.281283555 -466.420791101 + E_Fermi -0.161911912729 -2.20292458719 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103432663837 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108680650072 + + Density error is 4.52314980738e-07 + + Energy Rydberg eV + E_KohnSham -34.2812837808 -466.420794174 + E_Harris -34.2812837808 -466.420794174 + E_Fermi -0.161909609515 -2.20289325036 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103432766283 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108680685605 + + Density error is 1.54937121871e-07 + + Energy Rydberg eV + E_KohnSham -34.2812838072 -466.420794532 + E_Harris -34.2812838071 -466.420794532 + E_Fermi -0.161909420042 -2.20289067245 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00103432791801 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108680668109 + + Density error is 1.04197963377e-08 + + Energy Rydberg eV + E_KohnSham -34.2812838108 -466.420794582 + E_Harris -34.2812838108 -466.420794582 + E_band -7.92619295156 -107.841387589 + E_one_elec -69.0440768166 -939.392857855 + E_Hartree +35.9243821609 +488.776294518 + E_xc -8.19095675737 -111.443683972 + E_Ewald +7.15421347985 +97.3380680344 + E_demet -9.88978971247e-71 -1.34557492111e-69 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194341247851 -2.64414832721 + E_Fermi -0.161909272775 -2.20288866877 + + charge density convergence is achieved + final etot is -466.420794582 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1618 2.00000 + 2 -12.9612 2.00000 + 3 -9.08125 2.00000 + 4 -6.71641 2.00000 + 5 1.20351 0.00000 + 6 4.24961 0.00000 + 7 11.1045 0.00000 + 8 11.3548 0.00000 + + EFERMI = -2.202888668771819 eV + OUT.ABACUS/ final etot is -466.4207945817439 eV + correction force for each atom along direction 1 is 5.46612e-06 + correction force for each atom along direction 2 is 5.06816e-05 + correction force for each atom along direction 3 is -4.10149e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.32351748 -0.29618081 -0.26895630 + H1 -0.31344533 +0.31620631 +0.31561940 + H2 -0.010072145 -0.020025493 -0.046663101 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4207945817439 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7821 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7722 1 6.8 1.e+02% + Potential init_pot 0.28284 2 0.14 4.2% + PW_Basis recip2real 0.27970 17 0.016 4.1% + PW_Basis gathers_scatterp 0.12821 17 0.0075 1.9% + Potential v_of_rho 0.91953 14 0.066 14.% + XC_Functional v_xc 0.26075 15 0.017 3.8% + H_Hartree_pw v_hartree 0.62188 14 0.044 9.2% + PW_Basis real2recip 0.60507 41 0.015 8.9% + PW_Basis gatherp_scatters 0.24542 41 0.0060 3.6% + ORB_control set_orb_tables 1.1185 1 1.1 16.% + ORB_gen_tables gen_tables 1.1185 1 1.1 16.% + ORB_table_phi init_Table 0.49021 1 0.49 7.2% + ORB_table_phi cal_ST_Phi12_R 0.48527 126 0.0039 7.2% + ORB_table_beta init_Table_Beta 0.19138 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18985 56 0.0034 2.8% + ORB_table_alpha init_Table_Alpha 0.25640 1 0.26 3.8% + ORB_table_alpha S_PhiAlpha_R 0.25450 66 0.0039 3.8% + LOOP_ions opt_ions 5.1443 1 5.1 76.% + ESolver_KS_LCAO Run 4.5744 1 4.6 67.% + HSolverLCAO solve 2.4406 12 0.20 36.% + HamiltLCAO updateHk 1.2613 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2305 12 0.10 18.% + Gint_interface cal_gint 0.70935 25 0.028 10.% + Gint_Gamma distri_vl_value 0.58972 12 0.049 8.7% + Gint_Gamma distri_vl 2.3787 6 0.40 35.% + LCAO_Deepks cal_projected_DM 4.7823 14 0.34 71.% + LCAO_gen_fixedH add_v_delta 2.2453 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2452 6 0.37 33.% + ElecStateLCAO psiToRho 1.1597 12 0.097 17.% + Charge mix_rho 0.71219 11 0.065 11.% + LOOP_ions force_stress 0.56964 1 0.57 8.4% + Force_Stress_LCAO getForceStress 0.56961 1 0.57 8.4% + Force_LCAO_gamma ftable_gamma 0.36112 1 0.36 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.15404 1 0.15 2.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:44 2022 + Finish Time : Wed Sep 28 11:10:51 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..862e892074c3317b8bc71aed352b4eff554ec5db --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123621 ima = 3.65778e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123380928385 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112096654127 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112742249436 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112971723133 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112934078149 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112956689143 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112949852167 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112952502096 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112951820111 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011295173958 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112951722258 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112951714564 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7915b1eac607139a280ef8066a8a19d2011c6fb8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-25.452279661824 18.084772750629 10.263475698543 0 0 0 +H +0.0 +2 +-24.491266418801 17.003824173487 9.086359876194 0 0 0 +-27.026567126796 18.445274945477 9.376521700308 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/conv new file mode 100644 index 0000000000000000000000000000000000000000..5c4cf96e6b47d891846421894fb2177b10dac58f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/conv @@ -0,0 +1 @@ +78 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8bd28768443fbff9b8b454876d16a280f0b17ec2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749017666 0.0125946491 1.263516832 1.353917507 1.468741382 0.008368401705 0.01843617355 0.03902728407 +-2.236168564e-18 0.001001223948 0.002503380755 0.01205316671 0.04357636472 -3.607467e-19 1.839618147e-06 5.488847517e-06 +0.001649495608 0.005913052059 + +H atom_index 1 n_descriptor 18 +1.220515241 0.03522973048 0.09819261999 0.1370254362 0.3115998421 0.02073402206 0.02662120475 0.03845475555 +5.24542488e-18 4.039307641e-05 0.09298066036 0.1141768542 0.1174058453 4.318910478e-18 5.456073189e-06 0.01356775302 +0.02487814944 0.02936270735 + +H atom_index 2 n_descriptor 18 +1.238157427 0.03462633051 0.1039374156 0.1447878662 0.3176584043 0.02154861883 0.0276524951 0.03780196471 +-7.002462693e-17 4.194719073e-05 0.09761837222 0.1147033872 0.1241691706 1.042832552e-18 4.654494274e-06 0.01325510461 +0.025570044 0.03022298132 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ee18a062851ae3447f4df7ca7deac72f0beffce1 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:44 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.087682 SEC) : SETUP UNITCELL + DONE(0.0880753 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106247 SEC) : INIT PLANEWAVE + DONE(0.155119 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.432695 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651967e+02 0.000000e+00 2.140e-01 4.995e-01 + GE2 -4.664166e+02 -1.219864e+00 9.843e-02 4.224e-01 + GE3 -4.664219e+02 -5.286958e-03 6.333e-02 4.818e-01 + GE4 -4.664212e+02 6.539294e-04 1.987e-03 3.698e-01 + GE5 -4.664205e+02 7.124238e-04 9.440e-04 3.663e-01 + GE6 -4.664209e+02 -3.854485e-04 1.720e-04 3.620e-01 + GE7 -4.664208e+02 1.375249e-04 3.489e-05 3.491e-01 + GE8 -4.664208e+02 -5.318114e-05 1.607e-05 3.446e-01 + GE9 -4.664208e+02 1.786736e-05 2.387e-06 3.456e-01 + GE10 -4.664208e+02 -3.072968e-06 4.523e-07 3.425e-01 + GE11 -4.664208e+02 -3.585157e-07 1.549e-07 3.416e-01 + GE12 -4.664208e+02 -4.936857e-08 1.042e-08 2.870e-01 +E_delta_band = -6.94953703e-02 Ry = -9.45533020e-01 eV +E_delta_NN= -1.94341248e-01 Ry = -2.64414833e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7821 11 0.62 1e+02 % + Run_lcao lcao_line 6.7722 1 6.8 1e+02 % + Potential init_pot 0.28284 2 0.14 4.2 % + PW_Basis recip2real 0.2797 17 0.016 4.1 % + PW_Basis gathers_scatterp 0.12821 17 0.0075 1.9 % + Potential v_of_rho 0.91953 14 0.066 14 % + XC_Functional v_xc 0.26075 15 0.017 3.8 % + H_Hartree_pw v_hartree 0.62188 14 0.044 9.2 % + PW_Basis real2recip 0.60507 41 0.015 8.9 % + PW_Basis gatherp_scatters 0.24542 41 0.006 3.6 % + ORB_control set_orb_tables 1.1185 1 1.1 16 % + ORB_gen_tables gen_tables 1.1185 1 1.1 16 % + ORB_table_phi init_Table 0.49021 1 0.49 7.2 % + ORB_table_phi cal_ST_Phi12_R 0.48527 126 0.0039 7.2 % + ORB_table_beta init_Table_Beta 0.19138 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18985 56 0.0034 2.8 % + ORB_table_alpha init_Table_Alpha 0.2564 1 0.26 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.2545 66 0.0039 3.8 % + LOOP_ions opt_ions 5.1443 1 5.1 76 % + ESolver_KS_LCAO Run 4.5744 1 4.6 67 % + HSolverLCAO solve 2.4406 12 0.2 36 % + HamiltLCAO updateHk 1.2613 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.2305 12 0.1 18 % + Gint_interface cal_gint 0.70935 25 0.028 10 % + Gint_Gamma distri_vl_value 0.58972 12 0.049 8.7 % + Gint_Gamma distri_vl 2.3787 6 0.4 35 % + LCAO_Deepks cal_projected_DM 4.7823 14 0.34 71 % + LCAO_gen_fixedH add_v_delta 2.2453 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2452 6 0.37 33 % + ElecStateLCAO psiToRho 1.1597 12 0.097 17 % + Charge mix_rho 0.71219 11 0.065 11 % + LOOP_ions force_stress 0.56964 1 0.57 8.4 % + Force_Stress_LCAO getForceStress 0.56961 1 0.57 8.4 % + Force_LCAO_gamma ftable_gamma 0.36112 1 0.36 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.15404 1 0.15 2.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:44 2022 + FINISH Time : Wed Sep 28 11:10:51 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/78/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..41f625d8b5ceb902cf46407a097edc821b0dad2b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.10181 0.635837 0.35803 +H 0.0991718 0.572624 0.362979 +H 0.082755 0.64926 0.417374 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8d4ac649b862370f056a6a0106664947e0a4ff59 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.7808 2 + 2 -12.9496 2 + 3 -9.52837 2 + 4 -6.85006 2 + 5 1.50782 0 + 6 4.87124 0 + 7 10.9837 0 + 8 11.2713 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b83c2eb5b8653c11de98ac01ee592399cf1158fe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:29 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 2.85067850343 17.8034382175 10.0248324898 0 0 0 0 + tauc_H1 2.7768100414 16.0334835343 10.1634160818 0 0 0 0 + tauc_H2 2.31713898965 18.179269816 11.6864732838 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.102163433742 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.103682218277 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.121681218117 (SEC) + + DONE : INIT CHARGE Time : 0.164780964273 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443961 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000592 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105 + + Density error is 0.216723267369 + + Energy Rydberg eV + E_KohnSham -34.1838742232 -465.095469151 + E_Harris -34.3805245981 -467.771034763 + E_Fermi -0.426765471926 -5.80644212785 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000907131761007 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138316939505 + + Density error is 0.0967956406087 + + Energy Rydberg eV + E_KohnSham -34.2736626984 -466.317104029 + E_Harris -34.2803682784 -466.408338124 + E_Fermi -0.235661651587 -3.20634126167 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000868185735005 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132089171814 + + Density error is 0.0615539401536 + + Energy Rydberg eV + E_KohnSham -34.2737995848 -466.318966464 + E_Harris -34.2780595651 -466.376926469 + E_Fermi -0.219902831958 -2.99193152096 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000818888711357 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123572305773 + + Density error is 0.00208221628946 + + Energy Rydberg eV + E_KohnSham -34.2738675486 -466.319891158 + E_Harris -34.2738707866 -466.319935213 + E_Fermi -0.183832500518 -2.50116948464 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000823300084558 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124178017078 + + Density error is 0.000877782929929 + + Energy Rydberg eV + E_KohnSham -34.2737934885 -466.31888352 + E_Harris -34.2737964501 -466.318923813 + E_Fermi -0.182568356048 -2.48396991675 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000821673356494 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123957043755 + + Density error is 0.000166731858588 + + Energy Rydberg eV + E_KohnSham -34.2738498678 -466.319650599 + E_Harris -34.2738499721 -466.319652017 + E_Fermi -0.182961078994 -2.48931318655 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00082162570706 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123951724017 + + Density error is 4.39290482143e-05 + + Energy Rydberg eV + E_KohnSham -34.2738291238 -466.319368363 + E_Harris -34.2738289733 -466.319366314 + E_Fermi -0.182773674203 -2.48676341356 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000821558165577 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123943245146 + + Density error is 2.16022130646e-05 + + Energy Rydberg eV + E_KohnSham -34.2738338439 -466.319432582 + E_Harris -34.2738338456 -466.319432606 + E_Fermi -0.182828842117 -2.48751401154 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000821560904971 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123942402453 + + Density error is 1.96535890392e-06 + + Energy Rydberg eV + E_KohnSham -34.2738322387 -466.319410743 + E_Harris -34.2738322387 -466.319410743 + E_Fermi -0.182804422903 -2.48718177108 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000821563277637 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123942430687 + + Density error is 4.65584986797e-07 + + Energy Rydberg eV + E_KohnSham -34.2738325183 -466.319414547 + E_Harris -34.2738325183 -466.319414547 + E_Fermi -0.18280291242 -2.4871612199 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000821564331791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123942578187 + + Density error is 1.35264062063e-07 + + Energy Rydberg eV + E_KohnSham -34.2738325393 -466.319414832 + E_Harris -34.2738325393 -466.319414832 + E_Fermi -0.182802691663 -2.48715821636 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000821564516044 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123942594131 + + Density error is 1.08648239584e-08 + + Energy Rydberg eV + E_KohnSham -34.2738325442 -466.319414898 + E_Harris -34.2738325442 -466.319414898 + E_band -8.1008454384 -110.21765658 + E_one_elec -69.9969625962 -952.357534001 + E_Hartree +36.3598484011 +494.701116671 + E_xc -8.26121946386 -112.399657137 + E_Ewald +7.74733650492 +105.40792079 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196172827393 -2.66906824531 + E_Fermi -0.182802544249 -2.48715621068 + + charge density convergence is achieved + final etot is -466.319414898 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.7808 2.00000 + 2 -12.9496 2.00000 + 3 -9.52837 2.00000 + 4 -6.85006 2.00000 + 5 1.50782 0.00000 + 6 4.87124 0.00000 + 7 10.9837 0.00000 + 8 11.2713 0.00000 + + EFERMI = -2.487156210680744 eV + OUT.ABACUS/ final etot is -466.3194148982811 eV + correction force for each atom along direction 1 is -3.91322e-05 + correction force for each atom along direction 2 is -0.000129820 + correction force for each atom along direction 3 is 0.000137717 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.38011056 +1.1259513 -1.1128580 + H1 +0.13134000 -2.2319746 -0.51697766 + H2 -0.51145055 +1.1060233 +1.6298357 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3194148982811 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6310 11 0.69 1.0e+02% + Run_lcao lcao_line 7.6216 1 7.6 1.e+02% + Potential init_pot 0.28106 2 0.14 3.7% + PW_Basis recip2real 0.27095 17 0.016 3.6% + PW_Basis gathers_scatterp 0.12132 17 0.0071 1.6% + Potential v_of_rho 0.84167 14 0.060 11.% + XC_Functional v_xc 0.20493 15 0.014 2.7% + H_Hartree_pw v_hartree 0.59751 14 0.043 7.8% + PW_Basis real2recip 0.70339 41 0.017 9.2% + PW_Basis gatherp_scatters 0.28534 41 0.0070 3.7% + ORB_control set_orb_tables 1.0944 1 1.1 14.% + ORB_gen_tables gen_tables 1.0944 1 1.1 14.% + ORB_table_phi init_Table 0.47642 1 0.48 6.2% + ORB_table_phi cal_ST_Phi12_R 0.47113 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18301 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18145 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24775 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24583 66 0.0037 3.2% + LOOP_ions opt_ions 6.0016 1 6.0 79.% + ESolver_KS_LCAO Run 5.4185 1 5.4 71.% + HSolverLCAO solve 3.1784 12 0.26 42.% + HamiltLCAO updateHk 1.5904 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.5605 12 0.13 20.% + Gint_interface cal_gint 0.59913 25 0.024 7.9% + Gint_Gamma distri_vl_value 0.90916 12 0.076 12.% + Gint_Gamma distri_vl 2.8081 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.5961 14 0.40 73.% + LCAO_gen_fixedH add_v_delta 2.6803 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.6805 6 0.45 35.% + ElecStateLCAO psiToRho 1.5652 12 0.13 21.% + Charge mix_rho 0.79276 11 0.072 10.% + LOOP_ions force_stress 0.58291 1 0.58 7.6% + Force_Stress_LCAO getForceStress 0.58289 1 0.58 7.6% + Force_LCAO_gamma ftable_gamma 0.39035 1 0.39 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.14515 1 0.15 1.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:29 2022 + Finish Time : Wed Sep 28 11:09:37 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..9fa32fd58f915f930d3706bd30dbd7fab23f0cff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124138 ima = 3.68909e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8.00000000000001 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122078805044 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011135817128 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111742310519 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112052816389 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011197106119 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011201824629 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112010340146 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112013468397 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112012681055 + charge after normalized = 7.99999999999996 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112012615422 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112012596734 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011201259009 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/STRU new file mode 100644 index 0000000000000000000000000000000000000000..795dc05b2db6c30ae990b25c621ea4f47703d0e4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-25.149321496598 17.803438217456 10.024832489814 0 0 0 +H +0.0 +2 +-25.223189958605 16.033483534276 10.163416081826 0 0 0 +-25.682861010344 18.179269816013 11.686473283777 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/conv new file mode 100644 index 0000000000000000000000000000000000000000..c4a89aae5cdbf6518b68e75e34fcee9d929e5d50 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/conv @@ -0,0 +1 @@ +79 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..00614027e1208223da06a1ec009f0516f19a9d86 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754812947 0.01298098732 1.297431292 1.374738843 1.47134966 0.009915199574 0.01716019468 0.0391705124 +-7.32563398e-18 0.001021919594 0.003135977495 0.01452451538 0.05085316294 2.032877161e-20 3.58862436e-06 8.71663369e-06 +0.001592746331 0.006182630047 + +H atom_index 1 n_descriptor 18 +1.293738424 0.03366373997 0.1296271919 0.1711409595 0.3322390856 0.0259540672 0.03075738541 0.03717115205 +-3.323282098e-18 6.119949547e-05 0.1092261774 0.1257951059 0.1468849065 5.424144095e-18 6.190503094e-07 0.01379672137 +0.02952714861 0.03259432234 + +H atom_index 2 n_descriptor 18 +1.287252312 0.03385414356 0.1269906199 0.1677562123 0.330389213 0.02562685934 0.03038675145 0.03724043175 +-3.309281064e-17 6.059650582e-05 0.1093925739 0.1237622056 0.1440324066 -3.910215539e-18 8.729947511e-07 0.01366431199 +0.0293294145 0.03235576646 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..67e7b659feec98cf62669159b8d79934c56d20e2 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:29 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.102186 SEC) : SETUP UNITCELL + DONE(0.103698 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.121702 SEC) : INIT PLANEWAVE + DONE(0.164916 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444025 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650955e+02 0.000000e+00 2.167e-01 5.432e-01 + GE2 -4.663171e+02 -1.221635e+00 9.680e-02 5.042e-01 + GE3 -4.663190e+02 -1.862435e-03 6.155e-02 5.556e-01 + GE4 -4.663199e+02 -9.246944e-04 2.082e-03 4.345e-01 + GE5 -4.663189e+02 1.007639e-03 8.778e-04 4.335e-01 + GE6 -4.663197e+02 -7.670797e-04 1.667e-04 4.285e-01 + GE7 -4.663194e+02 2.822366e-04 4.393e-05 4.279e-01 + GE8 -4.663194e+02 -6.421973e-05 2.160e-05 4.178e-01 + GE9 -4.663194e+02 2.183954e-05 1.965e-06 4.173e-01 + GE10 -4.663194e+02 -3.804216e-06 4.656e-07 4.150e-01 + GE11 -4.663194e+02 -2.850188e-07 1.353e-07 4.163e-01 + GE12 -4.663194e+02 -6.622982e-08 1.086e-08 3.645e-01 +E_delta_band = -7.33374373e-02 Ry = -9.97807024e-01 eV +E_delta_NN= -1.96172827e-01 Ry = -2.66906825e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.631 11 0.69 1e+02 % + Run_lcao lcao_line 7.6216 1 7.6 1e+02 % + Potential init_pot 0.28106 2 0.14 3.7 % + PW_Basis recip2real 0.27095 17 0.016 3.6 % + PW_Basis gathers_scatterp 0.12132 17 0.0071 1.6 % + Potential v_of_rho 0.84167 14 0.06 11 % + XC_Functional v_xc 0.20493 15 0.014 2.7 % + H_Hartree_pw v_hartree 0.59751 14 0.043 7.8 % + PW_Basis real2recip 0.70339 41 0.017 9.2 % + PW_Basis gatherp_scatters 0.28534 41 0.007 3.7 % + ORB_control set_orb_tables 1.0944 1 1.1 14 % + ORB_gen_tables gen_tables 1.0944 1 1.1 14 % + ORB_table_phi init_Table 0.47642 1 0.48 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.47113 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18301 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18145 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24775 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24583 66 0.0037 3.2 % + LOOP_ions opt_ions 6.0016 1 6 79 % + ESolver_KS_LCAO Run 5.4185 1 5.4 71 % + HSolverLCAO solve 3.1784 12 0.26 42 % + HamiltLCAO updateHk 1.5904 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.5605 12 0.13 20 % + Gint_interface cal_gint 0.59913 25 0.024 7.9 % + Gint_Gamma distri_vl_value 0.90916 12 0.076 12 % + Gint_Gamma distri_vl 2.8081 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.5961 14 0.4 73 % + LCAO_gen_fixedH add_v_delta 2.6803 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.6805 6 0.45 35 % + ElecStateLCAO psiToRho 1.5652 12 0.13 21 % + Charge mix_rho 0.79276 11 0.072 10 % + LOOP_ions force_stress 0.58291 1 0.58 7.6 % + Force_Stress_LCAO getForceStress 0.58289 1 0.58 7.6 % + Force_LCAO_gamma ftable_gamma 0.39035 1 0.39 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.14515 1 0.15 1.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:29 2022 + FINISH Time : Wed Sep 28 11:09:37 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/79/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..05d887231c7f9201052c634faecee8d3d67042d4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.604043 0.136536 0.357977 +H 0.540623 0.117791 0.371331 +H 0.597588 0.198577 0.349303 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..26fa1af7ec8716599cea39ce41085979de904d2d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4072 2 + 2 -12.9689 2 + 3 -9.24277 2 + 4 -6.76802 2 + 5 1.27221 0 + 6 4.5189 0 + 7 11.0551 0 + 8 11.3049 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..77c55d027c55d596416c0cea1300ff74aa6ff933 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:04 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.9132035913 3.82302152919 10.0233430865 0 0 0 0 + tauc_H1 15.1374352462 3.2981495599 10.3972565624 0 0 0 0 + tauc_H2 16.7324548321 5.56016536652 9.78048314799 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.073091085212 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0733841821913 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0897154232163 (SEC) + + DONE : INIT CHARGE Time : 0.131314061398 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.379263 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00177 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000674 + + Density error is 0.215119653734 + + Energy Rydberg eV + E_KohnSham -34.1863907692 -465.129708516 + E_Harris -34.3793314897 -467.754801691 + E_Fermi -0.410258772274 -5.58185695741 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00156888425686 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000871565108519 + + Density error is 0.0978441831752 + + Energy Rydberg eV + E_KohnSham -34.2763046597 -466.353049756 + E_Harris -34.2830770139 -466.445192362 + E_Fermi -0.219437812241 -2.98560460314 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00143024958897 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000838679803406 + + Density error is 0.0626944195809 + + Energy Rydberg eV + E_KohnSham -34.2765464507 -466.356339491 + E_Harris -34.2809214499 -466.415864409 + E_Fermi -0.207619739987 -2.8248114811 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118394165369 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000801607781614 + + Density error is 0.0019880500979 + + Energy Rydberg eV + E_KohnSham -34.2765426061 -466.356287182 + E_Harris -34.2765432811 -466.356296366 + E_Fermi -0.171763954827 -2.33696849666 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118191628216 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803606946586 + + Density error is 0.000874921317806 + + Energy Rydberg eV + E_KohnSham -34.276484249 -466.355493194 + E_Harris -34.2764851669 -466.355505682 + E_Fermi -0.171099536303 -2.32792861888 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117926322859 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803058744164 + + Density error is 0.000111664239096 + + Energy Rydberg eV + E_KohnSham -34.2765186945 -466.355961848 + E_Harris -34.276518703 -466.355961965 + E_Fermi -0.171048783472 -2.32723809119 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117895120202 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803156805494 + + Density error is 4.25482782492e-05 + + Energy Rydberg eV + E_KohnSham -34.2765083202 -466.355820699 + E_Harris -34.2765083307 -466.355820842 + E_Fermi -0.170935624112 -2.32569847911 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117896811892 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803103178665 + + Density error is 1.28647440808e-05 + + Energy Rydberg eV + E_KohnSham -34.276511313 -466.355861418 + E_Harris -34.2765113137 -466.355861427 + E_Fermi -0.170980844666 -2.32631373631 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117893230218 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803108552603 + + Density error is 1.5065766541e-06 + + Energy Rydberg eV + E_KohnSham -34.2765098747 -466.355841849 + E_Harris -34.2765098747 -466.355841849 + E_Fermi -0.170966763308 -2.32612214961 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117892984064 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803108907526 + + Density error is 2.48022105859e-07 + + Energy Rydberg eV + E_KohnSham -34.2765100616 -466.355844392 + E_Harris -34.2765100616 -466.355844392 + E_Fermi -0.170965816611 -2.32610926913 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117892998113 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803109325558 + + Density error is 8.84464371659e-08 + + Energy Rydberg eV + E_KohnSham -34.2765100865 -466.355844731 + E_Harris -34.2765100865 -466.355844731 + E_band -7.99471711989 -108.773706729 + E_one_elec -69.4139234207 -944.424879057 + E_Hartree +36.0933379385 +491.075055803 + E_xc -8.21868276835 -111.820915704 + E_Ewald +7.38683663104 +100.503068377 + E_demet -1.29018514591e-78 -1.75538694594e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195134273531 -2.65493799511 + E_Fermi -0.170965761805 -2.32610852345 + + charge density convergence is achieved + final etot is -466.355844731 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4072 2.00000 + 2 -12.9689 2.00000 + 3 -9.24277 2.00000 + 4 -6.76802 2.00000 + 5 1.27221 0.00000 + 6 4.51890 0.00000 + 7 11.0551 0.00000 + 8 11.3049 0.00000 + + EFERMI = -2.326108523454735 eV + OUT.ABACUS/ final etot is -466.3558447306980 eV + correction force for each atom along direction 1 is -0.000160775 + correction force for each atom along direction 2 is 7.31574e-05 + correction force for each atom along direction 3 is 0.000140009 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0183963 -2.6078962 +0.58262135 + H1 +1.0603393 +0.10001880 -0.19291123 + H2 -0.041942955 +2.5078774 -0.38971012 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3558447306980 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5624 11 0.60 1.0e+02% + Run_lcao lcao_line 6.5551 1 6.6 1.e+02% + Potential init_pot 0.24549 2 0.12 3.7% + PW_Basis recip2real 0.22984 16 0.014 3.5% + PW_Basis gathers_scatterp 0.11096 16 0.0069 1.7% + Potential v_of_rho 0.88591 13 0.068 13.% + XC_Functional v_xc 0.29012 14 0.021 4.4% + H_Hartree_pw v_hartree 0.56436 13 0.043 8.6% + PW_Basis real2recip 0.60964 38 0.016 9.3% + PW_Basis gatherp_scatters 0.27477 38 0.0072 4.2% + ORB_control set_orb_tables 0.90607 1 0.91 14.% + ORB_gen_tables gen_tables 0.90607 1 0.91 14.% + ORB_table_phi init_Table 0.38269 1 0.38 5.8% + ORB_table_phi cal_ST_Phi12_R 0.37837 126 0.0030 5.8% + ORB_table_beta init_Table_Beta 0.15466 1 0.15 2.4% + ORB_table_beta VNL_PhiBeta_R 0.15333 56 0.0027 2.3% + ORB_table_alpha init_Table_Alpha 0.21046 1 0.21 3.2% + ORB_table_alpha S_PhiAlpha_R 0.20876 66 0.0032 3.2% + LOOP_ions opt_ions 5.1922 1 5.2 79.% + ESolver_KS_LCAO Run 4.6393 1 4.6 71.% + HSolverLCAO solve 2.4759 11 0.23 38.% + HamiltLCAO updateHk 1.2778 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2545 11 0.11 19.% + Gint_interface cal_gint 0.58857 23 0.026 9.0% + Gint_Gamma distri_vl_value 0.65225 11 0.059 9.9% + Gint_Gamma distri_vl 2.2259 6 0.37 34.% + LCAO_Deepks cal_projected_DM 4.8250 13 0.37 74.% + LCAO_gen_fixedH add_v_delta 2.0959 6 0.35 32.% + LCAO_DESCRIPTOR add_v_delta 2.0959 6 0.35 32.% + ElecStateLCAO psiToRho 1.1805 11 0.11 18.% + Charge mix_rho 0.75195 10 0.075 11.% + LOOP_ions force_stress 0.55268 1 0.55 8.4% + Force_Stress_LCAO getForceStress 0.55266 1 0.55 8.4% + Force_LCAO_gamma ftable_gamma 0.36158 1 0.36 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.13413 1 0.13 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:04 2022 + Finish Time : Wed Sep 28 11:10:11 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..26c4a9fb671cd983873c1d657338f82f49bea0ad --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124021 ima = 3.66247e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122939332521 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111907421157 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112446564931 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112706401193 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011265637256 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112682265494 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011267788046 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112680952121 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112680406903 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112680340493 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112680332053 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/STRU new file mode 100644 index 0000000000000000000000000000000000000000..41c85383c6f33b2cd8411b2779d3eec31f00e7ed --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.086796408712 3.823021529183 10.023343086484 0 0 0 +H +0.0 +2 +-12.862564753812 3.298149559891 10.397256562380 0 0 0 +-11.267545167967 5.560165366503 9.780483147984 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/conv new file mode 100644 index 0000000000000000000000000000000000000000..a0934d4c925ea9ef460f18b40ef16e90e1d8bb31 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/conv @@ -0,0 +1 @@ +8 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..3b2c250c31dfb59f0322f69e6f26cafd22e68a9a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751373269 0.01269794557 1.26937791 1.369298153 1.469885977 0.008970018932 0.01806680365 0.03911260282 +1.170809011e-18 0.001023642845 0.002737910074 0.01268687555 0.04659032704 -1.469602164e-19 2.307359523e-06 6.525091229e-06 +0.001600619638 0.005981765321 + +H atom_index 1 n_descriptor 18 +1.203231865 0.0360254148 0.09372956923 0.1292826076 0.3040504464 0.02033378371 0.02553223144 0.03934056659 +1.693884352e-18 4.41342085e-05 0.09024931957 0.1107095757 0.1132485283 -4.653834355e-18 6.209087938e-06 0.01415136198 +0.02473389737 0.02844664032 + +H atom_index 2 n_descriptor 18 +1.302327693 0.0328029362 0.1287868432 0.1759240983 0.3359349478 0.0250215942 0.03127891828 0.03667177464 +2.547160703e-18 5.348767586e-05 0.1079618539 0.1243237769 0.1508160269 9.284459892e-18 1.097340445e-06 0.01379958392 +0.02832720358 0.03283755913 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..606a16dbb1c93ddb65e8b23a12d6ad7f0134fb6b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/dm_eig.npy differ diff --git 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@@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:04 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0731084 SEC) : SETUP UNITCELL + DONE(0.0733932 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0897295 SEC) : INIT PLANEWAVE + DONE(0.131417 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.37931 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651297e+02 0.000000e+00 2.151e-01 4.984e-01 + GE2 -4.663530e+02 -1.223341e+00 9.784e-02 4.674e-01 + GE3 -4.663563e+02 -3.289735e-03 6.269e-02 5.324e-01 + GE4 -4.663563e+02 5.230904e-05 1.988e-03 4.060e-01 + GE5 -4.663555e+02 7.939887e-04 8.749e-04 4.029e-01 + GE6 -4.663560e+02 -4.686547e-04 1.117e-04 4.012e-01 + GE7 -4.663558e+02 1.411490e-04 4.255e-05 3.928e-01 + GE8 -4.663559e+02 -4.071866e-05 1.286e-05 3.855e-01 + GE9 -4.663558e+02 1.956863e-05 1.507e-06 3.910e-01 + GE10 -4.663558e+02 -2.542534e-06 2.480e-07 3.888e-01 + GE11 -4.663558e+02 -3.387923e-07 8.845e-08 3.197e-01 +E_delta_band = -7.10558066e-02 Ry = -9.66763845e-01 eV +E_delta_NN= -1.95134274e-01 Ry = -2.65493800e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5624 11 0.6 1e+02 % + Run_lcao lcao_line 6.5551 1 6.6 1e+02 % + Potential init_pot 0.24549 2 0.12 3.7 % + PW_Basis recip2real 0.22984 16 0.014 3.5 % + PW_Basis gathers_scatterp 0.11096 16 0.0069 1.7 % + Potential v_of_rho 0.88591 13 0.068 13 % + XC_Functional v_xc 0.29012 14 0.021 4.4 % + H_Hartree_pw v_hartree 0.56436 13 0.043 8.6 % + PW_Basis real2recip 0.60964 38 0.016 9.3 % + PW_Basis gatherp_scatters 0.27477 38 0.0072 4.2 % + ORB_control set_orb_tables 0.90607 1 0.91 14 % + ORB_gen_tables gen_tables 0.90607 1 0.91 14 % + ORB_table_phi init_Table 0.38269 1 0.38 5.8 % + ORB_table_phi cal_ST_Phi12_R 0.37837 126 0.003 5.8 % + ORB_table_beta init_Table_Beta 0.15466 1 0.15 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.15333 56 0.0027 2.3 % + ORB_table_alpha init_Table_Alpha 0.21046 1 0.21 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.20876 66 0.0032 3.2 % + LOOP_ions opt_ions 5.1922 1 5.2 79 % + ESolver_KS_LCAO Run 4.6393 1 4.6 71 % + HSolverLCAO solve 2.4759 11 0.23 38 % + HamiltLCAO updateHk 1.2778 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2545 11 0.11 19 % + Gint_interface cal_gint 0.58857 23 0.026 9 % + Gint_Gamma distri_vl_value 0.65225 11 0.059 9.9 % + Gint_Gamma distri_vl 2.2259 6 0.37 34 % + LCAO_Deepks cal_projected_DM 4.825 13 0.37 74 % + LCAO_gen_fixedH add_v_delta 2.0959 6 0.35 32 % + LCAO_DESCRIPTOR add_v_delta 2.0959 6 0.35 32 % + ElecStateLCAO psiToRho 1.1805 11 0.11 18 % + Charge mix_rho 0.75195 10 0.075 11 % + LOOP_ions force_stress 0.55268 1 0.55 8.4 % + Force_Stress_LCAO getForceStress 0.55266 1 0.55 8.4 % + Force_LCAO_gamma ftable_gamma 0.36158 1 0.36 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.13413 1 0.13 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:04 2022 + FINISH Time : Wed Sep 28 11:10:11 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/8/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3945dd1f9124311316a79d3c95724cbf5f3e2534 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.117549 0.622174 0.368142 +H 0.116294 0.56059 0.389096 +H 0.184151 0.636077 0.361303 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..09d6e79599cb0f0f7a984a5263a1d5f83084e0ff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0958 2 + 2 -12.8706 2 + 3 -9.08706 2 + 4 -6.70038 2 + 5 1.09502 0 + 6 4.14634 0 + 7 11.1217 0 + 8 11.3672 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e40d22d586aba9f2e925e84fe70300f901c1d78b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:58 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.29135980921 17.4208748678 10.3079897387 0 0 0 0 + tauc_H1 3.25622188031 15.6965247104 10.8946760082 0 0 0 0 + tauc_H2 5.15621654702 17.8101611525 10.1164835332 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870759617645 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.087439836052 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105538910331 (SEC) + + DONE : INIT CHARGE Time : 0.154152995806 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.435976 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00054 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00168 + + Density error is 0.212702246937 + + Energy Rydberg eV + E_KohnSham -34.190201237 -465.181552589 + E_Harris -34.3773086468 -467.727279501 + E_Fermi -0.393576667683 -5.35488528034 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000805839240954 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132142270096 + + Density error is 0.098590242759 + + Energy Rydberg eV + E_KohnSham -34.2786666339 -466.385186064 + E_Harris -34.2856325941 -466.479962814 + E_Fermi -0.203957930483 -2.77499000686 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000776359476826 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121723830502 + + Density error is 0.0634506540776 + + Energy Rydberg eV + E_KohnSham -34.2789919328 -466.389611982 + E_Harris -34.2834780261 -466.450648412 + E_Fermi -0.195511751224 -2.66007384261 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000743569964248 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102249757669 + + Density error is 0.00198921327266 + + Energy Rydberg eV + E_KohnSham -34.2789265807 -466.388722821 + E_Harris -34.2789286247 -466.388750631 + E_Fermi -0.160152972485 -2.17899297744 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000743110574754 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102097577117 + + Density error is 0.000892375632167 + + Energy Rydberg eV + E_KohnSham -34.2788879253 -466.388196887 + E_Harris -34.2788883633 -466.388202846 + E_Fermi -0.159890836072 -2.17542642856 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000742660363088 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010183634809 + + Density error is 0.000165870955941 + + Energy Rydberg eV + E_KohnSham -34.2789061083 -466.38844428 + E_Harris -34.2789061081 -466.388444278 + E_Fermi -0.159579921215 -2.17119621492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000742791857099 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101822752866 + + Density error is 2.99785193033e-05 + + Energy Rydberg eV + E_KohnSham -34.2789009445 -466.388374023 + E_Harris -34.2789009479 -466.388374069 + E_Fermi -0.159512214698 -2.1702750205 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000742730254673 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101820024194 + + Density error is 1.39685748262e-05 + + Energy Rydberg eV + E_KohnSham -34.2789036863 -466.388411327 + E_Harris -34.2789036872 -466.388411339 + E_Fermi -0.159534407424 -2.17057696801 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00074273549984 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101817946987 + + Density error is 1.51207820872e-06 + + Energy Rydberg eV + E_KohnSham -34.2789025413 -466.388395748 + E_Harris -34.2789025413 -466.388395749 + E_Fermi -0.15952018116 -2.17038340977 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000742737715971 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101817606847 + + Density error is 2.75843574341e-07 + + Energy Rydberg eV + E_KohnSham -34.2789027749 -466.388398926 + E_Harris -34.2789027749 -466.388398926 + E_Fermi -0.15951908762 -2.17036853139 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000742738235096 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001018176118 + + Density error is 5.28420639748e-08 + + Energy Rydberg eV + E_KohnSham -34.2789027921 -466.38839916 + E_Harris -34.2789027921 -466.38839916 + E_band -7.90167857328 -107.507852361 + E_one_elec -68.878441788 -937.139277678 + E_Hartree +35.8456602193 +487.705227554 + E_xc -8.17858011658 -111.275291135 + E_Ewald +7.05762275945 +96.0238838631 + E_demet -3.25954342318e-65 -4.43483634337e-64 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194093380633 -2.64077592069 + E_Fermi -0.159518961237 -2.17036681187 + + charge density convergence is achieved + final etot is -466.38839916 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0958 2.00000 + 2 -12.8706 2.00000 + 3 -9.08706 2.00000 + 4 -6.70038 2.00000 + 5 1.09502 0.00000 + 6 4.14634 0.00000 + 7 11.1217 0.00000 + 8 11.3672 0.00000 + + EFERMI = -2.170366811871121 eV + OUT.ABACUS/ final etot is -466.3883991600869 eV + correction force for each atom along direction 1 is 5.02152e-05 + correction force for each atom along direction 2 is -3.29110e-05 + correction force for each atom along direction 3 is -9.05542e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.5673717 +0.96342903 -0.38196021 + H1 +0.027845626 -0.59343629 +0.20307800 + H2 -1.5952173 -0.36999274 +0.17888221 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3883991600869 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7712 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7619 1 6.8 1.e+02% + Potential init_pot 0.28585 2 0.14 4.2% + PW_Basis recip2real 0.26639 16 0.017 3.9% + PW_Basis gathers_scatterp 0.12401 16 0.0078 1.8% + Potential v_of_rho 0.86628 13 0.067 13.% + XC_Functional v_xc 0.25741 14 0.018 3.8% + H_Hartree_pw v_hartree 0.57616 13 0.044 8.5% + PW_Basis real2recip 0.56301 38 0.015 8.3% + PW_Basis gatherp_scatters 0.23574 38 0.0062 3.5% + ORB_control set_orb_tables 1.0997 1 1.1 16.% + ORB_gen_tables gen_tables 1.0997 1 1.1 16.% + ORB_table_phi init_Table 0.48175 1 0.48 7.1% + ORB_table_phi cal_ST_Phi12_R 0.47677 126 0.0038 7.0% + ORB_table_beta init_Table_Beta 0.18880 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18734 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25029 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.24841 66 0.0038 3.7% + LOOP_ions opt_ions 5.1487 1 5.1 76.% + ESolver_KS_LCAO Run 4.5623 1 4.6 67.% + HSolverLCAO solve 2.5953 11 0.24 38.% + HamiltLCAO updateHk 1.3290 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3004 11 0.12 19.% + Gint_interface cal_gint 0.47354 23 0.021 7.0% + Gint_Gamma distri_vl_value 0.74283 11 0.068 11.% + Gint_Gamma distri_vl 2.1792 6 0.36 32.% + LCAO_Deepks cal_projected_DM 4.7393 13 0.36 70.% + LCAO_gen_fixedH add_v_delta 2.0483 6 0.34 30.% + LCAO_DESCRIPTOR add_v_delta 2.0484 6 0.34 30.% + ElecStateLCAO psiToRho 1.2496 11 0.11 18.% + Charge mix_rho 0.65261 10 0.065 9.6% + LOOP_ions force_stress 0.58627 1 0.59 8.7% + Force_Stress_LCAO getForceStress 0.58624 1 0.59 8.7% + Force_LCAO_gamma ftable_gamma 0.37387 1 0.37 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.13302 1 0.13 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:58 2022 + Finish Time : Wed Sep 28 11:09:05 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..08799edc3fa0bac58f778581331ee99ad8a3147d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012354 ima = 3.66646e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123411702279 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112204596355 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112877399257 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113085595165 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113062588798 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113075609188 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113071369394 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113073601955 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113072934558 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113072881695 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113072867772 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ef3eff0f46d335ce05ae54bf8e61c11956cd53e4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.708640190813 17.420874867746 10.307989738667 0 0 0 +H +0.0 +2 +-24.743778119688 15.696524710426 10.894676008207 0 0 0 +-22.843783452964 17.810161152470 10.116483533168 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/conv new file mode 100644 index 0000000000000000000000000000000000000000..cbb515072402d73ee68d91d7d6513e65c327a638 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/conv @@ -0,0 +1 @@ +80 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..fd7d3a0ca9cd48282d9d252b79cf4e9584dddb7d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749588597 0.01250453648 1.252813268 1.35113751 1.468521497 0.008431009337 0.01822731083 0.03906985309 +7.423043156e-18 0.0009556315417 0.002471148461 0.01176364428 0.04289975539 -1.24301204e-19 1.735987671e-06 5.317503118e-06 +0.001625532597 0.005868658351 + +H atom_index 1 n_descriptor 18 +1.25501187 0.03408896595 0.1094816881 0.1525742882 0.3232520923 0.02227065453 0.02863464279 0.03733288331 +-5.824573519e-18 4.234829465e-05 0.1010790784 0.1154517514 0.1308459983 5.680604289e-19 3.735544223e-06 0.01310818765 +0.02602735266 0.03098774417 + +H atom_index 2 n_descriptor 18 +1.181627088 0.03649424012 0.0863023345 0.1211458359 0.297204769 0.01888935766 0.02434797888 0.04010519865 +1.301599191e-17 3.607046523e-05 0.08217578103 0.1033685781 0.1126860435 3.704656644e-18 6.635691651e-06 0.01467108982 +0.02309162689 0.02730246237 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d4a8acf75128911777df3183899d09ebe3986da9 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..e9c71dee5a17002027180d078156911bbee0f0b6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..441a1b6cffce2aa78174480ea314b7c7c8b8ddee Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..d35586aacb6823b81530b8599cc017ee0fbbf3f0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..b8a0873c4bdc77681386b3a5a2b74df69c177273 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:58 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871009 SEC) : SETUP UNITCELL + DONE(0.0874541 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.10556 SEC) : INIT PLANEWAVE + DONE(0.154272 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.436035 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651816e+02 0.000000e+00 2.127e-01 5.297e-01 + GE2 -4.663852e+02 -1.203633e+00 9.859e-02 4.534e-01 + GE3 -4.663896e+02 -4.425919e-03 6.345e-02 5.079e-01 + GE4 -4.663887e+02 8.891613e-04 1.989e-03 4.024e-01 + GE5 -4.663882e+02 5.259338e-04 8.924e-04 3.970e-01 + GE6 -4.663884e+02 -2.473924e-04 1.659e-04 3.930e-01 + GE7 -4.663884e+02 7.025715e-05 2.998e-05 3.736e-01 + GE8 -4.663884e+02 -3.730384e-05 1.397e-05 3.796e-01 + GE9 -4.663884e+02 1.557808e-05 1.512e-06 3.743e-01 + GE10 -4.663884e+02 -3.178006e-06 2.758e-07 3.743e-01 + GE11 -4.663884e+02 -2.336353e-07 5.284e-08 3.164e-01 +E_delta_band = -6.89295144e-02 Ry = -9.37834156e-01 eV +E_delta_NN= -1.94093381e-01 Ry = -2.64077592e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7712 11 0.62 1e+02 % + Run_lcao lcao_line 6.7619 1 6.8 1e+02 % + Potential init_pot 0.28585 2 0.14 4.2 % + PW_Basis recip2real 0.26639 16 0.017 3.9 % + PW_Basis gathers_scatterp 0.12401 16 0.0078 1.8 % + Potential v_of_rho 0.86628 13 0.067 13 % + XC_Functional v_xc 0.25741 14 0.018 3.8 % + H_Hartree_pw v_hartree 0.57616 13 0.044 8.5 % + PW_Basis real2recip 0.56301 38 0.015 8.3 % + PW_Basis gatherp_scatters 0.23574 38 0.0062 3.5 % + ORB_control set_orb_tables 1.0997 1 1.1 16 % + ORB_gen_tables gen_tables 1.0997 1 1.1 16 % + ORB_table_phi init_Table 0.48175 1 0.48 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.47677 126 0.0038 7 % + ORB_table_beta init_Table_Beta 0.1888 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18734 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25029 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.24841 66 0.0038 3.7 % + LOOP_ions opt_ions 5.1487 1 5.1 76 % + ESolver_KS_LCAO Run 4.5623 1 4.6 67 % + HSolverLCAO solve 2.5953 11 0.24 38 % + HamiltLCAO updateHk 1.329 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3004 11 0.12 19 % + Gint_interface cal_gint 0.47354 23 0.021 7 % + Gint_Gamma distri_vl_value 0.74283 11 0.068 11 % + Gint_Gamma distri_vl 2.1792 6 0.36 32 % + LCAO_Deepks cal_projected_DM 4.7393 13 0.36 70 % + LCAO_gen_fixedH add_v_delta 2.0483 6 0.34 30 % + LCAO_DESCRIPTOR add_v_delta 2.0484 6 0.34 30 % + ElecStateLCAO psiToRho 1.2496 11 0.11 18 % + Charge mix_rho 0.65261 10 0.065 9.6 % + LOOP_ions force_stress 0.58627 1 0.59 8.7 % + Force_Stress_LCAO getForceStress 0.58624 1 0.59 8.7 % + Force_LCAO_gamma ftable_gamma 0.37387 1 0.37 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.13302 1 0.13 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:58 2022 + FINISH Time : Wed Sep 28 11:09:05 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/80/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9eb0f19c92b1c70d8be347a17d38fa4521e3b445 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.129014 0.616748 0.386793 +H 0.131482 0.560602 0.424335 +H 0.154367 0.595176 0.332745 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1909acaf49679a4a9de64c12da7c6385745fe844 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3851 2 + 2 -12.8412 2 + 3 -9.32151 2 + 4 -6.76428 2 + 5 1.22742 0 + 6 4.42899 0 + 7 11.066 0 + 8 11.3261 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ec976674404cedd86892b5c9e8aa9623dcfe6ea4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:10 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.61238423577 17.2689342608 10.8302131557 0 0 0 0 + tauc_H1 3.6815060544 15.6968678675 11.8813883524 0 0 0 0 + tauc_H2 4.32226804643 16.6649320736 9.31685757126 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.08663072274 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0878461897485 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105947885548 (SEC) + + DONE : INIT CHARGE Time : 0.149155933992 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.431384 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000718 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115 + + Density error is 0.213957237733 + + Energy Rydberg eV + E_KohnSham -34.1879381947 -465.15076232 + E_Harris -34.3783400396 -467.741312321 + E_Fermi -0.406732045394 -5.53387337655 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000948782361097 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138751010497 + + Density error is 0.0977252339632 + + Energy Rydberg eV + E_KohnSham -34.2768429529 -466.360373611 + E_Harris -34.2836614091 -466.453143467 + E_Fermi -0.217137784306 -2.95431111765 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000905058592114 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131794268993 + + Density error is 0.0626565733277 + + Energy Rydberg eV + E_KohnSham -34.2771006454 -466.363879698 + E_Harris -34.2815090922 -466.423859692 + E_Fermi -0.205924556953 -2.80174733268 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000850901918298 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122106418963 + + Density error is 0.001953427441 + + Energy Rydberg eV + E_KohnSham -34.2770831272 -466.36364135 + E_Harris -34.277083807 -466.363650598 + E_Fermi -0.170112133013 -2.31449430791 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000854232892753 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122523502036 + + Density error is 0.00083032268637 + + Energy Rydberg eV + E_KohnSham -34.2770306477 -466.36292733 + E_Harris -34.2770317012 -466.362941662 + E_Fermi -0.169521606976 -2.30645978899 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000853054572075 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122331509038 + + Density error is 0.000138277722777 + + Energy Rydberg eV + E_KohnSham -34.2770650011 -466.363394732 + E_Harris -34.2770650383 -466.363395237 + E_Fermi -0.169460367299 -2.30562658044 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00085311391425 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122332919611 + + Density error is 3.68614773129e-05 + + Energy Rydberg eV + E_KohnSham -34.2770525889 -466.363225854 + E_Harris -34.2770525948 -466.363225935 + E_Fermi -0.169365700585 -2.30433857372 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00085307841912 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012232618716 + + Density error is 1.8327316709e-05 + + Energy Rydberg eV + E_KohnSham -34.277056234 -466.363275449 + E_Harris -34.2770562355 -466.363275469 + E_Fermi -0.169399839038 -2.3048030512 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000853087353636 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122326689233 + + Density error is 2.84547773217e-06 + + Energy Rydberg eV + E_KohnSham -34.2770547739 -466.363255583 + E_Harris -34.2770547739 -466.363255583 + E_Fermi -0.169382473043 -2.30456677471 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000853087223725 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012232652349 + + Density error is 1.08864311807e-07 + + Energy Rydberg eV + E_KohnSham -34.2770550271 -466.363259028 + E_Harris -34.2770550271 -466.363259028 + E_Fermi -0.16937931546 -2.3045238136 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000853087536862 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122326578687 + + Density error is 5.27886105292e-08 + + Energy Rydberg eV + E_KohnSham -34.2770550863 -466.363259833 + E_Harris -34.2770550863 -466.363259833 + E_band -7.98373651799 -108.624307975 + E_one_elec -69.3120679104 -943.039063744 + E_Hartree +36.0423894532 +490.381866099 + E_xc -8.21033743853 -111.707371667 + E_Ewald +7.32722956758 +99.6920726731 + E_demet -7.69880281871e-76 -1.04747586113e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194948538936 -2.6524109463 + E_Fermi -0.169379355192 -2.30452435418 + + charge density convergence is achieved + final etot is -466.363259833 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3851 2.00000 + 2 -12.8412 2.00000 + 3 -9.32151 2.00000 + 4 -6.76428 2.00000 + 5 1.22742 0.00000 + 6 4.42899 0.00000 + 7 11.0660 0.00000 + 8 11.3261 0.00000 + + EFERMI = -2.304524354178242 eV + OUT.ABACUS/ final etot is -466.3632598329944 eV + correction force for each atom along direction 1 is 7.61613e-05 + correction force for each atom along direction 2 is -6.16475e-05 + correction force for each atom along direction 3 is -3.12448e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.62447480 -0.65193509 +2.2745326 + H1 -0.17331494 +1.0534254 -0.35155454 + H2 +0.79778973 -0.40149032 -1.9229781 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3632598329944 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4099 11 0.67 1.0e+02% + Run_lcao lcao_line 7.4010 1 7.4 1.e+02% + Potential init_pot 0.28387 2 0.14 3.8% + PW_Basis recip2real 0.24955 16 0.016 3.4% + PW_Basis gathers_scatterp 0.11119 16 0.0069 1.5% + Potential v_of_rho 0.78369 13 0.060 11.% + XC_Functional v_xc 0.19395 14 0.014 2.6% + H_Hartree_pw v_hartree 0.55200 13 0.042 7.4% + PW_Basis real2recip 0.65052 38 0.017 8.8% + PW_Basis gatherp_scatters 0.26600 38 0.0070 3.6% + ORB_control set_orb_tables 1.1062 1 1.1 15.% + ORB_gen_tables gen_tables 1.1061 1 1.1 15.% + ORB_table_phi init_Table 0.48046 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47517 126 0.0038 6.4% + ORB_table_beta init_Table_Beta 0.18582 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18428 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.25088 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24886 66 0.0038 3.4% + LOOP_ions opt_ions 5.7873 1 5.8 78.% + ESolver_KS_LCAO Run 5.1843 1 5.2 70.% + HSolverLCAO solve 3.1299 11 0.28 42.% + HamiltLCAO updateHk 1.5744 11 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.5466 11 0.14 21.% + Gint_interface cal_gint 0.57273 23 0.025 7.7% + Gint_Gamma distri_vl_value 0.90696 11 0.082 12.% + Gint_Gamma distri_vl 2.4725 6 0.41 33.% + LCAO_Deepks cal_projected_DM 5.3547 13 0.41 72.% + LCAO_gen_fixedH add_v_delta 2.3446 6 0.39 32.% + LCAO_DESCRIPTOR add_v_delta 2.3448 6 0.39 32.% + ElecStateLCAO psiToRho 1.5341 11 0.14 21.% + Charge mix_rho 0.71776 10 0.072 9.7% + LOOP_ions force_stress 0.60278 1 0.60 8.1% + Force_Stress_LCAO getForceStress 0.60276 1 0.60 8.1% + Force_LCAO_gamma ftable_gamma 0.41005 1 0.41 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.14408 1 0.14 1.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:10 2022 + Finish Time : Wed Sep 28 11:10:17 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..99b2675387caeec114d202e7f5c292f42f5c5cde --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124063 ima = 3.68546e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8.00000000000001 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122772195494 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011169246518 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011226346201 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112510802649 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112464181125 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011249240663 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112486249463 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112489089216 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112488263514 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112488120636 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112488117988 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/STRU new file mode 100644 index 0000000000000000000000000000000000000000..76c063cf8a291cdad4fd91c2dbfa987f792fa740 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.387615764223 17.268934260817 10.830213155695 0 0 0 +H +0.0 +2 +-24.318493945586 15.696867867494 11.881388352437 0 0 0 +-23.677731953567 16.664932073640 9.316857571263 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/conv new file mode 100644 index 0000000000000000000000000000000000000000..576344dc95b9b89b4b02889106cb4444879b6ac6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/conv @@ -0,0 +1 @@ +81 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c0576b8f33d9089adc228cedceb373622f19527b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752685778 0.01270705639 1.265532608 1.362183869 1.469715801 0.009184998796 0.01746617295 0.03914364617 +1.774832449e-18 0.0009612357953 0.002769294435 0.01279359131 0.04648151662 1.565370912e-19 2.448179722e-06 6.798334088e-06 +0.001585587364 0.006042313744 + +H atom_index 1 n_descriptor 18 +1.201913931 0.03623045834 0.09386859643 0.1286178738 0.3031031228 0.02045288504 0.02542963189 0.03957021239 +1.404236719e-17 4.431490119e-05 0.08995149626 0.1100541731 0.1132107139 2.383515972e-18 5.995083785e-06 0.01426161734 +0.02475493545 0.02835217059 + +H atom_index 2 n_descriptor 18 +1.292381509 0.03327621051 0.1255283869 0.1705604606 0.3330387931 0.02481607236 0.03070413204 0.03687876594 +-1.221209567e-17 5.282847017e-05 0.1078529035 0.1217432622 0.1462318657 -4.35432322e-18 1.311885583e-06 0.0135798083 +0.02810859442 0.03248908961 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a5baf3669b6a4b3074797393b987ecfde7048e67 Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..5747645542eacf055157ab957469a39a7b04280f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:10 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0866538 SEC) : SETUP UNITCELL + DONE(0.0878629 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.10597 SEC) : INIT PLANEWAVE + DONE(0.149306 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.431452 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651508e+02 0.000000e+00 2.140e-01 5.600e-01 + GE2 -4.663604e+02 -1.209611e+00 9.773e-02 5.242e-01 + GE3 -4.663639e+02 -3.506086e-03 6.266e-02 5.720e-01 + GE4 -4.663636e+02 2.383478e-04 1.953e-03 4.498e-01 + GE5 -4.663629e+02 7.140202e-04 8.303e-04 4.501e-01 + GE6 -4.663634e+02 -4.674025e-04 1.383e-04 4.472e-01 + GE7 -4.663632e+02 1.688778e-04 3.686e-05 4.378e-01 + GE8 -4.663633e+02 -4.959458e-05 1.833e-05 4.352e-01 + GE9 -4.663633e+02 1.986580e-05 2.845e-06 4.337e-01 + GE10 -4.663633e+02 -3.444606e-06 1.089e-07 4.325e-01 + GE11 -4.663633e+02 -8.054377e-07 5.279e-08 3.811e-01 +E_delta_band = -7.06797808e-02 Ry = -9.61647753e-01 eV +E_delta_NN= -1.94948539e-01 Ry = -2.65241095e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4099 11 0.67 1e+02 % + Run_lcao lcao_line 7.401 1 7.4 1e+02 % + Potential init_pot 0.28387 2 0.14 3.8 % + PW_Basis recip2real 0.24955 16 0.016 3.4 % + PW_Basis gathers_scatterp 0.11119 16 0.0069 1.5 % + Potential v_of_rho 0.78369 13 0.06 11 % + XC_Functional v_xc 0.19395 14 0.014 2.6 % + H_Hartree_pw v_hartree 0.552 13 0.042 7.4 % + PW_Basis real2recip 0.65052 38 0.017 8.8 % + PW_Basis gatherp_scatters 0.266 38 0.007 3.6 % + ORB_control set_orb_tables 1.1062 1 1.1 15 % + ORB_gen_tables gen_tables 1.1061 1 1.1 15 % + ORB_table_phi init_Table 0.48046 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.47517 126 0.0038 6.4 % + ORB_table_beta init_Table_Beta 0.18582 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18428 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.25088 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24886 66 0.0038 3.4 % + LOOP_ions opt_ions 5.7873 1 5.8 78 % + ESolver_KS_LCAO Run 5.1843 1 5.2 70 % + HSolverLCAO solve 3.1299 11 0.28 42 % + HamiltLCAO updateHk 1.5744 11 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.5466 11 0.14 21 % + Gint_interface cal_gint 0.57273 23 0.025 7.7 % + Gint_Gamma distri_vl_value 0.90696 11 0.082 12 % + Gint_Gamma distri_vl 2.4725 6 0.41 33 % + LCAO_Deepks cal_projected_DM 5.3547 13 0.41 72 % + LCAO_gen_fixedH add_v_delta 2.3446 6 0.39 32 % + LCAO_DESCRIPTOR add_v_delta 2.3448 6 0.39 32 % + ElecStateLCAO psiToRho 1.5341 11 0.14 21 % + Charge mix_rho 0.71776 10 0.072 9.7 % + LOOP_ions force_stress 0.60278 1 0.6 8.1 % + Force_Stress_LCAO getForceStress 0.60276 1 0.6 8.1 % + Force_LCAO_gamma ftable_gamma 0.41005 1 0.41 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.14408 1 0.14 1.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:10 2022 + FINISH Time : Wed Sep 28 11:10:17 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/81/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..40acc6ff54077b83613b9a0e85d4e641c3df391b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.129513 0.607687 0.385619 +H 0.117415 0.558468 0.424096 +H 0.10494 0.585609 0.327312 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ff07d4bd9d5ad251238374ff828d2b16c95393aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3828 2 + 2 -12.9459 2 + 3 -9.2499 2 + 4 -6.76425 2 + 5 1.28256 0 + 6 4.47397 0 + 7 11.0613 0 + 8 11.3183 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9675bcf2138c508afc3b2bddb3390bb0697e4b34 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/running_scf.log @@ -0,0 +1,780 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:37 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.62636334568 17.0152401704 10.7973187066 0 0 0 0 + tauc_H1 3.28762702885 15.6371167489 11.8746989108 0 0 0 0 + tauc_H2 2.93832222585 16.3970394958 9.16474318079 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0855683668635 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0923585308152 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.110552543871 (SEC) + + DONE : INIT CHARGE Time : 0.159327151181 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438943 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000615 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000945 + + Density error is 0.214685349767 + + Energy Rydberg eV + E_KohnSham -34.1888129137 -465.162663482 + E_Harris -34.3805210137 -467.770985995 + E_Fermi -0.408065039522 -5.55200969209 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000871165290512 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121232706577 + + Density error is 0.097776682263 + + Energy Rydberg eV + E_KohnSham -34.2782476083 -466.379484927 + E_Harris -34.2850213894 -466.471646948 + E_Fermi -0.217768471783 -2.962892061 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000835807832386 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116078575381 + + Density error is 0.0626436809022 + + Energy Rydberg eV + E_KohnSham -34.2785150139 -466.383123168 + E_Harris -34.2828931885 -466.442691289 + E_Fermi -0.206223458988 -2.8058141035 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000795826173291 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109498493333 + + Density error is 0.00196921012107 + + Energy Rydberg eV + E_KohnSham -34.2785061128 -466.383002061 + E_Harris -34.2785070222 -466.383014434 + E_Fermi -0.170465942224 -2.31930812918 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000797330031495 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109675737711 + + Density error is 0.000863397706033 + + Energy Rydberg eV + E_KohnSham -34.278447904 -466.382210091 + E_Harris -34.2784490558 -466.382225761 + E_Fermi -0.169780397008 -2.30998080801 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000796565288789 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109557578467 + + Density error is 0.000122507906592 + + Energy Rydberg eV + E_KohnSham -34.2784850009 -466.38271482 + E_Harris -34.278485025 -466.382715148 + E_Fermi -0.169763415428 -2.30974976176 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000796748824173 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109575268408 + + Density error is 4.08173971151e-05 + + Energy Rydberg eV + E_KohnSham -34.2784724001 -466.382543378 + E_Harris -34.2784724092 -466.382543501 + E_Fermi -0.16965104001 -2.30822081576 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000796671187836 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109564877213 + + Density error is 1.34778744835e-05 + + Energy Rydberg eV + E_KohnSham -34.2784758381 -466.382590154 + E_Harris -34.2784758388 -466.382590163 + E_Fermi -0.169692847459 -2.30878963529 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000796672555252 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109564460553 + + Density error is 2.23338851556e-06 + + Energy Rydberg eV + E_KohnSham -34.2784744872 -466.382571774 + E_Harris -34.2784744873 -466.382571774 + E_Fermi -0.169679131446 -2.30860301935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000796675993461 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109564822756 + + Density error is 1.65265960621e-07 + + Energy Rydberg eV + E_KohnSham -34.2784746287 -466.382573698 + E_Harris -34.2784746287 -466.382573698 + E_Fermi -0.169676947786 -2.30857330913 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000796676184263 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109564858041 + + Density error is 8.44687074069e-08 + + Energy Rydberg eV + E_KohnSham -34.278474674 -466.382574315 + E_Harris -34.278474674 -466.382574315 + E_band -7.98824107914 -108.685595674 + E_one_elec -69.371375066 -943.845978993 + E_Hartree +36.0729801812 +490.798074306 + E_xc -8.21516928325 -111.773112287 + E_Ewald +7.35924723682 +100.127695412 + E_demet -2.59206547024e-78 -3.52668599843e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19502350514 -2.65343091384 + E_Fermi -0.169676983553 -2.30857379578 + + charge density convergence is achieved + final etot is -466.382574315 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3828 2.00000 + 2 -12.9459 2.00000 + 3 -9.24990 2.00000 + 4 -6.76425 2.00000 + 5 1.28256 0.00000 + 6 4.47397 0.00000 + 7 11.0613 0.00000 + 8 11.3183 0.00000 + + EFERMI = -2.308573795776408 eV + OUT.ABACUS/ final etot is -466.3825743152930 eV + correction force for each atom along direction 1 is -1.48286e-05 + correction force for each atom along direction 2 is -2.83617e-05 + correction force for each atom along direction 3 is -6.26458e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.068754502 +0.92324674 -1.8924631 + H1 -0.26771319 -1.3584223 +1.3244281 + H2 +0.33646769 +0.43517561 +0.56803497 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3825743152930 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6288 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6199 1 6.6 1.e+02% + Potential init_pot 0.28453 2 0.14 4.3% + PW_Basis recip2real 0.26094 16 0.016 3.9% + PW_Basis gathers_scatterp 0.11833 16 0.0074 1.8% + Charge atomic_rho 0.10010 1 0.10 1.5% + Potential v_of_rho 0.86977 13 0.067 13.% + XC_Functional v_xc 0.24698 14 0.018 3.7% + H_Hartree_pw v_hartree 0.58676 13 0.045 8.9% + PW_Basis real2recip 0.58450 38 0.015 8.8% + PW_Basis gatherp_scatters 0.25206 38 0.0066 3.8% + ORB_control set_orb_tables 1.1103 1 1.1 17.% + ORB_gen_tables gen_tables 1.1103 1 1.1 17.% + ORB_table_phi init_Table 0.48357 1 0.48 7.3% + ORB_table_phi cal_ST_Phi12_R 0.47866 126 0.0038 7.2% + ORB_table_beta init_Table_Beta 0.19057 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18906 56 0.0034 2.9% + ORB_table_alpha init_Table_Alpha 0.25748 1 0.26 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25560 66 0.0039 3.9% + LOOP_ions opt_ions 4.9930 1 5.0 75.% + ESolver_KS_LCAO Run 4.4246 1 4.4 67.% + HSolverLCAO solve 2.4412 11 0.22 37.% + HamiltLCAO updateHk 1.2588 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2236 11 0.11 18.% + Gint_interface cal_gint 0.45902 23 0.020 6.9% + Gint_Gamma distri_vl_value 0.67575 11 0.061 10.% + Gint_Gamma distri_vl 2.1235 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.5974 13 0.35 69.% + LCAO_gen_fixedH add_v_delta 1.9906 6 0.33 30.% + LCAO_DESCRIPTOR add_v_delta 1.9906 6 0.33 30.% + ElecStateLCAO psiToRho 1.1646 11 0.11 18.% + Charge mix_rho 0.66002 10 0.066 10.% + LOOP_ions force_stress 0.56830 1 0.57 8.6% + Force_Stress_LCAO getForceStress 0.56827 1 0.57 8.6% + Force_LCAO_gamma ftable_gamma 0.36198 1 0.36 5.5% + Force_LCAO_gamma cal_fvl_dphi 0.12961 1 0.13 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:37 2022 + Finish Time : Wed Sep 28 11:05:44 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3d32bf4536fae4a19b7693098c4eb3d449503e2c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124046 ima = 3.65698e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122864453421 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111807569296 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112354346841 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112606388479 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112555062125 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011258448608 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112578790672 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112581715965 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112581227342 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112581116518 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011258111302 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/STRU new file mode 100644 index 0000000000000000000000000000000000000000..352f658de8d95c1f9b05d0655a5a4a13d136e27a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.373636654300 17.015240170388 10.797318706651 0 0 0 +H +0.0 +2 +-24.712372971173 15.637116748875 11.874698910740 0 0 0 +-25.061677774149 16.397039495739 9.164743180774 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/conv new file mode 100644 index 0000000000000000000000000000000000000000..f7b72241ec48e93af4278bf56122eac9d1944468 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/conv @@ -0,0 +1 @@ +82 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e07b9d1f351cba0f777838b16c8bdfc86b63a131 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751412808 0.01271851025 1.270837133 1.364548531 1.469717831 0.008947473501 0.01792977436 0.0390987287 +2.680776183e-18 0.001011790272 0.002726852972 0.01271423051 0.04635719301 1.609743247e-19 2.334991303e-06 6.54463835e-06 +0.001606459102 0.006019084877 + +H atom_index 1 n_descriptor 18 +1.288013535 0.03324310719 0.1231650144 0.1683604081 0.3319978353 0.02438345819 0.03046794568 0.0367795252 +-3.236192928e-18 5.201364184e-05 0.1077985829 0.1204345689 0.1444331632 8.208193619e-18 1.739532436e-06 0.01345113878 +0.02789068757 0.03233127961 + +H atom_index 2 n_descriptor 18 +1.213415611 0.03572211806 0.09695957506 0.1334990507 0.3077503567 0.02083686001 0.02612626453 0.03895309563 +1.226637948e-17 4.494979681e-05 0.09287308183 0.1136672755 0.114394145 -2.517153745e-18 5.727249947e-06 0.01388960432 +0.0251517473 0.02897155178 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..7af942c0e3054b7ead5cde81485bf36d12bd2a89 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..8d51c381e9991e76bd658ac9e3f4c62018761285 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..55f2ccaf65ed2a28131a54e7d1068066a77a07fb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..35a4ba5935960ed3b3393dfb4c3e8fb13f2b27b8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:37 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0855903 SEC) : SETUP UNITCELL + DONE(0.0923773 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.110573 SEC) : INIT PLANEWAVE + DONE(0.159455 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.439006 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651627e+02 0.000000e+00 2.147e-01 5.175e-01 + GE2 -4.663795e+02 -1.216821e+00 9.778e-02 4.425e-01 + GE3 -4.663831e+02 -3.638241e-03 6.264e-02 4.940e-01 + GE4 -4.663830e+02 1.211064e-04 1.969e-03 3.844e-01 + GE5 -4.663822e+02 7.919706e-04 8.634e-04 3.836e-01 + GE6 -4.663827e+02 -5.047290e-04 1.225e-04 3.752e-01 + GE7 -4.663825e+02 1.714422e-04 4.082e-05 3.706e-01 + GE8 -4.663826e+02 -4.677611e-05 1.348e-05 3.621e-01 + GE9 -4.663826e+02 1.837960e-05 2.233e-06 3.610e-01 + GE10 -4.663826e+02 -1.924194e-06 1.653e-07 3.657e-01 + GE11 -4.663826e+02 -6.169591e-07 8.447e-08 3.057e-01 +E_delta_band = -7.08657623e-02 Ry = -9.64178161e-01 eV +E_delta_NN= -1.95023505e-01 Ry = -2.65343091e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6288 11 0.6 1e+02 % + Run_lcao lcao_line 6.6199 1 6.6 1e+02 % + Potential init_pot 0.28453 2 0.14 4.3 % + PW_Basis recip2real 0.26094 16 0.016 3.9 % + PW_Basis gathers_scatterp 0.11833 16 0.0074 1.8 % + Charge atomic_rho 0.1001 1 0.1 1.5 % + Potential v_of_rho 0.86977 13 0.067 13 % + XC_Functional v_xc 0.24698 14 0.018 3.7 % + H_Hartree_pw v_hartree 0.58676 13 0.045 8.9 % + PW_Basis real2recip 0.5845 38 0.015 8.8 % + PW_Basis gatherp_scatters 0.25206 38 0.0066 3.8 % + ORB_control set_orb_tables 1.1103 1 1.1 17 % + ORB_gen_tables gen_tables 1.1103 1 1.1 17 % + ORB_table_phi init_Table 0.48357 1 0.48 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.47866 126 0.0038 7.2 % + ORB_table_beta init_Table_Beta 0.19057 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18906 56 0.0034 2.9 % + ORB_table_alpha init_Table_Alpha 0.25748 1 0.26 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.2556 66 0.0039 3.9 % + LOOP_ions opt_ions 4.993 1 5 75 % + ESolver_KS_LCAO Run 4.4246 1 4.4 67 % + HSolverLCAO solve 2.4412 11 0.22 37 % + HamiltLCAO updateHk 1.2588 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.2236 11 0.11 18 % + Gint_interface cal_gint 0.45902 23 0.02 6.9 % + Gint_Gamma distri_vl_value 0.67575 11 0.061 10 % + Gint_Gamma distri_vl 2.1235 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.5974 13 0.35 69 % + LCAO_gen_fixedH add_v_delta 1.9906 6 0.33 30 % + LCAO_DESCRIPTOR add_v_delta 1.9906 6 0.33 30 % + ElecStateLCAO psiToRho 1.1646 11 0.11 18 % + Charge mix_rho 0.66002 10 0.066 10 % + LOOP_ions force_stress 0.5683 1 0.57 8.6 % + Force_Stress_LCAO getForceStress 0.56827 1 0.57 8.6 % + Force_LCAO_gamma ftable_gamma 0.36198 1 0.36 5.5 % + Force_LCAO_gamma cal_fvl_dphi 0.12961 1 0.13 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:37 2022 + FINISH Time : Wed Sep 28 11:05:44 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/82/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..eb0b7ef49bac82ff0878f5abc42509f84b6844e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.134549 0.588354 0.376845 +H 0.0718758 0.576552 0.410114 +H 0.11648 0.582764 0.314141 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..60a838e1e767f54c945bf69117d2ff9b16eed26f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.8752 2 + 2 -12.4543 2 + 3 -9.20667 2 + 4 -6.6512 2 + 5 0.698511 0 + 6 3.72702 0 + 7 11.182 0 + 8 11.4186 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..64902a15e31c46ed76b8be5cf33632c637325bb4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/running_scf.log @@ -0,0 +1,802 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:50 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.7673666997 16.4739078164 10.5516726882 0 0 0 0 + tauc_H1 2.01252292063 16.1434578249 11.483186708 0 0 0 0 + tauc_H2 3.26142739702 16.3173855975 8.79595361977 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101499864315 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.114336926517 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.132412260766 (SEC) + + DONE : INIT CHARGE Time : 0.175574014389 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.460105 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000863 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000743 + + Density error is 0.210736575161 + + Energy Rydberg eV + E_KohnSham -34.1789988242 -465.029135945 + E_Harris -34.3631931711 -467.535228602 + E_Fermi -0.37861980717 -5.15138675317 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00128077657526 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000878966514729 + + Density error is 0.09982823214 + + Energy Rydberg eV + E_KohnSham -34.2688422136 -466.251517967 + E_Harris -34.2766184775 -466.357319466 + E_Fermi -0.189282585608 -2.57532169644 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122755563345 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00084263184648 + + Density error is 0.0646626595922 + + Energy Rydberg eV + E_KohnSham -34.2695573325 -466.26124766 + E_Harris -34.2743587203 -466.326573892 + E_Fermi -0.186541862993 -2.53803225225 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117242943215 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803133219272 + + Density error is 0.00196720190814 + + Energy Rydberg eV + E_KohnSham -34.2693893157 -466.258961674 + E_Harris -34.2693920724 -466.258999181 + E_Fermi -0.151358676114 -2.05934043688 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117377912232 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000804182534582 + + Density error is 0.00107978314585 + + Energy Rydberg eV + E_KohnSham -34.2693604793 -466.258569334 + E_Harris -34.2693608946 -466.258574984 + E_Fermi -0.151720165079 -2.06425874657 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117310024774 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803774710297 + + Density error is 0.000209668143541 + + Energy Rydberg eV + E_KohnSham -34.2693642008 -466.258619968 + E_Harris -34.2693642194 -466.258620221 + E_Fermi -0.151035843008 -2.05494806714 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117335058753 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803972050765 + + Density error is 3.36801992807e-05 + + Energy Rydberg eV + E_KohnSham -34.269364508 -466.258624147 + E_Harris -34.2693645092 -466.258624163 + E_Fermi -0.151092387623 -2.0557173961 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117330658404 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803959450926 + + Density error is 9.35039335977e-06 + + Energy Rydberg eV + E_KohnSham -34.2693659454 -466.258643704 + E_Harris -34.2693659457 -466.258643709 + E_Fermi -0.151090871959 -2.05569677444 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117330221414 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803957687815 + + Density error is 1.92083465558e-06 + + Energy Rydberg eV + E_KohnSham -34.269365251 -466.258634257 + E_Harris -34.269365251 -466.258634257 + E_Fermi -0.151080087617 -2.05555004593 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117329425544 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803953248682 + + Density error is 5.95007570848e-07 + + Energy Rydberg eV + E_KohnSham -34.2693654456 -466.258636905 + E_Harris -34.2693654456 -466.258636905 + E_Fermi -0.151080539941 -2.05555620011 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011732949353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803953657429 + + Density error is 2.33830941415e-07 + + Energy Rydberg eV + E_KohnSham -34.2693654067 -466.258636375 + E_Harris -34.2693654067 -466.258636375 + E_Fermi -0.151080240527 -2.05555212638 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011732953232 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000803953892976 + + Density error is 1.28044712709e-08 + + Energy Rydberg eV + E_KohnSham -34.26936541 -466.25863642 + E_Harris -34.26936541 -466.25863642 + E_band -7.81840890438 -106.374910393 + E_one_elec -68.2579789283 -928.697447389 + E_Hartree +35.5460788659 +483.629214134 + E_xc -8.13159897117 -110.636079859 + E_Ewald +6.70045986492 +91.1644333833 + E_demet -3.67971568851e-47 -5.00651003838e-46 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193208094117 -2.62873097972 + E_Fermi -0.151080028281 -2.05554923863 + + charge density convergence is achieved + final etot is -466.25863642 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.8752 2.00000 + 2 -12.4543 2.00000 + 3 -9.20667 2.00000 + 4 -6.65120 2.00000 + 5 0.698511 0.00000 + 6 3.72702 0.00000 + 7 11.1820 0.00000 + 8 11.4186 0.00000 + + EFERMI = -2.055549238628982 eV + OUT.ABACUS/ final etot is -466.2586364201411 eV + correction force for each atom along direction 1 is -0.000157766 + correction force for each atom along direction 2 is -0.000187662 + correction force for each atom along direction 3 is -9.64508e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -2.8617227 -0.53756140 +1.8126976 + H1 +2.8608216 +0.54618059 -1.3967384 + H2 +0.00090109696 -0.0086191912 -0.41595927 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2586364201411 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7549 11 0.70 1.0e+02% + Run_lcao lcao_line 7.7455 1 7.7 1.e+02% + Potential init_pot 0.28667 2 0.14 3.7% + PW_Basis recip2real 0.26604 17 0.016 3.4% + PW_Basis gathers_scatterp 0.11832 17 0.0070 1.5% + Charge atomic_rho 0.10016 1 0.10 1.3% + Potential v_of_rho 0.83535 14 0.060 11.% + XC_Functional v_xc 0.19836 15 0.013 2.6% + H_Hartree_pw v_hartree 0.59838 14 0.043 7.7% + PW_Basis real2recip 0.70447 41 0.017 9.1% + PW_Basis gatherp_scatters 0.28728 41 0.0070 3.7% + ORB_control set_orb_tables 1.0934 1 1.1 14.% + ORB_gen_tables gen_tables 1.0934 1 1.1 14.% + ORB_table_phi init_Table 0.47301 1 0.47 6.1% + ORB_table_phi cal_ST_Phi12_R 0.46763 126 0.0037 6.0% + ORB_table_beta init_Table_Beta 0.18109 1 0.18 2.3% + ORB_table_beta VNL_PhiBeta_R 0.17954 56 0.0032 2.3% + ORB_table_alpha init_Table_Alpha 0.24567 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24372 66 0.0037 3.1% + LOOP_ions opt_ions 6.1159 1 6.1 79.% + ESolver_KS_LCAO Run 5.5131 1 5.5 71.% + HSolverLCAO solve 3.2125 12 0.27 41.% + HamiltLCAO updateHk 1.6253 12 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.5950 12 0.13 21.% + Gint_interface cal_gint 0.73679 25 0.029 9.5% + Gint_Gamma distri_vl_value 0.88245 12 0.074 11.% + Gint_Gamma distri_vl 2.8552 6 0.48 37.% + LCAO_Deepks cal_projected_DM 5.7023 14 0.41 74.% + LCAO_gen_fixedH add_v_delta 2.7202 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.7203 6 0.45 35.% + ElecStateLCAO psiToRho 1.5651 12 0.13 20.% + Charge mix_rho 0.85583 11 0.078 11.% + LOOP_ions force_stress 0.60269 1 0.60 7.8% + Force_Stress_LCAO getForceStress 0.60267 1 0.60 7.8% + Force_LCAO_gamma ftable_gamma 0.40898 1 0.41 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.15757 1 0.16 2.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:50 2022 + Finish Time : Wed Sep 28 11:04:58 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1bd9b5dd076aa5dbf72adda1841e919a97c5c545 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012361 ima = 3.67675e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123826027219 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111889113926 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112908186586 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113126576333 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113125151212 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011312804333 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113126075523 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113127377957 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113126947089 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113127032405 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113127011427 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113126999519 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c2979494f809a376136bc8f5bab9962c25d4292f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.232633300300 16.473907816332 10.551672688233 0 0 0 +H +0.0 +2 +-25.987477079354 16.143457824928 11.483186707975 0 0 0 +-24.738572603005 16.317385597517 8.795953619786 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/conv new file mode 100644 index 0000000000000000000000000000000000000000..b8e0b1423aba4f299d59e61ebf2dce2068b59617 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/conv @@ -0,0 +1 @@ +83 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..cf2f3726dc6612e92e40d1591797e6254e4bdfa6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753413992 0.0121987753 1.216896074 1.332499378 1.467906427 0.008984659144 0.01694301135 0.03928244226 +-3.799150549e-18 0.0007630197676 0.002398902978 0.01097648755 0.04069565335 -4.588741021e-19 1.518404773e-06 5.028006587e-06 +0.001514183625 0.005749524289 + +H atom_index 1 n_descriptor 18 +1.108302837 0.03823818718 0.06722002362 0.09483093519 0.2652780606 0.01558544224 0.02007740421 0.04298512067 +1.12844087e-17 2.818139542e-05 0.06318229716 0.07968504053 0.1065071797 -4.097641455e-18 6.867772278e-06 0.01730736769 +0.01958522258 0.0229697244 + +H atom_index 2 n_descriptor 18 +1.248093291 0.03465310602 0.1070403874 0.1491434107 0.3208732479 0.02201939851 0.02819283291 0.03793167507 +4.021688881e-17 3.907696037e-05 0.0968712002 0.1156955458 0.1276790797 1.133423722e-18 3.571420312e-06 0.0132532431 +0.02530701609 0.03063258681 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..433ef3befc8e387c9a27ed4d15fa6b1767d156ec Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/log.scf @@ -0,0 +1,104 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:50 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101524 SEC) : SETUP UNITCELL + DONE(0.114355 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.132433 SEC) : INIT PLANEWAVE + DONE(0.17572 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.46017 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650291e+02 0.000000e+00 2.107e-01 5.522e-01 + GE2 -4.662515e+02 -1.222382e+00 9.983e-02 5.137e-01 + GE3 -4.662612e+02 -9.729692e-03 6.466e-02 5.724e-01 + GE4 -4.662590e+02 2.285986e-03 1.967e-03 4.408e-01 + GE5 -4.662586e+02 3.923403e-04 1.080e-03 4.388e-01 + GE6 -4.662586e+02 -5.063376e-05 2.097e-04 4.408e-01 + GE7 -4.662586e+02 -4.179398e-06 3.368e-05 4.307e-01 + GE8 -4.662586e+02 -1.955710e-05 9.350e-06 4.233e-01 + GE9 -4.662586e+02 9.447654e-06 1.921e-06 4.222e-01 + GE10 -4.662586e+02 -2.647974e-06 5.950e-07 4.237e-01 + GE11 -4.662586e+02 5.292973e-07 2.338e-07 4.233e-01 + GE12 -4.662586e+02 -4.485117e-08 1.280e-08 3.705e-01 +E_delta_band = -6.68818528e-02 Ry = -9.09974291e-01 eV +E_delta_NN= -1.93208094e-01 Ry = -2.62873098e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.7549 11 0.7 1e+02 % + Run_lcao lcao_line 7.7455 1 7.7 1e+02 % + Potential init_pot 0.28667 2 0.14 3.7 % + PW_Basis recip2real 0.26604 17 0.016 3.4 % + PW_Basis gathers_scatterp 0.11832 17 0.007 1.5 % + Charge atomic_rho 0.10016 1 0.1 1.3 % + Potential v_of_rho 0.83535 14 0.06 11 % + XC_Functional v_xc 0.19836 15 0.013 2.6 % + H_Hartree_pw v_hartree 0.59838 14 0.043 7.7 % + PW_Basis real2recip 0.70447 41 0.017 9.1 % + PW_Basis gatherp_scatters 0.28728 41 0.007 3.7 % + ORB_control set_orb_tables 1.0934 1 1.1 14 % + ORB_gen_tables gen_tables 1.0934 1 1.1 14 % + ORB_table_phi init_Table 0.47301 1 0.47 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.46763 126 0.0037 6 % + ORB_table_beta init_Table_Beta 0.18109 1 0.18 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.17954 56 0.0032 2.3 % + ORB_table_alpha init_Table_Alpha 0.24567 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24372 66 0.0037 3.1 % + LOOP_ions opt_ions 6.1159 1 6.1 79 % + ESolver_KS_LCAO Run 5.5131 1 5.5 71 % + HSolverLCAO solve 3.2125 12 0.27 41 % + HamiltLCAO updateHk 1.6253 12 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.595 12 0.13 21 % + Gint_interface cal_gint 0.73679 25 0.029 9.5 % + Gint_Gamma distri_vl_value 0.88245 12 0.074 11 % + Gint_Gamma distri_vl 2.8552 6 0.48 37 % + LCAO_Deepks cal_projected_DM 5.7023 14 0.41 74 % + LCAO_gen_fixedH add_v_delta 2.7202 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.7203 6 0.45 35 % + ElecStateLCAO psiToRho 1.5651 12 0.13 20 % + Charge mix_rho 0.85583 11 0.078 11 % + LOOP_ions force_stress 0.60269 1 0.6 7.8 % + Force_Stress_LCAO getForceStress 0.60267 1 0.6 7.8 % + Force_LCAO_gamma ftable_gamma 0.40898 1 0.41 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.15757 1 0.16 2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:50 2022 + FINISH Time : Wed Sep 28 11:04:58 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/83/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5a166875c7d7f854b5a89511221bf901ab4090a2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.130223 0.568046 0.36038 +H 0.106833 0.62318 0.371279 +H 0.169496 0.575163 0.310282 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..11de182ebcaad1c1279f415ed11f2c0691019102 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.8047 2 + 2 -13.5908 2 + 3 -9.10921 2 + 4 -6.8566 2 + 5 1.70552 0 + 6 5.1782 0 + 7 10.9427 0 + 8 11.1654 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..49c9dcefe953d2cd38505d62d1f738d761b660bb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:56 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.64623408161 15.9052819997 10.0906316231 0 0 0 0 + tauc_H1 2.99132059638 17.4490307777 10.3958059878 0 0 0 0 + tauc_H2 4.74588381006 16.1045723531 8.68790986769 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0722688245204 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0725470242187 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0881444200928 (SEC) + + DONE : INIT CHARGE Time : 0.129358801167 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374586 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000481 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013 + + Density error is 0.22172271541 + + Energy Rydberg eV + E_KohnSham -34.1753424677 -464.979388662 + E_Harris -34.3823369784 -467.795693462 + E_Fermi -0.439059222232 -5.9737071818 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000793439624347 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138610778326 + + Density error is 0.0969191897002 + + Energy Rydberg eV + E_KohnSham -34.2684229826 -466.245814037 + E_Harris -34.2750092444 -466.335424726 + E_Fermi -0.243951241364 -3.31912691673 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000769437724068 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130436581313 + + Density error is 0.0614123761346 + + Energy Rydberg eV + E_KohnSham -34.2686205071 -466.248501497 + E_Harris -34.2726877473 -466.303839139 + E_Fermi -0.22553337933 -3.06853904808 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000739512138577 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117598493191 + + Density error is 0.00220795387111 + + Energy Rydberg eV + E_KohnSham -34.2687396732 -466.250122835 + E_Harris -34.2687447351 -466.250191705 + E_Fermi -0.189712547697 -2.58117163078 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000742979751013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117664320039 + + Density error is 0.00100555243149 + + Energy Rydberg eV + E_KohnSham -34.2686445655 -466.248828828 + E_Harris -34.2686491806 -466.248891619 + E_Fermi -0.187776911036 -2.55483594293 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741724948129 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117521742222 + + Density error is 0.000133887786597 + + Energy Rydberg eV + E_KohnSham -34.2687134588 -466.249766169 + E_Harris -34.268713529 -466.249767125 + E_Fermi -0.188475321049 -2.56433829865 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00074183643596 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117504603901 + + Density error is 6.46452411976e-05 + + Energy Rydberg eV + E_KohnSham -34.2686899349 -466.249446109 + E_Harris -34.2686899559 -466.249446396 + E_Fermi -0.188265910533 -2.56148912241 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741753326207 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117501461655 + + Density error is 1.18460670753e-05 + + Energy Rydberg eV + E_KohnSham -34.2686943898 -466.249506722 + E_Harris -34.2686943902 -466.249506728 + E_Fermi -0.188339784376 -2.5624942276 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741758440603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117500059373 + + Density error is 2.04657162422e-06 + + Energy Rydberg eV + E_KohnSham -34.2686928277 -466.249485469 + E_Harris -34.2686928277 -466.249485469 + E_Fermi -0.188327787362 -2.56233099985 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741762529957 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117500198589 + + Density error is 1.65460580591e-07 + + Energy Rydberg eV + E_KohnSham -34.2686929199 -466.249486723 + E_Harris -34.2686929199 -466.249486723 + E_Fermi -0.188325803733 -2.5623040112 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741762336156 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117500174515 + + Density error is 1.11463836932e-07 + + Energy Rydberg eV + E_KohnSham -34.2686929608 -466.249487279 + E_Harris -34.2686929608 -466.249487279 + E_Fermi -0.188325856088 -2.56230472352 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000741762384401 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117500161411 + + Density error is 1.05383454832e-08 + + Energy Rydberg eV + E_KohnSham -34.2686929581 -466.249487242 + E_Harris -34.2686929581 -466.249487242 + E_band -8.13795372606 -110.722540735 + E_one_elec -70.3755224758 -957.508105398 + E_Hartree +36.5516198515 +497.31030111 + E_xc -8.29309046922 -112.833284411 + E_Ewald +7.97043862052 +108.443380798 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19692551175 -2.67930904137 + E_Fermi -0.188325733295 -2.56230305284 + + charge density convergence is achieved + final etot is -466.249487242 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.8047 2.00000 + 2 -13.5908 2.00000 + 3 -9.10921 2.00000 + 4 -6.85660 2.00000 + 5 1.70552 0.00000 + 6 5.17820 0.00000 + 7 10.9427 0.00000 + 8 11.1654 0.00000 + + EFERMI = -2.562303052844341 eV + OUT.ABACUS/ final etot is -466.2494872420440 eV + correction force for each atom along direction 1 is 0.000120096 + correction force for each atom along direction 2 is 0.000176353 + correction force for each atom along direction 3 is -9.78152e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.99707516 -4.3627580 +0.18233242 + H1 -1.8188275 +4.2393949 +0.86011594 + H2 +0.82175237 +0.12336313 -1.0424484 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2494872420440 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4712 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4647 1 7.5 1.e+02% + Potential init_pot 0.24522 2 0.12 3.3% + PW_Basis recip2real 0.24446 17 0.014 3.3% + PW_Basis gathers_scatterp 0.11768 17 0.0069 1.6% + Potential v_of_rho 1.0092 14 0.072 14.% + XC_Functional v_xc 0.36047 15 0.024 4.8% + H_Hartree_pw v_hartree 0.61784 14 0.044 8.3% + PW_Basis real2recip 0.67005 41 0.016 9.0% + PW_Basis gatherp_scatters 0.30329 41 0.0074 4.1% + ORB_control set_orb_tables 0.89573 1 0.90 12.% + ORB_gen_tables gen_tables 0.89573 1 0.90 12.% + ORB_table_phi init_Table 0.37274 1 0.37 5.0% + ORB_table_phi cal_ST_Phi12_R 0.36845 126 0.0029 4.9% + ORB_table_beta init_Table_Beta 0.15598 1 0.16 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15467 56 0.0028 2.1% + ORB_table_alpha init_Table_Alpha 0.20944 1 0.21 2.8% + ORB_table_alpha S_PhiAlpha_R 0.20784 66 0.0031 2.8% + LOOP_ions opt_ions 6.1244 1 6.1 82.% + ESolver_KS_LCAO Run 5.5533 1 5.6 74.% + HSolverLCAO solve 3.1695 12 0.26 42.% + HamiltLCAO updateHk 1.5821 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.5569 12 0.13 21.% + Gint_interface cal_gint 0.94636 25 0.038 13.% + Gint_Gamma distri_vl_value 0.80647 12 0.067 11.% + Gint_Gamma distri_vl 2.8884 6 0.48 39.% + LCAO_Deepks cal_projected_DM 5.7628 14 0.41 77.% + LCAO_gen_fixedH add_v_delta 2.7642 6 0.46 37.% + LCAO_DESCRIPTOR add_v_delta 2.7645 6 0.46 37.% + ElecStateLCAO psiToRho 1.5640 12 0.13 21.% + Charge mix_rho 0.77113 11 0.070 10.% + LOOP_ions force_stress 0.57105 1 0.57 7.6% + Force_Stress_LCAO getForceStress 0.57103 1 0.57 7.6% + Force_LCAO_gamma ftable_gamma 0.37492 1 0.37 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.16943 1 0.17 2.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:56 2022 + Finish Time : Wed Sep 28 11:10:03 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6f0758b1154263e50611a2d9c74cf2be90ac57d3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124247 ima = 3.67342e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122907498098 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112331237724 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112575981059 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011290807749 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112810100512 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112864314083 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112857134162 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112860673818 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112860329942 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112860236418 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112860238401 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112860233367 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4f2563fa619edc84abfb4866c4385acdac7cd4db --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.353765918405 15.905281999705 10.090631623037 0 0 0 +H +0.0 +2 +-25.008679403620 17.449030777699 10.395805987820 0 0 0 +-23.254116189936 16.104572353151 8.687909867674 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/conv new file mode 100644 index 0000000000000000000000000000000000000000..f3a39e9847f08ce20fc7201971ce32bf61cf6905 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/conv @@ -0,0 +1 @@ +84 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d4f8d0b9ba9129ddc6fa9f26e33958fac90d7bd6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748367012 0.01284658728 1.314608018 1.402469678 1.472066675 0.008828425822 0.02028410641 0.0390453986 +-9.560532298e-19 0.001350675969 0.00285618092 0.01376718129 0.04994735585 -1.191349831e-19 2.418598416e-06 6.686493424e-06 +0.001664747533 0.005766202366 + +H atom_index 1 n_descriptor 18 +1.344856399 0.03143119813 0.1476571267 0.2003632973 0.3453570166 0.02674709444 0.03358357703 0.03708026028 +-3.785264532e-17 6.258579692e-05 0.1053337279 0.1425120444 0.1714141053 6.769363015e-18 7.372262049e-08 0.01608764799 +0.0300847249 0.03398460593 + +H atom_index 2 n_descriptor 18 +1.275049718 0.03313836289 0.1184310406 0.1619181114 0.3281012956 0.02368733016 0.02974496694 0.03641210479 +-4.673430808e-17 5.596352328e-05 0.1090653029 0.1188164467 0.1394713088 -8.048014542e-18 2.874165305e-06 0.01323036696 +0.02821984756 0.03190231205 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..968d5d0b4b1e2124d130a7d2d4f88aa60453c1ec Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:56 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0722828 SEC) : SETUP UNITCELL + DONE(0.0725558 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0881565 SEC) : INIT PLANEWAVE + DONE(0.129462 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.37463 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.649794e+02 0.000000e+00 2.217e-01 5.361e-01 + GE2 -4.662458e+02 -1.266425e+00 9.692e-02 5.148e-01 + GE3 -4.662485e+02 -2.687460e-03 6.141e-02 5.786e-01 + GE4 -4.662501e+02 -1.621338e-03 2.208e-03 4.490e-01 + GE5 -4.662488e+02 1.294007e-03 1.006e-03 4.529e-01 + GE6 -4.662498e+02 -9.373407e-04 1.339e-04 4.354e-01 + GE7 -4.662494e+02 3.200592e-04 6.465e-05 4.405e-01 + GE8 -4.662495e+02 -6.061220e-05 1.185e-05 4.348e-01 + GE9 -4.662495e+02 2.125300e-05 2.047e-06 4.338e-01 + GE10 -4.662495e+02 -1.254196e-06 1.655e-07 4.307e-01 + GE11 -4.662495e+02 -5.564503e-07 1.115e-07 4.317e-01 + GE12 -4.662495e+02 3.729636e-08 1.054e-08 3.585e-01 +E_delta_band = -7.47870267e-02 Ry = -1.01752970e+00 eV +E_delta_NN= -1.96925512e-01 Ry = -2.67930904e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4712 11 0.68 1e+02 % + Run_lcao lcao_line 7.4647 1 7.5 1e+02 % + Potential init_pot 0.24522 2 0.12 3.3 % + PW_Basis recip2real 0.24446 17 0.014 3.3 % + PW_Basis gathers_scatterp 0.11768 17 0.0069 1.6 % + Potential v_of_rho 1.0092 14 0.072 14 % + XC_Functional v_xc 0.36047 15 0.024 4.8 % + H_Hartree_pw v_hartree 0.61784 14 0.044 8.3 % + PW_Basis real2recip 0.67005 41 0.016 9 % + PW_Basis gatherp_scatters 0.30329 41 0.0074 4.1 % + ORB_control set_orb_tables 0.89573 1 0.9 12 % + ORB_gen_tables gen_tables 0.89573 1 0.9 12 % + ORB_table_phi init_Table 0.37274 1 0.37 5 % + ORB_table_phi cal_ST_Phi12_R 0.36845 126 0.0029 4.9 % + ORB_table_beta init_Table_Beta 0.15598 1 0.16 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15467 56 0.0028 2.1 % + ORB_table_alpha init_Table_Alpha 0.20944 1 0.21 2.8 % + ORB_table_alpha S_PhiAlpha_R 0.20784 66 0.0031 2.8 % + LOOP_ions opt_ions 6.1244 1 6.1 82 % + ESolver_KS_LCAO Run 5.5533 1 5.6 74 % + HSolverLCAO solve 3.1695 12 0.26 42 % + HamiltLCAO updateHk 1.5821 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.5569 12 0.13 21 % + Gint_interface cal_gint 0.94636 25 0.038 13 % + Gint_Gamma distri_vl_value 0.80647 12 0.067 11 % + Gint_Gamma distri_vl 2.8884 6 0.48 39 % + LCAO_Deepks cal_projected_DM 5.7628 14 0.41 77 % + LCAO_gen_fixedH add_v_delta 2.7642 6 0.46 37 % + LCAO_DESCRIPTOR add_v_delta 2.7645 6 0.46 37 % + ElecStateLCAO psiToRho 1.564 12 0.13 21 % + Charge mix_rho 0.77113 11 0.07 10 % + LOOP_ions force_stress 0.57105 1 0.57 7.6 % + Force_Stress_LCAO getForceStress 0.57103 1 0.57 7.6 % + Force_LCAO_gamma ftable_gamma 0.37492 1 0.37 5 % + Force_LCAO_gamma cal_fvl_dphi 0.16943 1 0.17 2.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:56 2022 + FINISH Time : Wed Sep 28 11:10:03 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/84/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..cb828203114de77c3d2b7f2352b121938267c8f0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.125995 0.556142 0.342516 +H 0.127994 0.62472 0.336841 +H 0.147835 0.54363 0.281059 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8772b70ee758310a724b6ed051dada657e1afa76 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1091 2 + 2 -12.3442 2 + 3 -9.49767 2 + 4 -6.71162 2 + 5 0.935431 0 + 6 3.86153 0 + 7 11.1415 0 + 8 11.4255 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1f94255511f32774e1826902e9fa96acaebadd74 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:08 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.52786730993 15.5719801933 9.59044538213 0 0 0 0 + tauc_H1 3.58382738906 17.4921511902 9.43154646212 0 0 0 0 + tauc_H2 4.13937168091 15.2216306375 7.86966030372 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0872924721829 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0891583211121 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107305735744 (SEC) + + DONE : INIT CHARGE Time : 0.156898984984 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.436332 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000792 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102 + + Density error is 0.208774575827 + + Energy Rydberg eV + E_KohnSham -34.1895359633 -465.172501077 + E_Harris -34.3694052812 -467.619748696 + E_Fermi -0.385347101622 -5.24291628985 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00114578069901 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130475104049 + + Density error is 0.0982083726622 + + Energy Rydberg eV + E_KohnSham -34.2754336746 -466.341199396 + E_Harris -34.2826480759 -466.439356361 + E_Fermi -0.199463765244 -2.71384375186 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110437080785 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124381800939 + + Density error is 0.0632816400305 + + Energy Rydberg eV + E_KohnSham -34.2757933798 -466.346093436 + E_Harris -34.2804153493 -466.408978557 + E_Fermi -0.192944011245 -2.62513794791 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107218453491 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011713563038 + + Density error is 0.00186859206145 + + Energy Rydberg eV + E_KohnSham -34.27567731 -466.344514225 + E_Harris -34.2756775281 -466.344517193 + E_Fermi -0.157534390159 -2.14336533712 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107127806244 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117391553832 + + Density error is 0.000829042742317 + + Energy Rydberg eV + E_KohnSham -34.2756616047 -466.344300543 + E_Harris -34.2756619788 -466.344305634 + E_Fermi -0.157766734752 -2.14652654748 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107137672058 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117301036607 + + Density error is 0.000126174539957 + + Energy Rydberg eV + E_KohnSham -34.2756653759 -466.344351854 + E_Harris -34.275665373 -466.344351815 + E_Fermi -0.157246119091 -2.13944320803 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107158375003 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117286660512 + + Density error is 2.34506289529e-05 + + Energy Rydberg eV + E_KohnSham -34.2756664209 -466.344366072 + E_Harris -34.2756664211 -466.344366075 + E_Fermi -0.157215110339 -2.13902131231 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107151089584 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117283620034 + + Density error is 4.99041850379e-06 + + Energy Rydberg eV + E_KohnSham -34.2756669703 -466.344373547 + E_Harris -34.2756669704 -466.344373548 + E_Fermi -0.157214122394 -2.13900787063 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107151568692 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117283889483 + + Density error is 2.20884677543e-06 + + Energy Rydberg eV + E_KohnSham -34.2756665629 -466.344368004 + E_Harris -34.275666563 -466.344368004 + E_Fermi -0.157210824274 -2.1389629974 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107151615627 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117283445192 + + Density error is 3.0388490517e-07 + + Energy Rydberg eV + E_KohnSham -34.2756666201 -466.344368782 + E_Harris -34.2756666201 -466.344368782 + E_Fermi -0.157208964536 -2.13893769437 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107151660971 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117283508587 + + Density error is 1.01427531396e-07 + + Energy Rydberg eV + E_KohnSham -34.2756666354 -466.34436899 + E_Harris -34.2756666354 -466.34436899 + E_Fermi -0.157208769081 -2.13893503506 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00107151673371 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117283530138 + + Density error is 1.15599570151e-08 + + Energy Rydberg eV + E_KohnSham -34.2756666406 -466.34436906 + E_Harris -34.2756666406 -466.34436906 + E_band -7.88824238562 -107.325043649 + E_one_elec -68.6141139446 -933.542912868 + E_Hartree +35.7052684746 +485.795099874 + E_xc -8.15593992015 -110.96725546 + E_Ewald +6.91475554956 +94.0800757512 + E_demet -4.13251862236e-58 -5.62258003551e-57 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193697536679 -2.6353901874 + E_Fermi -0.157208754202 -2.13893483262 + + charge density convergence is achieved + final etot is -466.34436906 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1091 2.00000 + 2 -12.3442 2.00000 + 3 -9.49767 2.00000 + 4 -6.71162 2.00000 + 5 0.935431 0.00000 + 6 3.86153 0.00000 + 7 11.1415 0.00000 + 8 11.4255 0.00000 + + EFERMI = -2.138934832623474 eV + OUT.ABACUS/ final etot is -466.3443690600461 eV + correction force for each atom along direction 1 is -9.09200e-05 + correction force for each atom along direction 2 is 1.62969e-05 + correction force for each atom along direction 3 is -1.91503e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.31592232 +2.1340003 -0.90439382 + H1 -0.23185647 -1.5937935 +0.66058950 + H2 -0.084065853 -0.54020672 +0.24380432 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3443690600461 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9095 11 0.72 1.0e+02% + Run_lcao lcao_line 7.9000 1 7.9 1.e+02% + Potential init_pot 0.28529 2 0.14 3.6% + PW_Basis recip2real 0.29710 17 0.017 3.8% + PW_Basis gathers_scatterp 0.14557 17 0.0086 1.8% + Potential v_of_rho 1.1111 14 0.079 14.% + XC_Functional v_xc 0.36919 15 0.025 4.7% + H_Hartree_pw v_hartree 0.70162 14 0.050 8.9% + PW_Basis real2recip 0.72686 41 0.018 9.2% + PW_Basis gatherp_scatters 0.32498 41 0.0079 4.1% + ORB_control set_orb_tables 1.0963 1 1.1 14.% + ORB_gen_tables gen_tables 1.0963 1 1.1 14.% + ORB_table_phi init_Table 0.47377 1 0.47 6.0% + ORB_table_phi cal_ST_Phi12_R 0.46864 126 0.0037 5.9% + ORB_table_beta init_Table_Beta 0.18786 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18632 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.25214 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.25017 66 0.0038 3.2% + LOOP_ions opt_ions 6.2893 1 6.3 80.% + ESolver_KS_LCAO Run 5.6800 1 5.7 72.% + HSolverLCAO solve 3.1671 12 0.26 40.% + HamiltLCAO updateHk 1.5851 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.5554 12 0.13 20.% + Gint_interface cal_gint 1.3003 25 0.052 16.% + Gint_Gamma distri_vl_value 0.64660 12 0.054 8.2% + Gint_Gamma distri_vl 2.9452 6 0.49 37.% + LCAO_Deepks cal_projected_DM 5.9479 14 0.42 75.% + LCAO_gen_fixedH add_v_delta 2.8122 6 0.47 36.% + LCAO_DESCRIPTOR add_v_delta 2.8123 6 0.47 36.% + ElecStateLCAO psiToRho 1.5455 12 0.13 20.% + Charge mix_rho 0.79333 11 0.072 10.% + LOOP_ions force_stress 0.60908 1 0.61 7.7% + Force_Stress_LCAO getForceStress 0.60905 1 0.61 7.7% + Force_LCAO_gamma ftable_gamma 0.38848 1 0.39 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.22693 1 0.23 2.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:08 2022 + Finish Time : Wed Sep 28 11:12:16 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..722bb84159b96e0b5217a31976db0686b577cdf7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123556 ima = 3.70111e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8.00000000000001 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122818113263 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111493383271 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112300736353 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112492623318 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112491805183 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112491721493 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112491279835 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011249206955 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112491859475 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112491814039 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112491799865 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112491798792 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a484856dc390c520cd10f31b18399b33919ede00 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.472132690079 15.571980193315 9.590445382137 0 0 0 +H +0.0 +2 +-24.416172610943 17.492151190160 9.431546462144 0 0 0 +-23.860628319100 15.221630637487 7.869660303700 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/conv new file mode 100644 index 0000000000000000000000000000000000000000..e21e998829ccd9524117e9526e440f8c0a2e6f03 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/conv @@ -0,0 +1 @@ +85 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ebbede3d13eb0b638b3d9dbdb57778723a2d4fa1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75634865 0.01255478793 1.241364577 1.325024518 1.46860493 0.00972517039 0.01560619386 0.03930283472 +1.521474857e-17 0.0007235393114 0.00267430169 0.01260830044 0.04328131097 3.625168665e-19 2.360984529e-06 6.735117784e-06 +0.001557887576 0.006046803875 + +H atom_index 1 n_descriptor 18 +1.177654478 0.03730646856 0.08835264692 0.1189054607 0.2929542622 0.01969896935 0.02396642249 0.04099277902 +2.314812049e-17 3.770833003e-05 0.08230991455 0.1011579303 0.112180195 5.56824538e-18 5.536368637e-06 0.01516649951 +0.02350466798 0.02695631204 + +H atom_index 2 n_descriptor 18 +1.230585827 0.03571832302 0.1050290254 0.1408360215 0.313221393 0.02232249513 0.02709223822 0.03890726005 +-3.921098921e-17 4.215054757e-05 0.0955789181 0.1150295745 0.1204260796 -8.831491724e-18 3.413454972e-06 0.01368913677 +0.02570755303 0.02977858567 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..146db41fbda21f3d81eac73ac91bc789a7816050 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:08 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0873162 SEC) : SETUP UNITCELL + DONE(0.0891735 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107327 SEC) : INIT PLANEWAVE + DONE(0.15702 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.436404 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651725e+02 0.000000e+00 2.088e-01 5.750e-01 + GE2 -4.663412e+02 -1.168698e+00 9.821e-02 5.300e-01 + GE3 -4.663461e+02 -4.894040e-03 6.328e-02 5.964e-01 + GE4 -4.663445e+02 1.579210e-03 1.869e-03 4.564e-01 + GE5 -4.663443e+02 2.136819e-04 8.290e-04 4.558e-01 + GE6 -4.663444e+02 -5.131058e-05 1.262e-04 4.511e-01 + GE7 -4.663444e+02 -1.421806e-05 2.345e-05 4.354e-01 + GE8 -4.663444e+02 -7.474525e-06 4.990e-06 4.355e-01 + GE9 -4.663444e+02 5.542439e-06 2.209e-06 4.374e-01 + GE10 -4.663444e+02 -7.778025e-07 3.039e-07 4.394e-01 + GE11 -4.663444e+02 -2.084771e-07 1.014e-07 4.333e-01 + GE12 -4.663444e+02 -6.957224e-08 1.156e-08 3.626e-01 +E_delta_band = -6.80607368e-02 Ry = -9.26013830e-01 eV +E_delta_NN= -1.93697537e-01 Ry = -2.63539019e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9095 11 0.72 1e+02 % + Run_lcao lcao_line 7.9 1 7.9 1e+02 % + Potential init_pot 0.28529 2 0.14 3.6 % + PW_Basis recip2real 0.2971 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.14557 17 0.0086 1.8 % + Potential v_of_rho 1.1111 14 0.079 14 % + XC_Functional v_xc 0.36919 15 0.025 4.7 % + H_Hartree_pw v_hartree 0.70162 14 0.05 8.9 % + PW_Basis real2recip 0.72686 41 0.018 9.2 % + PW_Basis gatherp_scatters 0.32498 41 0.0079 4.1 % + ORB_control set_orb_tables 1.0963 1 1.1 14 % + ORB_gen_tables gen_tables 1.0963 1 1.1 14 % + ORB_table_phi init_Table 0.47377 1 0.47 6 % + ORB_table_phi cal_ST_Phi12_R 0.46864 126 0.0037 5.9 % + ORB_table_beta init_Table_Beta 0.18786 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18632 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.25214 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.25017 66 0.0038 3.2 % + LOOP_ions opt_ions 6.2893 1 6.3 80 % + ESolver_KS_LCAO Run 5.68 1 5.7 72 % + HSolverLCAO solve 3.1671 12 0.26 40 % + HamiltLCAO updateHk 1.5851 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.5554 12 0.13 20 % + Gint_interface cal_gint 1.3003 25 0.052 16 % + Gint_Gamma distri_vl_value 0.6466 12 0.054 8.2 % + Gint_Gamma distri_vl 2.9452 6 0.49 37 % + LCAO_Deepks cal_projected_DM 5.9479 14 0.42 75 % + LCAO_gen_fixedH add_v_delta 2.8122 6 0.47 36 % + LCAO_DESCRIPTOR add_v_delta 2.8123 6 0.47 36 % + ElecStateLCAO psiToRho 1.5455 12 0.13 20 % + Charge mix_rho 0.79333 11 0.072 10 % + LOOP_ions force_stress 0.60908 1 0.61 7.7 % + Force_Stress_LCAO getForceStress 0.60905 1 0.61 7.7 % + Force_LCAO_gamma ftable_gamma 0.38848 1 0.39 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.22693 1 0.23 2.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:08 2022 + FINISH Time : Wed Sep 28 11:12:16 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/85/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b011353bbd758fc75d99f098a5e83b12d371d70d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.133631 0.554799 0.312975 +H 0.126563 0.618355 0.307796 +H 0.119735 0.522905 0.255027 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b14e13c2c971e8a2aa2b0c06b2356fc945813f2b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0824 2 + 2 -13.3509 2 + 3 -8.70465 2 + 4 -6.68965 2 + 5 1.21749 0 + 6 4.40831 0 + 7 11.1042 0 + 8 11.3128 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ff5010342879227924922ad1d2a2d0086ea25800 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:43 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 3.74166729594 15.5343660025 8.7633120609 0 0 0 0 + tauc_H1 3.54375943025 17.313944386 8.61827965151 0 0 0 0 + tauc_H2 3.35259334427 14.6413380097 7.14075832124 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0731575845506 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0860196341245 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.101745725896 (SEC) + + DONE : INIT CHARGE Time : 0.142883505085 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.384365 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000962 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000847 + + Density error is 0.21533758494 + + Energy Rydberg eV + E_KohnSham -34.1875576744 -465.145585075 + E_Harris -34.3795955466 -467.758394369 + E_Fermi -0.399676461204 -5.43787722885 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00126166255592 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116580801714 + + Density error is 0.0983949978091 + + Energy Rydberg eV + E_KohnSham -34.2761312561 -466.350690478 + E_Harris -34.2828089957 -466.441545787 + E_Fermi -0.208973147229 -2.84322553131 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00121917231028 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112903411156 + + Density error is 0.0630561511687 + + Energy Rydberg eV + E_KohnSham -34.2762839577 -466.352768091 + E_Harris -34.2805556727 -466.410887755 + E_Fermi -0.19760483282 -2.68855167869 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116485099876 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108549004165 + + Density error is 0.00215907844386 + + Energy Rydberg eV + E_KohnSham -34.2762734338 -466.352624906 + E_Harris -34.2762787112 -466.352696708 + E_Fermi -0.162627502655 -2.21266068761 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116525718814 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108514380162 + + Density error is 0.000805916632805 + + Energy Rydberg eV + E_KohnSham -34.2762323604 -466.352066074 + E_Harris -34.276232783 -466.352071823 + E_Fermi -0.161834113559 -2.20186607519 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116453743729 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010845054313 + + Density error is 0.000202588153091 + + Energy Rydberg eV + E_KohnSham -34.2762596513 -466.352437385 + E_Harris -34.2762597345 -466.352438517 + E_Fermi -0.161764064024 -2.20091300236 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116489534884 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010848732062 + + Density error is 3.91391057864e-05 + + Energy Rydberg eV + E_KohnSham -34.2762486187 -466.352287278 + E_Harris -34.2762486267 -466.352287388 + E_Fermi -0.161625974493 -2.19903419791 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116481656507 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108475652013 + + Density error is 1.61834697734e-05 + + Energy Rydberg eV + E_KohnSham -34.2762537831 -466.352357545 + E_Harris -34.2762537842 -466.352357559 + E_Fermi -0.161665211744 -2.1995680481 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011648142277 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108475596487 + + Density error is 1.67623755662e-06 + + Energy Rydberg eV + E_KohnSham -34.2762523792 -466.352338444 + E_Harris -34.2762523792 -466.352338444 + E_Fermi -0.161647610743 -2.19932857419 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116481209935 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108475967784 + + Density error is 4.81306418238e-07 + + Energy Rydberg eV + E_KohnSham -34.2762526084 -466.352341562 + E_Harris -34.2762526084 -466.352341562 + E_Fermi -0.161646603199 -2.19931486586 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116481291952 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108476041292 + + Density error is 1.6335367101e-07 + + Energy Rydberg eV + E_KohnSham -34.2762526256 -466.352341796 + E_Harris -34.2762526256 -466.352341796 + E_Fermi -0.161646390977 -2.19931197843 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116481314908 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108476060276 + + Density error is 1.0954041322e-08 + + Energy Rydberg eV + E_KohnSham -34.2762526283 -466.352341832 + E_Harris -34.2762526283 -466.352341832 + E_band -7.91250288589 -107.65512469 + E_one_elec -69.1311851641 -940.578027724 + E_Hartree +35.9805367223 +489.540316522 + E_xc -8.19966113158 -111.562113059 + E_Ewald +7.19878250797 +97.9444607712 + E_demet -3.79364636565e-71 -5.16152067698e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19431964063 -2.64385434588 + E_Fermi -0.161646230151 -2.19930979027 + + charge density convergence is achieved + final etot is -466.352341832 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0824 2.00000 + 2 -13.3509 2.00000 + 3 -8.70465 2.00000 + 4 -6.68965 2.00000 + 5 1.21749 0.00000 + 6 4.40831 0.00000 + 7 11.1042 0.00000 + 8 11.3128 0.00000 + + EFERMI = -2.199309790268987 eV + OUT.ABACUS/ final etot is -466.3523418317961 eV + correction force for each atom along direction 1 is -0.000117504 + correction force for each atom along direction 2 is 3.06678e-05 + correction force for each atom along direction 3 is -9.07320e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.10319473 -2.2519430 -0.31200607 + H1 -0.28213161 +1.1093211 -0.64922162 + H2 +0.17893688 +1.1426219 +0.96122769 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3523418317961 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1038 11 0.65 1.0e+02% + Run_lcao lcao_line 7.0961 1 7.1 1.e+02% + Potential init_pot 0.24102 2 0.12 3.4% + PW_Basis recip2real 0.23715 17 0.014 3.3% + PW_Basis gathers_scatterp 0.10844 17 0.0064 1.5% + Potential v_of_rho 0.94179 14 0.067 13.% + XC_Functional v_xc 0.29965 15 0.020 4.2% + H_Hartree_pw v_hartree 0.60459 14 0.043 8.5% + PW_Basis real2recip 0.64015 41 0.016 9.0% + PW_Basis gatherp_scatters 0.26091 41 0.0064 3.7% + ORB_control set_orb_tables 0.89001 1 0.89 13.% + ORB_gen_tables gen_tables 0.89000 1 0.89 13.% + ORB_table_phi init_Table 0.37102 1 0.37 5.2% + ORB_table_phi cal_ST_Phi12_R 0.36682 126 0.0029 5.2% + ORB_table_beta init_Table_Beta 0.15228 1 0.15 2.1% + ORB_table_beta VNL_PhiBeta_R 0.15102 56 0.0027 2.1% + ORB_table_alpha init_Table_Alpha 0.20923 1 0.21 2.9% + ORB_table_alpha S_PhiAlpha_R 0.20757 66 0.0031 2.9% + LOOP_ions opt_ions 5.7526 1 5.8 81.% + ESolver_KS_LCAO Run 5.2059 1 5.2 73.% + HSolverLCAO solve 2.8503 12 0.24 40.% + HamiltLCAO updateHk 1.4384 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.4132 12 0.12 20.% + Gint_interface cal_gint 1.5894 25 0.064 22.% + Gint_Gamma distri_vl_value 0.44130 12 0.037 6.2% + Gint_Gamma distri_vl 2.7066 6 0.45 38.% + LCAO_Deepks cal_projected_DM 5.5015 14 0.39 77.% + LCAO_gen_fixedH add_v_delta 2.5788 6 0.43 36.% + LCAO_DESCRIPTOR add_v_delta 2.5787 6 0.43 36.% + ElecStateLCAO psiToRho 1.3946 12 0.12 20.% + Charge mix_rho 0.82572 11 0.075 12.% + LOOP_ions force_stress 0.54650 1 0.55 7.7% + Force_Stress_LCAO getForceStress 0.54648 1 0.55 7.7% + Force_LCAO_gamma ftable_gamma 0.34936 1 0.35 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.24405 1 0.24 3.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:43 2022 + Finish Time : Wed Sep 28 11:11:50 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a487ecf30f8ce3a12a162a2512ea7ef680b11308 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123257 ima = 3.64938e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123898212674 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113179509105 + charge after normalized = 8.00000000000004 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113661684378 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113855665142 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113822939212 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113844721438 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113835226622 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113838101887 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113837451967 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113837396168 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113837381111 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113837372778 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e265d09dbeb807f4ef26e37254ddf97fc20f92ca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-24.258332704053 15.534366002475 8.763312060884 0 0 0 +H +0.0 +2 +-24.456240569771 17.313944385986 8.618279651482 0 0 0 +-24.647406655748 14.641338009681 7.140758321263 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/conv new file mode 100644 index 0000000000000000000000000000000000000000..916d02b5368edd676145a64cb8128fb48d027cc6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/conv @@ -0,0 +1 @@ +86 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..72e2ea1957a7055a3b15e79b8c3bb53f1ab6b6f0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74216164 0.01247431377 1.268801561 1.372070964 1.468458738 0.007402076939 0.02084609399 0.03882885082 +-6.513661237e-18 0.001116504244 0.002239096989 0.01203480957 0.04073554673 -3.214705102e-19 1.250964989e-06 4.208148956e-06 +0.001825396184 0.005448114885 + +H atom_index 1 n_descriptor 18 +1.267337305 0.03284503519 0.1149914618 0.1605442766 0.3293946307 0.02240366958 0.02959906049 0.03629178807 +1.090491806e-17 3.555826446e-05 0.1053428804 0.1160742279 0.1377497628 -1.32776688e-18 3.165682414e-06 0.01278197824 +0.02648823949 0.03166557518 + +H atom_index 2 n_descriptor 18 +1.190273915 0.0355358401 0.08994843226 0.1265692392 0.304269562 0.01910802134 0.02516289507 0.03897023811 +1.657706398e-17 2.998062325e-05 0.08585556048 0.108220431 0.1132800549 2.448996479e-18 5.830457239e-06 0.01389328996 +0.02351704829 0.02804611796 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..040306da47c1d3960d635d6177a6c586ba6cd30a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:43 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0731734 SEC) : SETUP UNITCELL + DONE(0.0860308 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.101757 SEC) : INIT PLANEWAVE + DONE(0.142987 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.384407 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651456e+02 0.000000e+00 2.153e-01 5.119e-01 + GE2 -4.663507e+02 -1.205105e+00 9.839e-02 4.824e-01 + GE3 -4.663528e+02 -2.077613e-03 6.306e-02 5.437e-01 + GE4 -4.663526e+02 1.431852e-04 2.159e-03 4.249e-01 + GE5 -4.663521e+02 5.588323e-04 8.059e-04 4.254e-01 + GE6 -4.663524e+02 -3.713111e-04 2.026e-04 4.198e-01 + GE7 -4.663523e+02 1.501066e-04 3.914e-05 4.093e-01 + GE8 -4.663524e+02 -7.026625e-05 1.618e-05 3.992e-01 + GE9 -4.663523e+02 1.910099e-05 1.676e-06 3.983e-01 + GE10 -4.663523e+02 -3.118191e-06 4.813e-07 4.018e-01 + GE11 -4.663523e+02 -2.341842e-07 1.634e-07 4.000e-01 + GE12 -4.663523e+02 -3.584287e-08 1.095e-08 3.358e-01 +E_delta_band = -6.95940778e-02 Ry = -9.46876005e-01 eV +E_delta_NN= -1.94319641e-01 Ry = -2.64385435e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1038 11 0.65 1e+02 % + Run_lcao lcao_line 7.0961 1 7.1 1e+02 % + Potential init_pot 0.24102 2 0.12 3.4 % + PW_Basis recip2real 0.23715 17 0.014 3.3 % + PW_Basis gathers_scatterp 0.10844 17 0.0064 1.5 % + Potential v_of_rho 0.94179 14 0.067 13 % + XC_Functional v_xc 0.29965 15 0.02 4.2 % + H_Hartree_pw v_hartree 0.60459 14 0.043 8.5 % + PW_Basis real2recip 0.64015 41 0.016 9 % + PW_Basis gatherp_scatters 0.26091 41 0.0064 3.7 % + ORB_control set_orb_tables 0.89001 1 0.89 13 % + ORB_gen_tables gen_tables 0.89 1 0.89 13 % + ORB_table_phi init_Table 0.37102 1 0.37 5.2 % + ORB_table_phi cal_ST_Phi12_R 0.36682 126 0.0029 5.2 % + ORB_table_beta init_Table_Beta 0.15228 1 0.15 2.1 % + ORB_table_beta VNL_PhiBeta_R 0.15102 56 0.0027 2.1 % + ORB_table_alpha init_Table_Alpha 0.20923 1 0.21 2.9 % + ORB_table_alpha S_PhiAlpha_R 0.20757 66 0.0031 2.9 % + LOOP_ions opt_ions 5.7526 1 5.8 81 % + ESolver_KS_LCAO Run 5.2059 1 5.2 73 % + HSolverLCAO solve 2.8503 12 0.24 40 % + HamiltLCAO updateHk 1.4384 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.4132 12 0.12 20 % + Gint_interface cal_gint 1.5894 25 0.064 22 % + Gint_Gamma distri_vl_value 0.4413 12 0.037 6.2 % + Gint_Gamma distri_vl 2.7066 6 0.45 38 % + LCAO_Deepks cal_projected_DM 5.5015 14 0.39 77 % + LCAO_gen_fixedH add_v_delta 2.5788 6 0.43 36 % + LCAO_DESCRIPTOR add_v_delta 2.5787 6 0.43 36 % + ElecStateLCAO psiToRho 1.3946 12 0.12 20 % + Charge mix_rho 0.82572 11 0.075 12 % + LOOP_ions force_stress 0.5465 1 0.55 7.7 % + Force_Stress_LCAO getForceStress 0.54648 1 0.55 7.7 % + Force_LCAO_gamma ftable_gamma 0.34936 1 0.35 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.24405 1 0.24 3.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:43 2022 + FINISH Time : Wed Sep 28 11:11:50 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/86/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4f46c7b76e3d354081633a82d621e74731b08a0b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.143522 0.553895 0.29511 +H 0.089716 0.552521 0.333231 +H 0.113145 0.538128 0.243462 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8673f881d8f528366922d29b030afd5c47461dfd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.8033 2 + 2 -12.7448 2 + 3 -9.66277 2 + 4 -6.85071 2 + 5 1.38277 0 + 6 4.8118 0 + 7 10.9911 0 + 8 11.2793 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..469c7589535b9ae40d738143598237d6a4219a04 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:55 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.01862023172 15.5090535523 8.26308176328 0 0 0 0 + tauc_H1 2.51204766615 15.4705936104 9.33048082477 0 0 0 0 + tauc_H2 3.1680465781 15.0675815312 6.81694342967 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0881336803513 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0885770042329 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106878023276 (SEC) + + DONE : INIT CHARGE Time : 0.151761198569 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.431888 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00141 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000985 + + Density error is 0.217333436189 + + Energy Rydberg eV + E_KohnSham -34.1754097929 -464.980304668 + E_Harris -34.3745933857 -467.690336478 + E_Fermi -0.427088854162 -5.81084196889 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00121838111612 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107065393389 + + Density error is 0.097113860849 + + Energy Rydberg eV + E_KohnSham -34.2682564589 -466.243548366 + E_Harris -34.2751198887 -466.336930119 + E_Fermi -0.233910915081 -3.1825212695 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112234492451 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100883544679 + + Density error is 0.0621090235147 + + Energy Rydberg eV + E_KohnSham -34.2686080392 -466.248331862 + E_Harris -34.2730236794 -466.308409729 + E_Fermi -0.220522321952 -3.00036011473 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0009656249317 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000923939433695 + + Density error is 0.00210508673955 + + Energy Rydberg eV + E_KohnSham -34.2686366951 -466.248721746 + E_Harris -34.2686404628 -466.248773008 + E_Fermi -0.183889767914 -2.50194864753 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000965625374595 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092754747135 + + Density error is 0.00097639688196 + + Energy Rydberg eV + E_KohnSham -34.2685629574 -466.247718492 + E_Harris -34.2685645172 -466.247739715 + E_Fermi -0.18313944963 -2.49174004356 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000963730280416 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926207969621 + + Density error is 0.000180249205811 + + Energy Rydberg eV + E_KohnSham -34.2686078719 -466.248329586 + E_Harris -34.2686079712 -466.248330937 + E_Fermi -0.183195920086 -2.49250836352 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000963725258362 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926268558624 + + Density error is 4.55105141077e-05 + + Energy Rydberg eV + E_KohnSham -34.2685917271 -466.248109924 + E_Harris -34.2685917377 -466.248110068 + E_Fermi -0.183032952396 -2.49029107435 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000963713902572 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926225301021 + + Density error is 2.61360014787e-05 + + Energy Rydberg eV + E_KohnSham -34.2685967331 -466.248178035 + E_Harris -34.268596736 -466.248178074 + E_Fermi -0.183088339109 -2.49104464924 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000963683372798 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926220846218 + + Density error is 1.53241924604e-06 + + Energy Rydberg eV + E_KohnSham -34.268594822 -466.248152032 + E_Harris -34.268594822 -466.248152032 + E_Fermi -0.183058021633 -2.49063215882 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000963684079445 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926220741659 + + Density error is 4.11496525807e-07 + + Energy Rydberg eV + E_KohnSham -34.2685952363 -466.248157669 + E_Harris -34.2685952362 -466.248157669 + E_Fermi -0.183057777342 -2.49062883507 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000963683761984 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926221295884 + + Density error is 1.46782317189e-07 + + Energy Rydberg eV + E_KohnSham -34.2685952521 -466.248157885 + E_Harris -34.2685952521 -466.248157885 + E_Fermi -0.183057645095 -2.49062703576 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00096368353886 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926221381152 + + Density error is 1.22344706228e-08 + + Energy Rydberg eV + E_KohnSham -34.2685952542 -466.248157913 + E_Harris -34.2685952542 -466.248157913 + E_band -8.09390462179 -110.123221925 + E_one_elec -69.9018642953 -951.063655239 + E_Hartree +36.3105672512 +494.030612229 + E_xc -8.25333413444 -112.292371726 + E_Ewald +7.69907721599 +104.751319479 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196024807992 -2.66705433805 + E_Fermi -0.183057486812 -2.4906248822 + + charge density convergence is achieved + final etot is -466.248157913 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.8033 2.00000 + 2 -12.7448 2.00000 + 3 -9.66277 2.00000 + 4 -6.85071 2.00000 + 5 1.38277 0.00000 + 6 4.81180 0.00000 + 7 10.9911 0.00000 + 8 11.2793 0.00000 + + EFERMI = -2.490624882203717 eV + OUT.ABACUS/ final etot is -466.2481579134811 eV + correction force for each atom along direction 1 is -0.000189553 + correction force for each atom along direction 2 is 8.09573e-05 + correction force for each atom along direction 3 is 3.65953e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.67550963 +0.69995883 +2.8279809 + H1 +0.34508223 +0.23025225 +0.84894733 + H2 -1.0205919 -0.93021109 -3.6769282 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2481579134811 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6238 11 0.69 1.0e+02% + Run_lcao lcao_line 7.6131 1 7.6 1.e+02% + Potential init_pot 0.28078 2 0.14 3.7% + PW_Basis recip2real 0.27447 17 0.016 3.6% + PW_Basis gathers_scatterp 0.12401 17 0.0073 1.6% + Potential v_of_rho 0.85655 14 0.061 11.% + XC_Functional v_xc 0.20884 15 0.014 2.7% + H_Hartree_pw v_hartree 0.60612 14 0.043 8.0% + PW_Basis real2recip 0.69557 41 0.017 9.1% + PW_Basis gatherp_scatters 0.27782 41 0.0068 3.6% + ORB_control set_orb_tables 1.0927 1 1.1 14.% + ORB_gen_tables gen_tables 1.0927 1 1.1 14.% + ORB_table_phi init_Table 0.47698 1 0.48 6.3% + ORB_table_phi cal_ST_Phi12_R 0.47171 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18274 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18122 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24595 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24402 66 0.0037 3.2% + LOOP_ions opt_ions 6.0133 1 6.0 79.% + ESolver_KS_LCAO Run 5.4072 1 5.4 71.% + HSolverLCAO solve 2.9815 12 0.25 39.% + HamiltLCAO updateHk 1.5162 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4864 12 0.12 19.% + Gint_interface cal_gint 1.6659 25 0.067 22.% + Gint_Gamma distri_vl_value 0.43290 12 0.036 5.7% + Gint_Gamma distri_vl 2.8170 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.7130 14 0.41 75.% + LCAO_gen_fixedH add_v_delta 2.6702 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.6703 6 0.45 35.% + ElecStateLCAO psiToRho 1.4301 12 0.12 19.% + Charge mix_rho 0.96812 11 0.088 13.% + LOOP_ions force_stress 0.60592 1 0.61 7.9% + Force_Stress_LCAO getForceStress 0.60589 1 0.61 7.9% + Force_LCAO_gamma ftable_gamma 0.41220 1 0.41 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.27015 1 0.27 3.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:55 2022 + Finish Time : Wed Sep 28 11:04:03 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..95a117741b354dfb78fa25b77e7d679d226e85d2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124215 ima = 3.6837e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122348611506 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111081234238 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011162116914 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111954884303 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111883302994 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111920568295 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111912534161 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111916109054 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111915012048 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111914964217 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111914952019 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111914944472 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4f8c874189170e5a9c918b79bdb60bec16732b59 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.981379768296 15.509053552272 8.263081763287 0 0 0 +H +0.0 +2 +-25.487952333871 15.470593610347 9.330480824781 0 0 0 +-24.831953421907 15.067581531219 6.816943429647 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/conv new file mode 100644 index 0000000000000000000000000000000000000000..fc6d73796bb40615b24737519af488d1485c6e0d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/conv @@ -0,0 +1 @@ +87 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b202237ec4efd2413dd9fb9afd1b5a2e8b571e0a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.756988892 0.01295239455 1.285020749 1.374131497 1.471357484 0.01040113156 0.01636025196 0.03924543559 +5.626676717e-19 0.0009091246232 0.003231474026 0.01498282291 0.05082583696 -1.713124136e-19 3.846468169e-06 9.35042332e-06 +0.00159075709 0.006160226368 + +H atom_index 1 n_descriptor 18 +1.240215257 0.03570888048 0.1115116263 0.145168067 0.3152819265 0.02378760172 0.02765836077 0.03878003601 +-1.410934934e-17 5.422512834e-05 0.1057611873 0.1145924547 0.1245406667 -2.875959012e-18 2.537214397e-06 0.01368972748 +0.02803116886 0.03034778194 + +H atom_index 2 n_descriptor 18 +1.327273822 0.03322282909 0.1470302682 0.1901028306 0.3410890123 0.02831251291 0.03265884596 0.03769963645 +1.556635283e-17 6.152391342e-05 0.1071956485 0.1384521018 0.1624493027 1.427152953e-18 1.412791789e-07 0.01515082489 +0.03073817914 0.03366798836 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..541d5eac14fc14288d5d711fdcb31c9a7971efa6 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:55 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0881617 SEC) : SETUP UNITCELL + DONE(0.0885941 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106898 SEC) : INIT PLANEWAVE + DONE(0.151899 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.431951 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.649803e+02 0.000000e+00 2.173e-01 5.517e-01 + GE2 -4.662435e+02 -1.263244e+00 9.711e-02 5.009e-01 + GE3 -4.662483e+02 -4.783496e-03 6.211e-02 5.710e-01 + GE4 -4.662487e+02 -3.898834e-04 2.105e-03 4.284e-01 + GE5 -4.662477e+02 1.003253e-03 9.764e-04 4.286e-01 + GE6 -4.662483e+02 -6.110937e-04 1.802e-04 4.285e-01 + GE7 -4.662481e+02 2.196618e-04 4.551e-05 4.225e-01 + GE8 -4.662482e+02 -6.811043e-05 2.614e-05 4.117e-01 + GE9 -4.662482e+02 2.600255e-05 1.532e-06 4.134e-01 + GE10 -4.662482e+02 -5.636530e-06 4.115e-07 4.132e-01 + GE11 -4.662482e+02 -2.161937e-07 1.468e-07 4.143e-01 + GE12 -4.662482e+02 -2.862449e-08 1.223e-08 3.616e-01 +E_delta_band = -7.29835163e-02 Ry = -9.92991681e-01 eV +E_delta_NN= -1.96024808e-01 Ry = -2.66705434e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6238 11 0.69 1e+02 % + Run_lcao lcao_line 7.6131 1 7.6 1e+02 % + Potential init_pot 0.28078 2 0.14 3.7 % + PW_Basis recip2real 0.27447 17 0.016 3.6 % + PW_Basis gathers_scatterp 0.12401 17 0.0073 1.6 % + Potential v_of_rho 0.85655 14 0.061 11 % + XC_Functional v_xc 0.20884 15 0.014 2.7 % + H_Hartree_pw v_hartree 0.60612 14 0.043 8 % + PW_Basis real2recip 0.69557 41 0.017 9.1 % + PW_Basis gatherp_scatters 0.27782 41 0.0068 3.6 % + ORB_control set_orb_tables 1.0927 1 1.1 14 % + ORB_gen_tables gen_tables 1.0927 1 1.1 14 % + ORB_table_phi init_Table 0.47698 1 0.48 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.47171 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18274 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18122 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24595 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24402 66 0.0037 3.2 % + LOOP_ions opt_ions 6.0133 1 6 79 % + ESolver_KS_LCAO Run 5.4072 1 5.4 71 % + HSolverLCAO solve 2.9815 12 0.25 39 % + HamiltLCAO updateHk 1.5162 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4864 12 0.12 19 % + Gint_interface cal_gint 1.6659 25 0.067 22 % + Gint_Gamma distri_vl_value 0.4329 12 0.036 5.7 % + Gint_Gamma distri_vl 2.817 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.713 14 0.41 75 % + LCAO_gen_fixedH add_v_delta 2.6702 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.6703 6 0.45 35 % + ElecStateLCAO psiToRho 1.4301 12 0.12 19 % + Charge mix_rho 0.96812 11 0.088 13 % + LOOP_ions force_stress 0.60592 1 0.61 7.9 % + Force_Stress_LCAO getForceStress 0.60589 1 0.61 7.9 % + Force_LCAO_gamma ftable_gamma 0.4122 1 0.41 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.27015 1 0.27 3.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:55 2022 + FINISH Time : Wed Sep 28 11:04:03 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/87/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..f0fd2464e7a4937ee7884cfd0df3e804d8475bca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.14446 0.553445 0.289594 +H 0.178491 0.49849 0.299681 +H 0.121093 0.557909 0.22431 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..19f3f432b3929af467cecdbefae9a8cd33c255aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.8389 2 + 2 -13.1125 2 + 3 -8.66816 2 + 4 -6.63036 2 + 5 0.957457 0 + 6 4.05376 0 + 7 11.1658 0 + 8 11.3746 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b3ea1b347e7e44717f560fe97a7c4e014e327c8b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:32 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.04489155675 15.4964544022 8.10863451439 0 0 0 0 + tauc_H1 4.99775015473 13.9577196317 8.39105955864 0 0 0 0 + tauc_H2 3.39061563447 15.6214658846 6.28066852431 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0861636685349 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0875415273964 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105877732555 (SEC) + + DONE : INIT CHARGE Time : 0.156511560422 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.436656 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00117 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000833 + + Density error is 0.213499889473 + + Energy Rydberg eV + E_KohnSham -34.1844605773 -465.103446908 + E_Harris -34.3726329382 -467.663663223 + E_Fermi -0.38506052215 -5.23901717609 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00129853481204 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010614923237 + + Density error is 0.0993356754821 + + Energy Rydberg eV + E_KohnSham -34.2730252441 -466.308431018 + E_Harris -34.2800779551 -466.404388073 + E_Fermi -0.194855832569 -2.65114961148 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00123564266403 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102270467686 + + Density error is 0.0640230624711 + + Energy Rydberg eV + E_KohnSham -34.2733426117 -466.312749025 + E_Harris -34.2778215436 -466.37368802 + E_Fermi -0.187633217145 -2.55288088724 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113798881329 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973826146022 + + Density error is 0.00221478953242 + + Energy Rydberg eV + E_KohnSham -34.2732610675 -466.31163956 + E_Harris -34.2732686308 -466.311742463 + E_Fermi -0.152859125249 -2.07975509468 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113621558581 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000971231127704 + + Density error is 0.000865973260905 + + Energy Rydberg eV + E_KohnSham -34.273238119 -466.311327329 + E_Harris -34.2732381745 -466.311328084 + E_Fermi -0.152527725648 -2.0752461718 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113494852438 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000970627048868 + + Density error is 0.000201533460159 + + Energy Rydberg eV + E_KohnSham -34.2732494482 -466.311481471 + E_Harris -34.2732494443 -466.311481417 + E_Fermi -0.152126581397 -2.06978832426 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011351025692 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000970771099413 + + Density error is 2.77989413935e-05 + + Energy Rydberg eV + E_KohnSham -34.2732465985 -466.311442699 + E_Harris -34.2732466007 -466.311442729 + E_Fermi -0.152099708926 -2.06942270553 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113504728909 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000970687818149 + + Density error is 1.09053875755e-05 + + Energy Rydberg eV + E_KohnSham -34.273249078 -466.311476434 + E_Harris -34.2732490786 -466.311476442 + E_Fermi -0.152111239307 -2.06957958442 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011350394891 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000970689817403 + + Density error is 1.39565503579e-06 + + Energy Rydberg eV + E_KohnSham -34.2732481872 -466.311464314 + E_Harris -34.2732481872 -466.311464314 + E_Fermi -0.152099475127 -2.06941952453 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113503449569 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000970690443163 + + Density error is 5.57605869316e-07 + + Energy Rydberg eV + E_KohnSham -34.2732484013 -466.311467228 + E_Harris -34.2732484013 -466.311467228 + E_Fermi -0.152099507011 -2.06941995834 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113503494975 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000970691161384 + + Density error is 1.87365441783e-07 + + Energy Rydberg eV + E_KohnSham -34.2732483835 -466.311466985 + E_Harris -34.2732483835 -466.311466985 + E_Fermi -0.152099225245 -2.06941612471 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113503501616 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000970691318609 + + Density error is 1.14393959914e-08 + + Energy Rydberg eV + E_KohnSham -34.2732483872 -466.311467035 + E_Harris -34.2732483872 -466.311467035 + E_band -7.82759185068 -106.499850788 + E_one_elec -68.6024421492 -933.384109945 + E_Hartree +35.7323395619 +486.163420912 + E_xc -8.15982020459 -111.020049438 + E_Ewald +6.88244726752 +93.6404990228 + E_demet -2.06927833785e-56 -2.81539761427e-55 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193390616616 -2.63121432571 + E_Fermi -0.15209904189 -2.06941363004 + + charge density convergence is achieved + final etot is -466.311467035 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.8389 2.00000 + 2 -13.1125 2.00000 + 3 -8.66816 2.00000 + 4 -6.63036 2.00000 + 5 0.957457 0.00000 + 6 4.05376 0.00000 + 7 11.1658 0.00000 + 8 11.3746 0.00000 + + EFERMI = -2.069413630039190 eV + OUT.ABACUS/ final etot is -466.3114670354760 eV + correction force for each atom along direction 1 is 1.66056e-05 + correction force for each atom along direction 2 is -2.71442e-06 + correction force for each atom along direction 3 is -8.26263e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0650630 +0.99729324 -1.5895550 + H1 +0.00041518062 -0.32370414 -0.56407515 + H2 +1.0646478 -0.67358909 +2.1536301 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3114670354760 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5519 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5425 1 7.5 1.e+02% + Potential init_pot 0.28141 2 0.14 3.7% + PW_Basis recip2real 0.28648 17 0.017 3.8% + PW_Basis gathers_scatterp 0.12982 17 0.0076 1.7% + Potential v_of_rho 1.0389 14 0.074 14.% + XC_Functional v_xc 0.30300 15 0.020 4.0% + H_Hartree_pw v_hartree 0.69305 14 0.050 9.2% + PW_Basis real2recip 0.68755 41 0.017 9.1% + PW_Basis gatherp_scatters 0.26462 41 0.0065 3.5% + ORB_control set_orb_tables 1.1019 1 1.1 15.% + ORB_gen_tables gen_tables 1.1019 1 1.1 15.% + ORB_table_phi init_Table 0.48027 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47507 126 0.0038 6.3% + ORB_table_beta init_Table_Beta 0.18746 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18593 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24782 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24588 66 0.0037 3.3% + LOOP_ions opt_ions 5.9258 1 5.9 78.% + ESolver_KS_LCAO Run 5.3501 1 5.4 71.% + HSolverLCAO solve 2.8771 12 0.24 38.% + HamiltLCAO updateHk 1.4708 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4412 12 0.12 19.% + Gint_interface cal_gint 1.9509 25 0.078 26.% + Gint_Gamma distri_vl_value 0.29445 12 0.025 3.9% + Gint_Gamma distri_vl 2.7863 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.7063 14 0.41 76.% + LCAO_gen_fixedH add_v_delta 2.6413 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6413 6 0.44 35.% + ElecStateLCAO psiToRho 1.3826 12 0.12 18.% + Charge mix_rho 0.84507 11 0.077 11.% + LOOP_ions force_stress 0.57554 1 0.58 7.6% + Force_Stress_LCAO getForceStress 0.57552 1 0.58 7.6% + Force_LCAO_gamma ftable_gamma 0.35609 1 0.36 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.29580 1 0.30 3.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:32 2022 + Finish Time : Wed Sep 28 11:09:39 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c8fff607c634d5bc7f8be562db4bc1d5a8f5586b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012342 ima = 3.6807e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124332299721 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113152313442 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113841055605 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114002648802 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113993894683 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114001253923 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113997504232 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011399922689 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011399868972 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113998719267 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113998699714 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113998689928 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3f95c3ee3b74bcac46ab00a465fedbe9791c37b3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.955108443278 15.496454402190 8.108634514400 0 0 0 +H +0.0 +2 +-23.002249845261 13.957719631688 8.391059558631 0 0 0 +-24.609384365512 15.621465884610 6.280668524296 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/conv new file mode 100644 index 0000000000000000000000000000000000000000..86f25324db91190a426ccb34fc8a4e4ca9d50aac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/conv @@ -0,0 +1 @@ +88 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0e9de3d472fc84ab3309aa2741271d8a79fbca5b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742731074 0.01224082008 1.244907017 1.35609015 1.467312177 0.007318129904 0.02037918851 0.03885768461 +2.875171771e-18 0.0009901816195 0.002109944528 0.01122697593 0.03826273005 -4.623110525e-19 1.035204372e-06 3.651956043e-06 +0.001789732481 0.005368296295 + +H atom_index 1 n_descriptor 18 +1.239371143 0.03393013193 0.1046014355 0.1477093297 0.3214918371 0.02104156116 0.02804041686 0.03722132305 +1.902788047e-17 3.029207745e-05 0.09723326395 0.1147713057 0.1265313659 -1.990264977e-18 4.083568147e-06 0.01285115193 +0.02502848378 0.03046817025 + +H atom_index 2 n_descriptor 18 +1.148644718 0.03681183758 0.07795152801 0.1110934309 0.288691744 0.01712510666 0.02281051724 0.04087972693 +-5.429761981e-19 2.438360649e-05 0.07380492697 0.09430288552 0.1113454741 5.966691986e-18 5.909034675e-06 0.01530172668 +0.02131870179 0.02576257144 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d6ff6b2a87d4a2ddf2c7689ea247b8465f19d0b4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:32 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0861896 SEC) : SETUP UNITCELL + DONE(0.0875562 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105897 SEC) : INIT PLANEWAVE + DONE(0.156638 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.436721 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651034e+02 0.000000e+00 2.135e-01 5.532e-01 + GE2 -4.663084e+02 -1.204984e+00 9.934e-02 5.034e-01 + GE3 -4.663127e+02 -4.318007e-03 6.402e-02 5.658e-01 + GE4 -4.663116e+02 1.109466e-03 2.215e-03 4.299e-01 + GE5 -4.663113e+02 3.122309e-04 8.660e-04 4.292e-01 + GE6 -4.663115e+02 -1.541428e-04 2.015e-04 4.245e-01 + GE7 -4.663114e+02 3.877220e-05 2.780e-05 4.078e-01 + GE8 -4.663115e+02 -3.373502e-05 1.091e-05 4.074e-01 + GE9 -4.663115e+02 1.211982e-05 1.396e-06 4.076e-01 + GE10 -4.663115e+02 -2.913302e-06 5.576e-07 4.074e-01 + GE11 -4.663115e+02 2.428738e-07 1.874e-07 4.077e-01 + GE12 -4.663115e+02 -5.065260e-08 1.144e-08 3.426e-01 +E_delta_band = -6.76177538e-02 Ry = -9.19986738e-01 eV +E_delta_NN= -1.93390617e-01 Ry = -2.63121433e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5519 11 0.69 1e+02 % + Run_lcao lcao_line 7.5425 1 7.5 1e+02 % + Potential init_pot 0.28141 2 0.14 3.7 % + PW_Basis recip2real 0.28648 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.12982 17 0.0076 1.7 % + Potential v_of_rho 1.0389 14 0.074 14 % + XC_Functional v_xc 0.303 15 0.02 4 % + H_Hartree_pw v_hartree 0.69305 14 0.05 9.2 % + PW_Basis real2recip 0.68755 41 0.017 9.1 % + PW_Basis gatherp_scatters 0.26462 41 0.0065 3.5 % + ORB_control set_orb_tables 1.1019 1 1.1 15 % + ORB_gen_tables gen_tables 1.1019 1 1.1 15 % + ORB_table_phi init_Table 0.48027 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47507 126 0.0038 6.3 % + ORB_table_beta init_Table_Beta 0.18746 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18593 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24782 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24588 66 0.0037 3.3 % + LOOP_ions opt_ions 5.9258 1 5.9 78 % + ESolver_KS_LCAO Run 5.3501 1 5.4 71 % + HSolverLCAO solve 2.8771 12 0.24 38 % + HamiltLCAO updateHk 1.4708 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.4412 12 0.12 19 % + Gint_interface cal_gint 1.9509 25 0.078 26 % + Gint_Gamma distri_vl_value 0.29445 12 0.025 3.9 % + Gint_Gamma distri_vl 2.7863 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.7063 14 0.41 76 % + LCAO_gen_fixedH add_v_delta 2.6413 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6413 6 0.44 35 % + ElecStateLCAO psiToRho 1.3826 12 0.12 18 % + Charge mix_rho 0.84507 11 0.077 11 % + LOOP_ions force_stress 0.57554 1 0.58 7.6 % + Force_Stress_LCAO getForceStress 0.57552 1 0.58 7.6 % + Force_LCAO_gamma ftable_gamma 0.35609 1 0.36 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.2958 1 0.3 3.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:32 2022 + FINISH Time : Wed Sep 28 11:09:39 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/88/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..8ab465ec35d19765a1219982cfbf3ee8fa1ac1a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.152977 0.546991 0.280176 +H 0.187976 0.494235 0.261257 +H 0.106478 0.540663 0.237773 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ca60b035c2d23a2fb4fc372453b86beadbf37d6d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6053 2 + 2 -12.7811 2 + 3 -9.52134 2 + 4 -6.81253 2 + 5 1.34206 0 + 6 4.61837 0 + 7 11.0263 0 + 8 11.3111 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ac7328e73d53a5923111ce350ba28811037703d0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:26 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.28334332431 15.3157368812 7.84491440796 0 0 0 0 + tauc_H1 5.26332489661 13.8385761693 7.3152035738 0 0 0 0 + tauc_H2 2.98138652651 15.138570082 6.65763323815 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0883207975413 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0887153085419 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106985479784 (SEC) + + DONE : INIT CHARGE Time : 0.157701682133 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438847 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 144 0 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000682 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00152 + + Density error is 0.21529169723 + + Energy Rydberg eV + E_KohnSham -34.184743593 -465.107297534 + E_Harris -34.3785124852 -467.743658563 + E_Fermi -0.416480970511 -5.66651430752 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.001057126514 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00143391766695 + + Density error is 0.0971862799429 + + Energy Rydberg eV + E_KohnSham -34.2750278541 -466.335677924 + E_Harris -34.2818314244 -466.428245248 + E_Fermi -0.225622902145 -3.06975706847 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00101251373691 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132791369203 + + Density error is 0.0622033845326 + + Energy Rydberg eV + E_KohnSham -34.2753154956 -466.339591488 + E_Harris -34.2797109534 -466.399394759 + E_Fermi -0.213075353502 -2.89903891099 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000960965110538 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115362042872 + + Density error is 0.0019900098952 + + Energy Rydberg eV + E_KohnSham -34.2753257776 -466.339731382 + E_Harris -34.2753276044 -466.339756236 + E_Fermi -0.17692384563 -2.40717241265 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000966507752463 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115560749193 + + Density error is 0.000914209496863 + + Energy Rydberg eV + E_KohnSham -34.2752585359 -466.338816511 + E_Harris -34.2752604559 -466.338842634 + E_Fermi -0.176160647732 -2.39678857253 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00096482069456 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115310431159 + + Density error is 0.000130089231179 + + Energy Rydberg eV + E_KohnSham -34.2753045767 -466.339442929 + E_Harris -34.2753046185 -466.339443497 + E_Fermi -0.176239353921 -2.39785942517 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000964723818351 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115280506875 + + Density error is 4.1905581186e-05 + + Energy Rydberg eV + E_KohnSham -34.2752887001 -466.339226916 + E_Harris -34.2752887084 -466.339227029 + E_Fermi -0.176117854833 -2.39620634527 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000964656489388 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115277573518 + + Density error is 2.05672567089e-05 + + Energy Rydberg eV + E_KohnSham -34.2752921424 -466.339273752 + E_Harris -34.2752921441 -466.339273775 + E_Fermi -0.176163022417 -2.39682088177 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000964658447145 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115273878901 + + Density error is 2.20744565506e-06 + + Energy Rydberg eV + E_KohnSham -34.2752905639 -466.339252275 + E_Harris -34.275290564 -466.339252275 + E_Fermi -0.176140396347 -2.3965130383 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00096466079546 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115273926589 + + Density error is 6.93462930222e-07 + + Energy Rydberg eV + E_KohnSham -34.2752908405 -466.339256038 + E_Harris -34.2752908405 -466.339256038 + E_Fermi -0.176139267914 -2.39649768518 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000964662007025 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115273933018 + + Density error is 1.81330744499e-07 + + Energy Rydberg eV + E_KohnSham -34.2752908607 -466.339256313 + E_Harris -34.2752908607 -466.339256313 + E_Fermi -0.176138815517 -2.39649153 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000964662175549 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115273912528 + + Density error is 1.11541058813e-08 + + Energy Rydberg eV + E_KohnSham -34.2752908682 -466.339256415 + E_Harris -34.2752908682 -466.339256415 + E_band -8.04373293094 -109.440601051 + E_one_elec -69.6291098537 -947.352640678 + E_Hartree +36.185966078 +492.335326295 + E_xc -8.23316210251 -112.017917152 + E_Ewald +7.52461120934 +102.377587682 + E_demet -1.19129632105e-84 -1.62084179728e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195501666499 -2.65993663288 + E_Fermi -0.176138614342 -2.39648879287 + + charge density convergence is achieved + final etot is -466.339256415 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6053 2.00000 + 2 -12.7811 2.00000 + 3 -9.52134 2.00000 + 4 -6.81253 2.00000 + 5 1.34206 0.00000 + 6 4.61837 0.00000 + 7 11.0263 0.00000 + 8 11.3111 0.00000 + + EFERMI = -2.396488792874898 eV + OUT.ABACUS/ final etot is -466.3392564148616 eV + correction force for each atom along direction 1 is 1.60638e-05 + correction force for each atom along direction 2 is -5.85209e-05 + correction force for each atom along direction 3 is 1.05184e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.6077270 -0.42879729 +0.89635185 + H1 +0.47171111 +0.10028047 +0.46074517 + H2 -2.0794381 +0.32851682 -1.3570970 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3392564148616 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3487 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3390 1 7.3 1.e+02% + Potential init_pot 0.28418 2 0.14 3.9% + PW_Basis recip2real 0.29203 17 0.017 4.0% + PW_Basis gathers_scatterp 0.12442 17 0.0073 1.7% + Potential v_of_rho 1.0539 14 0.075 14.% + XC_Functional v_xc 0.30218 15 0.020 4.1% + H_Hartree_pw v_hartree 0.70473 14 0.050 9.6% + PW_Basis real2recip 0.69595 41 0.017 9.5% + PW_Basis gatherp_scatters 0.26509 41 0.0065 3.6% + ORB_control set_orb_tables 1.0985 1 1.1 15.% + ORB_gen_tables gen_tables 1.0985 1 1.1 15.% + ORB_table_phi init_Table 0.47493 1 0.47 6.5% + ORB_table_phi cal_ST_Phi12_R 0.46980 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18545 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18390 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.25191 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.25001 66 0.0038 3.4% + LOOP_ions opt_ions 5.7246 1 5.7 78.% + ESolver_KS_LCAO Run 5.1657 1 5.2 70.% + HSolverLCAO solve 2.7196 12 0.23 37.% + HamiltLCAO updateHk 1.4001 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.3705 12 0.11 19.% + Gint_interface cal_gint 2.1221 25 0.085 29.% + Gint_Gamma distri_vl_value 0.15894 12 0.013 2.2% + Gint_Gamma distri_vl 2.6954 6 0.45 37.% + LCAO_Deepks cal_projected_DM 5.5372 14 0.40 75.% + LCAO_gen_fixedH add_v_delta 2.5492 6 0.42 35.% + LCAO_DESCRIPTOR add_v_delta 2.5492 6 0.42 35.% + ElecStateLCAO psiToRho 1.2984 12 0.11 18.% + Charge mix_rho 0.84686 11 0.077 12.% + LOOP_ions force_stress 0.55867 1 0.56 7.6% + Force_Stress_LCAO getForceStress 0.55864 1 0.56 7.6% + Force_LCAO_gamma ftable_gamma 0.34227 1 0.34 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.30894 1 0.31 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:26 2022 + Finish Time : Wed Sep 28 11:14:33 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..66e162a1aae1deaea0a30736a1cd3c5cca6d3c97 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124011 ima = 3.69702e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122417113079 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111321316809 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111857992944 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112149158169 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112081490942 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112119611768 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112114540364 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112117649737 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112116846709 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112116769873 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112116742659 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112116733024 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e2273a7080b89dfa17fa54e67efb199809a5a753 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.716656675711 15.315736881242 7.844914407940 0 0 0 +H +0.0 +2 +-22.736675103378 13.838576169349 7.315203573809 0 0 0 +-25.018613473515 15.138570081982 6.657633238164 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/conv new file mode 100644 index 0000000000000000000000000000000000000000..a4c6b24663b535a0f8f1f3dacce48b2af2434894 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/conv @@ -0,0 +1 @@ +89 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7d5e75ae3d77a54bc03ca25ff1d87842f4aa401b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755121112 0.01288500142 1.279506112 1.364782016 1.470543806 0.009834863667 0.01672136632 0.03918936613 +9.020717749e-19 0.0009334546429 0.003019437086 0.01399074989 0.04892238335 4.614022259e-19 3.242013888e-06 8.239139405e-06 +0.00158774411 0.006168908239 + +H atom_index 1 n_descriptor 18 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:26 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0883443 SEC) : SETUP UNITCELL + DONE(0.0887326 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107009 SEC) : INIT PLANEWAVE + DONE(0.157837 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438908 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651073e+02 0.000000e+00 2.153e-01 5.338e-01 + GE2 -4.663357e+02 -1.228380e+00 9.719e-02 4.858e-01 + GE3 -4.663396e+02 -3.913564e-03 6.220e-02 5.556e-01 + GE4 -4.663397e+02 -1.398943e-04 1.990e-03 4.178e-01 + GE5 -4.663388e+02 9.148711e-04 9.142e-04 4.164e-01 + GE6 -4.663394e+02 -6.264179e-04 1.301e-04 4.087e-01 + GE7 -4.663392e+02 2.160126e-04 4.191e-05 4.012e-01 + GE8 -4.663393e+02 -4.683583e-05 2.057e-05 3.899e-01 + GE9 -4.663393e+02 2.147670e-05 2.207e-06 3.905e-01 + GE10 -4.663393e+02 -3.762851e-06 6.935e-07 3.903e-01 + GE11 -4.663393e+02 -2.746785e-07 1.813e-07 3.895e-01 + GE12 -4.663393e+02 -1.021377e-07 1.115e-08 3.238e-01 +E_delta_band = -7.19054672e-02 Ry = -9.78324071e-01 eV +E_delta_NN= -1.95501666e-01 Ry = -2.65993663e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3487 11 0.67 1e+02 % + Run_lcao lcao_line 7.339 1 7.3 1e+02 % + Potential init_pot 0.28418 2 0.14 3.9 % + PW_Basis recip2real 0.29203 17 0.017 4 % + PW_Basis gathers_scatterp 0.12442 17 0.0073 1.7 % + Potential v_of_rho 1.0539 14 0.075 14 % + XC_Functional v_xc 0.30218 15 0.02 4.1 % + H_Hartree_pw v_hartree 0.70473 14 0.05 9.6 % + PW_Basis real2recip 0.69595 41 0.017 9.5 % + PW_Basis gatherp_scatters 0.26509 41 0.0065 3.6 % + ORB_control set_orb_tables 1.0985 1 1.1 15 % + ORB_gen_tables gen_tables 1.0985 1 1.1 15 % + ORB_table_phi init_Table 0.47493 1 0.47 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.4698 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18545 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.1839 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.25191 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.25001 66 0.0038 3.4 % + LOOP_ions opt_ions 5.7246 1 5.7 78 % + ESolver_KS_LCAO Run 5.1657 1 5.2 70 % + HSolverLCAO solve 2.7196 12 0.23 37 % + HamiltLCAO updateHk 1.4001 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.3705 12 0.11 19 % + Gint_interface cal_gint 2.1221 25 0.085 29 % + Gint_Gamma distri_vl_value 0.15894 12 0.013 2.2 % + Gint_Gamma distri_vl 2.6954 6 0.45 37 % + LCAO_Deepks cal_projected_DM 5.5372 14 0.4 75 % + LCAO_gen_fixedH add_v_delta 2.5492 6 0.42 35 % + LCAO_DESCRIPTOR add_v_delta 2.5492 6 0.42 35 % + ElecStateLCAO psiToRho 1.2984 12 0.11 18 % + Charge mix_rho 0.84686 11 0.077 12 % + LOOP_ions force_stress 0.55867 1 0.56 7.6 % + Force_Stress_LCAO getForceStress 0.55864 1 0.56 7.6 % + Force_LCAO_gamma ftable_gamma 0.34227 1 0.34 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.30894 1 0.31 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:26 2022 + FINISH Time : Wed Sep 28 11:14:33 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/89/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..19a1d253c5453f00747847b0323d853aa33adc5d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.587076 0.161558 0.36255 +H 0.531112 0.14653 0.336898 +H 0.588079 0.231168 0.354267 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ce1a2a4e82240e0fdd304dd2a2ec33d84851040d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1834 2 + 2 -12.7463 2 + 3 -9.2166 2 + 4 -6.71562 2 + 5 0.979286 0 + 6 4.20823 0 + 7 11.1097 0 + 8 11.3461 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9a1947223f51119ab0e2820e0810eb45781c54e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:41 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.4381224436 4.5236203678 10.151394502 0 0 0 0 + tauc_H1 14.8711481172 4.10284186354 9.4331546769 0 0 0 0 + tauc_H2 16.4662249557 6.47269419474 9.9194733178 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870825268218 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0972023587732 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115310741691 (SEC) + + DONE : INIT CHARGE Time : 0.165569575266 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44703 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00149 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000515 + + Density error is 0.212616075145 + + Energy Rydberg eV + E_KohnSham -34.1834164022 -465.089240177 + E_Harris -34.3714519839 -467.647595514 + E_Fermi -0.397063623948 -5.40232775422 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00132486194044 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000765049342241 + + Density error is 0.0983752235163 + + Energy Rydberg eV + E_KohnSham -34.2720480821 -466.295136047 + E_Harris -34.2790813801 -466.390828976 + E_Fermi -0.207804082588 -2.82731959086 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00122244306986 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000743186695033 + + Density error is 0.0632680261649 + + Energy Rydberg eV + E_KohnSham -34.2723507159 -466.29925359 + E_Harris -34.2768697775 -466.360738578 + E_Fermi -0.199146677719 -2.70952955475 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010242444822 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000731010836216 + + Density error is 0.00197336034711 + + Energy Rydberg eV + E_KohnSham -34.272281995 -466.298318595 + E_Harris -34.2722834922 -466.298338965 + E_Fermi -0.16347813628 -2.22423415183 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00102114925993 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00072949437633 + + Density error is 0.000832684186859 + + Energy Rydberg eV + E_KohnSham -34.2722514982 -466.297903664 + E_Harris -34.272251733 -466.297906859 + E_Fermi -0.163307793679 -2.22191652184 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010186944574 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729575027839 + + Density error is 0.000167929760708 + + Energy Rydberg eV + E_KohnSham -34.2722641922 -466.298076376 + E_Harris -34.2722641886 -466.298076327 + E_Fermi -0.162941077858 -2.21692709713 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001018619723 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729751677894 + + Density error is 3.00814240878e-05 + + Energy Rydberg eV + E_KohnSham -34.2722611856 -466.298035468 + E_Harris -34.2722611863 -466.298035478 + E_Fermi -0.16290680557 -2.21646079873 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101857620461 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729697177215 + + Density error is 1.09205543603e-05 + + Energy Rydberg eV + E_KohnSham -34.2722631137 -466.298061702 + E_Harris -34.2722631143 -466.298061709 + E_Fermi -0.162915301623 -2.21657639346 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101856804748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729709187123 + + Density error is 2.59679207609e-06 + + Energy Rydberg eV + E_KohnSham -34.2722623235 -466.29805095 + E_Harris -34.2722623235 -466.29805095 + E_Fermi -0.162906685956 -2.2164591713 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101856047586 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729710561264 + + Density error is 4.9065071098e-07 + + Energy Rydberg eV + E_KohnSham -34.272262498 -466.298053324 + E_Harris -34.272262498 -466.298053324 + E_Fermi -0.162904347822 -2.21642735935 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101856020445 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729711171484 + + Density error is 1.77587646543e-07 + + Energy Rydberg eV + E_KohnSham -34.2722625152 -466.298053558 + E_Harris -34.2722625152 -466.298053558 + E_Fermi -0.162904130922 -2.21642440828 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00101855987351 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729711475986 + + Density error is 1.08940236622e-08 + + Energy Rydberg eV + E_KohnSham -34.2722625183 -466.298053601 + E_Harris -34.2722625183 -466.298053601 + E_band -7.91755980695 -107.72392763 + E_one_elec -68.9136996585 -937.618985617 + E_Hartree +35.8571079659 +487.860982138 + E_xc -8.18123981505 -111.311478189 + E_Ewald +7.09062579146 +96.4729131496 + E_demet -1.4249925548e-62 -1.93880183529e-61 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194325682557 -2.64393655051 + E_Fermi -0.162903963678 -2.2164221328 + + charge density convergence is achieved + final etot is -466.298053601 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1834 2.00000 + 2 -12.7463 2.00000 + 3 -9.21660 2.00000 + 4 -6.71562 2.00000 + 5 0.979286 0.00000 + 6 4.20823 0.00000 + 7 11.1097 0.00000 + 8 11.3461 0.00000 + + EFERMI = -2.216422132799959 eV + OUT.ABACUS/ final etot is -466.2980536007074 eV + correction force for each atom along direction 1 is -0.000118086 + correction force for each atom along direction 2 is 0.000120836 + correction force for each atom along direction 3 is -0.000156001 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.8024527 +3.1328525 +0.48829196 + H1 -1.8961546 -0.66985861 -0.84701111 + H2 +0.093701839 -2.4629939 +0.35871915 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2980536007074 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5597 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5503 1 7.6 1.e+02% + Potential init_pot 0.28425 2 0.14 3.8% + PW_Basis recip2real 0.28756 17 0.017 3.8% + PW_Basis gathers_scatterp 0.13381 17 0.0079 1.8% + Potential v_of_rho 1.0841 14 0.077 14.% + XC_Functional v_xc 0.34207 15 0.023 4.5% + H_Hartree_pw v_hartree 0.70229 14 0.050 9.3% + PW_Basis real2recip 0.73026 41 0.018 9.7% + PW_Basis gatherp_scatters 0.33019 41 0.0081 4.4% + ORB_control set_orb_tables 1.1024 1 1.1 15.% + ORB_gen_tables gen_tables 1.1024 1 1.1 15.% + ORB_table_phi init_Table 0.47386 1 0.47 6.3% + ORB_table_phi cal_ST_Phi12_R 0.46863 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18977 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18818 56 0.0034 2.5% + ORB_table_alpha init_Table_Alpha 0.25280 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.25080 66 0.0038 3.3% + LOOP_ions opt_ions 5.9221 1 5.9 78.% + ESolver_KS_LCAO Run 5.3053 1 5.3 70.% + HSolverLCAO solve 2.7489 12 0.23 36.% + HamiltLCAO updateHk 1.4164 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.3851 12 0.12 18.% + Gint_interface cal_gint 0.78384 25 0.031 10.% + Gint_Gamma distri_vl_value 0.66564 12 0.055 8.8% + Gint_Gamma distri_vl 2.7293 6 0.45 36.% + LCAO_Deepks cal_projected_DM 5.5474 14 0.40 73.% + LCAO_gen_fixedH add_v_delta 2.5887 6 0.43 34.% + LCAO_DESCRIPTOR add_v_delta 2.5889 6 0.43 34.% + ElecStateLCAO psiToRho 1.2991 12 0.11 17.% + Charge mix_rho 0.86692 11 0.079 11.% + LOOP_ions force_stress 0.61658 1 0.62 8.2% + Force_Stress_LCAO getForceStress 0.61655 1 0.62 8.2% + Force_LCAO_gamma ftable_gamma 0.39654 1 0.40 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.17917 1 0.18 2.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:41 2022 + Finish Time : Wed Sep 28 11:04:49 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..26db7c646cb571192f3025ef4151199e47d9c1ae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123834 ima = 3.66673e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 7.99999999999999 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123221861271 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112008018733 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112703785098 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112923672522 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112907867333 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011291650626 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112913796199 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112915205056 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112914683555 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011291463015 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112914612725 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112914603604 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/STRU new file mode 100644 index 0000000000000000000000000000000000000000..58a23de4432dde25cedf93eb3ff3c7ae1ac45fd2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.561877556411 4.523620367813 10.151394501968 0 0 0 +H +0.0 +2 +-13.128851882759 4.102841863552 9.433154676902 0 0 0 +-11.533775044260 6.472694194720 9.919473317783 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/conv new file mode 100644 index 0000000000000000000000000000000000000000..8c9a13a2aabefc0887334ac8d8df3c2a36c41b85 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/conv @@ -0,0 +1 @@ +9 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e6d46d20d342123c39e0dc95f3126e64be2efd74 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752120324 0.01245908005 1.241535178 1.358929921 1.469020459 0.008968238202 0.01765910725 0.03918325607 +-3.319477741e-18 0.0009064078248 0.002594061201 0.01181045427 0.04413374666 5.494358177e-20 1.886519109e-06 5.829902787e-06 +0.001559018002 0.005855095083 + +H atom_index 1 n_descriptor 18 +1.29408388 0.03306569961 0.1245996321 0.1717315115 0.3343130916 0.024367669 0.03083451906 0.03680416126 +-2.375135191e-17 4.79652084e-05 0.1069629352 0.1207195091 0.1471266711 2.586553849e-18 1.492822298e-06 0.01353308054 +0.02748286188 0.03254014954 + +H atom_index 2 n_descriptor 18 +1.146065424 0.03756733338 0.07697171617 0.107591802 0.2816859727 0.0174485718 0.02222378939 0.04168756058 +1.079097144e-17 3.504277639e-05 0.07374792461 0.09128935002 0.1100313457 5.186177445e-18 7.307493575e-06 0.01607533096 +0.0216685595 0.02523807287 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fc6fa500ccb1da1239509691564995b2130afe54 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/e_base.npy 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/dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..69981377ab7f80969d20e7cbce034151675f1c0a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..32293a6acc1af271369528a34b604e8739da1d80 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:41 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871058 SEC) : SETUP UNITCELL + DONE(0.0972197 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115333 SEC) : INIT PLANEWAVE + DONE(0.165689 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447095 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650892e+02 0.000000e+00 2.126e-01 5.409e-01 + GE2 -4.662951e+02 -1.205896e+00 9.838e-02 4.828e-01 + GE3 -4.662993e+02 -4.117544e-03 6.327e-02 5.527e-01 + GE4 -4.662983e+02 9.349953e-04 1.973e-03 4.194e-01 + GE5 -4.662979e+02 4.149308e-04 8.327e-04 4.437e-01 + GE6 -4.662981e+02 -1.727112e-04 1.679e-04 4.185e-01 + GE7 -4.662980e+02 4.090739e-05 3.008e-05 4.371e-01 + GE8 -4.662981e+02 -2.623365e-05 1.092e-05 4.161e-01 + GE9 -4.662981e+02 1.075175e-05 2.597e-06 4.034e-01 + GE10 -4.662981e+02 -2.374424e-06 4.907e-07 3.955e-01 + GE11 -4.662981e+02 -2.337148e-07 1.776e-07 3.937e-01 + GE12 -4.662981e+02 -4.254501e-08 1.089e-08 3.357e-01 +E_delta_band = -6.92688805e-02 Ry = -9.42451468e-01 eV +E_delta_NN= -1.94325683e-01 Ry = -2.64393655e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5597 11 0.69 1e+02 % + Run_lcao lcao_line 7.5503 1 7.6 1e+02 % + Potential init_pot 0.28425 2 0.14 3.8 % + PW_Basis recip2real 0.28756 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.13381 17 0.0079 1.8 % + Potential v_of_rho 1.0841 14 0.077 14 % + XC_Functional v_xc 0.34207 15 0.023 4.5 % + H_Hartree_pw v_hartree 0.70229 14 0.05 9.3 % + PW_Basis real2recip 0.73026 41 0.018 9.7 % + PW_Basis gatherp_scatters 0.33019 41 0.0081 4.4 % + ORB_control set_orb_tables 1.1024 1 1.1 15 % + ORB_gen_tables gen_tables 1.1024 1 1.1 15 % + ORB_table_phi init_Table 0.47386 1 0.47 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.46863 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18977 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18818 56 0.0034 2.5 % + ORB_table_alpha init_Table_Alpha 0.2528 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.2508 66 0.0038 3.3 % + LOOP_ions opt_ions 5.9221 1 5.9 78 % + ESolver_KS_LCAO Run 5.3053 1 5.3 70 % + HSolverLCAO solve 2.7489 12 0.23 36 % + HamiltLCAO updateHk 1.4164 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.3851 12 0.12 18 % + Gint_interface cal_gint 0.78384 25 0.031 10 % + Gint_Gamma distri_vl_value 0.66564 12 0.055 8.8 % + Gint_Gamma distri_vl 2.7293 6 0.45 36 % + LCAO_Deepks cal_projected_DM 5.5474 14 0.4 73 % + LCAO_gen_fixedH add_v_delta 2.5887 6 0.43 34 % + LCAO_DESCRIPTOR add_v_delta 2.5889 6 0.43 34 % + ElecStateLCAO psiToRho 1.2991 12 0.11 17 % + Charge mix_rho 0.86692 11 0.079 11 % + LOOP_ions force_stress 0.61658 1 0.62 8.2 % + Force_Stress_LCAO getForceStress 0.61655 1 0.62 8.2 % + Force_LCAO_gamma ftable_gamma 0.39654 1 0.4 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.17917 1 0.18 2.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:41 2022 + FINISH Time : Wed Sep 28 11:04:49 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/9/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..202ecd441951f1cd08c72b9d9d94f9856ad124d1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.169919 0.532764 0.273486 +H 0.18164 0.482487 0.235978 +H 0.1042 0.539037 0.270529 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d8fd1fb35d6b74215c0a13a984985803cc06f5e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4036 2 + 2 -13.0866 2 + 3 -9.17062 2 + 4 -6.76964 2 + 5 1.36409 0 + 6 4.56152 0 + 7 11.0499 0 + 8 11.302 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7137e3a833da3b6716bde89bb39253f7d71f1e35 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:33 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 4.75772586879 14.9173869776 7.65759545741 0 0 0 0 + tauc_H1 5.08592862525 13.5096370066 6.60737073338 0 0 0 0 + tauc_H2 2.91760373711 15.093036326 7.57480641512 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0730131105403 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0849606643506 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.100741479625 (SEC) + + DONE : INIT CHARGE Time : 0.142322314817 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.385856 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 144 0 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000604 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00186 + + Density error is 0.215970702628 + + Energy Rydberg eV + E_KohnSham -34.1888298179 -465.162893476 + E_Harris -34.3830989928 -467.8060612 + E_Fermi -0.411665056039 -5.60099042962 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000960313728228 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00145362361222 + + Density error is 0.0978402162793 + + Energy Rydberg eV + E_KohnSham -34.27941579 -466.395378855 + E_Harris -34.2861303096 -466.486734582 + E_Fermi -0.219666290985 -2.98871321592 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000926060636109 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00132923899392 + + Density error is 0.0626744893947 + + Energy Rydberg eV + E_KohnSham -34.2797179199 -466.399489543 + E_Harris -34.2840543222 -466.458489324 + E_Fermi -0.207600953655 -2.82455587995 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000886755342989 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110775564698 + + Density error is 0.0020049333149 + + Energy Rydberg eV + E_KohnSham -34.279722783 -466.399555709 + E_Harris -34.2797242463 -466.399575618 + E_Fermi -0.171860941307 -2.33828806542 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000888993713137 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110517990448 + + Density error is 0.000920960989578 + + Energy Rydberg eV + E_KohnSham -34.2796555028 -466.398640315 + E_Harris -34.2796569479 -466.398659977 + E_Fermi -0.171042613299 -2.32715414167 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000888042112081 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110290379609 + + Density error is 0.000120594766273 + + Energy Rydberg eV + E_KohnSham -34.2796971031 -466.399206316 + E_Harris -34.2796971163 -466.399206496 + E_Fermi -0.171089457425 -2.32779148871 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000888126848736 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110260712255 + + Density error is 4.28380925367e-05 + + Energy Rydberg eV + E_KohnSham -34.27968376 -466.399024774 + E_Harris -34.2796837706 -466.399024918 + E_Fermi -0.170962437864 -2.32606329891 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000888044965571 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110263757851 + + Density error is 1.39313218012e-05 + + Energy Rydberg eV + E_KohnSham -34.2796870063 -466.399068942 + E_Harris -34.2796870071 -466.399068954 + E_Fermi -0.171011373934 -2.32672910831 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000888052061186 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110260520889 + + Density error is 1.22168330329e-06 + + Energy Rydberg eV + E_KohnSham -34.2796855355 -466.399048931 + E_Harris -34.2796855355 -466.399048931 + E_Fermi -0.170995991525 -2.3265198199 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000888054008479 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110260181716 + + Density error is 1.42127586169e-07 + + Energy Rydberg eV + E_KohnSham -34.2796857624 -466.399052018 + E_Harris -34.2796857624 -466.399052018 + E_Fermi -0.170995050688 -2.32650701916 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000888054371677 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110260217278 + + Density error is 4.64440671458e-08 + + Energy Rydberg eV + E_KohnSham -34.2796857806 -466.399052266 + E_Harris -34.2796857806 -466.399052266 + E_band -8.00111987445 -108.860820674 + E_one_elec -69.4887739755 -945.443273101 + E_Hartree +36.1313999637 +491.592916223 + E_xc -8.22450295533 -111.90010341 + E_Ewald +7.42611251486 +101.037444191 + E_demet -1.46414037727e-82 -1.99206518027e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195196258468 -2.65578134345 + E_Fermi -0.170995099095 -2.32650767777 + + charge density convergence is achieved + final etot is -466.399052266 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4036 2.00000 + 2 -13.0866 2.00000 + 3 -9.17062 2.00000 + 4 -6.76964 2.00000 + 5 1.36409 0.00000 + 6 4.56152 0.00000 + 7 11.0499 0.00000 + 8 11.3020 0.00000 + + EFERMI = -2.326507677768757 eV + OUT.ABACUS/ final etot is -466.3990522656546 eV + correction force for each atom along direction 1 is -1.49847e-05 + correction force for each atom along direction 2 is -0.000140906 + correction force for each atom along direction 3 is -2.92732e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.58728885 +1.2481208 +0.89990788 + H1 +0.41056358 -1.3137300 -0.96966642 + H2 +0.17672527 +0.065609121 +0.069758533 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3990522656546 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4283 11 0.58 1.0e+02% + Run_lcao lcao_line 6.4207 1 6.4 1.e+02% + Potential init_pot 0.24078 2 0.12 3.7% + PW_Basis recip2real 0.24548 16 0.015 3.8% + PW_Basis gathers_scatterp 0.10421 16 0.0065 1.6% + Potential v_of_rho 0.89631 13 0.069 14.% + XC_Functional v_xc 0.26869 14 0.019 4.2% + H_Hartree_pw v_hartree 0.58931 13 0.045 9.2% + PW_Basis real2recip 0.58871 38 0.015 9.2% + PW_Basis gatherp_scatters 0.21512 38 0.0057 3.3% + ORB_control set_orb_tables 0.90715 1 0.91 14.% + ORB_gen_tables gen_tables 0.90714 1 0.91 14.% + ORB_table_phi init_Table 0.38325 1 0.38 6.0% + ORB_table_phi cal_ST_Phi12_R 0.37891 126 0.0030 5.9% + ORB_table_beta init_Table_Beta 0.15674 1 0.16 2.4% + ORB_table_beta VNL_PhiBeta_R 0.15547 56 0.0028 2.4% + ORB_table_alpha init_Table_Alpha 0.20966 1 0.21 3.3% + ORB_table_alpha S_PhiAlpha_R 0.20801 66 0.0032 3.2% + LOOP_ions opt_ions 5.0593 1 5.1 79.% + ESolver_KS_LCAO Run 4.5460 1 4.5 71.% + HSolverLCAO solve 2.4085 11 0.22 37.% + HamiltLCAO updateHk 1.2438 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.2172 11 0.11 19.% + Gint_interface cal_gint 1.9552 23 0.085 30.% + Gint_Gamma distri_vl_value 0.12364 11 0.011 1.9% + Gint_Gamma distri_vl 2.1897 6 0.36 34.% + LCAO_Deepks cal_projected_DM 4.8915 13 0.38 76.% + LCAO_gen_fixedH add_v_delta 2.0610 6 0.34 32.% + LCAO_DESCRIPTOR add_v_delta 2.0611 6 0.34 32.% + ElecStateLCAO psiToRho 1.1478 11 0.10 18.% + Charge mix_rho 0.75116 10 0.075 12.% + LOOP_ions force_stress 0.51315 1 0.51 8.0% + Force_Stress_LCAO getForceStress 0.51313 1 0.51 8.0% + Force_LCAO_gamma ftable_gamma 0.31952 1 0.32 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.28944 1 0.29 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:33 2022 + Finish Time : Wed Sep 28 11:07:39 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2cd976ff2e3db0e1f666b3dea1c7554c5f61e9cc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123699 ima = 3.67525e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123028915488 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111991434387 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112508505731 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112776153585 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112717154802 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011274918962 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112744220611 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011274729459 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112746674579 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112746630485 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112746626763 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/STRU new file mode 100644 index 0000000000000000000000000000000000000000..51db28a5b2986d99cad46fcc3546dd37691e1978 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-23.242274131226 14.917386977561 7.657595457399 0 0 0 +H +0.0 +2 +-22.914071374727 13.509637006611 6.607370733372 0 0 0 +-25.082396262916 15.093036325987 7.574806415097 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/conv new file mode 100644 index 0000000000000000000000000000000000000000..212c707d29fa2ebac208365b1750566f7c62220c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/conv @@ -0,0 +1 @@ +90 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4310d23dcea948b228a51fe3c64fe349ba0b1c49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749884345 0.01274694856 1.279066217 1.368856898 1.469848868 0.008698507594 0.01852520332 0.0390484468 +1.811749005e-18 0.001079613901 0.002690994979 0.01274204154 0.04638478941 2.865712845e-19 2.234763205e-06 6.321090994e-06 +0.001637976053 0.00598148944 + +H atom_index 1 n_descriptor 18 +1.282892897 0.03320866045 0.1207537293 0.1658614717 0.3307470156 0.02394738138 0.03019456007 0.03666866499 +3.390079979e-18 5.110645865e-05 0.1077426176 0.1191859598 0.1423993322 1.454391128e-17 2.223517909e-06 0.01331856698 +0.02770871771 0.0321484511 + +H atom_index 2 n_descriptor 18 +1.232614069 0.03490532201 0.102831015 0.1419609456 0.3149369395 0.02159968382 0.02727979734 0.03802701099 +-5.354024115e-17 4.633469302e-05 0.09817726495 0.1142363947 0.1218613777 4.209418057e-18 5.014412745e-06 0.01341802906 +0.02590494816 0.02995711512 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fab46e1d9135e45d2aeab9bf0ce8779c03b165f6 Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..65710e74f265c32823c7fa4531c74165a829f62a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:33 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0730283 SEC) : SETUP UNITCELL + DONE(0.0849723 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.100756 SEC) : INIT PLANEWAVE + DONE(0.142426 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.385918 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651629e+02 0.000000e+00 2.160e-01 4.908e-01 + GE2 -4.663954e+02 -1.232485e+00 9.784e-02 4.624e-01 + GE3 -4.663995e+02 -4.110688e-03 6.267e-02 5.231e-01 + GE4 -4.663996e+02 -6.616629e-05 2.005e-03 3.988e-01 + GE5 -4.663986e+02 9.153945e-04 9.210e-04 3.979e-01 + GE6 -4.663992e+02 -5.660017e-04 1.206e-04 3.892e-01 + GE7 -4.663990e+02 1.815420e-04 4.284e-05 3.855e-01 + GE8 -4.663991e+02 -4.416739e-05 1.393e-05 3.784e-01 + GE9 -4.663990e+02 2.001074e-05 1.222e-06 3.790e-01 + GE10 -4.663991e+02 -3.086964e-06 1.421e-07 3.763e-01 + GE11 -4.663991e+02 -2.477043e-07 4.644e-08 3.115e-01 +E_delta_band = -7.12749302e-02 Ry = -9.69745175e-01 eV +E_delta_NN= -1.95196258e-01 Ry = -2.65578134e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4283 11 0.58 1e+02 % + Run_lcao lcao_line 6.4207 1 6.4 1e+02 % + Potential init_pot 0.24078 2 0.12 3.7 % + PW_Basis recip2real 0.24548 16 0.015 3.8 % + PW_Basis gathers_scatterp 0.10421 16 0.0065 1.6 % + Potential v_of_rho 0.89631 13 0.069 14 % + XC_Functional v_xc 0.26869 14 0.019 4.2 % + H_Hartree_pw v_hartree 0.58931 13 0.045 9.2 % + PW_Basis real2recip 0.58871 38 0.015 9.2 % + PW_Basis gatherp_scatters 0.21512 38 0.0057 3.3 % + ORB_control set_orb_tables 0.90715 1 0.91 14 % + ORB_gen_tables gen_tables 0.90714 1 0.91 14 % + ORB_table_phi init_Table 0.38325 1 0.38 6 % + ORB_table_phi cal_ST_Phi12_R 0.37891 126 0.003 5.9 % + ORB_table_beta init_Table_Beta 0.15674 1 0.16 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.15547 56 0.0028 2.4 % + ORB_table_alpha init_Table_Alpha 0.20966 1 0.21 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.20801 66 0.0032 3.2 % + LOOP_ions opt_ions 5.0593 1 5.1 79 % + ESolver_KS_LCAO Run 4.546 1 4.5 71 % + HSolverLCAO solve 2.4085 11 0.22 37 % + HamiltLCAO updateHk 1.2438 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.2172 11 0.11 19 % + Gint_interface cal_gint 1.9552 23 0.085 30 % + Gint_Gamma distri_vl_value 0.12364 11 0.011 1.9 % + Gint_Gamma distri_vl 2.1897 6 0.36 34 % + LCAO_Deepks cal_projected_DM 4.8915 13 0.38 76 % + LCAO_gen_fixedH add_v_delta 2.061 6 0.34 32 % + LCAO_DESCRIPTOR add_v_delta 2.0611 6 0.34 32 % + ElecStateLCAO psiToRho 1.1478 11 0.1 18 % + Charge mix_rho 0.75116 10 0.075 12 % + LOOP_ions force_stress 0.51315 1 0.51 8 % + Force_Stress_LCAO getForceStress 0.51313 1 0.51 8 % + Force_LCAO_gamma ftable_gamma 0.31952 1 0.32 5 % + Force_LCAO_gamma cal_fvl_dphi 0.28944 1 0.29 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:33 2022 + FINISH Time : Wed Sep 28 11:07:39 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/90/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d127f968f1e984fbf5b5e1af8200809c90830770 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.180058 0.524382 0.267284 +H 0.171734 0.458868 0.245806 +H 0.122328 0.532958 0.298138 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..122e46dd06bcc2dd41fafca6c8360ebc06130c6f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0269 2 + 2 -12.507 2 + 3 -9.3102 2 + 4 -6.69007 2 + 5 0.927496 0 + 6 3.87071 0 + 7 11.1503 0 + 8 11.4133 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f080d43f13a01cabb1389fc16fa862e2888d2b4f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:22 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.04163743074 14.6826887384 7.48394853989 0 0 0 0 + tauc_H1 4.80856105223 12.8483150056 6.88256304681 0 0 0 0 + tauc_H2 3.42519794931 14.9228309471 8.34785898832 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0876882767917 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0973250598415 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115491088584 (SEC) + + DONE : INIT CHARGE Time : 0.164102114982 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.444465 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000618 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00162 + + Density error is 0.209848227305 + + Energy Rydberg eV + E_KohnSham -34.1891629495 -465.167425963 + E_Harris -34.370856517 -467.639493772 + E_Fermi -0.384995866432 -5.23813748992 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000905262091894 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00135873771122 + + Density error is 0.098598303522 + + Energy Rydberg eV + E_KohnSham -34.2760927797 -466.350166981 + E_Harris -34.2833328451 -466.448673125 + E_Fermi -0.197329986691 -2.68481220526 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000867077559165 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125897286295 + + Density error is 0.0636048745456 + + Energy Rydberg eV + E_KohnSham -34.2764991881 -466.35569645 + E_Harris -34.2811227142 -466.41860275 + E_Fermi -0.191198930385 -2.60139490474 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000825129383968 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107655369299 + + Density error is 0.00191961181142 + + Energy Rydberg eV + E_KohnSham -34.2763829399 -466.354114813 + E_Harris -34.2763843722 -466.3541343 + E_Fermi -0.155892281695 -2.12102330527 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000826171636299 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107743217812 + + Density error is 0.000881445408744 + + Energy Rydberg eV + E_KohnSham -34.2763619993 -466.353829901 + E_Harris -34.2763624211 -466.35383564 + E_Fermi -0.156029577249 -2.12289130712 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000825832578236 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107482833804 + + Density error is 0.000167706366399 + + Energy Rydberg eV + E_KohnSham -34.2763674496 -466.353904057 + E_Harris -34.2763672802 -466.353901751 + E_Fermi -0.155530233076 -2.1160973811 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000825886624092 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107466315569 + + Density error is 2.6274249236e-05 + + Energy Rydberg eV + E_KohnSham -34.2763676083 -466.353906215 + E_Harris -34.2763676087 -466.353906221 + E_Fermi -0.155505202671 -2.11575682497 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000825869041366 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107464538898 + + Density error is 7.14077088914e-06 + + Energy Rydberg eV + E_KohnSham -34.2763686841 -466.353920853 + E_Harris -34.2763686843 -466.353920856 + E_Fermi -0.155508639996 -2.11580359218 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00082587150213 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107463943377 + + Density error is 2.39416524722e-06 + + Energy Rydberg eV + E_KohnSham -34.27636814 -466.353913449 + E_Harris -34.27636814 -466.353913449 + E_Fermi -0.155502720577 -2.11572305435 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000825867403999 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107462936165 + + Density error is 4.85609866666e-07 + + Energy Rydberg eV + E_KohnSham -34.2763682685 -466.353915197 + E_Harris -34.2763682685 -466.353915197 + E_Fermi -0.155501151872 -2.11570171103 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000825868070819 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107462928919 + + Density error is 1.92999755266e-07 + + Energy Rydberg eV + E_KohnSham -34.2763682619 -466.353915108 + E_Harris -34.2763682619 -466.353915108 + E_Fermi -0.155500917064 -2.1156985163 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000825868398801 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107462897279 + + Density error is 1.14988630913e-08 + + Energy Rydberg eV + E_KohnSham -34.2763682648 -466.353915147 + E_Harris -34.2763682648 -466.353915147 + E_band -7.86936396707 -107.068189588 + E_one_elec -68.5649368858 -932.873824658 + E_Hartree +35.688551335 +485.567651521 + E_xc -8.15355326103 -110.934783296 + E_Ewald +6.87932088235 +93.5979623704 + E_demet -5.42920178702e-57 -7.38680798952e-56 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193625203869 -2.63440604903 + E_Fermi -0.155500754059 -2.1156962985 + + charge density convergence is achieved + final etot is -466.353915147 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0269 2.00000 + 2 -12.5070 2.00000 + 3 -9.31020 2.00000 + 4 -6.69007 2.00000 + 5 0.927496 0.00000 + 6 3.87071 0.00000 + 7 11.1503 0.00000 + 8 11.4133 0.00000 + + EFERMI = -2.115696298499544 eV + OUT.ABACUS/ final etot is -466.3539151469909 eV + correction force for each atom along direction 1 is -8.56254e-05 + correction force for each atom along direction 2 is -9.71868e-05 + correction force for each atom along direction 3 is -0.000114454 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.54508657 -2.2368614 -0.61491053 + H1 +0.49601831 +1.9638368 +0.52919631 + H2 +0.049068266 +0.27302460 +0.085714220 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3539151469909 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6325 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6226 1 6.6 1.e+02% + Potential init_pot 0.28535 2 0.14 4.3% + PW_Basis recip2real 0.28098 17 0.017 4.2% + PW_Basis gathers_scatterp 0.12123 17 0.0071 1.8% + Potential v_of_rho 0.92166 14 0.066 14.% + XC_Functional v_xc 0.24839 15 0.017 3.7% + H_Hartree_pw v_hartree 0.63105 14 0.045 9.5% + PW_Basis real2recip 0.59204 41 0.014 8.9% + PW_Basis gatherp_scatters 0.22859 41 0.0056 3.4% + ORB_control set_orb_tables 1.0982 1 1.1 17.% + ORB_gen_tables gen_tables 1.0982 1 1.1 17.% + ORB_table_phi init_Table 0.48153 1 0.48 7.3% + ORB_table_phi cal_ST_Phi12_R 0.47660 126 0.0038 7.2% + ORB_table_beta init_Table_Beta 0.18554 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18406 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25151 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24960 66 0.0038 3.8% + LOOP_ions opt_ions 5.0044 1 5.0 75.% + ESolver_KS_LCAO Run 4.4685 1 4.5 67.% + HSolverLCAO solve 2.3558 12 0.20 36.% + HamiltLCAO updateHk 1.2227 12 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1866 12 0.099 18.% + Gint_interface cal_gint 1.7065 25 0.068 26.% + Gint_Gamma distri_vl_value 0.19008 12 0.016 2.9% + Gint_Gamma distri_vl 2.3264 6 0.39 35.% + LCAO_Deepks cal_projected_DM 4.7995 14 0.34 72.% + LCAO_gen_fixedH add_v_delta 2.1936 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.1936 6 0.37 33.% + ElecStateLCAO psiToRho 1.1162 12 0.093 17.% + Charge mix_rho 0.71231 11 0.065 11.% + LOOP_ions force_stress 0.53573 1 0.54 8.1% + Force_Stress_LCAO getForceStress 0.53569 1 0.54 8.1% + Force_LCAO_gamma ftable_gamma 0.32432 1 0.32 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.27552 1 0.28 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:22 2022 + Finish Time : Wed Sep 28 11:08:28 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..32a284103fa729802df1bacb3546202e6c232438 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123341 ima = 3.64978e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123202288692 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111770041812 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112585198189 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112774940285 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112771615933 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773664772 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112772518654 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773520877 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773178258 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773184311 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773167438 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773158436 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/STRU new file mode 100644 index 0000000000000000000000000000000000000000..160ecb3c88c03c00993f2770cf63f990c6e2fe7e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.958362569277 14.682688738413 7.483948539875 0 0 0 +H +0.0 +2 +-23.191438947765 12.848315005628 6.882563046825 0 0 0 +-24.574802050699 14.922830947068 8.347858988334 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/conv new file mode 100644 index 0000000000000000000000000000000000000000..5501b99aefd239673974cdf60d24b0da3a9e40f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/conv @@ -0,0 +1 @@ +91 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..80880347cd9d9be40c0037d869ffc7b4f03c0127 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753812869 0.01244930221 1.237927699 1.332000247 1.468301798 0.009138558156 0.01660469252 0.0392312763 +-2.006701289e-18 0.0007939824688 0.002538418037 0.01184190056 0.04247341399 1.919910281e-20 1.955101456e-06 5.821200496e-06 +0.001552034657 0.005956583272 + +H atom_index 1 n_descriptor 18 +1.162458717 0.03738842996 0.08195141715 0.113330302 0.2878590085 0.01837395334 0.02312667057 0.04130104117 +-3.327128677e-18 3.531669503e-05 0.07710843977 0.09627959549 0.1113598955 3.192105944e-18 6.570862433e-06 0.01556426726 +0.02233185846 0.02612241691 + +H atom_index 2 n_descriptor 18 +1.237407027 0.03515250222 0.1047845553 0.1439958177 0.3164671913 0.02194815327 0.02752814019 0.03836139363 +1.345465778e-17 4.166539532e-05 0.09597246179 0.115196245 0.1232626221 3.437695484e-19 3.925517961e-06 0.01345381693 +0.02544745578 0.03011968456 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..dda3d74c6624928ac184ccf703291b27c158c021 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:22 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0877129 SEC) : SETUP UNITCELL + DONE(0.0973435 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115512 SEC) : INIT PLANEWAVE + DONE(0.164221 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444533 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651674e+02 0.000000e+00 2.098e-01 4.952e-01 + GE2 -4.663502e+02 -1.182741e+00 9.860e-02 4.121e-01 + GE3 -4.663557e+02 -5.529469e-03 6.360e-02 4.700e-01 + GE4 -4.663541e+02 1.581637e-03 1.920e-03 3.606e-01 + GE5 -4.663538e+02 2.849123e-04 8.814e-04 3.579e-01 + GE6 -4.663539e+02 -7.415613e-05 1.677e-04 3.539e-01 + GE7 -4.663539e+02 -2.158454e-06 2.627e-05 3.349e-01 + GE8 -4.663539e+02 -1.463750e-05 7.141e-06 3.363e-01 + GE9 -4.663539e+02 7.403675e-06 2.394e-06 3.365e-01 + GE10 -4.663539e+02 -1.748294e-06 4.856e-07 3.337e-01 + GE11 -4.663539e+02 8.934948e-08 1.930e-07 3.382e-01 + GE12 -4.663539e+02 -3.887931e-08 1.150e-08 2.783e-01 +E_delta_band = -6.78748687e-02 Ry = -9.23484965e-01 eV +E_delta_NN= -1.93625204e-01 Ry = -2.63440605e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6325 11 0.6 1e+02 % + Run_lcao lcao_line 6.6226 1 6.6 1e+02 % + Potential init_pot 0.28535 2 0.14 4.3 % + PW_Basis recip2real 0.28098 17 0.017 4.2 % + PW_Basis gathers_scatterp 0.12123 17 0.0071 1.8 % + Potential v_of_rho 0.92166 14 0.066 14 % + XC_Functional v_xc 0.24839 15 0.017 3.7 % + H_Hartree_pw v_hartree 0.63105 14 0.045 9.5 % + PW_Basis real2recip 0.59204 41 0.014 8.9 % + PW_Basis gatherp_scatters 0.22859 41 0.0056 3.4 % + ORB_control set_orb_tables 1.0982 1 1.1 17 % + ORB_gen_tables gen_tables 1.0982 1 1.1 17 % + ORB_table_phi init_Table 0.48153 1 0.48 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.4766 126 0.0038 7.2 % + ORB_table_beta init_Table_Beta 0.18554 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18406 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25151 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.2496 66 0.0038 3.8 % + LOOP_ions opt_ions 5.0044 1 5 75 % + ESolver_KS_LCAO Run 4.4685 1 4.5 67 % + HSolverLCAO solve 2.3558 12 0.2 36 % + HamiltLCAO updateHk 1.2227 12 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1866 12 0.099 18 % + Gint_interface cal_gint 1.7065 25 0.068 26 % + Gint_Gamma distri_vl_value 0.19008 12 0.016 2.9 % + Gint_Gamma distri_vl 2.3264 6 0.39 35 % + LCAO_Deepks cal_projected_DM 4.7995 14 0.34 72 % + LCAO_gen_fixedH add_v_delta 2.1936 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.1936 6 0.37 33 % + ElecStateLCAO psiToRho 1.1162 12 0.093 17 % + Charge mix_rho 0.71231 11 0.065 11 % + LOOP_ions force_stress 0.53573 1 0.54 8.1 % + Force_Stress_LCAO getForceStress 0.53569 1 0.54 8.1 % + Force_LCAO_gamma ftable_gamma 0.32432 1 0.32 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.27552 1 0.28 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:22 2022 + FINISH Time : Wed Sep 28 11:08:28 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/91/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..786a75ddb8193bf22c7f2d82eab93b8fc360eb6e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.190975 0.502052 0.26503 +H 0.158209 0.448225 0.27571 +H 0.152012 0.545284 0.291179 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bc23ae1a9dfc9938f64af793a0402d772677ffd6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6464 2 + 2 -13.1177 2 + 3 -9.3276 2 + 4 -6.82311 2 + 5 1.51152 0 + 6 4.81289 0 + 7 11.0003 0 + 8 11.2668 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..81446f1bfb7c67e251c740b071ab96e20fed6620 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/running_scf.log @@ -0,0 +1,780 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:09 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.34730803665 14.0574513259 7.42084914195 0 0 0 0 + tauc_H1 4.42984051783 12.5503040263 7.71988255274 0 0 0 0 + tauc_H2 4.25634381543 15.2679566886 8.1530028302 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0891451801778 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0895497080565 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107978680948 (SEC) + + DONE : INIT CHARGE Time : 0.157882526416 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437704 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 9 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00116 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114 + + Density error is 0.216763642211 + + Energy Rydberg eV + E_KohnSham -34.1873503048 -465.142763667 + E_Harris -34.3836907889 -467.814113 + E_Fermi -0.423553227971 -5.76273730669 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0012164660996 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116806981971 + + Density error is 0.0970779880774 + + Energy Rydberg eV + E_KohnSham -34.2771297112 -466.364275158 + E_Harris -34.2837695481 -466.454614773 + E_Fermi -0.231531506006 -3.1501477482 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00112759811971 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109736417109 + + Density error is 0.0618243604691 + + Energy Rydberg eV + E_KohnSham -34.2772736757 -466.366233895 + E_Harris -34.2815035208 -466.42378389 + E_Fermi -0.216208880026 -2.94167272656 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000983725543978 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991557099168 + + Density error is 0.00204347286848 + + Energy Rydberg eV + E_KohnSham -34.277333579 -466.367048922 + E_Harris -34.2773361325 -466.367083663 + E_Fermi -0.180352214471 -2.45381776373 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000983493646635 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000993372744175 + + Density error is 0.00089888795452 + + Energy Rydberg eV + E_KohnSham -34.2772559077 -466.365992149 + E_Harris -34.2772589727 -466.366033851 + E_Fermi -0.178978634371 -2.4351292477 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000982032431998 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991958029488 + + Density error is 0.000105124046595 + + Energy Rydberg eV + E_KohnSham -34.2773150332 -466.366796593 + E_Harris -34.2773150523 -466.366796853 + E_Fermi -0.179398911107 -2.44084740605 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000981622870643 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991774891755 + + Density error is 4.60617961733e-05 + + Energy Rydberg eV + E_KohnSham -34.277296008 -466.366537742 + E_Harris -34.2772960191 -466.366537893 + E_Fermi -0.17926165223 -2.43897990322 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000981684117391 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991792466245 + + Density error is 1.77923642141e-05 + + Energy Rydberg eV + E_KohnSham -34.2772984316 -466.366570716 + E_Harris -34.2772984329 -466.366570734 + E_Fermi -0.179327725456 -2.43987887558 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00098166759739 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991787223401 + + Density error is 1.83914445964e-06 + + Energy Rydberg eV + E_KohnSham -34.2772969681 -466.366550804 + E_Harris -34.2772969681 -466.366550804 + E_Fermi -0.17930787632 -2.43960881424 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000981667414493 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991785793407 + + Density error is 1.96951845495e-07 + + Energy Rydberg eV + E_KohnSham -34.2772972224 -466.366554264 + E_Harris -34.2772972224 -466.366554265 + E_Fermi -0.179306279284 -2.43958708545 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000981667991465 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991786532974 + + Density error is 6.60793802322e-08 + + Energy Rydberg eV + E_KohnSham -34.2772972536 -466.366554688 + E_Harris -34.2772972536 -466.366554688 + E_band -8.07232075079 -109.829558294 + E_one_elec -69.884900998 -950.832857738 + E_Hartree +36.3132182394 +494.066680774 + E_xc -8.25384474613 -112.299318955 + E_Ewald +7.67131060943 +104.373535416 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195958705469 -2.66615496709 + E_Fermi -0.179306285239 -2.43958716646 + + charge density convergence is achieved + final etot is -466.366554688 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6464 2.00000 + 2 -13.1177 2.00000 + 3 -9.32760 2.00000 + 4 -6.82311 2.00000 + 5 1.51152 0.00000 + 6 4.81289 0.00000 + 7 11.0003 0.00000 + 8 11.2668 0.00000 + + EFERMI = -2.439587166464963 eV + OUT.ABACUS/ final etot is -466.3665546881859 eV + correction force for each atom along direction 1 is -0.000175154 + correction force for each atom along direction 2 is -6.80645e-05 + correction force for each atom along direction 3 is 8.57564e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.3987245 +0.12520276 -0.72802363 + H1 -0.57336098 -1.5770861 +0.10703374 + H2 -0.82536348 +1.4518833 +0.62098989 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3665546881859 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4190 11 0.58 1.0e+02% + Run_lcao lcao_line 6.4084 1 6.4 1.e+02% + Potential init_pot 0.28566 2 0.14 4.5% + PW_Basis recip2real 0.26170 16 0.016 4.1% + PW_Basis gathers_scatterp 0.11141 16 0.0070 1.7% + Charge atomic_rho 0.10003 1 0.10 1.6% + Potential v_of_rho 0.85492 13 0.066 13.% + XC_Functional v_xc 0.23968 14 0.017 3.7% + H_Hartree_pw v_hartree 0.58064 13 0.045 9.0% + PW_Basis real2recip 0.55447 38 0.015 8.6% + PW_Basis gatherp_scatters 0.21540 38 0.0057 3.4% + ORB_control set_orb_tables 1.1149 1 1.1 17.% + ORB_gen_tables gen_tables 1.1149 1 1.1 17.% + ORB_table_phi init_Table 0.48857 1 0.49 7.6% + ORB_table_phi cal_ST_Phi12_R 0.48359 126 0.0038 7.5% + ORB_table_beta init_Table_Beta 0.18813 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18663 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25627 1 0.26 4.0% + ORB_table_alpha S_PhiAlpha_R 0.25435 66 0.0039 4.0% + LOOP_ions opt_ions 4.7807 1 4.8 74.% + ESolver_KS_LCAO Run 4.2357 1 4.2 66.% + HSolverLCAO solve 2.2832 11 0.21 36.% + HamiltLCAO updateHk 1.1862 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1534 11 0.10 18.% + Gint_interface cal_gint 1.5381 23 0.067 24.% + Gint_Gamma distri_vl_value 0.23221 11 0.021 3.6% + Gint_Gamma distri_vl 2.0448 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.5612 13 0.35 71.% + LCAO_gen_fixedH add_v_delta 1.9139 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9139 6 0.32 30.% + ElecStateLCAO psiToRho 1.0793 11 0.098 17.% + Charge mix_rho 0.65541 10 0.066 10.% + LOOP_ions force_stress 0.54480 1 0.54 8.5% + Force_Stress_LCAO getForceStress 0.54477 1 0.54 8.5% + Force_LCAO_gamma ftable_gamma 0.33214 1 0.33 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.27206 1 0.27 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:09 2022 + Finish Time : Wed Sep 28 11:05:15 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..cb5e6d51703ffcf7f90f3aac793edac6fe927f2e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124138 ima = 3.66533e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122409355263 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111703995326 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112085410268 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112380712997 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112296565547 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112343421551 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112340605454 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112343432556 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112342698736 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112342620749 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112342612874 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/STRU new file mode 100644 index 0000000000000000000000000000000000000000..734b927790c5ddc9c902a74faa1fa64a35815b87 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.652691963359 14.057451325931 7.420849141959 0 0 0 +H +0.0 +2 +-23.570159482143 12.550304026233 7.719882552761 0 0 0 +-23.743656184581 15.267956688561 8.153002830185 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/conv new file mode 100644 index 0000000000000000000000000000000000000000..fe6779c9f9e9308eb1821edfcd6db750ed023a9b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/conv @@ -0,0 +1 @@ +92 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8bee7c5ad770b3d5b1347d0d4ad34dd7f978ade3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751917967 0.01289960646 1.295315233 1.376438262 1.470903286 0.009239218728 0.01815362053 0.03909702345 +3.696661239e-18 0.001110223729 0.002927070527 0.01364871192 0.04929842993 -2.561729353e-19 2.883552669e-06 7.483519891e-06 +0.00161227249 0.006090593315 + +H atom_index 1 n_descriptor 18 +1.282028735 0.03352814985 0.1220618602 0.1650503684 0.3294967377 0.02452513084 0.03009625352 0.03688004568 +-2.872884533e-17 5.731935513e-05 0.108829748 0.1203960495 0.1418207326 -6.379361546e-18 1.86396493e-06 0.01344227997 +0.02843740385 0.03212877619 + +H atom_index 2 n_descriptor 18 +1.28445825 0.03345255611 0.1230102865 0.1662930022 0.3302052624 0.02464230224 0.03023587646 0.03684417222 +-1.383227651e-17 5.756472647e-05 0.1088731111 0.12105261 0.1428738505 -4.971101973e-18 1.733928924e-06 0.01347871715 +0.02851527308 0.03222215083 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d5fe03826aabbe059c3179c2f238b154e15e447c Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..9a430509ac08660a8c6488bf010cb550280f7dea Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..e6a607fd79975a4bef7c940baaa189342d00bf1b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..07c1d657ac54f268ee2bed6a9933c1904d10813b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:09 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0891709 SEC) : SETUP UNITCELL + DONE(0.0895673 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.108008 SEC) : INIT PLANEWAVE + DONE(0.158014 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.437769 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651428e+02 0.000000e+00 2.168e-01 4.961e-01 + GE2 -4.663643e+02 -1.221511e+00 9.708e-02 4.251e-01 + GE3 -4.663662e+02 -1.958737e-03 6.182e-02 4.819e-01 + GE4 -4.663670e+02 -8.150269e-04 2.043e-03 3.685e-01 + GE5 -4.663660e+02 1.056773e-03 8.989e-04 3.716e-01 + GE6 -4.663668e+02 -8.044439e-04 1.051e-04 3.489e-01 + GE7 -4.663665e+02 2.588511e-04 4.606e-05 3.559e-01 + GE8 -4.663666e+02 -3.297472e-05 1.779e-05 3.493e-01 + GE9 -4.663666e+02 1.991252e-05 1.839e-06 3.436e-01 + GE10 -4.663666e+02 -3.460714e-06 1.970e-07 3.440e-01 + GE11 -4.663666e+02 -4.236942e-07 6.608e-08 2.876e-01 +E_delta_band = -7.28783472e-02 Ry = -9.91560782e-01 eV +E_delta_NN= -1.95958705e-01 Ry = -2.66615497e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.419 11 0.58 1e+02 % + Run_lcao lcao_line 6.4084 1 6.4 1e+02 % + Potential init_pot 0.28566 2 0.14 4.5 % + PW_Basis recip2real 0.2617 16 0.016 4.1 % + PW_Basis gathers_scatterp 0.11141 16 0.007 1.7 % + Charge atomic_rho 0.10003 1 0.1 1.6 % + Potential v_of_rho 0.85492 13 0.066 13 % + XC_Functional v_xc 0.23968 14 0.017 3.7 % + H_Hartree_pw v_hartree 0.58064 13 0.045 9 % + PW_Basis real2recip 0.55447 38 0.015 8.6 % + PW_Basis gatherp_scatters 0.2154 38 0.0057 3.4 % + ORB_control set_orb_tables 1.1149 1 1.1 17 % + ORB_gen_tables gen_tables 1.1149 1 1.1 17 % + ORB_table_phi init_Table 0.48857 1 0.49 7.6 % + ORB_table_phi cal_ST_Phi12_R 0.48359 126 0.0038 7.5 % + ORB_table_beta init_Table_Beta 0.18813 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18663 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.25627 1 0.26 4 % + ORB_table_alpha S_PhiAlpha_R 0.25435 66 0.0039 4 % + LOOP_ions opt_ions 4.7807 1 4.8 74 % + ESolver_KS_LCAO Run 4.2357 1 4.2 66 % + HSolverLCAO solve 2.2832 11 0.21 36 % + HamiltLCAO updateHk 1.1862 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1534 11 0.1 18 % + Gint_interface cal_gint 1.5381 23 0.067 24 % + Gint_Gamma distri_vl_value 0.23221 11 0.021 3.6 % + Gint_Gamma distri_vl 2.0448 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.5612 13 0.35 71 % + LCAO_gen_fixedH add_v_delta 1.9139 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9139 6 0.32 30 % + ElecStateLCAO psiToRho 1.0793 11 0.098 17 % + Charge mix_rho 0.65541 10 0.066 10 % + LOOP_ions force_stress 0.5448 1 0.54 8.5 % + Force_Stress_LCAO getForceStress 0.54477 1 0.54 8.5 % + Force_LCAO_gamma ftable_gamma 0.33214 1 0.33 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.27206 1 0.27 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:09 2022 + FINISH Time : Wed Sep 28 11:05:15 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/92/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3deb2cca0d605aae4b39f73eb8b45707cc486d4c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.20052 0.48062 0.266862 +H 0.148145 0.452872 0.292486 +H 0.184291 0.54222 0.246562 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..a32535589b26c6993d4976e13e202e872261850b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1664 2 + 2 -13.2246 2 + 3 -8.88121 2 + 4 -6.71358 2 + 5 1.26632 0 + 6 4.40647 0 + 7 11.0919 0 + 8 11.3197 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c0c7b9858e0b19d00591ba456f88d4068278310c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.61454660095 13.4573556962 7.47214585703 0 0 0 0 + tauc_H1 4.1480562291 12.6804296072 8.18961753391 0 0 0 0 + tauc_H2 5.16015160993 15.1821722882 6.90374430855 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0876044890655 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0899067442426 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107997122508 (SEC) + + DONE : INIT CHARGE Time : 0.157317853533 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.439556 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 4 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00145 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000599 + + Density error is 0.214934429872 + + Energy Rydberg eV + E_KohnSham -34.1904719321 -465.185235586 + E_Harris -34.3818684054 -467.7893182 + E_Fermi -0.4025041347 -5.47634970048 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00125902543784 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000777859317042 + + Density error is 0.0982496238722 + + Energy Rydberg eV + E_KohnSham -34.2793363555 -466.394298094 + E_Harris -34.2860367522 -466.485461668 + E_Fermi -0.211011812799 -2.87096299938 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00117057683133 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000754158666391 + + Density error is 0.0629737737019 + + Energy Rydberg eV + E_KohnSham -34.2795444649 -466.397129568 + E_Harris -34.2838531209 -466.455751839 + E_Fermi -0.19976943086 -2.71800254592 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102407792969 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000730479341684 + + Density error is 0.00207493541282 + + Energy Rydberg eV + E_KohnSham -34.2795325651 -466.396967662 + E_Harris -34.2795358335 -466.39701213 + E_Fermi -0.164554282504 -2.23887587235 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102400681706 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000730064660649 + + Density error is 0.000838822214533 + + Energy Rydberg eV + E_KohnSham -34.2794844366 -466.39631284 + E_Harris -34.2794850908 -466.396321741 + E_Fermi -0.163817812935 -2.22885568981 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010221831207 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729754847712 + + Density error is 0.000196535757637 + + Energy Rydberg eV + E_KohnSham -34.2795148019 -466.396725981 + E_Harris -34.2795148824 -466.396727076 + E_Fermi -0.163763133916 -2.2281117436 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102217243101 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000730051583065 + + Density error is 3.56112689061e-05 + + Energy Rydberg eV + E_KohnSham -34.2795027289 -466.396561719 + E_Harris -34.279502735 -466.396561803 + E_Fermi -0.163631485959 -2.22632058125 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102217066548 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00072997603222 + + Density error is 1.89727419994e-05 + + Energy Rydberg eV + E_KohnSham -34.2795076791 -466.396629071 + E_Harris -34.2795076807 -466.396629092 + E_Fermi -0.163670218609 -2.22684756599 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102215647327 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729986061328 + + Density error is 2.78465954227e-06 + + Energy Rydberg eV + E_KohnSham -34.2795062357 -466.396609432 + E_Harris -34.2795062357 -466.396609432 + E_Fermi -0.16365153676 -2.22659338639 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102214763618 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729987815957 + + Density error is 5.14471405841e-07 + + Energy Rydberg eV + E_KohnSham -34.2795065318 -466.396613461 + E_Harris -34.2795065318 -466.396613461 + E_Fermi -0.1636488372 -2.22655665699 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102214775941 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729988179721 + + Density error is 1.8359397752e-07 + + Energy Rydberg eV + E_KohnSham -34.279506555 -466.396613776 + E_Harris -34.279506555 -466.396613776 + E_Fermi -0.163648612724 -2.22655360284 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102214753815 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000729988374779 + + Density error is 9.93569336791e-09 + + Energy Rydberg eV + E_KohnSham -34.2795065578 -466.396613815 + E_Harris -34.2795065578 -466.396613815 + E_band -7.93575634564 -107.97150424 + E_one_elec -69.1953152791 -941.450562702 + E_Hartree +36.0035484166 +489.853406685 + E_xc -8.20357121131 -111.615312423 + E_Ewald +7.24040071534 +98.5107055319 + E_demet -3.1339495296e-74 -4.26395708469e-73 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194531873668 -2.6467419245 + E_Fermi -0.163648432268 -2.22655114761 + + charge density convergence is achieved + final etot is -466.396613815 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1664 2.00000 + 2 -13.2246 2.00000 + 3 -8.88121 2.00000 + 4 -6.71358 2.00000 + 5 1.26632 0.00000 + 6 4.40647 0.00000 + 7 11.0919 0.00000 + 8 11.3197 0.00000 + + EFERMI = -2.226551147612249 eV + OUT.ABACUS/ final etot is -466.3966138150060 eV + correction force for each atom along direction 1 is -5.52710e-05 + correction force for each atom along direction 2 is 7.12406e-05 + correction force for each atom along direction 3 is -9.10249e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.0001175 +0.93335545 -0.65551430 + H1 -0.90311590 -0.11063036 +0.29581388 + H2 -0.097001565 -0.82272509 +0.35970042 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3966138150060 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5895 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5792 1 7.6 1.e+02% + Potential init_pot 0.28434 2 0.14 3.7% + PW_Basis recip2real 0.29681 17 0.017 3.9% + PW_Basis gathers_scatterp 0.13294 17 0.0078 1.8% + Potential v_of_rho 1.0533 14 0.075 14.% + XC_Functional v_xc 0.31042 15 0.021 4.1% + H_Hartree_pw v_hartree 0.70005 14 0.050 9.2% + PW_Basis real2recip 0.69628 41 0.017 9.2% + PW_Basis gatherp_scatters 0.26721 41 0.0065 3.5% + ORB_control set_orb_tables 1.0897 1 1.1 14.% + ORB_gen_tables gen_tables 1.0897 1 1.1 14.% + ORB_table_phi init_Table 0.47271 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46762 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18289 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18134 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24837 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24640 66 0.0037 3.2% + LOOP_ions opt_ions 5.9727 1 6.0 79.% + ESolver_KS_LCAO Run 5.4004 1 5.4 71.% + HSolverLCAO solve 2.9174 12 0.24 38.% + HamiltLCAO updateHk 1.4919 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.4625 12 0.12 19.% + Gint_interface cal_gint 2.1325 25 0.085 28.% + Gint_Gamma distri_vl_value 0.24353 12 0.020 3.2% + Gint_Gamma distri_vl 2.8107 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.7653 14 0.41 76.% + LCAO_gen_fixedH add_v_delta 2.6673 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6673 6 0.44 35.% + ElecStateLCAO psiToRho 1.4018 12 0.12 18.% + Charge mix_rho 0.84573 11 0.077 11.% + LOOP_ions force_stress 0.57213 1 0.57 7.5% + Force_Stress_LCAO getForceStress 0.57211 1 0.57 7.5% + Force_LCAO_gamma ftable_gamma 0.35296 1 0.35 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.30509 1 0.31 4.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:17 2022 + Finish Time : Wed Sep 28 11:14:25 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..baa7003e5effc518691883f6befaed986cd678b9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123761 ima = 3.64944e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123515688997 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112636879468 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113147713478 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113362790009 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113324435917 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113349174762 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113340042733 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113342817913 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113341971024 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113341899451 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113341882605 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113341873337 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/STRU new file mode 100644 index 0000000000000000000000000000000000000000..f0d4a6e44d96abd9667b7e153ab6612e52478b45 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.385453399071 13.457355696250 7.472145857010 0 0 0 +H +0.0 +2 +-23.851943770890 12.680429607190 8.189617533918 0 0 0 +-22.839848390083 15.182172288244 6.903744308544 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/conv new file mode 100644 index 0000000000000000000000000000000000000000..81900884056fec38151e599d298e712c840a9337 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/conv @@ -0,0 +1 @@ +93 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7220649ae32bf37af4c0cea22d84f6c584bf2bf7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745315319 0.01257004833 1.270846284 1.367035214 1.468819422 0.007840624976 0.01983380963 0.03891704044 +4.4741746e-19 0.00110093831 0.002388352661 0.01209413694 0.04269897318 -5.157041615e-19 1.540519199e-06 4.87332422e-06 +0.001740651076 0.005696890071 + +H atom_index 1 n_descriptor 18 +1.261695409 0.03338099688 0.1121738241 0.156631838 0.3264141216 0.02233715164 0.0291352024 0.03668699256 +1.802158023e-17 4.023999917e-05 0.1039638657 0.1155737828 0.1344526055 2.18398138e-18 3.59229951e-06 0.01291707756 +0.02638922097 0.03135615081 + +H atom_index 2 n_descriptor 18 +1.210635961 0.03516326314 0.09527241217 0.1337355749 0.3097125753 0.02007905747 0.026177685 0.03842668635 +7.82170966e-18 3.605831638e-05 0.09093767916 0.1138214101 0.114584082 -1.083700826e-18 5.77791829e-06 0.01356755725 +0.02443864694 0.028971795 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..86a32ff887142b061f3b37970bceb6f07ef13455 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0876399 SEC) : SETUP UNITCELL + DONE(0.0899221 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.108016 SEC) : INIT PLANEWAVE + DONE(0.157453 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.439622 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651852e+02 0.000000e+00 2.149e-01 5.528e-01 + GE2 -4.663943e+02 -1.209063e+00 9.825e-02 5.044e-01 + GE3 -4.663971e+02 -2.831474e-03 6.297e-02 5.700e-01 + GE4 -4.663970e+02 1.619056e-04 2.075e-03 4.342e-01 + GE5 -4.663963e+02 6.548226e-04 8.388e-04 4.332e-01 + GE6 -4.663967e+02 -4.131413e-04 1.965e-04 4.317e-01 + GE7 -4.663966e+02 1.642614e-04 3.561e-05 4.209e-01 + GE8 -4.663966e+02 -6.735130e-05 1.897e-05 4.094e-01 + GE9 -4.663966e+02 1.963888e-05 2.785e-06 4.123e-01 + GE10 -4.663966e+02 -4.028864e-06 5.145e-07 4.127e-01 + GE11 -4.663966e+02 -3.149517e-07 1.836e-07 4.118e-01 + GE12 -4.663966e+02 -3.931338e-08 9.936e-09 3.449e-01 +E_delta_band = -6.99626743e-02 Ry = -9.51891018e-01 eV +E_delta_NN= -1.94531874e-01 Ry = -2.64674192e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5895 11 0.69 1e+02 % + Run_lcao lcao_line 7.5792 1 7.6 1e+02 % + Potential init_pot 0.28434 2 0.14 3.7 % + PW_Basis recip2real 0.29681 17 0.017 3.9 % + PW_Basis gathers_scatterp 0.13294 17 0.0078 1.8 % + Potential v_of_rho 1.0533 14 0.075 14 % + XC_Functional v_xc 0.31042 15 0.021 4.1 % + H_Hartree_pw v_hartree 0.70005 14 0.05 9.2 % + PW_Basis real2recip 0.69628 41 0.017 9.2 % + PW_Basis gatherp_scatters 0.26721 41 0.0065 3.5 % + ORB_control set_orb_tables 1.0897 1 1.1 14 % + ORB_gen_tables gen_tables 1.0897 1 1.1 14 % + ORB_table_phi init_Table 0.47271 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.46762 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18289 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18134 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24837 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.2464 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9727 1 6 79 % + ESolver_KS_LCAO Run 5.4004 1 5.4 71 % + HSolverLCAO solve 2.9174 12 0.24 38 % + HamiltLCAO updateHk 1.4919 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.4625 12 0.12 19 % + Gint_interface cal_gint 2.1325 25 0.085 28 % + Gint_Gamma distri_vl_value 0.24353 12 0.02 3.2 % + Gint_Gamma distri_vl 2.8107 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.7653 14 0.41 76 % + LCAO_gen_fixedH add_v_delta 2.6673 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6673 6 0.44 35 % + ElecStateLCAO psiToRho 1.4018 12 0.12 18 % + Charge mix_rho 0.84573 11 0.077 11 % + LOOP_ions force_stress 0.57213 1 0.57 7.5 % + Force_Stress_LCAO getForceStress 0.57211 1 0.57 7.5 % + Force_LCAO_gamma ftable_gamma 0.35296 1 0.35 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.30509 1 0.31 4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:17 2022 + FINISH Time : Wed Sep 28 11:14:25 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/93/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9cb479947a0e1fcdc12e80d855ba010ec52beaa7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.190325 0.478089 0.275495 +H 0.1502 0.425279 0.281137 +H 0.157816 0.520383 0.23861 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..032a60dfe28f15f27c428f24fb010781bbe8f0d0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.231 2 + 2 -13.07 2 + 3 -9.0526 2 + 4 -6.73097 2 + 5 1.27005 0 + 6 4.38046 0 + 7 11.0856 0 + 8 11.3307 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a391c656e713d5c0faf65813063afb9634b9f038 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:38 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.32909847148 13.3865039086 7.71385923312 0 0 0 0 + tauc_H1 4.20560889685 11.9078140397 7.87183805845 0 0 0 0 + tauc_H2 4.41885865794 14.5707345516 6.68108548958 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0857683331698 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0979254250094 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116224316953 (SEC) + + DONE : INIT CHARGE Time : 0.165727961739 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44674 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 144 0 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00113 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000945 + + Density error is 0.21409184231 + + Energy Rydberg eV + E_KohnSham -34.1922287792 -465.209138717 + E_Harris -34.3821552635 -467.793221105 + E_Fermi -0.402971647444 -5.48271053768 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00120448278055 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102217115348 + + Density error is 0.0980214948722 + + Energy Rydberg eV + E_KohnSham -34.2806911204 -466.412730616 + E_Harris -34.2874220493 -466.504309601 + E_Fermi -0.212280988471 -2.88823102028 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00112486340727 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000971328900288 + + Density error is 0.0628476877775 + + Energy Rydberg eV + E_KohnSham -34.2809002304 -466.415575703 + E_Harris -34.2852469021 -466.474715205 + E_Fermi -0.201135933535 -2.73659476862 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000988667634332 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000900319078327 + + Density error is 0.0019967332829 + + Energy Rydberg eV + E_KohnSham -34.2808842429 -466.415358182 + E_Harris -34.2808859446 -466.415381335 + E_Fermi -0.165745636396 -2.25508507362 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000987095305201 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000901595757338 + + Density error is 0.000833962762331 + + Energy Rydberg eV + E_KohnSham -34.2808337694 -466.414671455 + E_Harris -34.2808346135 -466.41468294 + E_Fermi -0.165067555501 -2.24585930975 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000985511069506 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000900538812898 + + Density error is 0.000174435502961 + + Energy Rydberg eV + E_KohnSham -34.2808664723 -466.4151164 + E_Harris -34.2808665516 -466.415117479 + E_Fermi -0.165016059852 -2.2451586755 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000985597631485 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000900736424112 + + Density error is 3.63230350291e-05 + + Energy Rydberg eV + E_KohnSham -34.2808535963 -466.414941213 + E_Harris -34.2808536029 -466.414941304 + E_Fermi -0.164899699095 -2.24357550617 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00098556524066 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000900699403743 + + Density error is 1.63429797813e-05 + + Energy Rydberg eV + E_KohnSham -34.2808582552 -466.415004602 + E_Harris -34.2808582563 -466.415004616 + E_Fermi -0.164938196491 -2.24409929012 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000985542263548 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000900697138611 + + Density error is 2.00268011895e-06 + + Energy Rydberg eV + E_KohnSham -34.2808569092 -466.414986287 + E_Harris -34.2808569092 -466.414986287 + E_Fermi -0.164920856727 -2.24386337053 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000985539863258 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000900694803239 + + Density error is 4.23249741543e-07 + + Energy Rydberg eV + E_KohnSham -34.2808571284 -466.41498927 + E_Harris -34.2808571284 -466.41498927 + E_Fermi -0.164919129726 -2.24383987348 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000985540406048 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000900695313639 + + Density error is 1.47974537061e-07 + + Energy Rydberg eV + E_KohnSham -34.280857153 -466.414989605 + E_Harris -34.280857153 -466.414989605 + E_Fermi -0.164918962457 -2.24383759767 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000985540403076 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000900695401776 + + Density error is 1.01859563248e-08 + + Energy Rydberg eV + E_KohnSham -34.2808571559 -466.414989645 + E_Harris -34.2808571559 -466.414989645 + E_band -7.95028222603 -108.169138982 + E_one_elec -69.2118544314 -941.675589414 + E_Hartree +36.0047926978 +489.870335999 + E_xc -8.20393866769 -111.620311923 + E_Ewald +7.25464890951 +98.7045621588 + E_demet -4.28916287069e-75 -5.83570546915e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194638965299 -2.64819898089 + E_Fermi -0.164918820809 -2.24383567044 + + charge density convergence is achieved + final etot is -466.414989645 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2310 2.00000 + 2 -13.0700 2.00000 + 3 -9.05260 2.00000 + 4 -6.73097 2.00000 + 5 1.27005 0.00000 + 6 4.38046 0.00000 + 7 11.0856 0.00000 + 8 11.3307 0.00000 + + EFERMI = -2.243835670442499 eV + OUT.ABACUS/ final etot is -466.4149896446075 eV + correction force for each atom along direction 1 is -0.000196128 + correction force for each atom along direction 2 is -6.62462e-05 + correction force for each atom along direction 3 is -0.000166307 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.15091047 -0.90907075 +0.51348728 + H1 +0.28104639 +0.47666013 -0.088850261 + H2 -0.43195686 +0.43241062 -0.42463702 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4149896446075 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5215 11 0.68 1.0e+02% + Run_lcao lcao_line 7.5128 1 7.5 1.e+02% + Potential init_pot 0.28340 2 0.14 3.8% + PW_Basis recip2real 0.28663 17 0.017 3.8% + PW_Basis gathers_scatterp 0.13159 17 0.0077 1.7% + Potential v_of_rho 1.0375 14 0.074 14.% + XC_Functional v_xc 0.30277 15 0.020 4.0% + H_Hartree_pw v_hartree 0.69108 14 0.049 9.2% + PW_Basis real2recip 0.69716 41 0.017 9.3% + PW_Basis gatherp_scatters 0.27405 41 0.0067 3.6% + ORB_control set_orb_tables 1.1014 1 1.1 15.% + ORB_gen_tables gen_tables 1.1014 1 1.1 15.% + ORB_table_phi init_Table 0.47788 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47266 126 0.0038 6.3% + ORB_table_beta init_Table_Beta 0.18578 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18422 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.25186 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24986 66 0.0038 3.3% + LOOP_ions opt_ions 5.8861 1 5.9 78.% + ESolver_KS_LCAO Run 5.3215 1 5.3 71.% + HSolverLCAO solve 2.8659 12 0.24 38.% + HamiltLCAO updateHk 1.4574 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4279 12 0.12 19.% + Gint_interface cal_gint 2.1495 25 0.086 29.% + Gint_Gamma distri_vl_value 0.20171 12 0.017 2.7% + Gint_Gamma distri_vl 2.7744 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.6845 14 0.41 76.% + LCAO_gen_fixedH add_v_delta 2.6312 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6313 6 0.44 35.% + ElecStateLCAO psiToRho 1.3854 12 0.12 18.% + Charge mix_rho 0.84759 11 0.077 11.% + LOOP_ions force_stress 0.56442 1 0.56 7.5% + Force_Stress_LCAO getForceStress 0.56439 1 0.56 7.5% + Force_LCAO_gamma ftable_gamma 0.34786 1 0.35 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.30362 1 0.30 4.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:38 2022 + Finish Time : Wed Sep 28 11:01:45 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..56dc46264beb0c80b2f2bc12f84d30cbbb176720 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123636 ima = 3.68292e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123184888256 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112259361466 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112792746689 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113018678215 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112976952488 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113003948194 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112995158234 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112997881198 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112997241549 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112997168874 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112997153951 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112997146581 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8a23b7e932d0a5100b0ca7253b74083e859bded1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.670901528512 13.386503908557 7.713859233097 0 0 0 +H +0.0 +2 +-23.794391103141 11.907814039733 7.871838058479 0 0 0 +-23.581141342057 14.570734551654 6.681085489591 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/conv new file mode 100644 index 0000000000000000000000000000000000000000..9cfc173a44fba6c2f2dc78064de9d7ffe419f403 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/conv @@ -0,0 +1 @@ +94 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e40d5ea247f383ee8c80e7270b9e9b7fe3ba7d17 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748278134 0.01263702517 1.269999659 1.361663249 1.469071635 0.008308836967 0.01882911221 0.03900260914 +-3.630758075e-19 0.001054157785 0.002525394391 0.01222534641 0.04419091169 -3.975297675e-19 1.85673881e-06 5.546999549e-06 +0.001668124327 0.005886817549 + +H atom_index 1 n_descriptor 18 +1.220530023 0.03514157378 0.09828434636 0.137115066 0.3117288863 0.02073225626 0.02663567986 0.0383457379 +-2.027972323e-17 4.088879367e-05 0.09358963631 0.1140635252 0.1175479064 -1.903481278e-18 5.556007983e-06 0.01353349718 +0.02499490969 0.02938397008 + +H atom_index 2 n_descriptor 18 +1.258509814 0.03383013095 0.111021841 0.1542888245 0.3242974298 0.02247156241 0.02884731938 0.03706035311 +2.496501751e-17 4.427206265e-05 0.1032071758 0.1154789546 0.1324401519 4.738852411e-18 3.703157196e-06 0.01306760684 +0.02644138272 0.0311625962 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..6db02d86ae2529e951bca524b7dd32c200366482 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:38 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0857946 SEC) : SETUP UNITCELL + DONE(0.0979451 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116252 SEC) : INIT PLANEWAVE + DONE(0.165864 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446814 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652091e+02 0.000000e+00 2.141e-01 5.459e-01 + GE2 -4.664127e+02 -1.203592e+00 9.802e-02 4.987e-01 + GE3 -4.664156e+02 -2.845087e-03 6.285e-02 5.668e-01 + GE4 -4.664154e+02 2.175211e-04 1.997e-03 4.289e-01 + GE5 -4.664147e+02 6.867265e-04 8.340e-04 4.252e-01 + GE6 -4.664151e+02 -4.449450e-04 1.744e-04 4.180e-01 + GE7 -4.664149e+02 1.751872e-04 3.632e-05 4.142e-01 + GE8 -4.664150e+02 -6.338887e-05 1.634e-05 4.076e-01 + GE9 -4.664150e+02 1.831437e-05 2.003e-06 4.059e-01 + GE10 -4.664150e+02 -2.982208e-06 4.232e-07 4.063e-01 + GE11 -4.664150e+02 -3.359217e-07 1.480e-07 4.041e-01 + GE12 -4.664150e+02 -3.913849e-08 1.019e-08 3.376e-01 +E_delta_band = -7.01333011e-02 Ry = -9.54212515e-01 eV +E_delta_NN= -1.94638965e-01 Ry = -2.64819898e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5215 11 0.68 1e+02 % + Run_lcao lcao_line 7.5128 1 7.5 1e+02 % + Potential init_pot 0.2834 2 0.14 3.8 % + PW_Basis recip2real 0.28663 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.13159 17 0.0077 1.7 % + Potential v_of_rho 1.0375 14 0.074 14 % + XC_Functional v_xc 0.30277 15 0.02 4 % + H_Hartree_pw v_hartree 0.69108 14 0.049 9.2 % + PW_Basis real2recip 0.69716 41 0.017 9.3 % + PW_Basis gatherp_scatters 0.27405 41 0.0067 3.6 % + ORB_control set_orb_tables 1.1014 1 1.1 15 % + ORB_gen_tables gen_tables 1.1014 1 1.1 15 % + ORB_table_phi init_Table 0.47788 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47266 126 0.0038 6.3 % + ORB_table_beta init_Table_Beta 0.18578 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18422 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.25186 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24986 66 0.0038 3.3 % + LOOP_ions opt_ions 5.8861 1 5.9 78 % + ESolver_KS_LCAO Run 5.3215 1 5.3 71 % + HSolverLCAO solve 2.8659 12 0.24 38 % + HamiltLCAO updateHk 1.4574 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.4279 12 0.12 19 % + Gint_interface cal_gint 2.1495 25 0.086 29 % + Gint_Gamma distri_vl_value 0.20171 12 0.017 2.7 % + Gint_Gamma distri_vl 2.7744 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.6845 14 0.41 76 % + LCAO_gen_fixedH add_v_delta 2.6312 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6313 6 0.44 35 % + ElecStateLCAO psiToRho 1.3854 12 0.12 18 % + Charge mix_rho 0.84759 11 0.077 11 % + LOOP_ions force_stress 0.56442 1 0.56 7.5 % + Force_Stress_LCAO getForceStress 0.56439 1 0.56 7.5 % + Force_LCAO_gamma ftable_gamma 0.34786 1 0.35 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.30362 1 0.3 4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:38 2022 + FINISH Time : Wed Sep 28 11:01:45 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/94/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4062b670c87db5ba44941cd12c59eb851ca5bc03 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.179919 0.463589 0.283863 +H 0.14976 0.406725 0.274113 +H 0.151153 0.503742 0.239684 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..04880aa957ab3851e4816652aef642f7c50c61d0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2755 2 + 2 -12.9731 2 + 3 -9.16017 2 + 4 -6.74235 2 + 5 1.27093 0 + 6 4.3707 0 + 7 11.0811 0 + 8 11.3374 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..5cacc739814b8e1bdefa0ce247d9d929e55a54ac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:49 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.03772625944 12.9804993172 7.94816051221 0 0 0 0 + tauc_H1 4.19327390949 11.3883001623 7.67515974968 0 0 0 0 + tauc_H2 4.23227020181 14.1047868844 6.71116120122 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870245748822 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877014144924 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105847727491 (SEC) + + DONE : INIT CHARGE Time : 0.154779081566 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.433484 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 337 ; sender_size of each process is: +144 144 49 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00115 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00093 + + Density error is 0.213533827547 + + Energy Rydberg eV + E_KohnSham -34.1930810173 -465.220734012 + E_Harris -34.3819171701 -467.789981678 + E_Fermi -0.403124501408 -5.48479022256 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00120214877744 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110292239556 + + Density error is 0.09784626618 + + Energy Rydberg eV + E_KohnSham -34.2810343314 -466.417400241 + E_Harris -34.2877780125 -466.509152729 + E_Fermi -0.213378350719 -2.90316139962 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00122422282479 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105281027061 + + Density error is 0.0627183984481 + + Energy Rydberg eV + E_KohnSham -34.2812261062 -466.42000947 + E_Harris -34.2855851631 -466.479317483 + E_Fermi -0.202101762776 -2.7497355496 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00126103033915 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000986280757667 + + Density error is 0.00196676354398 + + Energy Rydberg eV + E_KohnSham -34.281210559 -466.41979794 + E_Harris -34.2812115796 -466.419811826 + E_Fermi -0.16663097537 -2.26713072833 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00125709364342 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098760933736 + + Density error is 0.000814961204873 + + Energy Rydberg eV + E_KohnSham -34.2811599208 -466.419108972 + E_Harris -34.2811608794 -466.419122014 + E_Fermi -0.165961664789 -2.2580242907 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00125832733911 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000986555463054 + + Density error is 0.000146325306886 + + Energy Rydberg eV + E_KohnSham -34.2811940142 -466.419572837 + E_Harris -34.2811940604 -466.419573465 + E_Fermi -0.165928395798 -2.25757164285 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.0012587490498 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000986756987818 + + Density error is 3.52602829954e-05 + + Energy Rydberg eV + E_KohnSham -34.281181447 -466.419401852 + E_Harris -34.2811814536 -466.419401941 + E_Fermi -0.165819583123 -2.25609117046 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00125873287074 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000986689301641 + + Density error is 1.4637602586e-05 + + Energy Rydberg eV + E_KohnSham -34.2811853362 -466.419454766 + E_Harris -34.281185337 -466.419454778 + E_Fermi -0.165857419056 -2.25660595474 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00125871767148 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000986687239761 + + Density error is 1.42792683777e-06 + + Energy Rydberg eV + E_KohnSham -34.2811840382 -466.419437106 + E_Harris -34.2811840382 -466.419437106 + E_Fermi -0.165841034504 -2.25638303147 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00125871964009 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000986688698899 + + Density error is 1.51496431088e-07 + + Energy Rydberg eV + E_KohnSham -34.2811842494 -466.419439979 + E_Harris -34.2811842494 -466.419439979 + E_Fermi -0.165840033122 -2.25636940697 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00125872035753 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000986689087007 + + Density error is 3.05479284865e-08 + + Energy Rydberg eV + E_KohnSham -34.2811842728 -466.419440298 + E_Harris -34.2811842728 -466.419440298 + E_band -7.96006700378 -108.302267713 + E_one_elec -69.2294581497 -941.915100288 + E_Hartree +36.0091812608 +489.930045461 + E_xc -8.20466927777 -111.630252383 + E_Ewald +7.26821400115 +98.8891246991 + E_demet -1.19869265439e-75 -1.63090502504e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194702335908 -2.64906118226 + E_Fermi -0.165840001625 -2.25636897843 + + charge density convergence is achieved + final etot is -466.419440298 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2755 2.00000 + 2 -12.9731 2.00000 + 3 -9.16017 2.00000 + 4 -6.74235 2.00000 + 5 1.27093 0.00000 + 6 4.37070 0.00000 + 7 11.0811 0.00000 + 8 11.3374 0.00000 + + EFERMI = -2.256368978430227 eV + OUT.ABACUS/ final etot is -466.4194402983579 eV + correction force for each atom along direction 1 is -6.26690e-05 + correction force for each atom along direction 2 is -7.32924e-05 + correction force for each atom along direction 3 is -0.000183534 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.060300105 +0.66603401 -0.19162691 + H1 -0.23119174 -0.55258587 -0.027970599 + H2 +0.17089164 -0.11344814 +0.21959751 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4194402983579 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3478 11 0.58 1.0e+02% + Run_lcao lcao_line 6.3389 1 6.3 1.e+02% + Potential init_pot 0.28486 2 0.14 4.5% + PW_Basis recip2real 0.26852 16 0.017 4.2% + PW_Basis gathers_scatterp 0.11812 16 0.0074 1.9% + Potential v_of_rho 0.87732 13 0.067 14.% + XC_Functional v_xc 0.24753 14 0.018 3.9% + H_Hartree_pw v_hartree 0.59121 13 0.045 9.3% + PW_Basis real2recip 0.56492 38 0.015 8.9% + PW_Basis gatherp_scatters 0.22373 38 0.0059 3.5% + ORB_control set_orb_tables 1.1160 1 1.1 18.% + ORB_gen_tables gen_tables 1.1160 1 1.1 18.% + ORB_table_phi init_Table 0.48727 1 0.49 7.7% + ORB_table_phi cal_ST_Phi12_R 0.48234 126 0.0038 7.6% + ORB_table_beta init_Table_Beta 0.18878 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18726 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25969 1 0.26 4.1% + ORB_table_alpha S_PhiAlpha_R 0.25778 66 0.0039 4.1% + LOOP_ions opt_ions 4.7115 1 4.7 74.% + ESolver_KS_LCAO Run 4.1725 1 4.2 66.% + HSolverLCAO solve 2.1890 11 0.20 34.% + HamiltLCAO updateHk 1.1389 11 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1072 11 0.10 17.% + Gint_interface cal_gint 1.6140 23 0.070 25.% + Gint_Gamma distri_vl_value 0.16195 11 0.015 2.6% + Gint_Gamma distri_vl 2.0118 6 0.34 32.% + LCAO_Deepks cal_projected_DM 4.5095 13 0.35 71.% + LCAO_gen_fixedH add_v_delta 1.8809 6 0.31 30.% + LCAO_DESCRIPTOR add_v_delta 1.8808 6 0.31 30.% + ElecStateLCAO psiToRho 1.0308 11 0.094 16.% + Charge mix_rho 0.66010 10 0.066 10.% + LOOP_ions force_stress 0.53881 1 0.54 8.5% + Force_Stress_LCAO getForceStress 0.53878 1 0.54 8.5% + Force_LCAO_gamma ftable_gamma 0.32709 1 0.33 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.27888 1 0.28 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:49 2022 + Finish Time : Wed Sep 28 11:06:55 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..50da75b0ab9068f2fa691facf96a6d2ae33a81ab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123644 ima = 3.70719e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122944020882 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112038237141 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112573689921 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112802472548 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112758319274 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112785786785 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011277872235 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112781365163 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112780763837 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112780701986 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112780693626 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/STRU new file mode 100644 index 0000000000000000000000000000000000000000..04d610893582b559ce86d1ab471a919a5b5a0ae5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.962273740539 12.980499317153 7.948160512218 0 0 0 +H +0.0 +2 +-23.806726090486 11.388300162289 7.675159749678 0 0 0 +-23.767729798178 14.104786884385 6.711161201227 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/conv new file mode 100644 index 0000000000000000000000000000000000000000..8f1db8709d15893d509c58c321de4652a35122e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/conv @@ -0,0 +1 @@ +95 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a887dcef1c5fcf7d56bb3458af59820b6750f5c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750017087 0.01268167848 1.270041859 1.358427369 1.469240137 0.008615571361 0.01821997394 0.03905271603 +-3.257979056e-19 0.001017631104 0.002612297403 0.01241551641 0.04502094118 4.372545104e-19 2.091065818e-06 6.01736694e-06 +0.001634043838 0.005986314088 + +H atom_index 1 n_descriptor 18 +1.254680221 0.03417380229 0.1101035102 0.1521144265 0.3224470608 0.02254078208 0.02857564302 0.03735430127 +1.192277292e-17 4.628902169e-05 0.1025657864 0.1153512276 0.1305546513 6.790405266e-18 3.749206565e-06 0.01316976297 +0.02647645962 0.03096986774 + +H atom_index 2 n_descriptor 18 +1.228828577 0.03506069912 0.1013319884 0.1403537233 0.3138479236 0.02132993232 0.02706607286 0.03822315175 +-1.342542041e-17 4.390673217e-05 0.0960868549 0.1143014782 0.1203644765 1.559871447e-19 5.097758227e-06 0.01347434983 +0.02549506358 0.02975957035 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..8a247aa5a86afecff85dedc11e57e95ecc49feaa Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..20557e2cdcbd03f7868ce8f7f388dcf7ce666a44 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:49 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870461 SEC) : SETUP UNITCELL + DONE(0.0877154 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105868 SEC) : INIT PLANEWAVE + DONE(0.154913 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.433558 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652207e+02 0.000000e+00 2.135e-01 4.935e-01 + GE2 -4.664174e+02 -1.196666e+00 9.785e-02 4.196e-01 + GE3 -4.664200e+02 -2.609230e-03 6.272e-02 4.767e-01 + GE4 -4.664198e+02 2.115304e-04 1.967e-03 3.651e-01 + GE5 -4.664191e+02 6.889676e-04 8.150e-04 3.601e-01 + GE6 -4.664196e+02 -4.638649e-04 1.463e-04 3.507e-01 + GE7 -4.664194e+02 1.709855e-04 3.526e-05 3.474e-01 + GE8 -4.664195e+02 -5.291441e-05 1.464e-05 3.407e-01 + GE9 -4.664194e+02 1.766021e-05 1.428e-06 3.366e-01 + GE10 -4.664194e+02 -2.873570e-06 1.515e-07 3.383e-01 + GE11 -4.664194e+02 -3.188838e-07 3.055e-08 2.824e-01 +E_delta_band = -7.02502286e-02 Ry = -9.55803395e-01 eV +E_delta_NN= -1.94702336e-01 Ry = -2.64906118e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3478 11 0.58 1e+02 % + Run_lcao lcao_line 6.3389 1 6.3 1e+02 % + Potential init_pot 0.28486 2 0.14 4.5 % + PW_Basis recip2real 0.26852 16 0.017 4.2 % + PW_Basis gathers_scatterp 0.11812 16 0.0074 1.9 % + Potential v_of_rho 0.87732 13 0.067 14 % + XC_Functional v_xc 0.24753 14 0.018 3.9 % + H_Hartree_pw v_hartree 0.59121 13 0.045 9.3 % + PW_Basis real2recip 0.56492 38 0.015 8.9 % + PW_Basis gatherp_scatters 0.22373 38 0.0059 3.5 % + ORB_control set_orb_tables 1.116 1 1.1 18 % + ORB_gen_tables gen_tables 1.116 1 1.1 18 % + ORB_table_phi init_Table 0.48727 1 0.49 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.48234 126 0.0038 7.6 % + ORB_table_beta init_Table_Beta 0.18878 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18726 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.25969 1 0.26 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.25778 66 0.0039 4.1 % + LOOP_ions opt_ions 4.7115 1 4.7 74 % + ESolver_KS_LCAO Run 4.1725 1 4.2 66 % + HSolverLCAO solve 2.189 11 0.2 34 % + HamiltLCAO updateHk 1.1389 11 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1072 11 0.1 17 % + Gint_interface cal_gint 1.614 23 0.07 25 % + Gint_Gamma distri_vl_value 0.16195 11 0.015 2.6 % + Gint_Gamma distri_vl 2.0118 6 0.34 32 % + LCAO_Deepks cal_projected_DM 4.5095 13 0.35 71 % + LCAO_gen_fixedH add_v_delta 1.8809 6 0.31 30 % + LCAO_DESCRIPTOR add_v_delta 1.8808 6 0.31 30 % + ElecStateLCAO psiToRho 1.0308 11 0.094 16 % + Charge mix_rho 0.6601 10 0.066 10 % + LOOP_ions force_stress 0.53881 1 0.54 8.5 % + Force_Stress_LCAO getForceStress 0.53878 1 0.54 8.5 % + Force_LCAO_gamma ftable_gamma 0.32709 1 0.33 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.27888 1 0.28 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:49 2022 + FINISH Time : Wed Sep 28 11:06:55 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/95/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..0cd664df802edaf1f922e11520a04c63c09f9a32 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.191799 0.454117 0.293157 +H 0.146655 0.405985 0.291415 +H 0.160185 0.503163 0.264177 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..73255d5845886559f760963a3ff9cb6a0e77b029 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3206 2 + 2 -12.9209 2 + 3 -9.23257 2 + 4 -6.75275 2 + 5 1.28042 0 + 6 4.38722 0 + 7 11.0748 0 + 8 11.3384 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a2fd81e06671a6f88a6d6df82411f8bca14cf844 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:28 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.37038486092 12.715265168 8.20838371925 0 0 0 0 + tauc_H1 4.10634815581 11.3675678749 8.15962068548 0 0 0 0 + tauc_H2 4.48518031916 14.0885631313 7.39696578222 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0736109259452 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0868290028276 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.102620847597 (SEC) + + DONE : INIT CHARGE Time : 0.14426928942 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388566 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000898 + + Density error is 0.213647640852 + + Energy Rydberg eV + E_KohnSham -34.1926166747 -465.214416306 + E_Harris -34.3817242668 -467.787357093 + E_Fermi -0.404833511292 -5.50804249492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00111533087265 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000988284571516 + + Density error is 0.0977178446951 + + Energy Rydberg eV + E_KohnSham -34.2808494638 -466.414884987 + E_Harris -34.2876075909 -466.506834024 + E_Fermi -0.214658436528 -2.92057786055 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00104494729567 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000938814126737 + + Density error is 0.0626512851734 + + Energy Rydberg eV + E_KohnSham -34.2810606344 -466.417758111 + E_Harris -34.2854343929 -466.477266149 + E_Fermi -0.203377029288 -2.76708644063 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000935104408472 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000871239682334 + + Density error is 0.00195208986392 + + Energy Rydberg eV + E_KohnSham -34.2810456833 -466.417554691 + E_Harris -34.2810462557 -466.417562479 + E_Fermi -0.167808627052 -2.28315350146 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000935505710542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000872688176875 + + Density error is 0.000835970967862 + + Energy Rydberg eV + E_KohnSham -34.2809914202 -466.416816404 + E_Harris -34.2809925944 -466.41683238 + E_Fermi -0.167138894154 -2.27404131791 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000934145638654 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000871647442447 + + Density error is 0.000123523769009 + + Energy Rydberg eV + E_KohnSham -34.2810282825 -466.417317942 + E_Harris -34.2810283083 -466.417318292 + E_Fermi -0.167122893539 -2.27382361837 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000934208167291 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000871757745133 + + Density error is 3.46195844519e-05 + + Energy Rydberg eV + E_KohnSham -34.2810154778 -466.417143724 + E_Harris -34.2810154845 -466.417143815 + E_Fermi -0.1670170839 -2.27238400439 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000934180734083 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000871718386567 + + Density error is 1.37808955596e-05 + + Energy Rydberg eV + E_KohnSham -34.2810187241 -466.417187893 + E_Harris -34.2810187249 -466.417187903 + E_Fermi -0.167056763552 -2.27292387374 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000934169003905 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000871717401108 + + Density error is 1.23104914063e-06 + + Energy Rydberg eV + E_KohnSham -34.2810174457 -466.417170499 + E_Harris -34.2810174457 -466.417170499 + E_Fermi -0.167040988242 -2.27270923964 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000934169274801 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000871717386456 + + Density error is 1.71718240997e-07 + + Energy Rydberg eV + E_KohnSham -34.2810176599 -466.417173413 + E_Harris -34.2810176599 -466.417173413 + E_Fermi -0.167040395355 -2.272701173 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000934169559009 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000871717803667 + + Density error is 3.48158752771e-08 + + Energy Rydberg eV + E_KohnSham -34.2810176773 -466.41717365 + E_Harris -34.2810176773 -466.41717365 + E_band -7.9712002915 -108.453743864 + E_one_elec -69.2713298147 -942.484793517 + E_Hartree +36.0263494297 +490.163630383 + E_xc -8.20740000264 -111.667405801 + E_Ewald +7.29571680846 +99.2633195894 + E_demet -1.0148616506e-76 -1.38079011299e-75 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19479427869 -2.65031212798 + E_Fermi -0.167040354139 -2.27270061223 + + charge density convergence is achieved + final etot is -466.41717365 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3206 2.00000 + 2 -12.9209 2.00000 + 3 -9.23257 2.00000 + 4 -6.75275 2.00000 + 5 1.28042 0.00000 + 6 4.38722 0.00000 + 7 11.0748 0.00000 + 8 11.3384 0.00000 + + EFERMI = -2.272700612232676 eV + OUT.ABACUS/ final etot is -466.4171736499924 eV + correction force for each atom along direction 1 is -0.000121481 + correction force for each atom along direction 2 is -2.94690e-05 + correction force for each atom along direction 3 is -4.85246e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.038773989 -0.49069623 +0.14883830 + H1 +0.16901224 -0.068164083 +0.090303798 + H2 -0.13023825 +0.55886031 -0.23914210 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4171736499924 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8545 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8469 1 6.8 1.e+02% + Potential init_pot 0.24246 2 0.12 3.5% + PW_Basis recip2real 0.22844 16 0.014 3.3% + PW_Basis gathers_scatterp 0.11027 16 0.0069 1.6% + Potential v_of_rho 0.88226 13 0.068 13.% + XC_Functional v_xc 0.28441 14 0.020 4.1% + H_Hartree_pw v_hartree 0.56463 13 0.043 8.2% + PW_Basis real2recip 0.59855 38 0.016 8.7% + PW_Basis gatherp_scatters 0.24562 38 0.0065 3.6% + ORB_control set_orb_tables 0.89554 1 0.90 13.% + ORB_gen_tables gen_tables 0.89554 1 0.90 13.% + ORB_table_phi init_Table 0.37542 1 0.38 5.5% + ORB_table_phi cal_ST_Phi12_R 0.37113 126 0.0029 5.4% + ORB_table_beta init_Table_Beta 0.15466 1 0.15 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15337 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20807 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20638 66 0.0031 3.0% + LOOP_ions opt_ions 5.4921 1 5.5 80.% + ESolver_KS_LCAO Run 4.9487 1 4.9 72.% + HSolverLCAO solve 2.7678 11 0.25 40.% + HamiltLCAO updateHk 1.3969 11 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.3736 11 0.12 20.% + Gint_interface cal_gint 1.7536 23 0.076 26.% + Gint_Gamma distri_vl_value 0.34084 11 0.031 5.0% + Gint_Gamma distri_vl 2.3717 6 0.40 35.% + LCAO_Deepks cal_projected_DM 5.2667 13 0.41 77.% + LCAO_gen_fixedH add_v_delta 2.2446 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2447 6 0.37 33.% + ElecStateLCAO psiToRho 1.3539 11 0.12 20.% + Charge mix_rho 0.74921 10 0.075 11.% + LOOP_ions force_stress 0.54319 1 0.54 7.9% + Force_Stress_LCAO getForceStress 0.54317 1 0.54 7.9% + Force_LCAO_gamma ftable_gamma 0.34519 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.26868 1 0.27 3.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:28 2022 + Finish Time : Wed Sep 28 11:03:35 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a723ab708b7ac9f35f24efe1aff0fcd636b20a22 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123951 ima = 3.68088e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122803275767 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111793748575 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112340637641 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011257729485 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112528097446 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112557577997 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112551969462 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112554586538 + charge after normalized = 8.00000000000004 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112553994447 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112553946147 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011255393689 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/STRU new file mode 100644 index 0000000000000000000000000000000000000000..81d35c05fc30e722d6ec8e9782a64f7b952ae9e7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.629615139096 12.715265167980 8.208383719224 0 0 0 +H +0.0 +2 +-23.893651844186 11.367567874931 8.159620685466 0 0 0 +-23.514819680852 14.088563131316 7.396965782209 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/conv new file mode 100644 index 0000000000000000000000000000000000000000..4deba72cc21b55e840bdf563561d8f07d3807edd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/conv @@ -0,0 +1 @@ +96 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..095c043a8c9822a760552562206ab9618fdaa540 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751117345 0.01272004832 1.271259424 1.357433789 1.469402501 0.008836475725 0.017850078 0.03907961161 +-5.968302401e-19 0.0009970760027 0.002679442488 0.01262386094 0.04567274623 4.448908207e-19 2.277865231e-06 6.388113909e-06 +0.00161740371 0.006043811379 + +H atom_index 1 n_descriptor 18 +1.235466423 0.03496960855 0.1039963628 0.1431137842 0.3156650649 0.02183224286 0.02742614246 0.03810495433 +8.079588988e-18 4.607841913e-05 0.09825125165 0.1145146732 0.1227584598 4.987420104e-18 4.632061236e-06 0.013427129 +0.02592687111 0.03006768352 + +H atom_index 2 n_descriptor 18 +1.254491245 0.03432033514 0.1105459229 0.151848922 0.3219768555 0.02273715309 0.02853852309 0.03748125847 +1.908010959e-17 4.787096974e-05 0.1028927238 0.1154190892 0.1303161719 5.865410501e-18 3.59620012e-06 0.01322933517 +0.02664313003 0.03095143227 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a6d05ddd4199f6417336c0ec36671143f7bdc251 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..f4262c113fef2d8bd9dabf2c80e6a9b0633b8ebd Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..f8e9302ddfa62d6fa755a5eb2e39fd25ce0bc9f4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..91c118e95072585073f09318caaab284d001c0ca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:28 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0736279 SEC) : SETUP UNITCELL + DONE(0.0868407 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.102636 SEC) : INIT PLANEWAVE + DONE(0.144372 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.38861 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652144e+02 0.000000e+00 2.136e-01 5.223e-01 + GE2 -4.664149e+02 -1.200469e+00 9.772e-02 4.975e-01 + GE3 -4.664178e+02 -2.873124e-03 6.265e-02 5.587e-01 + GE4 -4.664176e+02 2.034200e-04 1.952e-03 4.366e-01 + GE5 -4.664168e+02 7.382867e-04 8.360e-04 4.339e-01 + GE6 -4.664173e+02 -5.015370e-04 1.235e-04 4.235e-01 + GE7 -4.664171e+02 1.742171e-04 3.462e-05 4.246e-01 + GE8 -4.664172e+02 -4.416834e-05 1.378e-05 4.192e-01 + GE9 -4.664172e+02 1.739388e-05 1.231e-06 4.151e-01 + GE10 -4.664172e+02 -2.913894e-06 1.717e-07 4.150e-01 + GE11 -4.664172e+02 -2.372171e-07 3.482e-08 3.485e-01 +E_delta_band = -7.04401806e-02 Ry = -9.58387824e-01 eV +E_delta_NN= -1.94794279e-01 Ry = -2.65031213e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8545 11 0.62 1e+02 % + Run_lcao lcao_line 6.8469 1 6.8 1e+02 % + Potential init_pot 0.24246 2 0.12 3.5 % + PW_Basis recip2real 0.22844 16 0.014 3.3 % + PW_Basis gathers_scatterp 0.11027 16 0.0069 1.6 % + Potential v_of_rho 0.88226 13 0.068 13 % + XC_Functional v_xc 0.28441 14 0.02 4.1 % + H_Hartree_pw v_hartree 0.56463 13 0.043 8.2 % + PW_Basis real2recip 0.59855 38 0.016 8.7 % + PW_Basis gatherp_scatters 0.24562 38 0.0065 3.6 % + ORB_control set_orb_tables 0.89554 1 0.9 13 % + ORB_gen_tables gen_tables 0.89554 1 0.9 13 % + ORB_table_phi init_Table 0.37542 1 0.38 5.5 % + ORB_table_phi cal_ST_Phi12_R 0.37113 126 0.0029 5.4 % + ORB_table_beta init_Table_Beta 0.15466 1 0.15 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15337 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20807 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20638 66 0.0031 3 % + LOOP_ions opt_ions 5.4921 1 5.5 80 % + ESolver_KS_LCAO Run 4.9487 1 4.9 72 % + HSolverLCAO solve 2.7678 11 0.25 40 % + HamiltLCAO updateHk 1.3969 11 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.3736 11 0.12 20 % + Gint_interface cal_gint 1.7536 23 0.076 26 % + Gint_Gamma distri_vl_value 0.34084 11 0.031 5 % + Gint_Gamma distri_vl 2.3717 6 0.4 35 % + LCAO_Deepks cal_projected_DM 5.2667 13 0.41 77 % + LCAO_gen_fixedH add_v_delta 2.2446 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2447 6 0.37 33 % + ElecStateLCAO psiToRho 1.3539 11 0.12 20 % + Charge mix_rho 0.74921 10 0.075 11 % + LOOP_ions force_stress 0.54319 1 0.54 7.9 % + Force_Stress_LCAO getForceStress 0.54317 1 0.54 7.9 % + Force_LCAO_gamma ftable_gamma 0.34519 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.26868 1 0.27 3.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:28 2022 + FINISH Time : Wed Sep 28 11:03:35 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/96/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..86fdf61fcb65cc8288aae373ff4af9129b906674 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.197398 0.4575 0.31026 +H 0.145957 0.429906 0.338628 +H 0.173834 0.505819 0.276743 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..7475fb44fa137b1ca42da56fa24545456b7238c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5083 2 + 2 -13.2941 2 + 3 -9.10421 2 + 4 -6.79272 2 + 5 1.49521 0 + 6 4.7645 0 + 7 11.0186 0 + 8 11.2608 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ecbc342c4f865cbd95654dc5bff822386e96441a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:47 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.52713859233 12.8099998611 8.68726860556 0 0 0 0 + tauc_H1 4.08679432905 12.0373774999 9.4815817185 0 0 0 0 + tauc_H2 4.86736070961 14.1629394096 7.74879938926 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0883808836369 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101052110417 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119444815731 (SEC) + + DONE : INIT CHARGE Time : 0.169892354818 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449917 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00136 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000762 + + Density error is 0.217600450897 + + Energy Rydberg eV + E_KohnSham -34.1873685783 -465.143012291 + E_Harris -34.3850383425 -467.832447406 + E_Fermi -0.420181927543 -5.7168684112 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00119792144993 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000894623475418 + + Density error is 0.0974858008445 + + Energy Rydberg eV + E_KohnSham -34.278301852 -466.380222951 + E_Harris -34.2849010546 -466.470009709 + E_Fermi -0.226848435222 -3.0864313014 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00111001634073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856118721573 + + Density error is 0.0622153756349 + + Energy Rydberg eV + E_KohnSham -34.2785265585 -466.383280239 + E_Harris -34.2827484368 -466.440721841 + E_Fermi -0.212526259653 -2.89156810591 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000969445988355 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000806089559094 + + Density error is 0.00205628658525 + + Energy Rydberg eV + E_KohnSham -34.2785717996 -466.383895777 + E_Harris -34.2785738478 -466.383923644 + E_Fermi -0.176825136047 -2.40582939987 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000968898795745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000808065341389 + + Density error is 0.000907040544507 + + Energy Rydberg eV + E_KohnSham -34.2784953225 -466.382855252 + E_Harris -34.2784977381 -466.382888118 + E_Fermi -0.175585449764 -2.38896260269 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967579359274 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000807137087618 + + Density error is 0.000121926374112 + + Energy Rydberg eV + E_KohnSham -34.2785479224 -466.383570911 + E_Harris -34.2785479508 -466.383571297 + E_Fermi -0.175889393339 -2.39309796718 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967459680589 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000807239829212 + + Density error is 4.83766221901e-05 + + Energy Rydberg eV + E_KohnSham -34.2785301545 -466.383329166 + E_Harris -34.2785301677 -466.383329346 + E_Fermi -0.175732055126 -2.39095727096 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967471434114 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000807195047194 + + Density error is 1.33081691337e-05 + + Energy Rydberg eV + E_KohnSham -34.2785338372 -466.383379272 + E_Harris -34.278533838 -466.383379282 + E_Fermi -0.175791387849 -2.39176453407 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967454860961 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000807197203754 + + Density error is 9.16708907822e-07 + + Energy Rydberg eV + E_KohnSham -34.2785323236 -466.383358678 + E_Harris -34.2785323236 -466.383358678 + E_Fermi -0.175775774267 -2.3915521004 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967453744029 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000807197227772 + + Density error is 1.30426319931e-07 + + Energy Rydberg eV + E_KohnSham -34.2785325496 -466.383361752 + E_Harris -34.2785325496 -466.383361752 + E_Fermi -0.175775388202 -2.39154684771 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000967454018809 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000807197534668 + + Density error is 2.98914702314e-08 + + Energy Rydberg eV + E_KohnSham -34.2785325608 -466.383361906 + E_Harris -34.2785325608 -466.383361906 + E_band -8.04064103727 -109.398533679 + E_one_elec -69.7679761545 -949.242013629 + E_Hartree +36.2655299601 +493.417848446 + E_xc -8.24615834454 -112.194740096 + E_Ewald +7.5934253836 +103.313852555 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195694637308 -2.66256213543 + E_Fermi -0.175775465761 -2.39154790295 + + charge density convergence is achieved + final etot is -466.383361906 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5083 2.00000 + 2 -13.2941 2.00000 + 3 -9.10421 2.00000 + 4 -6.79272 2.00000 + 5 1.49521 0.00000 + 6 4.76450 0.00000 + 7 11.0186 0.00000 + 8 11.2608 0.00000 + + EFERMI = -2.391547902949470 eV + OUT.ABACUS/ final etot is -466.3833619058802 eV + correction force for each atom along direction 1 is -0.000179596 + correction force for each atom along direction 2 is 6.55164e-05 + correction force for each atom along direction 3 is 8.54745e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.2794263 -1.2734394 +0.79511724 + H1 -0.52551724 -0.29064107 +0.29379959 + H2 -0.75390907 +1.5640804 -1.0889168 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3833619058802 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6051 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5946 1 7.6 1.e+02% + Potential init_pot 0.28256 2 0.14 3.7% + PW_Basis recip2real 0.27040 16 0.017 3.6% + PW_Basis gathers_scatterp 0.12577 16 0.0079 1.7% + Potential v_of_rho 0.97393 13 0.075 13.% + XC_Functional v_xc 0.29185 14 0.021 3.8% + H_Hartree_pw v_hartree 0.64394 13 0.050 8.5% + PW_Basis real2recip 0.66034 38 0.017 8.7% + PW_Basis gatherp_scatters 0.29090 38 0.0077 3.8% + ORB_control set_orb_tables 1.1023 1 1.1 14.% + ORB_gen_tables gen_tables 1.1023 1 1.1 14.% + ORB_table_phi init_Table 0.47670 1 0.48 6.3% + ORB_table_phi cal_ST_Phi12_R 0.47144 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18774 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18617 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.25197 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.25001 66 0.0038 3.3% + LOOP_ions opt_ions 5.9609 1 6.0 78.% + ESolver_KS_LCAO Run 5.3583 1 5.4 70.% + HSolverLCAO solve 3.0726 11 0.28 40.% + HamiltLCAO updateHk 1.5547 11 0.14 20.% + LCAO_Hamilt cal_Hgamma 1.5275 11 0.14 20.% + Gint_interface cal_gint 1.4542 23 0.063 19.% + Gint_Gamma distri_vl_value 0.56489 11 0.051 7.4% + Gint_Gamma distri_vl 2.5731 6 0.43 34.% + LCAO_Deepks cal_projected_DM 5.6621 13 0.44 74.% + LCAO_gen_fixedH add_v_delta 2.4284 6 0.40 32.% + LCAO_DESCRIPTOR add_v_delta 2.4284 6 0.40 32.% + ElecStateLCAO psiToRho 1.4955 11 0.14 20.% + Charge mix_rho 0.76579 10 0.077 10.% + LOOP_ions force_stress 0.60249 1 0.60 7.9% + Force_Stress_LCAO getForceStress 0.60247 1 0.60 7.9% + Force_LCAO_gamma ftable_gamma 0.38351 1 0.38 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.25688 1 0.26 3.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:47 2022 + Finish Time : Wed Sep 28 11:07:54 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b88728406a42e146194f945cf851937e835f92d2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124059 ima = 3.66053e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122948482308 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112121185543 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112528359729 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112809322465 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011273580768 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112777195367 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112771313485 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112774494954 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773909259 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773884564 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773882975 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5fcbc48550c28cd4b91444cace450bfe9cb69114 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.472861407665 12.809999861133 8.687268605554 0 0 0 +H +0.0 +2 +-23.913205670932 12.037377499922 9.481581718489 0 0 0 +-23.132639290377 14.162939409598 7.748799389284 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/conv new file mode 100644 index 0000000000000000000000000000000000000000..ec03cfac369bdb2ac1d9fb5c1467fbc0adffc4bc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/conv @@ -0,0 +1 @@ +97 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..afaae277eff8e28e5738b83075a2f4135daed265 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748448359 0.01280031427 1.292672315 1.379498266 1.470399818 0.008551984445 0.01931124982 0.03900284603 +5.039560654e-20 0.001183564318 0.002703702569 0.01302727432 0.04717954678 3.948365883e-19 2.21611246e-06 6.287245767e-06 +0.00167209957 0.005911634283 + +H atom_index 1 n_descriptor 18 +1.257253005 0.03386059574 0.111314214 0.1534076471 0.3232063634 0.02268873401 0.02873787942 0.03700566143 +2.559918607e-17 4.935566653e-05 0.1051539884 0.1152869343 0.1318962711 7.746719896e-18 3.852275436e-06 0.01312359571 +0.02700469716 0.03112399618 + +H atom_index 2 n_descriptor 18 +1.291633176 0.03273292257 0.1241556822 0.1704941355 0.3332465596 0.02425232086 0.03070666989 0.03636816674 +5.170852724e-18 5.26359856e-05 0.1084164471 0.1218590352 0.1464475911 1.09258051e-17 1.921374894e-06 0.01345249194 +0.02815449334 0.03248953095 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e57f885aa741b5e754ed1b3adc3de93f11e42a3a Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..2f6df25d7deccaaeb2794551f6721ec9db002474 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..d11bd74ebbab537cb4daea8574f55bdb10d3ceb4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..598b04e0e09186d5ba51bb1d04b4b32f0bd32dbb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:47 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0884034 SEC) : SETUP UNITCELL + DONE(0.101072 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119466 SEC) : INIT PLANEWAVE + DONE(0.170019 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449987 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651430e+02 0.000000e+00 2.176e-01 5.865e-01 + GE2 -4.663802e+02 -1.237211e+00 9.749e-02 5.387e-01 + GE3 -4.663833e+02 -3.057288e-03 6.222e-02 6.055e-01 + GE4 -4.663839e+02 -6.155373e-04 2.056e-03 4.711e-01 + GE5 -4.663829e+02 1.040525e-03 9.070e-04 4.682e-01 + GE6 -4.663836e+02 -7.156588e-04 1.219e-04 4.442e-01 + GE7 -4.663833e+02 2.417451e-04 4.838e-05 4.565e-01 + GE8 -4.663834e+02 -5.010591e-05 1.331e-05 4.488e-01 + GE9 -4.663834e+02 2.059393e-05 9.167e-07 4.479e-01 + GE10 -4.663834e+02 -3.074466e-06 1.304e-07 4.478e-01 + GE11 -4.663834e+02 -1.534528e-07 2.989e-08 3.808e-01 +E_delta_band = -7.23412318e-02 Ry = -9.84252953e-01 eV +E_delta_NN= -1.95694637e-01 Ry = -2.66256214e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6051 11 0.69 1e+02 % + Run_lcao lcao_line 7.5946 1 7.6 1e+02 % + Potential init_pot 0.28256 2 0.14 3.7 % + PW_Basis recip2real 0.2704 16 0.017 3.6 % + PW_Basis gathers_scatterp 0.12577 16 0.0079 1.7 % + Potential v_of_rho 0.97393 13 0.075 13 % + XC_Functional v_xc 0.29185 14 0.021 3.8 % + H_Hartree_pw v_hartree 0.64394 13 0.05 8.5 % + PW_Basis real2recip 0.66034 38 0.017 8.7 % + PW_Basis gatherp_scatters 0.2909 38 0.0077 3.8 % + ORB_control set_orb_tables 1.1023 1 1.1 14 % + ORB_gen_tables gen_tables 1.1023 1 1.1 14 % + ORB_table_phi init_Table 0.4767 1 0.48 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.47144 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18774 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18617 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.25197 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.25001 66 0.0038 3.3 % + LOOP_ions opt_ions 5.9609 1 6 78 % + ESolver_KS_LCAO Run 5.3583 1 5.4 70 % + HSolverLCAO solve 3.0726 11 0.28 40 % + HamiltLCAO updateHk 1.5547 11 0.14 20 % + LCAO_Hamilt cal_Hgamma 1.5275 11 0.14 20 % + Gint_interface cal_gint 1.4542 23 0.063 19 % + Gint_Gamma distri_vl_value 0.56489 11 0.051 7.4 % + Gint_Gamma distri_vl 2.5731 6 0.43 34 % + LCAO_Deepks cal_projected_DM 5.6621 13 0.44 74 % + LCAO_gen_fixedH add_v_delta 2.4284 6 0.4 32 % + LCAO_DESCRIPTOR add_v_delta 2.4284 6 0.4 32 % + ElecStateLCAO psiToRho 1.4955 11 0.14 20 % + Charge mix_rho 0.76579 10 0.077 10 % + LOOP_ions force_stress 0.60249 1 0.6 7.9 % + Force_Stress_LCAO getForceStress 0.60247 1 0.6 7.9 % + Force_LCAO_gamma ftable_gamma 0.38351 1 0.38 5 % + Force_LCAO_gamma cal_fvl_dphi 0.25688 1 0.26 3.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:47 2022 + FINISH Time : Wed Sep 28 11:07:54 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/97/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..6625871fb8f72ccb86a2f8c05597f34e48aaf281 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.194881 0.455057 0.324208 +H 0.131754 0.453869 0.340558 +H 0.184831 0.461798 0.257164 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9293d853c62509cb53fcea09f4ed38ccdb7eb68b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2664 2 + 2 -12.4772 2 + 3 -9.5079 2 + 4 -6.74322 2 + 5 1.06124 0 + 6 4.10821 0 + 7 11.1061 0 + 8 11.3913 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..8170b6ab7dc109ae79892631557149402e38e8c6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:25 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.45666302324 12.741597681 9.07781518963 0 0 0 0 + tauc_H1 3.68911271946 12.708338396 9.53563427256 0 0 0 0 + tauc_H2 5.1752550929 12.9303360736 7.20058197966 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0999961499168 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100393196841 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118396218854 (SEC) + + DONE : INIT CHARGE Time : 0.161582418297 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443831 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00183 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000553 + + Density error is 0.212121767951 + + Energy Rydberg eV + E_KohnSham -34.1861415499 -465.126317713 + E_Harris -34.3733338883 -467.673200137 + E_Fermi -0.396551535493 -5.39536043336 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00142428385232 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000782357461197 + + Density error is 0.0982777500541 + + Energy Rydberg eV + E_KohnSham -34.2761739511 -466.351271374 + E_Harris -34.2833870038 -466.449409991 + E_Fermi -0.206346921475 -2.80749389681 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00130708265701 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000751808996401 + + Density error is 0.0634730266888 + + Energy Rydberg eV + E_KohnSham -34.2767243453 -466.358759872 + E_Harris -34.2813483111 -466.421672154 + E_Fermi -0.199327811009 -2.7119939996 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108433954076 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000730676469593 + + Density error is 0.00188357960264 + + Energy Rydberg eV + E_KohnSham -34.2766359014 -466.357556531 + E_Harris -34.2766355274 -466.357551442 + E_Fermi -0.163548218973 -2.22518767579 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108588706918 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00073189957123 + + Density error is 0.00111420711608 + + Energy Rydberg eV + E_KohnSham -34.2765800859 -466.356797122 + E_Harris -34.2765818051 -466.356820512 + E_Fermi -0.163546389264 -2.22516278131 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108224273291 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000731450596233 + + Density error is 0.000101541892147 + + Energy Rydberg eV + E_KohnSham -34.276608762 -466.35718728 + E_Harris -34.2766087652 -466.357187323 + E_Fermi -0.163183821929 -2.22022979966 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108194375269 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000731563999697 + + Density error is 3.19930095467e-05 + + Energy Rydberg eV + E_KohnSham -34.2766007001 -466.357077592 + E_Harris -34.2766007042 -466.357077647 + E_Fermi -0.163103921541 -2.2191426991 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108194073954 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00073149228854 + + Density error is 1.52635726099e-05 + + Energy Rydberg eV + E_KohnSham -34.2766023796 -466.357100443 + E_Harris -34.2766023806 -466.357100457 + E_Fermi -0.163131124057 -2.21951280832 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108191873348 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000731507004461 + + Density error is 2.61945283503e-06 + + Energy Rydberg eV + E_KohnSham -34.2766011477 -466.357083682 + E_Harris -34.2766011477 -466.357083682 + E_Fermi -0.163117010261 -2.21932078027 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108191174076 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000731511330876 + + Density error is 2.25354312127e-07 + + Energy Rydberg eV + E_KohnSham -34.2766013583 -466.357086548 + E_Harris -34.2766013583 -466.357086548 + E_Fermi -0.163114561008 -2.21928745648 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108191201231 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000731511560761 + + Density error is 3.52295112702e-08 + + Energy Rydberg eV + E_KohnSham -34.2766014084 -466.357087229 + E_Harris -34.2766014084 -466.357087229 + E_band -7.93708170751 -107.989536714 + E_one_elec -68.9350210086 -937.909077467 + E_Hartree +35.8573413855 +487.864157974 + E_xc -8.18025359108 -111.298059924 + E_Ewald +7.10632929175 +96.6865702321 + E_demet -8.55386043731e-66 -1.16381241844e-64 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194252113836 -2.64293559671 + E_Fermi -0.163114436345 -2.21928576035 + + charge density convergence is achieved + final etot is -466.357087229 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2664 2.00000 + 2 -12.4772 2.00000 + 3 -9.50790 2.00000 + 4 -6.74322 2.00000 + 5 1.06124 0.00000 + 6 4.10821 0.00000 + 7 11.1061 0.00000 + 8 11.3913 0.00000 + + EFERMI = -2.219285760347039 eV + OUT.ABACUS/ final etot is -466.3570872285183 eV + correction force for each atom along direction 1 is -5.64834e-05 + correction force for each atom along direction 2 is -0.000159324 + correction force for each atom along direction 3 is -8.32804e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.23849726 +0.18564918 -1.9341353 + H1 -0.53697106 -0.069675772 +0.78013052 + H2 +0.77546832 -0.11597340 +1.1540048 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3570872285183 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4139 11 0.67 1.0e+02% + Run_lcao lcao_line 7.4042 1 7.4 1.e+02% + Potential init_pot 0.28383 2 0.14 3.8% + PW_Basis recip2real 0.25589 16 0.016 3.5% + PW_Basis gathers_scatterp 0.11430 16 0.0071 1.5% + Potential v_of_rho 0.79548 13 0.061 11.% + XC_Functional v_xc 0.19224 14 0.014 2.6% + H_Hartree_pw v_hartree 0.56693 13 0.044 7.6% + PW_Basis real2recip 0.64868 38 0.017 8.7% + PW_Basis gatherp_scatters 0.26114 38 0.0069 3.5% + ORB_control set_orb_tables 1.0993 1 1.1 15.% + ORB_gen_tables gen_tables 1.0993 1 1.1 15.% + ORB_table_phi init_Table 0.47680 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47162 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18529 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18376 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24805 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24608 66 0.0037 3.3% + LOOP_ions opt_ions 5.7858 1 5.8 78.% + ESolver_KS_LCAO Run 5.1430 1 5.1 69.% + HSolverLCAO solve 2.9184 11 0.27 39.% + HamiltLCAO updateHk 1.4859 11 0.14 20.% + LCAO_Hamilt cal_Hgamma 1.4583 11 0.13 20.% + Gint_interface cal_gint 1.3902 23 0.060 19.% + Gint_Gamma distri_vl_value 0.51992 11 0.047 7.0% + Gint_Gamma distri_vl 2.4624 6 0.41 33.% + LCAO_Deepks cal_projected_DM 5.4237 13 0.42 73.% + LCAO_gen_fixedH add_v_delta 2.3158 6 0.39 31.% + LCAO_DESCRIPTOR add_v_delta 2.3158 6 0.39 31.% + ElecStateLCAO psiToRho 1.4087 11 0.13 19.% + Charge mix_rho 0.87896 10 0.088 12.% + LOOP_ions force_stress 0.64270 1 0.64 8.7% + Force_Stress_LCAO getForceStress 0.64268 1 0.64 8.7% + Force_LCAO_gamma ftable_gamma 0.45053 1 0.45 6.1% + Force_LCAO_gamma cal_fvl_dphi 0.24761 1 0.25 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:25 2022 + Finish Time : Wed Sep 28 11:06:33 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6df7ba636799ef1f2f5313f72aafe163f1f7749b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123855 ima = 3.66445e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012292900025 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111250856014 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112059528871 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112315867267 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112273458974 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112296104297 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112294245299 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011229666287 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112295959572 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112295827531 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112295814383 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7af60b9d85ac7d1ba67f0ca82da6717d7c021351 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.543336976776 12.741597681007 9.077815189638 0 0 0 +H +0.0 +2 +-24.310887280527 12.708338395957 9.535634272548 0 0 0 +-22.824744907101 12.930336073627 7.200581979665 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/conv new file mode 100644 index 0000000000000000000000000000000000000000..65be9d2ff4ecb9617667d8dc7a837254052b14c8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/conv @@ -0,0 +1 @@ +98 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5734120fde2042f39b7f205d8d96b7c0c41a369e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755891494 0.01267941191 1.252580721 1.338583045 1.469162129 0.009742713696 0.01591715821 0.03925488696 +2.580980622e-18 0.0007845347175 0.002787030568 0.01305161654 0.04510600894 -3.797093005e-20 2.637492668e-06 7.263274553e-06 +0.001572280278 0.006107754027 + +H atom_index 1 n_descriptor 18 +1.256371076 0.0348598835 0.1143518371 0.1526359434 0.3217793542 0.02372773616 0.02860816368 0.0380119314 +2.977068983e-18 4.714592757e-05 0.1030150703 0.1163839172 0.1307247431 1.069515746e-17 2.230018972e-06 0.01339331377 +0.02703156953 0.03101543279 + +H atom_index 2 n_descriptor 18 +1.19280266 0.0368885905 0.09308867047 0.1248357846 0.2987878553 0.02054387312 0.02485606462 0.04035701634 +-5.021272026e-17 4.155610241e-05 0.08749540839 0.1064942473 0.1128729999 -6.476035541e-18 5.255877635e-06 0.01467650812 +0.02450083785 0.02781601862 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3fc4d521ad1f0dda71a9303c7a85feb3a3f12592 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..e586ad2b26e5252488a52ea2ebf663a681617109 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..bd76bfe17c575e0c316687358d9e37f422bb27f2 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..5107155fd5c1eee6cb5bb200f23b80f005e52c46 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:25 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.100019 SEC) : SETUP UNITCELL + DONE(0.100409 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118417 SEC) : INIT PLANEWAVE + DONE(0.161717 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443891 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651263e+02 0.000000e+00 2.121e-01 5.561e-01 + GE2 -4.663513e+02 -1.224954e+00 9.828e-02 5.165e-01 + GE3 -4.663588e+02 -7.488498e-03 6.347e-02 5.848e-01 + GE4 -4.663576e+02 1.203341e-03 1.884e-03 4.437e-01 + GE5 -4.663568e+02 7.594093e-04 1.114e-03 4.429e-01 + GE6 -4.663572e+02 -3.901579e-04 1.015e-04 4.432e-01 + GE7 -4.663571e+02 1.096877e-04 3.199e-05 4.358e-01 + GE8 -4.663571e+02 -2.285090e-05 1.526e-05 4.308e-01 + GE9 -4.663571e+02 1.676065e-05 2.619e-06 4.271e-01 + GE10 -4.663571e+02 -2.865434e-06 2.254e-07 4.265e-01 + GE11 -4.663571e+02 -6.809723e-07 3.523e-08 3.750e-01 +E_delta_band = -6.92546279e-02 Ry = -9.42257553e-01 eV +E_delta_NN= -1.94252114e-01 Ry = -2.64293560e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4139 11 0.67 1e+02 % + Run_lcao lcao_line 7.4042 1 7.4 1e+02 % + Potential init_pot 0.28383 2 0.14 3.8 % + PW_Basis recip2real 0.25589 16 0.016 3.5 % + PW_Basis gathers_scatterp 0.1143 16 0.0071 1.5 % + Potential v_of_rho 0.79548 13 0.061 11 % + XC_Functional v_xc 0.19224 14 0.014 2.6 % + H_Hartree_pw v_hartree 0.56693 13 0.044 7.6 % + PW_Basis real2recip 0.64868 38 0.017 8.7 % + PW_Basis gatherp_scatters 0.26114 38 0.0069 3.5 % + ORB_control set_orb_tables 1.0993 1 1.1 15 % + ORB_gen_tables gen_tables 1.0993 1 1.1 15 % + ORB_table_phi init_Table 0.4768 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47162 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18529 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18376 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24805 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24608 66 0.0037 3.3 % + LOOP_ions opt_ions 5.7858 1 5.8 78 % + ESolver_KS_LCAO Run 5.143 1 5.1 69 % + HSolverLCAO solve 2.9184 11 0.27 39 % + HamiltLCAO updateHk 1.4859 11 0.14 20 % + LCAO_Hamilt cal_Hgamma 1.4583 11 0.13 20 % + Gint_interface cal_gint 1.3902 23 0.06 19 % + Gint_Gamma distri_vl_value 0.51992 11 0.047 7 % + Gint_Gamma distri_vl 2.4624 6 0.41 33 % + LCAO_Deepks cal_projected_DM 5.4237 13 0.42 73 % + LCAO_gen_fixedH add_v_delta 2.3158 6 0.39 31 % + LCAO_DESCRIPTOR add_v_delta 2.3158 6 0.39 31 % + ElecStateLCAO psiToRho 1.4087 11 0.13 19 % + Charge mix_rho 0.87896 10 0.088 12 % + LOOP_ions force_stress 0.6427 1 0.64 8.7 % + Force_Stress_LCAO getForceStress 0.64268 1 0.64 8.7 % + Force_LCAO_gamma ftable_gamma 0.45053 1 0.45 6.1 % + Force_LCAO_gamma cal_fvl_dphi 0.24761 1 0.25 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:25 2022 + FINISH Time : Wed Sep 28 11:06:33 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/98/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..77d7db7830f7c902ae7edc3f82e9829726fcf54c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.189228 0.452792 0.322104 +H 0.151551 0.493767 0.287504 +H 0.167551 0.393156 0.314046 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..870d9b71809ceceaa5fbaa25346676e198cc2ded --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3233 2 + 2 -13.3748 2 + 3 -8.90203 2 + 4 -6.75026 2 + 5 1.41641 0 + 6 4.63099 0 + 7 11.0524 0 + 8 11.2783 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..12519dc14456f3161d3afa042a1db296645ac771 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:52 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 5.29837430712 12.6781623361 9.01891259847 0 0 0 0 + tauc_H1 4.24343338437 13.8254665969 8.05012478503 0 0 0 0 + tauc_H2 4.69144042776 11.0083594164 8.79327679909 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871718308835 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0894439741585 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107416067243 (SEC) + + DONE : INIT CHARGE Time : 0.156803298106 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438005 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00162 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000859 + + Density error is 0.216438168925 + + Energy Rydberg eV + E_KohnSham -34.1899156402 -465.177666846 + E_Harris -34.3845564344 -467.82589071 + E_Fermi -0.411776996704 -5.6025134605 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00145929623919 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104633188568 + + Density error is 0.0977525134115 + + Energy Rydberg eV + E_KohnSham -34.2791424241 -466.391659521 + E_Harris -34.285712042 -466.481043758 + E_Fermi -0.219953475841 -2.99262056635 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00133374180539 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100539583962 + + Density error is 0.0624340335673 + + Energy Rydberg eV + E_KohnSham -34.2792819356 -466.393557673 + E_Harris -34.2834817423 -466.450698974 + E_Fermi -0.206239916968 -2.80603802581 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111394118806 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000951106468506 + + Density error is 0.00207774690031 + + Energy Rydberg eV + E_KohnSham -34.2793140541 -466.393994667 + E_Harris -34.2793167389 -466.394031196 + E_Fermi -0.170938863228 -2.32574254954 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110938251099 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000952434290919 + + Density error is 0.000842281628768 + + Energy Rydberg eV + E_KohnSham -34.2792522734 -466.393154097 + E_Harris -34.2792537711 -466.393174475 + E_Fermi -0.169824314333 -2.31057833387 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110764861842 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000951542833499 + + Density error is 0.000204649803935 + + Energy Rydberg eV + E_KohnSham -34.2792959393 -466.393748203 + E_Harris -34.2792960812 -466.393750133 + E_Fermi -0.170044817909 -2.31357843894 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110734506227 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000951831989363 + + Density error is 4.25275075326e-05 + + Energy Rydberg eV + E_KohnSham -34.2792781575 -466.393506269 + E_Harris -34.2792781676 -466.393506406 + E_Fermi -0.169843882963 -2.31084457874 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110738276946 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000951772215316 + + Density error is 1.75246958853e-05 + + Energy Rydberg eV + E_KohnSham -34.2792840382 -466.39358628 + E_Harris -34.2792840394 -466.393586297 + E_Fermi -0.169896004418 -2.31155372752 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110732915931 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000951769325481 + + Density error is 1.37236053579e-06 + + Energy Rydberg eV + E_KohnSham -34.2792825404 -466.393565902 + E_Harris -34.2792825404 -466.393565902 + E_Fermi -0.16987610961 -2.31128304477 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011073267541 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000951769207886 + + Density error is 1.51837084291e-07 + + Energy Rydberg eV + E_KohnSham -34.2792827848 -466.393569227 + E_Harris -34.2792827848 -466.393569227 + E_Fermi -0.169875085695 -2.31126911369 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110732715766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000951769724625 + + Density error is 3.82720810942e-08 + + Energy Rydberg eV + E_KohnSham -34.2792828054 -466.393569507 + E_Harris -34.2792828054 -466.393569507 + E_band -7.98936743161 -108.700920486 + E_one_elec -69.5281656057 -945.979223725 + E_Hartree +36.1598328927 +491.979766068 + E_xc -8.22883149186 -111.958996171 + E_Ewald +7.44176016444 +101.250341386 + E_demet -3.5669178765e-84 -4.85304074184e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195146990383 -2.65511101676 + E_Fermi -0.169875069539 -2.31126889388 + + charge density convergence is achieved + final etot is -466.393569507 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3233 2.00000 + 2 -13.3748 2.00000 + 3 -8.90203 2.00000 + 4 -6.75026 2.00000 + 5 1.41641 0.00000 + 6 4.63099 0.00000 + 7 11.0524 0.00000 + 8 11.2783 0.00000 + + EFERMI = -2.311268893877494 eV + OUT.ABACUS/ final etot is -466.3935695074728 eV + correction force for each atom along direction 1 is -0.000185111 + correction force for each atom along direction 2 is -1.04501e-05 + correction force for each atom along direction 3 is -0.000184255 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.89287387 +1.3796186 +0.48305830 + H1 -0.20455138 -0.17767465 -0.12983588 + H2 -0.68832249 -1.2019440 -0.35322242 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3935695074728 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6735 11 0.70 1.0e+02% + Run_lcao lcao_line 7.6634 1 7.7 1.e+02% + Potential init_pot 0.28564 2 0.14 3.7% + PW_Basis recip2real 0.26816 16 0.017 3.5% + PW_Basis gathers_scatterp 0.12629 16 0.0079 1.6% + Potential v_of_rho 0.98812 13 0.076 13.% + XC_Functional v_xc 0.31702 14 0.023 4.1% + H_Hartree_pw v_hartree 0.63344 13 0.049 8.3% + PW_Basis real2recip 0.65884 38 0.017 8.6% + PW_Basis gatherp_scatters 0.29462 38 0.0078 3.8% + ORB_control set_orb_tables 1.1057 1 1.1 14.% + ORB_gen_tables gen_tables 1.1057 1 1.1 14.% + ORB_table_phi init_Table 0.48321 1 0.48 6.3% + ORB_table_phi cal_ST_Phi12_R 0.47797 126 0.0038 6.2% + ORB_table_beta init_Table_Beta 0.18412 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18256 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.25124 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24931 66 0.0038 3.2% + LOOP_ions opt_ions 6.0427 1 6.0 79.% + ESolver_KS_LCAO Run 5.4316 1 5.4 71.% + HSolverLCAO solve 3.1374 11 0.29 41.% + HamiltLCAO updateHk 1.5831 11 0.14 21.% + LCAO_Hamilt cal_Hgamma 1.5554 11 0.14 20.% + Gint_interface cal_gint 1.3797 23 0.060 18.% + Gint_Gamma distri_vl_value 0.62175 11 0.057 8.1% + Gint_Gamma distri_vl 2.6046 6 0.43 34.% + LCAO_Deepks cal_projected_DM 5.7294 13 0.44 75.% + LCAO_gen_fixedH add_v_delta 2.4607 6 0.41 32.% + LCAO_DESCRIPTOR add_v_delta 2.4608 6 0.41 32.% + ElecStateLCAO psiToRho 1.5324 11 0.14 20.% + Charge mix_rho 0.76624 10 0.077 10.% + LOOP_ions force_stress 0.61094 1 0.61 8.0% + Force_Stress_LCAO getForceStress 0.61091 1 0.61 8.0% + Force_LCAO_gamma ftable_gamma 0.39041 1 0.39 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.25195 1 0.25 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:52 2022 + Finish Time : Wed Sep 28 11:03:59 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..dc7f430c730fc50e02d05e9bb61cb79a34e5702f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123568 ima = 3.64645e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123276142318 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112623302043 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113023196681 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113265861894 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113208827185 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113245020897 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113233784931 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113236823509 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113236152718 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113236100207 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011323609383 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/STRU new file mode 100644 index 0000000000000000000000000000000000000000..91618db4cddd61e81d4ea571beb4b2471236df6d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-22.701625692865 12.678162336084 9.018912598490 0 0 0 +H +0.0 +2 +-23.756566615641 13.825466596871 8.050124785030 0 0 0 +-23.308559572239 11.008359416446 8.793276799109 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/conv new file mode 100644 index 0000000000000000000000000000000000000000..0ef562f788814ea34d6eb1bab63d0977b8a3b868 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/conv @@ -0,0 +1 @@ +99 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f3e0338bb210a93cf0e8c1766b156a21c1659be8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745145143 0.01268545188 1.285770867 1.376961812 1.469590112 0.007934799784 0.02017442701 0.03890821535 +-4.278750537e-18 0.001184461526 0.002476245053 0.01259096302 0.04430460722 -3.545551405e-19 1.702510559e-06 5.24395872e-06 +0.001753322777 0.005714691616 + +H atom_index 1 n_descriptor 18 +1.239770502 0.03410380171 0.1050285516 0.1462566394 0.3192352476 0.02150788836 0.02784871946 0.0372368528 +-1.159053467e-17 4.090395195e-05 0.0999730802 0.1143948603 0.1256348408 8.101904058e-18 4.761738767e-06 0.01304488897 +0.02590947196 0.03039633466 + +H atom_index 2 n_descriptor 18 +1.275018962 0.03287720057 0.1174631124 0.1629728381 0.3299352789 0.02304960123 0.02987459587 0.03631116509 +2.214163585e-17 4.393821086e-05 0.1070778798 0.1173818704 0.1399965852 6.50928295e-18 2.977904806e-06 0.01301335555 +0.0271693528 0.03190231833 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..bd457d9ded4769392f0abd5ca799e881110b61d0 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..3263b42b237c6cffd6debc93c4fe95300a4e4235 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..1d9028a8bdb579555ad94776b3f9f1ee6babb824 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..06eef2f8f45d6961f3154412668d381f3ac3a510 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:52 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871995 SEC) : SETUP UNITCELL + DONE(0.0894607 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107436 SEC) : INIT PLANEWAVE + DONE(0.156929 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438065 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651777e+02 0.000000e+00 2.164e-01 5.903e-01 + GE2 -4.663917e+02 -1.213993e+00 9.775e-02 5.451e-01 + GE3 -4.663936e+02 -1.898152e-03 6.243e-02 6.123e-01 + GE4 -4.663940e+02 -4.369938e-04 2.078e-03 4.764e-01 + GE5 -4.663932e+02 8.405696e-04 8.423e-04 4.748e-01 + GE6 -4.663937e+02 -5.941062e-04 2.046e-04 4.640e-01 + GE7 -4.663935e+02 2.419339e-04 4.253e-05 4.527e-01 + GE8 -4.663936e+02 -8.001084e-05 1.752e-05 4.561e-01 + GE9 -4.663936e+02 2.037879e-05 1.372e-06 4.578e-01 + GE10 -4.663936e+02 -3.325536e-06 1.518e-07 4.528e-01 + GE11 -4.663936e+02 -2.804220e-07 3.827e-08 3.871e-01 +E_delta_band = -7.12682254e-02 Ry = -9.69653951e-01 eV +E_delta_NN= -1.95146990e-01 Ry = -2.65511102e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6735 11 0.7 1e+02 % + Run_lcao lcao_line 7.6634 1 7.7 1e+02 % + Potential init_pot 0.28564 2 0.14 3.7 % + PW_Basis recip2real 0.26816 16 0.017 3.5 % + PW_Basis gathers_scatterp 0.12629 16 0.0079 1.6 % + Potential v_of_rho 0.98812 13 0.076 13 % + XC_Functional v_xc 0.31702 14 0.023 4.1 % + H_Hartree_pw v_hartree 0.63344 13 0.049 8.3 % + PW_Basis real2recip 0.65884 38 0.017 8.6 % + PW_Basis gatherp_scatters 0.29462 38 0.0078 3.8 % + ORB_control set_orb_tables 1.1057 1 1.1 14 % + ORB_gen_tables gen_tables 1.1057 1 1.1 14 % + ORB_table_phi init_Table 0.48321 1 0.48 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.47797 126 0.0038 6.2 % + ORB_table_beta init_Table_Beta 0.18412 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18256 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.25124 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24931 66 0.0038 3.2 % + LOOP_ions opt_ions 6.0427 1 6 79 % + ESolver_KS_LCAO Run 5.4316 1 5.4 71 % + HSolverLCAO solve 3.1374 11 0.29 41 % + HamiltLCAO updateHk 1.5831 11 0.14 21 % + LCAO_Hamilt cal_Hgamma 1.5554 11 0.14 20 % + Gint_interface cal_gint 1.3797 23 0.06 18 % + Gint_Gamma distri_vl_value 0.62175 11 0.057 8.1 % + Gint_Gamma distri_vl 2.6046 6 0.43 34 % + LCAO_Deepks cal_projected_DM 5.7294 13 0.44 75 % + LCAO_gen_fixedH add_v_delta 2.4607 6 0.41 32 % + LCAO_DESCRIPTOR add_v_delta 2.4608 6 0.41 32 % + ElecStateLCAO psiToRho 1.5324 11 0.14 20 % + Charge mix_rho 0.76624 10 0.077 10 % + LOOP_ions force_stress 0.61094 1 0.61 8 % + Force_Stress_LCAO getForceStress 0.61091 1 0.61 8 % + Force_LCAO_gamma ftable_gamma 0.39041 1 0.39 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.25195 1 0.25 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:52 2022 + FINISH Time : Wed Sep 28 11:03:59 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/99/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/H_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/H_ONCV_PBE-1.0.upf new file mode 120000 index 0000000000000000000000000000000000000000..9880d5f3474a67f84e7a20ef438603329c983a07 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/H_ONCV_PBE-1.0.upf @@ -0,0 +1 @@ +../../../../iter/H_ONCV_PBE-1.0.upf \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/H_gga_6au_60Ry_2s1p.orb b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/H_gga_6au_60Ry_2s1p.orb new file mode 120000 index 0000000000000000000000000000000000000000..c79b62f8b6dcf731268379ef0ddf2f3217ed86e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/H_gga_6au_60Ry_2s1p.orb @@ -0,0 +1 @@ +../../../../iter/H_gga_6au_60Ry_2s1p.orb \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..76ee9d71bec143675cb6f16507d7e9525a195f13 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/INPUT @@ -0,0 +1,21 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 100.000000 +scf_thr 1.000000e-07 +scf_nmax 100 +basis_type lcao +dft_functional hse +gamma_only 1 +mixing_type pulay +mixing_beta 0.40000 +cal_force 0 +cal_stress 0 +deepks_scf 1 +deepks_model model.ptg +exx_pca_threshold 1e-4 +exx_c_threshold 1e-4 +exx_dm_threshold 1e-4 +exx_schwarz_threshold 1e-5 +exx_cauchy_threshold 1e-7 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..057908475a5a9cc1da334d2032e0a903015ec447 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/INPUT @@ -0,0 +1,282 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional hse #exchange correlation functional +xc_temperature 0 #temperature for finite temperature functionals +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 0 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #the control of symmetry +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group +out_freq_elec 0 #the frequency ( >= 0) of electronic iter to output charge density and wavefunction. 0: output only when converged +dft_plus_dmft 0 #true:DFT+U correction; false: standard DFT calcullation(default) +printe 100 #Print out energy for each band for every printe steps +mem_saver 0 #Only for nscf calculations. if set to 1, then a memory saving technique will be used for many k point calculations. +diago_proc 2 #the number of procs used to do diagonalization +nbspline -1 #the order of B-spline basis +wannier_card #input card for wannier functions +soc_lambda 1 #The fraction of averaged SOC pseudopotential is given by (1-soc_lambda) +cal_force 0 #if calculate the force at the end of the electronic iteration +out_freq_ion 0 #the frequency ( >= 0 ) of ionic step to output charge density and wavefunction. 0: output only when ion steps are finished + +#Parameters (2.PW) +ecutwfc 100 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables +pw_seed 1 #random seed for initializing wave functions + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 100 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 0 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model model.ptg #file dir of traced pytorch model: 'model.ptg +bessel_lmax 2 #lmax used in generating bessel functions +bessel_rcut 6 #rcut used in generating bessel functions +bessel_rcut 6 #tolerence level when generating bessel functions + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +gamma_only 1 #Only for localized orbitals set and gamma point. If set to 1, a fast algorithm is used +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 100 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_element_info 0 #output (projected) wavefunction of each element +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method fixed #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.01 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force +test_skip_ewald 0 #skip ewald energy + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0.0001 # +exx_c_threshold 0.0001 # +exx_v_threshold 0 # +exx_dm_threshold 0.0001 # +exx_schwarz_threshold1e-05 # +exx_cauchy_threshold1e-07 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) + +#Parameters (20.dft+u) +dft_plus_u 0 #true:DFT+U correction; false: standard DFT calcullation(default) +dftu_type 2 #1:rotationally invarient formalism; 2:simplified form(default) +double_counting 1 #1:FLL(fully localized limit)(default); 2:AMF(around mean field) +yukawa_lambda 0 #default:0.0 +yukawa_potential 0 #default: false +omc 0 #whether turn on occupation matrix control method or not +hund_j 0 0 #Hund exchange parameter J(ev) +hubbard_u 0 0 #Hubbard Coulomb interaction parameter U(ev) +orbital_corr -1 -1 #which correlated orbitals need corrected ; d:2 ,f:3, do not need correction:-1 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..fec4395ee7d7dee5f840e56d8986a953a6a4af38 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.68499 0.0198613 0.206681 +H 0.737263 0.0609936 0.208978 +H 0.703007 0.991759 0.151281 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e4265cdb99b891d72f8bf3abb48ab76618e6d1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/istate.info @@ -0,0 +1,17 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4774 2 + 2 -12.4601 2 + 3 -9.54393 2 + 4 -6.6771 2 + 5 1.43203 0 + 6 4.78989 0 + 7 11.3487 0 + 8 11.7462 0 + 9 12.735 0 + 10 19.1996 0 + 11 24.3926 0 + 12 26.2999 0 + 13 31.7396 0 + 14 32.2056 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0cac0b58ee4cf2253ed2e1a911fb1c65564d43fa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/running_scf.log @@ -0,0 +1,727 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 2 + Start Time is Wed Oct 12 12:59:43 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 2 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + The esolver type has been set to : ksdft_lcao + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.179723531 0.556117645516 5.78706081801 0 0 0 0 + tauc_H1 20.6433699266 1.70781947776 5.85137512725 0 0 0 0 + tauc_H2 19.6841906027 27.7692630016 4.23586843828 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ./O_gga_6au_60Ry_2s2p1d.orb + orbital file: ./H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ./O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : hse + exchange-correlation functional = HSE + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ./H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : hse + exchange-correlation functional = HSE + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 400 + [fft grid for charge/potential] = 180, 180, 180 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 90, 90, 90 + nbxx = 364500 + nrxx = 2916000 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 2965459 + number of sticks = 24961 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 12481 1482731 + 2 12480 1482728 + --------------- sum ------------------- + 2 24961 2965459 + number of |g| = 6617 + max |g| = 10.1301020408 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 14 + NBANDS = 14 + DONE : SETUP UNITCELL Time : 0.362527398509 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Doing symmetry analysis: | + | We calculate the norm of 3 vectors and the angles between them, | + | the type of Bravais lattice is given. We can judge if the unticell | + | is a primitive cell. Finally we give the point group operation for | + | this unitcell. We we use the point group operations to do symmetry | + | analysis on given k-point mesh and the charge density. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + LATTICE VECTORS: (CARTESIAN COORDINATE: IN UNIT OF A0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + right hand lattice = 1 + NORM_A = 28 + NORM_B = 28 + NORM_C = 28 + ALPHA (DEGREE) = 90 + BETA (DEGREE) = 90 + GAMMA (DEGREE) = 90 + BRAVAIS TYPE = 1 + BRAVAIS LATTICE NAME = 01. Cubic P (simple) + IBRAV = 1 + BRAVAIS = SIMPLE CUBIC + LATTICE CONSTANT A = 122.049170419 + ibrav = 1 + ROTATION MATRICES = 48 + PURE POINT GROUP OPERATIONS = 1 + SPACE GROUP OPERATIONS = 1 + POINT GROUP = C_1 +Warning : If the optimal symmetric configuration is not the input configuration, +you have to manually change configurations, ABACUS would only calculate the input structure! + DONE : SYMMETRY Time : 0.389037732588 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.397740276181 (SEC) + + DONE : INIT CHARGE Time : 0.553953263327 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 2.46804 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 1005 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 276 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 180, 180, 180 + [big cell numbers in grid] = 90, 90, 90 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 20, 20, 20 + [dimension of extened grid] = 131, 131, 131 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 23 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 23 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +276 253 +sender_size is 552 ; sender_size of each process is: +276 276 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.000891 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000234 + + Density error is 0.220930940636 + + Energy Rydberg eV + E_KohnSham -34.3458688681 -467.299519367 + E_Harris -34.5623556538 -470.244973195 + E_Fermi -0.852047612528 -11.5927024977 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00121780297773 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000225553183416 + + Density error is 0.0969136823804 + + Energy Rydberg eV + E_KohnSham -34.4466585976 -468.670833988 + E_Harris -34.4528133171 -468.754573243 + E_Fermi -0.546431597809 -7.43458329745 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00115390748625 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000212342093579 + + Density error is 0.0622379319468 + + Energy Rydberg eV + E_KohnSham -34.4473967583 -468.68087718 + E_Harris -34.4518102993 -468.740926486 + E_Fermi -0.531065111706 -7.22551152821 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00105878165305 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000187772045163 + + Density error is 0.00217915829897 + + Energy Rydberg eV + E_KohnSham -34.447434781 -468.681394505 + E_Harris -34.447441892 -468.681491255 + E_Fermi -0.483448789772 -6.57765823211 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00106714935426 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000188099842837 + + Density error is 0.00143076123858 + + Energy Rydberg eV + E_KohnSham -34.4473324277 -468.680001916 + E_Harris -34.4473370476 -468.680064773 + E_Fermi -0.484809184655 -6.59616735404 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00106233312496 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000187437927234 + + Density error is 0.000266640980591 + + Energy Rydberg eV + E_KohnSham -34.4473634904 -468.680424547 + E_Harris -34.4473635469 -468.680425315 + E_Fermi -0.483386824101 -6.57681514589 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00106292150603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000187522290411 + + Density error is 6.91083762356e-05 + + Energy Rydberg eV + E_KohnSham -34.4473529743 -468.680281468 + E_Harris -34.4473529967 -468.680281773 + E_Fermi -0.483548565551 -6.57901575122 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00106266027887 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000187492701656 + + Density error is 7.53959971159e-06 + + Energy Rydberg eV + E_KohnSham -34.4473560976 -468.680323962 + E_Harris -34.4473560976 -468.680323963 + E_Fermi -0.48350780745 -6.57846120881 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00106267610728 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000187492913427 + + Density error is 1.6842299835e-06 + + Energy Rydberg eV + E_KohnSham -34.4473550805 -468.680310123 + E_Harris -34.4473550807 -468.680310127 + E_Fermi -0.483500370398 -6.57836002252 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00106266960407 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000187491433464 + + Density error is 4.90077786444e-07 + + Energy Rydberg eV + E_KohnSham -34.4473552941 -468.68031303 + E_Harris -34.4473552941 -468.68031303 + E_Fermi -0.483499724658 -6.57835123677 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.0010626711011 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000187491512836 + + Density error is 4.81058246304e-08 + + Energy Rydberg eV + E_KohnSham -34.4473552638 -468.680312617 + E_Harris -34.4473552638 -468.680312617 + E_band -7.91187779057 -107.646619831 + E_one_elec -69.4519004109 -944.941582517 + E_Hartree +36.2495542931 +493.200488347 + E_xc -8.45103269053 -114.982198575 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195185721161 -2.65563797603 + E_Fermi -0.483499411519 -6.5783469763 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00115493406681 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000246084574375 + + Density error is 0.0924500987149 + + Energy Rydberg eV + E_KohnSham -34.3421145707 -467.24843953 + E_Harris -39.6778831856 -539.845295902 + E_Fermi -0.904745875756 -12.3096991523 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00125228096955 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000207617892903 + + Density error is 0.09386530433 + + Energy Rydberg eV + E_KohnSham -34.4402059014 -468.583040553 + E_Harris -34.4700283379 -468.988795617 + E_Fermi -0.476653086314 -6.48519794316 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00120949585099 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000208973480892 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/running_scf.ref b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/running_scf.ref new file mode 100644 index 0000000000000000000000000000000000000000..f2fa322ff438300825de5c4207f716e5cfc1bf68 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/running_scf.ref @@ -0,0 +1,2491 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 2 + Start Time is Fri Sep 30 11:21:05 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 2 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + The esolver type has been set to : ksdft_lcao + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.179723531 0.556117645516 5.78706081801 0 0 0 0 + tauc_H1 20.6433699266 1.70781947776 5.85137512725 0 0 0 0 + tauc_H2 19.6841906027 27.7692630016 4.23586843828 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ./O_gga_6au_60Ry_2s2p1d.orb + orbital file: ./H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ./O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : hf + exchange-correlation functional = HF + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ./H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : hf + exchange-correlation functional = HF + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 400 + [fft grid for charge/potential] = 180, 180, 180 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 90, 90, 90 + nbxx = 364500 + nrxx = 2916000 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 2965459 + number of sticks = 24961 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 12481 1482731 + 2 12480 1482728 + --------------- sum ------------------- + 2 24961 2965459 + number of |g| = 6617 + max |g| = 10.1301020408 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 14 + NBANDS = 14 + DONE : SETUP UNITCELL Time : 0.359533677343 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Doing symmetry analysis: | + | We calculate the norm of 3 vectors and the angles between them, | + | the type of Bravais lattice is given. We can judge if the unticell | + | is a primitive cell. Finally we give the point group operation for | + | this unitcell. We we use the point group operations to do symmetry | + | analysis on given k-point mesh and the charge density. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + LATTICE VECTORS: (CARTESIAN COORDINATE: IN UNIT OF A0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + right hand lattice = 1 + NORM_A = 28 + NORM_B = 28 + NORM_C = 28 + ALPHA (DEGREE) = 90 + BETA (DEGREE) = 90 + GAMMA (DEGREE) = 90 + BRAVAIS TYPE = 1 + BRAVAIS LATTICE NAME = 01. Cubic P (simple) + IBRAV = 1 + BRAVAIS = SIMPLE CUBIC + LATTICE CONSTANT A = 122.049170419 + ibrav = 1 + ROTATION MATRICES = 48 + PURE POINT GROUP OPERATIONS = 1 + SPACE GROUP OPERATIONS = 1 + POINT GROUP = C_1 +Warning : If the optimal symmetric configuration is not the input configuration, +you have to manually change configurations, ABACUS would only calculate the input structure! + DONE : SYMMETRY Time : 0.386135323439 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.395966864657 (SEC) + + DONE : INIT CHARGE Time : 0.552855394082 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 2.41678 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 1005 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 276 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 180, 180, 180 + [big cell numbers in grid] = 90, 90, 90 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 20, 20, 20 + [dimension of extened grid] = 131, 131, 131 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 23 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 23 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +276 253 +sender_size is 552 ; sender_size of each process is: +276 276 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.000979 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000239 + + Density error is 0.223511968482 + + Energy Rydberg eV + E_KohnSham -34.1810999257 -465.057722897 + E_Harris -34.4049152034 -468.102885972 + E_Fermi -0.860157284124 -11.7030402403 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00123619605385 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000226847718047 + + Density error is 0.0972045552349 + + Energy Rydberg eV + E_KohnSham -34.2563449141 -466.081483484 + E_Harris -34.262509559 -466.165357782 + E_Fermi -0.552946712086 -7.52322597473 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00117282983461 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000214400382995 + + Density error is 0.0624989257094 + + Energy Rydberg eV + E_KohnSham -34.2521409817 -466.02428605 + E_Harris -34.2565662723 -466.084495218 + E_Fermi -0.538340279074 -7.32449525831 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00108007237208 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.00018980873405 + + Density error is 0.00209092482909 + + Energy Rydberg eV + E_KohnSham -34.2523041943 -466.026506672 + E_Harris -34.2523123699 -466.026617907 + E_Fermi -0.489994380991 -6.66671556946 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00108611079106 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000190090806547 + + Density error is 0.00140023000925 + + Energy Rydberg eV + E_KohnSham -34.2523043253 -466.026508455 + E_Harris -34.2523105977 -466.026593794 + E_Fermi -0.492606296043 -6.70225249686 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00108305049477 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000189447646977 + + Density error is 0.000338923606122 + + Energy Rydberg eV + E_KohnSham -34.252306204 -466.026534016 + E_Harris -34.2523064762 -466.026537719 + E_Fermi -0.490179403143 -6.66923292499 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.0010832908574 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.00018954909386 + + Density error is 3.92929996697e-05 + + Energy Rydberg eV + E_KohnSham -34.2523062992 -466.026535311 + E_Harris -34.2523063131 -466.026535499 + E_Fermi -0.490629701479 -6.67535954815 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00108322111189 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000189533583892 + + Density error is 1.05379449385e-05 + + Energy Rydberg eV + E_KohnSham -34.2523063003 -466.026535325 + E_Harris -34.2523063005 -466.026535328 + E_Fermi -0.490567658469 -6.67451540969 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00108320042396 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000189533444357 + + Density error is 1.66778163184e-06 + + Energy Rydberg eV + E_KohnSham -34.2523063004 -466.026535327 + E_Harris -34.2523063006 -466.02653533 + E_Fermi -0.490579722747 -6.67467955262 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00108319569337 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000189532055788 + + Density error is 2.43068026145e-07 + + Energy Rydberg eV + E_KohnSham -34.2523063004 -466.026535327 + E_Harris -34.2523063004 -466.026535327 + E_Fermi -0.490579192323 -6.67467233583 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00108319519284 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000189532045853 + + Density error is 7.23361254598e-08 + + Energy Rydberg eV + E_KohnSham -34.2523063004 -466.026535327 + E_Harris -34.2523063004 -466.026535327 + E_band -7.8185600888 -106.376967363 + E_one_elec -69.4018814905 -944.261040192 + E_Hartree +36.2726949717 +493.515333431 + E_xc -8.4532182109 -115.011934106 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_Fermi -0.490579469776 -6.67467611077 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.000994763264882 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000327540125143 + + Density error is 0.212574544588 + + Energy Rydberg eV + E_KohnSham -32.8983777176 -447.605391916 + E_Harris -58.4540783481 -795.308536873 + E_Fermi -2.4777978833 -33.7121697052 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00160950636763 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000265583783825 + + Density error is 0.192034784776 + + Energy Rydberg eV + E_KohnSham -33.698646651 -458.493609342 + E_Harris -33.8504863105 -460.559493894 + E_Fermi -0.715398236649 -9.73349235757 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00150927952214 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000274022138436 + + Density error is 0.0982444893033 + + Energy Rydberg eV + E_KohnSham -33.6799746193 -458.239563318 + E_Harris -33.7222009337 -458.8140818 + E_Fermi -0.850730211127 -11.5747783321 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143755165059 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000272792691201 + + Density error is 0.0479206799885 + + Energy Rydberg eV + E_KohnSham -33.6736398026 -458.153373715 + E_Harris -33.6867891498 -458.332279761 + E_Fermi -0.926069950743 -12.5998280767 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00138618202813 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000268433900886 + + Density error is 0.0147571444994 + + Energy Rydberg eV + E_KohnSham -33.6750134178 -458.172062709 + E_Harris -33.6765878081 -458.193483387 + E_Fermi -0.976156723655 -13.2812935827 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00136298272542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000266627253611 + + Density error is 0.00108312070673 + + Energy Rydberg eV + E_KohnSham -33.675507382 -458.178783436 + E_Harris -33.6755174152 -458.178919945 + E_Fermi -0.997143576151 -13.5668343598 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00136077838398 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000266756557798 + + Density error is 0.00020273092603 + + Energy Rydberg eV + E_KohnSham -33.6755114539 -458.178838838 + E_Harris -33.6755117825 -458.178843308 + E_Fermi -0.999125815188 -13.5938041055 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00136135751338 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000266899629665 + + Density error is 3.29451792249e-05 + + Energy Rydberg eV + E_KohnSham -33.6755115734 -458.178840463 + E_Harris -33.6755115837 -458.178840603 + E_Fermi -0.99883638588 -13.5898662177 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00136126209654 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.00026688015466 + + Density error is 1.60476419738e-05 + + Energy Rydberg eV + E_KohnSham -33.6755115786 -458.178840533 + E_Harris -33.6755115806 -458.178840561 + E_Fermi -0.998904518673 -13.5907932119 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00136130043785 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000266884113491 + + Density error is 4.4284690611e-07 + + Energy Rydberg eV + E_KohnSham -33.6755115789 -458.178840538 + E_Harris -33.6755115789 -458.178840538 + E_Fermi -0.998882677732 -13.5904960507 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00136129933728 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000266883633666 + + Density error is 1.09317533485e-07 + + Energy Rydberg eV + E_KohnSham -33.6755115789 -458.178840538 + E_Harris -33.6755115789 -458.178840538 + E_Fermi -0.998882877861 -13.5904987735 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00136129919554 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000266883532274 + + Density error is 3.48977537816e-08 + + Energy Rydberg eV + E_KohnSham -33.6755115789 -458.178840538 + E_Harris -33.6755115789 -458.178840538 + E_band -12.5704214515 -171.029358001 + E_one_elec -69.4407993754 -944.79054518 + E_Hartree +36.3078901273 +493.99418809 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.87270076017 -107.113588987 + E_Fermi -0.99888278752 -13.5904975444 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00142505379974 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000289451145148 + + Density error is 0.00198215305397 + + Energy Rydberg eV + E_KohnSham -33.6764775777 -458.191983626 + E_Harris -33.6999756914 -458.511691864 + E_Fermi -1.00197840244 -13.6326155462 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.0014249121231 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000288461337771 + + Density error is 0.00109117814286 + + Energy Rydberg eV + E_KohnSham -33.6764754599 -458.191954811 + E_Harris -33.6764792327 -458.192006143 + E_Fermi -1.00062343618 -13.6141802844 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00142337410982 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000287486544304 + + Density error is 0.000247187323394 + + Energy Rydberg eV + E_KohnSham -33.6764755784 -458.191956424 + E_Harris -33.6764757627 -458.191958932 + E_Fermi -1.00012223218 -13.6073610542 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00142268260039 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.00028725765797 + + Density error is 3.41684816725e-05 + + Energy Rydberg eV + E_KohnSham -33.6764755899 -458.191956581 + E_Harris -33.676475596 -458.191956663 + E_Fermi -1.00010501761 -13.6071268379 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00142259305509 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000287257831079 + + Density error is 3.89401216115e-06 + + Energy Rydberg eV + E_KohnSham -33.6764755909 -458.191956595 + E_Harris -33.676475591 -458.191956595 + E_Fermi -1.00008778685 -13.6068924014 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.0014226005173 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000287259827421 + + Density error is 2.85100288704e-07 + + Energy Rydberg eV + E_KohnSham -33.676475591 -458.191956595 + E_Harris -33.676475591 -458.191956595 + E_Fermi -1.00008937348 -13.6069139886 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00142260028458 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000287260059903 + + Density error is 4.49103464776e-08 + + Energy Rydberg eV + E_KohnSham -33.676475591 -458.191956595 + E_Harris -33.676475591 -458.191956595 + E_band -12.5710140417 -171.037420606 + E_one_elec -69.4421334484 -944.808696174 + E_Hartree +36.3200027112 +494.158988248 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88444328317 -107.273354209 + E_Fermi -1.00008936094 -13.606913818 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143521928825 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292162287198 + + Density error is 0.000537604499586 + + Energy Rydberg eV + E_KohnSham -33.6765267474 -458.192652614 + E_Harris -33.6835035635 -458.287577066 + E_Fermi -1.00098145932 -13.6190514391 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143535383681 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000291909540919 + + Density error is 0.000280935356287 + + Energy Rydberg eV + E_KohnSham -33.6765266526 -458.192651324 + E_Harris -33.6765269165 -458.192654915 + E_Fermi -1.00054414024 -13.6131014078 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143507347172 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000291675215606 + + Density error is 7.28221869375e-05 + + Energy Rydberg eV + E_KohnSham -33.6765266586 -458.192651406 + E_Harris -33.6765266754 -458.192651634 + E_Fermi -1.00040268708 -13.6111768388 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143490210603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000291604102418 + + Density error is 1.06562262222e-05 + + Energy Rydberg eV + E_KohnSham -33.6765266598 -458.192651422 + E_Harris -33.6765266603 -458.192651429 + E_Fermi -1.0003957812 -13.6110828795 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143488020299 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000291600764321 + + Density error is 1.20866994117e-06 + + Energy Rydberg eV + E_KohnSham -33.6765266599 -458.192651423 + E_Harris -33.6765266599 -458.192651423 + E_Fermi -1.00039094283 -13.61101705 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143488211132 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000291600653958 + + Density error is 1.07002304951e-07 + + Energy Rydberg eV + E_KohnSham -33.6765266599 -458.192651423 + E_Harris -33.6765266599 -458.192651423 + E_Fermi -1.00039129209 -13.6110218021 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.0014348818909 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.00029160076914 + + Density error is 1.08389114073e-08 + + Energy Rydberg eV + E_KohnSham -33.6765266599 -458.192651423 + E_Harris -33.6765266599 -458.192651423 + E_band -12.5704692378 -171.030008167 + E_one_elec -69.4427807954 -944.817503782 + E_Hartree +36.3240868362 +494.214555618 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88793112996 -107.320808799 + E_Fermi -1.00039126851 -13.6110214812 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143726902545 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292758963718 + + Density error is 0.000178116888626 + + Energy Rydberg eV + E_KohnSham -33.6765305458 -458.192704294 + E_Harris -33.6787331422 -458.222672156 + E_Fermi -1.00066664049 -13.6147681091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.001437336751 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292687638673 + + Density error is 8.90977918384e-05 + + Energy Rydberg eV + E_KohnSham -33.676530531 -458.192704093 + E_Harris -33.6765305607 -458.192704497 + E_Fermi -1.00053125137 -13.6129260457 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143728196149 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292617764693 + + Density error is 1.82388272481e-05 + + Energy Rydberg eV + E_KohnSham -33.6765305322 -458.192704109 + E_Harris -33.6765305335 -458.192704126 + E_Fermi -1.00048520406 -13.61229954 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143724844098 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292600604668 + + Density error is 3.27399969585e-06 + + Energy Rydberg eV + E_KohnSham -33.6765305324 -458.192704111 + E_Harris -33.6765305324 -458.192704112 + E_Fermi -1.00048585793 -13.6123084362 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143724553533 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292598962496 + + Density error is 3.86686201907e-07 + + Energy Rydberg eV + E_KohnSham -33.6765305324 -458.192704111 + E_Harris -33.6765305324 -458.192704111 + E_Fermi -1.00048480836 -13.6122941561 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143724619872 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292598767383 + + Density error is 3.95919159583e-08 + + Energy Rydberg eV + E_KohnSham -33.6765305324 -458.192704111 + E_Harris -33.6765305324 -458.192704111 + E_band -12.5702393495 -171.026880377 + E_one_elec -69.4430187826 -944.820741764 + E_Hartree +36.3254221908 +494.23272405 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88903236985 -107.335791936 + E_Fermi -1.00048489491 -13.6122953337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143763627419 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292930947062 + + Density error is 7.12607777051e-05 + + Energy Rydberg eV + E_KohnSham -33.6765310328 -458.192710919 + E_Harris -33.6772467969 -458.20244939 + E_Fermi -1.00057534089 -13.6135259145 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143765843124 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.0002929082253 + + Density error is 3.65470616098e-05 + + Energy Rydberg eV + E_KohnSham -33.6765310286 -458.192710862 + E_Harris -33.6765310337 -458.192710932 + E_Fermi -1.00053522464 -13.6129801048 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143764898708 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.0002928831424 + + Density error is 4.20223797095e-06 + + Energy Rydberg eV + E_KohnSham -33.6765310288 -458.192710865 + E_Harris -33.6765310289 -458.192710867 + E_Fermi -1.00051881566 -13.6127568492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143764421251 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292879684178 + + Density error is 1.10991239682e-06 + + Energy Rydberg eV + E_KohnSham -33.6765310288 -458.192710866 + E_Harris -33.6765310288 -458.192710866 + E_Fermi -1.00052034087 -13.6127776008 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143764501826 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292878994567 + + Density error is 1.2212195406e-07 + + Energy Rydberg eV + E_KohnSham -33.6765310288 -458.192710866 + E_Harris -33.6765310288 -458.192710866 + E_Fermi -1.00052023326 -13.6127761366 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143764528053 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292878917198 + + Density error is 1.46215515298e-08 + + Energy Rydberg eV + E_KohnSham -33.6765310288 -458.192710866 + E_Harris -33.6765310288 -458.192710866 + E_band -12.5701693496 -171.025927979 + E_one_elec -69.443089637 -944.821705788 + E_Hartree +36.3258504231 +494.238550449 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88939024419 -107.340661067 + E_Fermi -1.00052026283 -13.6127765389 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143767108021 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292999438143 + + Density error is 3.21849802076e-05 + + Energy Rydberg eV + E_KohnSham -33.6765311243 -458.192712165 + E_Harris -33.6767707426 -458.19597234 + E_Fermi -1.00055188862 -13.61320683 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143767671364 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292991158824 + + Density error is 1.69271917441e-05 + + Energy Rydberg eV + E_KohnSham -33.6765311232 -458.19271215 + E_Harris -33.6765311243 -458.192712165 + E_Fermi -1.00054067545 -13.6130542669 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143767655007 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292981115178 + + Density error is 1.0995739558e-06 + + Energy Rydberg eV + E_KohnSham -33.6765311232 -458.19271215 + E_Harris -33.6765311232 -458.19271215 + E_Fermi -1.00053472446 -13.6129732995 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143767665449 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000292980425612 + + Density error is 4.35960197515e-07 + + Energy Rydberg eV + E_KohnSham -33.6765311232 -458.19271215 + E_Harris -33.6765311232 -458.19271215 + E_Fermi -1.00053545847 -13.6129832862 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143767761334 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.00029298011432 + + Density error is 4.13276011025e-08 + + Energy Rydberg eV + E_KohnSham -33.6765311232 -458.19271215 + E_Harris -33.6765311232 -458.19271215 + E_band -12.5701529708 -171.025705134 + E_one_elec -69.443106016 -944.821928636 + E_Hartree +36.3259865155 +494.240402081 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88951005198 -107.342291135 + E_Fermi -1.00053550952 -13.6129839809 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143765357614 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293032592855 + + Density error is 1.52918631829e-05 + + Energy Rydberg eV + E_KohnSham -33.6765311447 -458.192712443 + E_Harris -33.6766144263 -458.193845546 + E_Fermi -1.00054724417 -13.613143639 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143765461473 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293029171046 + + Density error is 8.14661161644e-06 + + Energy Rydberg eV + E_KohnSham -33.6765311444 -458.192712439 + E_Harris -33.6765311447 -458.192712442 + E_Fermi -1.00054441265 -13.6131051141 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143765576419 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293024865601 + + Density error is 4.48109982387e-07 + + Energy Rydberg eV + E_KohnSham -33.6765311444 -458.192712439 + E_Harris -33.6765311444 -458.192712439 + E_Fermi -1.00054225213 -13.6130757187 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143765648553 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293024630083 + + Density error is 1.57865993074e-07 + + Energy Rydberg eV + E_KohnSham -33.6765311444 -458.192712439 + E_Harris -33.6765311444 -458.192712439 + E_Fermi -1.00054248571 -13.6130788967 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143765699678 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293024505894 + + Density error is 1.72525151807e-08 + + Energy Rydberg eV + E_KohnSham -33.6765311444 -458.192712439 + E_Harris -33.6765311444 -458.192712439 + E_band -12.5701514355 -171.025684245 + E_one_elec -69.4431077076 -944.821951651 + E_Hartree +36.3260298264 +494.240991356 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88955169246 -107.342857683 + E_Fermi -1.00054251489 -13.6130792938 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143763664808 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293049695061 + + Density error is 7.39707069032e-06 + + Energy Rydberg eV + E_KohnSham -33.6765311495 -458.192712508 + E_Harris -33.6765614772 -458.193125137 + E_Fermi -1.00054709694 -13.6131416358 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143763657407 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293048166981 + + Density error is 3.96244214024e-06 + + Energy Rydberg eV + E_KohnSham -33.6765311495 -458.192712507 + E_Harris -33.6765311495 -458.192712508 + E_Fermi -1.00054652269 -13.6131338226 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143763753642 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293046207687 + + Density error is 2.02635776337e-07 + + Energy Rydberg eV + E_KohnSham -33.6765311495 -458.192712507 + E_Harris -33.6765311495 -458.192712507 + E_Fermi -1.00054572365 -13.6131229512 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143763819142 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.00029304606843 + + Density error is 4.53600789793e-08 + + Energy Rydberg eV + E_KohnSham -33.6765311495 -458.192712507 + E_Harris -33.6765311495 -458.192712507 + E_band -12.5701524312 -171.025697793 + E_one_elec -69.4431063151 -944.821932705 + E_Hartree +36.3260435925 +494.241178655 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88956685621 -107.343063996 + E_Fermi -1.00054575987 -13.613123444 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143762603917 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293058661079 + + Density error is 3.60147015508e-06 + + Energy Rydberg eV + E_KohnSham -33.6765311507 -458.192712524 + E_Harris -33.6765427059 -458.192869741 + E_Fermi -1.0005476146 -13.6131486789 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143762601433 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293057893145 + + Density error is 1.93980520227e-06 + + Energy Rydberg eV + E_KohnSham -33.6765311507 -458.192712524 + E_Harris -33.6765311507 -458.192712524 + E_Fermi -1.00054762979 -13.6131488856 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143762662765 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293056964094 + + Density error is 9.64100837133e-08 + + Energy Rydberg eV + E_KohnSham -33.6765311507 -458.192712524 + E_Harris -33.6765311507 -458.192712524 + E_band -12.5701536265 -171.025714056 + E_one_elec -69.4431052823 -944.821918653 + E_Hartree +36.3260483361 +494.241243194 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88957263379 -107.343142604 + E_Fermi -1.00054729329 -13.6131443072 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143762002262 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293063349629 + + Density error is 1.75874744234e-06 + + Energy Rydberg eV + E_KohnSham -33.676531151 -458.192712528 + E_Harris -33.6765358855 -458.192776945 + E_Fermi -1.00054806918 -13.6131548637 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143762050357 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293062880997 + + Density error is 9.55007401254e-07 + + Energy Rydberg eV + E_KohnSham -33.676531151 -458.192712528 + E_Harris -33.676531151 -458.192712528 + E_Fermi -1.00054812266 -13.6131555914 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143762068642 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293062434226 + + Density error is 5.55225408594e-08 + + Energy Rydberg eV + E_KohnSham -33.676531151 -458.192712528 + E_Harris -33.676531151 -458.192712528 + E_band -12.5701548067 -171.025730113 + E_one_elec -69.4431048558 -944.821912851 + E_Hartree +36.3260502766 +494.241269597 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88957500106 -107.343174813 + E_Fermi -1.00054804049 -13.6131544733 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143761735961 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293065656159 + + Density error is 8.63147745815e-07 + + Energy Rydberg eV + E_KohnSham -33.676531151 -458.192712529 + E_Harris -33.6765332771 -458.192741455 + E_Fermi -1.00054837598 -13.6131590379 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143761773813 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293065422444 + + Density error is 4.69045049138e-07 + + Energy Rydberg eV + E_KohnSham -33.676531151 -458.192712529 + E_Harris -33.676531151 -458.192712529 + E_Fermi -1.00054832823 -13.6131583884 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143761770858 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293065198433 + + Density error is 5.22420997671e-08 + + Energy Rydberg eV + E_KohnSham -33.676531151 -458.192712529 + E_Harris -33.676531151 -458.192712529 + E_band -12.5701554965 -171.025739499 + E_one_elec -69.4431047271 -944.821911099 + E_Hartree +36.3260512108 +494.241282307 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88957606408 -107.343189276 + E_Fermi -1.00054839296 -13.613159269 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143761605358 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293066825591 + + Density error is 4.23878363441e-07 + + Energy Rydberg eV + E_KohnSham -33.6765311511 -458.192712529 + E_Harris -33.6765321656 -458.192726332 + E_Fermi -1.00054854116 -13.6131612854 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143761639965 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293066710066 + + Density error is 2.3303432046e-07 + + Energy Rydberg eV + E_KohnSham -33.6765311511 -458.192712529 + E_Harris -33.6765311511 -458.192712529 + E_Fermi -1.00054840481 -13.6131594302 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.0014376162338 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293066598742 + + Density error is 6.1065984333e-08 + + Energy Rydberg eV + E_KohnSham -33.6765311511 -458.192712529 + E_Harris -33.6765311511 -458.192712529 + E_band -12.5701558998 -171.025744985 + E_one_elec -69.4431047493 -944.821911401 + E_Hartree +36.3260517403 +494.24128951 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88957657133 -107.343196177 + E_Fermi -1.00054856092 -13.6131615542 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143761541481 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293067421719 + + Density error is 2.08794347262e-07 + + Energy Rydberg eV + E_KohnSham -33.6765311511 -458.192712529 + E_Harris -33.6765316662 -458.192719538 + E_Fermi -1.00054862796 -13.6131624663 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.0014376157627 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.00029306736185 + + Density error is 1.28926638293e-07 + + Energy Rydberg eV + E_KohnSham -33.6765311511 -458.192712529 + E_Harris -33.6765311511 -458.192712529 + E_Fermi -1.00054842562 -13.6131597134 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.001437615564 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293067317797 + + Density error is 4.26608725387e-08 + + Energy Rydberg eV + E_KohnSham -33.6765311511 -458.192712529 + E_Harris -33.6765311511 -458.192712529 + E_band -12.570155808 -171.025743737 + E_one_elec -69.4431043905 -944.82190652 + E_Hartree +36.3260516391 +494.241288134 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.8895768289 -107.343199682 + E_Fermi -1.00054859509 -13.6131620191 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143761517758 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293067738106 + + Density error is 1.04805511512e-07 + + Energy Rydberg eV + E_KohnSham -33.6765311511 -458.192712529 + E_Harris -33.6765312716 -458.192714169 + E_Fermi -1.00054861491 -13.6131622888 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143761537896 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293067694947 + + Density error is 6.87393537568e-08 + + Energy Rydberg eV + E_KohnSham -33.6765311511 -458.192712529 + E_Harris -33.6765311511 -458.192712529 + E_band -12.5701549144 -171.025731579 + E_one_elec -69.4431030517 -944.821888304 + E_Hartree +36.3260503605 +494.241270738 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88957688915 -107.343200502 + E_Fermi -1.00054849046 -13.6131605956 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00143761523463 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = -0.000293067911243 + + Density error is 6.40558903716e-08 + + Energy Rydberg eV + E_KohnSham -33.6765311511 -458.192712529 + E_Harris -33.6765307646 -458.192707271 + E_band -12.5701547212 -171.02572895 + E_one_elec -69.4431023077 -944.821878182 + E_Hartree +36.3260494232 +494.241257986 + E_xc +0 +0 + E_Ewald +7.3300984293 +99.7311055393 + E_demet +0 +0 + E_descf +0 +0 + E_efield +0 +0 + E_exx -7.88957669592 -107.343197872 + E_Fermi -1.00054846604 -13.6131602633 + + charge density convergence is achieved + final etot is -458.192712529 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (0 pws) + 1 -37.0838 2.00000 + 2 -18.6526 2.00000 + 3 -16.1634 2.00000 + 4 -13.6132 2.00000 + 5 6.25993 0.00000 + 6 10.5899 0.00000 + 7 17.2039 0.00000 + 8 17.7147 0.00000 + 9 18.4000 0.00000 + 10 26.8644 0.00000 + 11 30.3067 0.00000 + 12 33.8498 0.00000 + 13 39.7478 0.00000 + 14 40.4541 0.00000 + + EFERMI = -13.61316026332539 eV + OUT.ABACUS/ final etot is -458.1927125289770 eV + + + -------------------------------------------- + !FINAL_ETOT_IS -458.1927125289770 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 167.13 11 15. 1.0e+02% + Driver driver_line 167.12 1 1.7e+02 1.e+02% + mymath heapsort 0.21006 290 0.00072 0.13% + Potential init_pot 1.7611 1 1.8 1.1% + Potential set_local_pot 0.12969 1 0.13 0.078% + PW_Basis recip2real 31.282 412 0.076 19.% + PW_Basis gathers_scatterp 12.259 412 0.030 7.3% + Charge atomic_rho 0.18931 1 0.19 0.11% + Potential v_of_rho 99.206 82 1.2 59.% + XC_Functional v_xc 81.701 82 1.0 49.% + PW_Basis real2recip 45.156 654 0.069 27.% + PW_Basis gatherp_scatters 16.578 654 0.025 9.9% + H_Hartree_pw v_hartree 16.498 82 0.20 9.9% + Potential set_vr_eff 0.56547 82 0.0069 0.34% + NOrbital_Lm extra_uniform 0.63370 2492 0.00025 0.38% + Mathzone_Add1Cubic_Spline_Interpolation 0.15528 2492 6.2e-05 0.093% + ORB_control set_orb_tables 0.51048 1 0.51 0.31% + ORB_gen_tables gen_tables 0.51048 1 0.51 0.31% + ORB_table_phi cal_ST_Phi12_R 1.6817 4573 0.00037 1.0% + ORB_table_beta init_Table_Beta 0.21553 1 0.22 0.13% + ORB_table_beta VNL_PhiBeta_R 0.21425 56 0.0038 0.13% + ORB_gaunt_table init_Gaunt_CH 0.14148 4 0.035 0.085% + ORB_gaunt_table init_Gaunt 1.5424 4 0.39 0.92% + ORB_gaunt_table Get_Gaunt_SH 8.4364 3636325 2.3e-06 5.0% + ESolver_KS_LCAO Run 154.87 1 1.5e+02 93.% + ESolver_KS_LCAO beforescf 2.8807 1 2.9 1.7% + ESolver_KS_LCAO beforesolver 0.10976 1 0.11 0.066% + ESolver_KS_LCAO set_matrix_grid 0.10916 1 0.11 0.065% + Grid_Technique init 0.10906 1 0.11 0.065% + Exx_Lcao cal_exx_ions 2.6880 1 2.7 1.6% + HSolverLCAO solve 22.711 81 0.28 14.% + HamiltLCAO updateHk 10.597 81 0.13 6.3% + LCAO_Hamilt cal_Hgamma 9.2234 81 0.11 5.5% + Gint_interface cal_gint 20.460 162 0.13 12.% + Gint_Gamma distri_vl 75.120 41 1.8 45.% + ElecStateLCAO psiToRho 12.030 81 0.15 7.2% + Charge_Mixing rhog_dot_product 0.50422 81 0.0062 0.30% + Charge mix_rho 14.331 65 0.22 8.6% + Exx_Lcao cal_exx_elec 0.32190 15 0.021 0.19% + Exx_Lcao Rexx_to_Km2D 0.28687 15 0.019 0.17% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 8495. + ORB_table_phi Jl(x) 921.9 + Charge_Pulay Rrho 178.0 + Charge_Pulay dRrho 155.7 + Charge_Pulay drho 155.7 + PW_Basis struc_fac 45.25 + Charge rho 22.25 + Charge rho_save 22.25 + Charge rho_core 22.25 + Potential vltot 22.25 + Potential vr 22.25 + Potential vr_eff 22.25 + Potential vr_eff1 22.25 + Potential vnew 22.25 + Charge_Pulay rho_save2 22.25 + Charge rhog 11.31 + Charge rhog_save 11.31 + Charge kin_r 11.31 + Charge kin_r_save 11.31 + Charge rhog_core 11.31 + Grid_Meshcell index2normal 8.576 + Grid_Meshcell index2ucell 8.576 + atoms_on_grid start_ind 1.390 + atoms_on_grid how_many_atoms 1.390 + atoms_on_grid bcell_start 1.390 + ---------------------------------------------------------- + + Start Time : Fri Sep 30 11:21:05 2022 + Finish Time : Fri Sep 30 11:23:53 2022 + Total Time : 0 h 2 mins 48 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..868e64dc1926c3eab8fea38e1eb6952f6c64d075 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/OUT.ABACUS/warning.log @@ -0,0 +1,85 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 100 + smearing_decision warning : Fixed occupations,gauss broadening ignored + AUTO_SET gaussian_parameter to 0 + In SCAN_BEGIN, can't find: ABFS_ORBITAL block. + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: hse + dft_functional in pseudopot file is: PBE + dft_functional readin is: hse + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 0 + AUTO_SET NBANDS to 14 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.00019443 ima = 4.48669e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00000714344087 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001589214966 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001547018833 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001555921775 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001552283419 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001553409333 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001553202966 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001553193653 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001553234745 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001553232108 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001553234113 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00000769021125 + charge after normalized = 8.00000000000007 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0000214628366 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00001819140448 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/O_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/O_ONCV_PBE-1.0.upf new file mode 120000 index 0000000000000000000000000000000000000000..ff914a6806b2192868a9bc36694ff03c0dc9e450 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/O_ONCV_PBE-1.0.upf @@ -0,0 +1 @@ +../../../../iter/O_ONCV_PBE-1.0.upf \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/O_gga_6au_60Ry_2s2p1d.orb b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/O_gga_6au_60Ry_2s2p1d.orb new file mode 120000 index 0000000000000000000000000000000000000000..5d2ff63b151809f86337680c77401e9918d3ca92 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/O_gga_6au_60Ry_2s2p1d.orb @@ -0,0 +1 @@ +../../../../iter/O_gga_6au_60Ry_2s2p1d.orb \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4179a854538bff4c70927c2d6e66e35c9832cede --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ./O_ONCV_PBE-1.0.upf +H 1.00 ./H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.820276468984 0.556117645521 5.787060818012 0 0 0 +H +0.0 +2 +-7.356630073377 1.707819477768 5.851375127279 0 0 0 +-8.315809397290 -0.230736998458 4.235868438293 0 0 0 + +NUMERICAL_ORBITAL +./O_gga_6au_60Ry_2s2p1d.orb +./H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +./jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/conv new file mode 100644 index 0000000000000000000000000000000000000000..ad4f2b2bd146eb43e6bc53593e024b152bdd6377 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/conv @@ -0,0 +1 @@ +0 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b5779cabee4d968c961213a88a3fcde8a113011d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.758581718 0.01284203554 1.265033145 1.344810407 1.471051213 0.01007398078 0.01579005391 0.04005933564 +-3.200059422e-18 0.0007911704557 0.002969625941 0.01412052535 0.04762125346 2.514761411e-19 3.12426363e-06 8.458066978e-06 +0.001627433065 0.006305533123 + +H atom_index 1 n_descriptor 18 +1.230280138 0.03608334904 0.1056460747 0.1391344859 0.3100727911 0.02274681256 0.02685681118 0.03924322461 +1.672025869e-17 4.73544709e-05 0.09892987143 0.1144079993 0.1195215668 -4.241039086e-18 3.266489826e-06 0.0138877745 +0.02664619417 0.02970028214 + +H atom_index 2 n_descriptor 18 +1.271114926 0.03477267875 0.1204853378 0.1582611061 0.3240707721 0.02485681349 0.02927341376 0.0379594944 +1.682098609e-17 5.100372004e-05 0.1069195295 0.1185414433 0.1360624162 4.960492564e-18 1.240598128e-06 0.01349641237 +0.02816851617 0.03161715576 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d7bfa193ad865ca366caf3e9b71b1a0d762750e5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/e_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..13fa93ceaf9e5b7a3f3d7cf9e9eb0245857427a9 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..67b1206ae0b0f71735dd479b7832fcc223c22bd1 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/jle.orb b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/jle.orb new file mode 120000 index 0000000000000000000000000000000000000000..ec013d36e71b0af8561def26fd6025ab0b7550d0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/jle.orb @@ -0,0 +1 @@ +../../../../iter/jle.orb \ No newline at end of file diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..555d110b9127e05d9c11224569ff1ebb44c9e694 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:52 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871682 SEC) : SETUP UNITCELL + DONE(0.0916797 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11062 SEC) : INIT PLANEWAVE + DONE(0.15892 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438702 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651319e+02 0.000000e+00 2.128e-01 5.205e-01 + GE2 -4.663446e+02 -1.212774e+00 9.747e-02 4.425e-01 + GE3 -4.663494e+02 -4.706967e-03 6.254e-02 5.010e-01 + GE4 -4.663488e+02 5.060499e-04 1.925e-03 3.956e-01 + GE5 -4.663481e+02 7.717992e-04 9.324e-04 3.878e-01 + GE6 -4.663486e+02 -4.999855e-04 1.050e-04 3.858e-01 + GE7 -4.663484e+02 1.499420e-04 3.525e-05 3.822e-01 + GE8 -4.663485e+02 -2.490778e-05 1.899e-05 3.668e-01 + GE9 -4.663484e+02 1.925364e-05 1.864e-06 3.682e-01 + GE10 -4.663484e+02 -3.857833e-06 3.397e-07 3.644e-01 + GE11 -4.663484e+02 -3.954001e-07 1.048e-07 3.631e-01 + GE12 -4.663484e+02 -4.990182e-08 1.140e-08 3.090e-01 +E_delta_band = -7.06291448e-02 Ry = -9.60958814e-01 eV +E_delta_NN= -1.94870538e-01 Ry = -2.65134969e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0351 11 0.64 1e+02 % + Run_lcao lcao_line 7.0246 1 7 1e+02 % + Potential init_pot 0.28445 2 0.14 4 % + PW_Basis recip2real 0.28292 17 0.017 4 % + PW_Basis gathers_scatterp 0.12039 17 0.0071 1.7 % + Potential v_of_rho 0.942 14 0.067 13 % + XC_Functional v_xc 0.26372 15 0.018 3.7 % + H_Hartree_pw v_hartree 0.63869 14 0.046 9.1 % + PW_Basis real2recip 0.59981 41 0.015 8.5 % + PW_Basis gatherp_scatters 0.23393 41 0.0057 3.3 % + ORB_control set_orb_tables 1.1004 1 1.1 16 % + ORB_gen_tables gen_tables 1.1004 1 1.1 16 % + ORB_table_phi init_Table 0.48314 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47826 126 0.0038 6.8 % + ORB_table_beta init_Table_Beta 0.18653 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18509 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.25323 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.2514 66 0.0038 3.6 % + LOOP_ions opt_ions 5.4093 1 5.4 77 % + ESolver_KS_LCAO Run 4.8485 1 4.8 69 % + HSolverLCAO solve 2.7071 12 0.23 38 % + HamiltLCAO updateHk 1.3821 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3406 12 0.11 19 % + Gint_interface cal_gint 2.5809 25 0.1 37 % + Gint_Gamma distri_vl 2.5127 6 0.42 36 % + LCAO_Deepks cal_projected_DM 5.2315 14 0.37 74 % + LCAO_gen_fixedH add_v_delta 2.3815 6 0.4 34 % + LCAO_DESCRIPTOR add_v_delta 2.3815 6 0.4 34 % + ElecStateLCAO psiToRho 1.3101 12 0.11 19 % + Charge mix_rho 0.71337 11 0.065 10 % + LOOP_ions force_stress 0.56066 1 0.56 8 % + Force_Stress_LCAO getForceStress 0.56063 1 0.56 8 % + Force_LCAO_gamma ftable_gamma 0.34779 1 0.35 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.34108 1 0.34 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:52 2022 + FINISH Time : Wed Sep 28 11:05:59 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/model.ptg b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/model.ptg new file 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/dm3_0 b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/dm3_0 new file mode 100644 index 0000000000000000000000000000000000000000..0bb86e45dde7a780861d6f221f77e050f2081593 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/dm3_0 @@ -0,0 +1,20 @@ +[4232 +4232 +] +4232 +73 +80 1 +85 1 +91 1 +94 1 593 +105 1 +121 1 +125 1 4744 +133 1 0 +135 1 1 +138 1 1 +143 1 +148 +154 +165 +169 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/dm3_1 b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/dm3_1 new file mode 100644 index 0000000000000000000000000000000000000000..96a40215fba86d95e4511a5f753114e145e6d9c3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/dm3_1 @@ -0,0 +1,20 @@ +[4232 +4232 +] +4232 +73 +80 0 +85 0 +121 0 +125 0 4744 +133 0 0 +135 0 1 +138 0 1 +143 0 +91 0 +94 0 593 +105 0 +148 +154 +165 +169 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/time_0 b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/time_0 new file mode 100644 index 0000000000000000000000000000000000000000..d2893ea6b5b3602e3cdfc1f22d0be8fc2d644e46 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/time_0 @@ -0,0 +1,2764 @@ +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.045241 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 1.3e-05 1.36314 + 1 1 3e-06 0.08705 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.45031 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+eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.31789 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.10128 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.96547 +TIME@ m_abfs_abfs.init_radial 9.3e-05 +TIME@ m_abfslcaos_lcaos.init 0.862251 +TIME@ m_abfslcaos_lcaos.init_radial 0.000267 +TIME@ Exx_Lcao::init 9.29273 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000613 +TIME@ radial_R_C 7e-06 + 0 0 2e-06 0.785316 + 0 1 3e-06 0.521292 + 1 0 4e-06 0.12927 + 1 1 3e-06 0.077208 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.51327 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.51329 +TIME@ radial_R_V 0.000725 + 0 0 2e-06 0.075499 + 0 1 3e-05 0.451528 + 1 0 1.8e-05 0.452158 + 1 1 2e-05 0.162803 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.14221 +TIME@ m_abfs_abfs.init_radial_table 1.14226 +TIME@ init_radial_table_ions 2.65634 +TIME@ Abfs::cal_Vs 0.028068 +TIME@ Abfs::cal_Vps 1e-06 +atom_pairs_core 0 +atom_centres_core 0 +H_atom_pairs_core 0 +TIME@ Exx_Lcao::allocate_Hexx 1.5e-05 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.040846 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 1e-05 1.13788 + 1 1 3e-06 0.065263 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.20325 +TIME@LapackConnector::dsyev 0.000268 +TIME@LapackConnector::dsyev 2.1e-05 +TIME@LapackConnector::dsyev 1.2e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 6e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 1e-06 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -5.34664e-20 +0 1 1 4.33321e-22 +0 1 2 6.18542e-20 +0 1 3 6.77848e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 -1.57373e-20 +0 2 1 2.76318e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.04127 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.06631 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.89364 +TIME@ m_abfs_abfs.init_radial 9.3e-05 +TIME@ m_abfslcaos_lcaos.init 0.830123 +TIME@ m_abfslcaos_lcaos.init_radial 0.000269 +TIME@ Exx_Lcao::init 8.87278 +atom_pairs_core_origin 6 +TIME@ Htime::distribute 0.000612 +TIME@ radial_R_C 8e-06 + 0 0 2e-06 0.57848 + 0 1 4e-06 0.356166 + 1 0 3e-06 0.140094 + 1 1 3e-06 0.061307 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.13624 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.13626 +TIME@ radial_R_V 0.001195 + 0 0 4e-06 0.174393 + 0 1 5.1e-05 0.799029 + 1 0 3.3e-05 0.833186 + 1 1 1.9e-05 0.161591 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.96849 +TIME@ m_abfs_abfs.init_radial_table 1.96855 +TIME@ init_radial_table_ions 3.10608 +TIME@ Abfs::cal_Vs 0.070482 +TIME@ Abfs::cal_Vps 0.000306 +atom_pairs_core 6 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.8e-05 +TIME@ Abfs::cal_Cs 0.027547 +TIME@ Abfs::cal_Cps 7e-06 +TIME@ schwarz::init 0.002241 +TIME@ cauchy::init 0.000296 +TIME@ Exx_Lcao::cal_exx_ions 3.208 +sizeof_Cs: 174580 +sizeof_Vs: 2856452 +sizeof_Cps: 174580 +sizeof_Vps: 50576 +sizeof_Cws: 171296 +sizeof_Vws: 2754552 +TIME@ Exx_Lcao::cal_DM 6.1e-05 +TIME@ cauchy.cal_norm_D_max 2.8e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001584 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 6e-06 +E_exx -6.89189 +TIME@ Exx_Lcao::cal_energy 6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 9.9e-05 +sizeof_Hexx2D 4248 +TIME@ Exx_Lcao::cal_exx_elec 0.001886 +TIME@ Exx_Lcao::cal_DM 6.6e-05 +TIME@ cauchy.cal_norm_D_max 2.9e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002264 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -6.90168 +TIME@ Exx_Lcao::cal_energy 5.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 7.5e-05 +sizeof_Hexx2D 4248 +TIME@ Exx_Lcao::cal_exx_elec 0.002522 +TIME@ Exx_Lcao::cal_DM 6.6e-05 +TIME@ cauchy.cal_norm_D_max 2.7e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001195 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -6.90244 +TIME@ Exx_Lcao::cal_energy 5.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 6.8e-05 +sizeof_Hexx2D 4248 +TIME@ Exx_Lcao::cal_exx_elec 0.001449 +TIME@ Exx_Lcao::cal_DM 6.7e-05 +TIME@ cauchy.cal_norm_D_max 2.7e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001206 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -6.9025 +TIME@ Exx_Lcao::cal_energy 5.3e-05 +TIME@ Hexx_para.Rexx_to_Km2D 6.9e-05 +sizeof_Hexx2D 4248 +TIME@ Exx_Lcao::cal_exx_elec 0.001461 +TIME@ Exx_Lcao::cal_DM 6.6e-05 +TIME@ cauchy.cal_norm_D_max 2.7e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001212 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -6.90251 +TIME@ Exx_Lcao::cal_energy 5.5e-05 +TIME@ Hexx_para.Rexx_to_Km2D 8.2e-05 +sizeof_Hexx2D 4248 +TIME@ Exx_Lcao::cal_exx_elec 0.001483 +TIME@ Exx_Lcao::cal_DM 6.7e-05 +TIME@ cauchy.cal_norm_D_max 2.6e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001606 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -6.90251 +TIME@ Exx_Lcao::cal_energy 6.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 6.6e-05 +sizeof_Hexx2D 4248 +TIME@ Exx_Lcao::cal_exx_elec 0.001868 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.041809 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 1.1e-05 1.41248 + 1 1 3e-06 0.08697 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.49958 +TIME@LapackConnector::dsyev 0.000213 +TIME@LapackConnector::dsyev 2e-05 +TIME@LapackConnector::dsyev 1.1e-05 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 7e-06 +TIME@LapackConnector::dsyev 3e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.38671 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.09596 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.95298 +TIME@ m_abfs_abfs.init_radial 0.000106 +TIME@ m_abfslcaos_lcaos.init 0.839114 +TIME@ m_abfslcaos_lcaos.init_radial 0.000273 +TIME@ Exx_Lcao::init 9.3172 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000599 +TIME@ radial_R_C 8e-06 + 0 0 2e-06 0.765072 + 0 1 3e-06 0.516492 + 1 0 4e-06 0.126705 + 1 1 3e-06 0.08005 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.4885 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.48853 +TIME@ radial_R_V 0.000714 + 0 0 3e-06 0.076687 + 0 1 3.1e-05 0.445975 + 1 0 1.7e-05 0.454123 + 1 1 1.9e-05 0.175507 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.15253 +TIME@ m_abfs_abfs.init_radial_table 1.15258 +TIME@ init_radial_table_ions 2.64189 +TIME@ Abfs::cal_Vs 0.026861 +TIME@ Abfs::cal_Vps 6.5e-05 +atom_pairs_core 3 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.2e-05 +TIME@ Abfs::cal_Cs 0.028177 +TIME@ Abfs::cal_Cps 6e-06 +TIME@ schwarz::init 0.006134 +TIME@ cauchy::init 0.000252 +TIME@ Exx_Lcao::cal_exx_ions 2.74971 +sizeof_Cs: 174580 +sizeof_Vs: 632144 +sizeof_Cps: 174580 +sizeof_Vps: 11388 +sizeof_Cws: 171296 +sizeof_Vws: 634096 +TIME@ Exx_Lcao::cal_DM 0.00088 +TIME@ cauchy.cal_norm_D_max 3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000834 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -6.89189 +TIME@ Exx_Lcao::cal_energy 0.000507 +TIME@ Hexx_para.Rexx_to_Km2D 0.01658 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.018878 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.041817 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 9e-06 1.38525 + 1 1 2e-06 0.09061 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.47597 +TIME@LapackConnector::dsyev 0.000188 +TIME@LapackConnector::dsyev 1.9e-05 +TIME@LapackConnector::dsyev 1.1e-05 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 7e-06 +TIME@LapackConnector::dsyev 3e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.34318 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.09579 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.96224 +TIME@ m_abfs_abfs.init_radial 8.9e-05 +TIME@ m_abfslcaos_lcaos.init 0.842665 +TIME@ m_abfslcaos_lcaos.init_radial 0.000268 +TIME@ Exx_Lcao::init 9.28628 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000611 +TIME@ radial_R_C 8e-06 + 0 0 2e-06 0.776034 + 0 1 4e-06 0.478882 + 1 0 3e-06 0.129815 + 1 1 3e-06 0.092961 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.47788 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.47791 +TIME@ radial_R_V 0.00074 + 0 0 3e-06 0.076525 + 0 1 2.9e-05 0.449081 + 1 0 1.8e-05 0.458606 + 1 1 1.9e-05 0.171776 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.15621 +TIME@ m_abfs_abfs.init_radial_table 1.15628 +TIME@ init_radial_table_ions 2.63501 +TIME@ Abfs::cal_Vs 0.026876 +TIME@ Abfs::cal_Vps 6.6e-05 +atom_pairs_core 3 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.7e-05 +TIME@ Abfs::cal_Cs 0.028464 +TIME@ Abfs::cal_Cps 7e-06 +TIME@ schwarz::init 0.006078 +TIME@ cauchy::init 0.000269 +TIME@ Exx_Lcao::cal_exx_ions 2.7215 +sizeof_Cs: 174580 +sizeof_Vs: 632144 +sizeof_Cps: 174580 +sizeof_Vps: 11388 +sizeof_Cws: 171296 +sizeof_Vws: 634096 +TIME@ Exx_Lcao::cal_DM 0.000337 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000825 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -26.4745 +TIME@ Exx_Lcao::cal_energy 0.001516 +TIME@ Hexx_para.Rexx_to_Km2D 0.01797 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020717 +TIME@ Exx_Lcao::cal_DM 0.000296 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000823 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -26.4835 +TIME@ Exx_Lcao::cal_energy 0.000498 +TIME@ Hexx_para.Rexx_to_Km2D 0.009617 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.011305 +TIME@ Exx_Lcao::cal_DM 0.00107 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.008073 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -26.4863 +TIME@ Exx_Lcao::cal_energy 6.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.010442 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.01972 +TIME@ Exx_Lcao::cal_DM 0.000668 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000807 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -26.4872 +TIME@ Exx_Lcao::cal_energy 0.002127 +TIME@ Hexx_para.Rexx_to_Km2D 0.017311 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020982 +TIME@ Exx_Lcao::cal_DM 0.000664 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002202 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -26.4875 +TIME@ Exx_Lcao::cal_energy 7.7e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018127 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021139 +TIME@ Exx_Lcao::cal_DM 0.000707 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000982 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -26.4876 +TIME@ Exx_Lcao::cal_energy 0.000286 +TIME@ Hexx_para.Rexx_to_Km2D 0.018948 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021002 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.044248 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 9e-06 1.34688 + 1 1 3e-06 0.084619 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.43162 +TIME@LapackConnector::dsyev 0.000224 +TIME@LapackConnector::dsyev 3.3e-05 +TIME@LapackConnector::dsyev 1.1e-05 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 6e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.31042 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.10877 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.96945 +TIME@ m_abfs_abfs.init_radial 9e-05 +TIME@ m_abfslcaos_lcaos.init 0.837318 +TIME@ m_abfslcaos_lcaos.init_radial 0.000268 +TIME@ Exx_Lcao::init 9.2708 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000605 +TIME@ radial_R_C 6e-06 + 0 0 1e-06 0.754652 + 0 1 4e-06 0.480785 + 1 0 4e-06 0.128753 + 1 1 4e-06 0.085032 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.44942 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.44945 +TIME@ radial_R_V 0.000713 + 0 0 2e-06 0.076564 + 0 1 2.7e-05 0.454107 + 1 0 1.7e-05 0.457918 + 1 1 1.9e-05 0.171529 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.16035 +TIME@ m_abfs_abfs.init_radial_table 1.16041 +TIME@ init_radial_table_ions 2.61064 +TIME@ Abfs::cal_Vs 0.027056 +TIME@ Abfs::cal_Vps 6.4e-05 +atom_pairs_core 3 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.2e-05 +TIME@ Abfs::cal_Cs 0.028573 +TIME@ Abfs::cal_Cps 7e-06 +TIME@ schwarz::init 0.006126 +TIME@ cauchy::init 0.000255 +TIME@ Exx_Lcao::cal_exx_ions 2.70087 +sizeof_Cs: 174580 +sizeof_Vs: 632144 +sizeof_Cps: 174580 +sizeof_Vps: 11388 +sizeof_Cws: 171296 +sizeof_Vws: 634096 +TIME@ Exx_Lcao::cal_DM 0.000684 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000871 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 0.00048 +TIME@ Hexx_para.Rexx_to_Km2D 0.018833 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020939 +TIME@ Exx_Lcao::cal_DM 0.000669 +TIME@ cauchy.cal_norm_D_max 3.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000772 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88288 +TIME@ Exx_Lcao::cal_energy 0.003462 +TIME@ Hexx_para.Rexx_to_Km2D 0.015963 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020942 +TIME@ Exx_Lcao::cal_DM 0.000578 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000873 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88384 +TIME@ Exx_Lcao::cal_energy 0.001148 +TIME@ Hexx_para.Rexx_to_Km2D 0.018185 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020852 +TIME@ Exx_Lcao::cal_DM 0.000774 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000943 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88393 +TIME@ Exx_Lcao::cal_energy 0.000281 +TIME@ Hexx_para.Rexx_to_Km2D 0.019421 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021482 +TIME@ Exx_Lcao::cal_DM 0.000632 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000883 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88394 +TIME@ Exx_Lcao::cal_energy 0.000308 +TIME@ Hexx_para.Rexx_to_Km2D 0.020833 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.02272 +TIME@ Exx_Lcao::cal_DM 0.000588 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000796 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88394 +TIME@ Exx_Lcao::cal_energy 0.002232 +TIME@ Hexx_para.Rexx_to_Km2D 0.018757 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.02244 +TIME@ Exx_Lcao::cal_DM 0.000815 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000835 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88394 +TIME@ Exx_Lcao::cal_energy 0.000436 +TIME@ Hexx_para.Rexx_to_Km2D 0.018975 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021125 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.042132 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 8e-06 1.36594 + 1 1 2e-06 0.089359 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.45541 +TIME@LapackConnector::dsyev 0.000183 +TIME@LapackConnector::dsyev 1.9e-05 +TIME@LapackConnector::dsyev 1e-05 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +TIME@LapackConnector::dsyev 6e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 1e-06 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.32696 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.09817 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.9622 +TIME@ m_abfs_abfs.init_radial 8.6e-05 +TIME@ m_abfslcaos_lcaos.init 0.833261 +TIME@ m_abfslcaos_lcaos.init_radial 0.000273 +TIME@ Exx_Lcao::init 9.26333 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000614 +TIME@ radial_R_C 8e-06 + 0 0 2e-06 0.748313 + 0 1 3e-06 0.510564 + 1 0 4e-06 0.126639 + 1 1 4e-06 0.079015 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.46472 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.46474 +TIME@ radial_R_V 0.000717 + 0 0 2e-06 0.076033 + 0 1 2.8e-05 0.453565 + 1 0 1.7e-05 0.455029 + 1 1 2e-05 0.169219 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.15408 +TIME@ m_abfs_abfs.init_radial_table 1.15415 +TIME@ init_radial_table_ions 2.61966 +TIME@ Abfs::cal_Vs 0.026724 +TIME@ Abfs::cal_Vps 6.6e-05 +atom_pairs_core 3 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.1e-05 +TIME@ Abfs::cal_Cs 0.028262 +TIME@ Abfs::cal_Cps 6e-06 +TIME@ schwarz::init 0.006199 +TIME@ cauchy::init 0.00026 +TIME@ Exx_Lcao::cal_exx_ions 2.68792 +sizeof_Cs: 174580 +sizeof_Vs: 632144 +sizeof_Cps: 174580 +sizeof_Vps: 11388 +sizeof_Cws: 171296 +sizeof_Vws: 634096 +TIME@ Exx_Lcao::cal_DM 0.000749 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.004338 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 6.8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.015839 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021067 +TIME@ Exx_Lcao::cal_DM 0.000578 +TIME@ cauchy.cal_norm_D_max 3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000789 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88444 +TIME@ Exx_Lcao::cal_energy 0.000443 +TIME@ Hexx_para.Rexx_to_Km2D 0.018953 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020838 +TIME@ Exx_Lcao::cal_DM 0.000499 +TIME@ cauchy.cal_norm_D_max 3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000812 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88793 +TIME@ Exx_Lcao::cal_energy 0.00038 +TIME@ Hexx_para.Rexx_to_Km2D 0.019446 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021216 +TIME@ Exx_Lcao::cal_DM 0.000512 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000813 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88903 +TIME@ Exx_Lcao::cal_energy 0.000471 +TIME@ Hexx_para.Rexx_to_Km2D 0.021737 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.023615 +TIME@ Exx_Lcao::cal_DM 0.000235 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000879 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88939 +TIME@ Exx_Lcao::cal_energy 0.000545 +TIME@ Hexx_para.Rexx_to_Km2D 0.018893 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020624 +TIME@ Exx_Lcao::cal_DM 0.000479 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000824 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88951 +TIME@ Exx_Lcao::cal_energy 0.00052 +TIME@ Hexx_para.Rexx_to_Km2D 0.019006 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020899 +TIME@ Exx_Lcao::cal_DM 0.000231 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001992 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88955 +TIME@ Exx_Lcao::cal_energy 7.2e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018739 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021103 +TIME@ Exx_Lcao::cal_DM 0.000448 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.003075 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 6.8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018627 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.02229 +TIME@ Exx_Lcao::cal_DM 0.000869 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000805 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 0.000392 +TIME@ Hexx_para.Rexx_to_Km2D 0.019568 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021702 +TIME@ Exx_Lcao::cal_DM 0.000595 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000843 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000374 +TIME@ Hexx_para.Rexx_to_Km2D 0.019487 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021382 +TIME@ Exx_Lcao::cal_DM 0.000224 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000889 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000668 +TIME@ Hexx_para.Rexx_to_Km2D 0.01934 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021194 +TIME@ Exx_Lcao::cal_DM 0.000561 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000794 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000481 +TIME@ Hexx_para.Rexx_to_Km2D 0.020403 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.022307 +TIME@ Exx_Lcao::cal_DM 0.000779 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000986 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000432 +TIME@ Hexx_para.Rexx_to_Km2D 0.01896 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021231 +TIME@ Exx_Lcao::cal_DM 0.000604 +TIME@ cauchy.cal_norm_D_max 2.6e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000796 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000447 +TIME@ Hexx_para.Rexx_to_Km2D 0.018899 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020817 +TIME@ Exx_Lcao::cal_DM 0.000885 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00079 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000463 +TIME@ Hexx_para.Rexx_to_Km2D 0.01887 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021078 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.044345 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 9e-06 2.36668 + 1 1 3e-06 0.173421 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 2.54023 +TIME@LapackConnector::dsyev 0.000192 +TIME@LapackConnector::dsyev 2.4e-05 +TIME@LapackConnector::dsyev 1.2e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 0 +TIME@LapackConnector::dsyev 1e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 1e-06 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 4.52038 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.38144 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.95689 +TIME@ m_abfs_abfs.init_radial 8.8e-05 +TIME@ m_abfslcaos_lcaos.init 0.832836 +TIME@ m_abfslcaos_lcaos.init_radial 0.000278 +TIME@ Exx_Lcao::init 10.737 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000624 +TIME@ radial_R_C 7e-06 + 0 0 1e-06 1.66521 + 0 1 3e-06 0.86036 + 1 0 3e-06 0.280107 + 1 1 3e-06 0.169293 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 2.97515 +TIME@ m_abfslcaos_lcaos.init_radial_table 2.97518 +TIME@ radial_R_V 0.000714 + 0 0 2e-06 0.076919 + 0 1 2.9e-05 0.483279 + 1 0 1.7e-05 0.409894 + 1 1 1.8e-05 0.159357 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.12967 +TIME@ m_abfs_abfs.init_radial_table 1.12974 +TIME@ init_radial_table_ions 4.10569 +TIME@ Abfs::cal_Vs 0.027505 +TIME@ Abfs::cal_Vps 6.5e-05 +atom_pairs_core 3 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.6e-05 +TIME@ Abfs::cal_Cs 0.029021 +TIME@ Abfs::cal_Cps 7e-06 +TIME@ schwarz::init 0.006367 +TIME@ cauchy::init 0.000289 +TIME@ Exx_Lcao::cal_exx_ions 4.17008 +sizeof_Cs: 174580 +sizeof_Vs: 632144 +sizeof_Cps: 174580 +sizeof_Vps: 11388 +sizeof_Cws: 171296 +sizeof_Vws: 634096 +TIME@ Exx_Lcao::cal_DM 0.010688 +TIME@ cauchy.cal_norm_D_max 2.9e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000916 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 0.000561 +TIME@ Hexx_para.Rexx_to_Km2D 0.025708 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.037959 +TIME@ Exx_Lcao::cal_DM 0.00024 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000798 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -9.02854 +TIME@ Exx_Lcao::cal_energy 0.000465 +TIME@ Hexx_para.Rexx_to_Km2D 0.025554 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.027124 +TIME@ Exx_Lcao::cal_DM 0.000252 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000791 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.66979 +TIME@ Exx_Lcao::cal_energy 0.000484 +TIME@ Hexx_para.Rexx_to_Km2D 0.018864 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020459 +TIME@ Exx_Lcao::cal_DM 0.000249 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002809 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.75746 +TIME@ Exx_Lcao::cal_energy 5.9e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.020001 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.02319 +TIME@ Exx_Lcao::cal_DM 0.000245 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000869 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.8643 +TIME@ Exx_Lcao::cal_energy 0.000507 +TIME@ Hexx_para.Rexx_to_Km2D 0.019282 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020971 +TIME@ Exx_Lcao::cal_DM 0.000246 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000783 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.87342 +TIME@ Exx_Lcao::cal_energy 0.000509 +TIME@ Hexx_para.Rexx_to_Km2D 0.018859 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020467 +TIME@ Exx_Lcao::cal_DM 0.000303 +TIME@ cauchy.cal_norm_D_max 2.9e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000779 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88942 +TIME@ Exx_Lcao::cal_energy 0.00081 +TIME@ Hexx_para.Rexx_to_Km2D 0.019998 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021973 +TIME@ Exx_Lcao::cal_DM 0.000244 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000789 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 9e-06 +E_exx -7.88906 +TIME@ Exx_Lcao::cal_energy 0.000476 +TIME@ Hexx_para.Rexx_to_Km2D 0.01889 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020469 +TIME@ Exx_Lcao::cal_DM 0.000255 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000795 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88956 +TIME@ Exx_Lcao::cal_energy 0.001766 +TIME@ Hexx_para.Rexx_to_Km2D 0.020189 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.023071 +TIME@ Exx_Lcao::cal_DM 0.000259 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00084 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8896 +TIME@ Exx_Lcao::cal_energy 0.000417 +TIME@ Hexx_para.Rexx_to_Km2D 0.019566 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021148 +TIME@ Exx_Lcao::cal_DM 0.00025 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000804 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 0.000445 +TIME@ Hexx_para.Rexx_to_Km2D 0.019618 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.02119 +TIME@ Exx_Lcao::cal_DM 0.000244 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002928 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 5.9e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019933 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.023237 +TIME@ Exx_Lcao::cal_DM 0.00024 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000799 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.002343 +TIME@ Hexx_para.Rexx_to_Km2D 0.019983 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.023446 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.041728 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 8e-06 1.36142 + 1 1 4e-06 0.086598 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.44814 +TIME@LapackConnector::dsyev 0.001123 +TIME@LapackConnector::dsyev 2.1e-05 +TIME@LapackConnector::dsyev 1.1e-05 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +TIME@LapackConnector::dsyev 6e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.32254 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.09985 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 4.0001 +TIME@ m_abfs_abfs.init_radial 9e-05 +TIME@ m_abfslcaos_lcaos.init 0.835642 +TIME@ m_abfslcaos_lcaos.init_radial 0.000271 +TIME@ Exx_Lcao::init 9.30046 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000613 +TIME@ radial_R_C 7e-06 + 0 0 2e-06 0.781473 + 0 1 3e-06 0.518272 + 1 0 3e-06 0.129015 + 1 1 3e-06 0.074214 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.50317 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.50319 +TIME@ radial_R_V 0.000723 + 0 0 2e-06 0.076413 + 0 1 2.9e-05 0.457249 + 1 0 1.7e-05 0.454982 + 1 1 1.9e-05 0.162578 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.15144 +TIME@ m_abfs_abfs.init_radial_table 1.15151 +TIME@ init_radial_table_ions 2.65548 +TIME@ Abfs::cal_Vs 0.027571 +TIME@ Abfs::cal_Vps 6.4e-05 +atom_pairs_core 3 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.1e-05 +TIME@ Abfs::cal_Cs 0.028532 +TIME@ Abfs::cal_Cps 7e-06 +TIME@ schwarz::init 0.006151 +TIME@ cauchy::init 0.000252 +TIME@ Exx_Lcao::cal_exx_ions 2.71916 +sizeof_Cs: 174580 +sizeof_Vs: 632144 +sizeof_Cps: 174580 +sizeof_Vps: 11388 +sizeof_Cws: 171296 +sizeof_Vws: 634096 +TIME@ Exx_Lcao::cal_DM 0.000322 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000846 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 0.00731 +TIME@ Hexx_para.Rexx_to_Km2D 0.014238 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.022793 +TIME@ Exx_Lcao::cal_DM 0.000255 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000805 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -9.02854 +TIME@ Exx_Lcao::cal_energy 0.000416 +TIME@ Hexx_para.Rexx_to_Km2D 0.021449 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.022997 +TIME@ Exx_Lcao::cal_DM 0.000264 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000827 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.66979 +TIME@ Exx_Lcao::cal_energy 0.000402 +TIME@ Hexx_para.Rexx_to_Km2D 0.018919 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020481 +TIME@ Exx_Lcao::cal_DM 0.000245 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000808 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.75746 +TIME@ Exx_Lcao::cal_energy 0.000438 +TIME@ Hexx_para.Rexx_to_Km2D 0.018963 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020535 +TIME@ Exx_Lcao::cal_DM 0.000254 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000804 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8643 +TIME@ Exx_Lcao::cal_energy 0.000437 +TIME@ Hexx_para.Rexx_to_Km2D 0.018904 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020467 +TIME@ Exx_Lcao::cal_DM 0.000262 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000812 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.87342 +TIME@ Exx_Lcao::cal_energy 0.000425 +TIME@ Hexx_para.Rexx_to_Km2D 0.020285 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021851 +TIME@ Exx_Lcao::cal_DM 0.000251 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000797 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88942 +TIME@ Exx_Lcao::cal_energy 0.000408 +TIME@ Hexx_para.Rexx_to_Km2D 0.02038 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021901 +TIME@ Exx_Lcao::cal_DM 0.000253 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000794 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88906 +TIME@ Exx_Lcao::cal_energy 0.007343 +TIME@ Hexx_para.Rexx_to_Km2D 0.014502 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.022959 +TIME@ Exx_Lcao::cal_DM 0.000247 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000862 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88956 +TIME@ Exx_Lcao::cal_energy 0.000374 +TIME@ Hexx_para.Rexx_to_Km2D 0.019007 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020558 +TIME@ Exx_Lcao::cal_DM 0.000243 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000838 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8896 +TIME@ Exx_Lcao::cal_energy 0.000385 +TIME@ Hexx_para.Rexx_to_Km2D 0.01952 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021052 +TIME@ Exx_Lcao::cal_DM 0.000251 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00083 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 0.000407 +TIME@ Hexx_para.Rexx_to_Km2D 0.01982 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.02138 +TIME@ Exx_Lcao::cal_DM 0.000247 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000835 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000383 +TIME@ Hexx_para.Rexx_to_Km2D 0.021128 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.022662 +TIME@ Exx_Lcao::cal_DM 0.000259 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001755 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 7.8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019987 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.02215 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.041597 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 9e-06 1.35227 + 1 1 3e-06 0.11433 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.46672 +TIME@LapackConnector::dsyev 0.000246 +TIME@LapackConnector::dsyev 2.2e-05 +TIME@LapackConnector::dsyev 1.2e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 7e-06 +TIME@LapackConnector::dsyev 3e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.33541 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.09479 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.96592 +TIME@ m_abfs_abfs.init_radial 8.7e-05 +TIME@ m_abfslcaos_lcaos.init 0.835738 +TIME@ m_abfslcaos_lcaos.init_radial 0.000262 +TIME@ Exx_Lcao::init 9.27404 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000619 +TIME@ radial_R_C 7e-06 + 0 0 1e-06 0.809422 + 0 1 2e-06 0.519245 + 1 0 3e-06 0.139913 + 1 1 4e-06 0.073675 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.54245 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.54247 +TIME@ radial_R_V 0.000716 + 0 0 2e-06 0.076076 + 0 1 3e-05 0.459494 + 1 0 1.8e-05 0.455848 + 1 1 2e-05 0.160373 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.15203 +TIME@ m_abfs_abfs.init_radial_table 1.15208 +TIME@ init_radial_table_ions 2.69532 +TIME@ Abfs::cal_Vs 0.03438 +TIME@ Abfs::cal_Vps 6.8e-05 +atom_pairs_core 3 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.2e-05 +TIME@ Abfs::cal_Cs 0.028231 +TIME@ Abfs::cal_Cps 7e-06 +TIME@ schwarz::init 0.006053 +TIME@ cauchy::init 0.000262 +TIME@ Exx_Lcao::cal_exx_ions 2.7654 +sizeof_Cs: 174580 +sizeof_Vs: 632144 +sizeof_Cps: 174580 +sizeof_Vps: 11388 +sizeof_Cws: 171296 +sizeof_Vws: 634096 +TIME@ Exx_Lcao::cal_DM 0.000325 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000865 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 0.000436 +TIME@ Hexx_para.Rexx_to_Km2D 0.019318 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.02102 +TIME@ Exx_Lcao::cal_DM 0.000248 +TIME@ cauchy.cal_norm_D_max 2.6e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.003148 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -9.02854 +TIME@ Exx_Lcao::cal_energy 7.2e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.017063 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020601 +TIME@ Exx_Lcao::cal_DM 0.000245 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000833 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.66979 +TIME@ Exx_Lcao::cal_energy 0.000415 +TIME@ Hexx_para.Rexx_to_Km2D 0.016315 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.01788 +TIME@ Exx_Lcao::cal_DM 0.000259 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000819 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.75746 +TIME@ Exx_Lcao::cal_energy 0.000445 +TIME@ Hexx_para.Rexx_to_Km2D 0.019609 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021209 +TIME@ Exx_Lcao::cal_DM 0.000244 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.0008 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8643 +TIME@ Exx_Lcao::cal_energy 0.000458 +TIME@ Hexx_para.Rexx_to_Km2D 0.019964 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.021542 +TIME@ Exx_Lcao::cal_DM 0.000249 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000808 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.87342 +TIME@ Exx_Lcao::cal_energy 0.000431 +TIME@ Hexx_para.Rexx_to_Km2D 0.018962 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020524 +TIME@ Exx_Lcao::cal_DM 0.000253 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000866 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88942 +TIME@ Exx_Lcao::cal_energy 0.000491 +TIME@ Hexx_para.Rexx_to_Km2D 0.018765 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020449 +TIME@ Exx_Lcao::cal_DM 0.000261 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.008055 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88906 +TIME@ Exx_Lcao::cal_energy 6.2e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.013894 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.022347 +TIME@ Exx_Lcao::cal_DM 0.000247 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.008088 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88956 +TIME@ Exx_Lcao::cal_energy 6.9e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.014439 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.022924 +TIME@ Exx_Lcao::cal_DM 0.000251 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000876 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8896 +TIME@ Exx_Lcao::cal_energy 0.000498 +TIME@ Hexx_para.Rexx_to_Km2D 0.018758 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020453 +TIME@ Exx_Lcao::cal_DM 0.000262 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.008076 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019931 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.028399 +TIME@ Exx_Lcao::cal_DM 0.000243 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.007611 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 6.7e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.012824 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020814 +TIME@ Exx_Lcao::cal_DM 0.000247 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000788 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.004624 +TIME@ Hexx_para.Rexx_to_Km2D 0.014836 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020566 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.043463 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 9e-06 1.51447 + 1 1 2e-06 0.092894 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.6075 +TIME@LapackConnector::dsyev 0.000202 +TIME@LapackConnector::dsyev 2.2e-05 +TIME@LapackConnector::dsyev 1.3e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 0 +TIME@LapackConnector::dsyev 8e-06 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.5027 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.11588 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.98612 +TIME@ m_abfs_abfs.init_radial 9e-05 +TIME@ m_abfslcaos_lcaos.init 0.837924 +TIME@ m_abfslcaos_lcaos.init_radial 0.000267 +TIME@ Exx_Lcao::init 9.4867 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000676 +TIME@ radial_R_C 1.1e-05 + 0 0 2e-06 0.815964 + 0 1 4e-06 0.531769 + 1 0 3e-06 0.143411 + 1 1 3e-06 0.086772 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.57813 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.57816 +TIME@ radial_R_V 0.000741 + 0 0 2e-06 0.077261 + 0 1 2.9e-05 0.465982 + 1 0 1.8e-05 0.463457 + 1 1 1.9e-05 0.170312 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.17723 +TIME@ m_abfs_abfs.init_radial_table 1.17729 +TIME@ init_radial_table_ions 2.75627 +TIME@ Abfs::cal_Vs 0.029717 +TIME@ Abfs::cal_Vps 7.1e-05 +atom_pairs_core 3 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.4e-05 +TIME@ Abfs::cal_Cs 0.031862 +TIME@ Abfs::cal_Cps 8e-06 +TIME@ schwarz::init 0.006789 +TIME@ cauchy::init 0.000304 +TIME@ Exx_Lcao::cal_exx_ions 2.82621 +sizeof_Cs: 174580 +sizeof_Vs: 632144 +sizeof_Cps: 174580 +sizeof_Vps: 11388 +sizeof_Cws: 171296 +sizeof_Vws: 634096 +TIME@ Exx_Lcao::cal_DM 0.000243 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000973 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 0.000586 +TIME@ Hexx_para.Rexx_to_Km2D 0.018614 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020518 +TIME@ Exx_Lcao::cal_DM 0.000284 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000935 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88444 +TIME@ Exx_Lcao::cal_energy 0.000581 +TIME@ Hexx_para.Rexx_to_Km2D 0.017288 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.019156 +TIME@ Exx_Lcao::cal_DM 0.000384 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000953 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88793 +TIME@ Exx_Lcao::cal_energy 0.000498 +TIME@ Hexx_para.Rexx_to_Km2D 0.018798 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020705 +TIME@ Exx_Lcao::cal_DM 0.000271 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000956 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88903 +TIME@ Exx_Lcao::cal_energy 0.000593 +TIME@ Hexx_para.Rexx_to_Km2D 0.018775 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020667 +TIME@ Exx_Lcao::cal_DM 0.000271 +TIME@ cauchy.cal_norm_D_max 2.8e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002381 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88939 +TIME@ Exx_Lcao::cal_energy 6.5e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.017701 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020495 +TIME@ Exx_Lcao::cal_DM 0.000205 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000944 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88951 +TIME@ Exx_Lcao::cal_energy 0.001949 +TIME@ Hexx_para.Rexx_to_Km2D 0.015234 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.018399 +TIME@ Exx_Lcao::cal_DM 0.000219 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000933 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88955 +TIME@ Exx_Lcao::cal_energy 0.000512 +TIME@ Hexx_para.Rexx_to_Km2D 0.008291 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.010023 +TIME@ Exx_Lcao::cal_DM 0.000596 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001263 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 0.000194 +TIME@ Hexx_para.Rexx_to_Km2D 0.018778 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020911 +TIME@ Exx_Lcao::cal_DM 0.000227 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.004353 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 7e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 7.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.01584 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020559 +TIME@ Exx_Lcao::cal_DM 0.000225 +TIME@ cauchy.cal_norm_D_max 2.6e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000933 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 6e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 0.003101 +TIME@ Hexx_para.Rexx_to_Km2D 0.016642 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020987 +TIME@ Exx_Lcao::cal_DM 0.000268 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000931 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000671 +TIME@ Hexx_para.Rexx_to_Km2D 0.018514 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020454 +TIME@ Exx_Lcao::cal_DM 0.000224 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000936 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000292 +TIME@ Hexx_para.Rexx_to_Km2D 0.001199 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.00272 +TIME@ Exx_Lcao::cal_DM 0.000372 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000934 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000594 +TIME@ Hexx_para.Rexx_to_Km2D 0.01862 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020588 +TIME@ Exx_Lcao::cal_DM 0.000218 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000947 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000572 +TIME@ Hexx_para.Rexx_to_Km2D 0.018612 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020434 +TIME@ Exx_Lcao::cal_DM 0.000214 +TIME@ cauchy.cal_norm_D_max 3.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000913 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000547 +TIME@ Hexx_para.Rexx_to_Km2D 0.008293 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.010054 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.042324 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 9e-06 1.46784 + 1 1 2e-06 0.094733 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.5627 +TIME@LapackConnector::dsyev 0.000201 +TIME@LapackConnector::dsyev 2.2e-05 +TIME@LapackConnector::dsyev 1.3e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 7e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 1e-06 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.47238 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.11543 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 4.07254 +TIME@ m_abfs_abfs.init_radial 9e-05 +TIME@ m_abfslcaos_lcaos.init 0.833854 +TIME@ m_abfslcaos_lcaos.init_radial 0.000269 +TIME@ Exx_Lcao::init 9.53714 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000627 +TIME@ radial_R_C 7e-06 + 0 0 2e-06 0.868328 + 0 1 4e-06 0.557491 + 1 0 4e-06 0.145306 + 1 1 3e-06 0.089124 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.66046 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.66048 +TIME@ radial_R_V 0.000724 + 0 0 2e-06 0.0764 + 0 1 2.9e-05 0.466981 + 1 0 1.7e-05 0.464611 + 1 1 2.1e-05 0.16651 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.17473 +TIME@ m_abfs_abfs.init_radial_table 1.17479 +TIME@ init_radial_table_ions 2.83605 +TIME@ Abfs::cal_Vs 0.029468 +TIME@ Abfs::cal_Vps 6.5e-05 +atom_pairs_core 3 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.3e-05 +TIME@ Abfs::cal_Cs 0.031072 +TIME@ Abfs::cal_Cps 8e-06 +TIME@ schwarz::init 0.006831 +TIME@ cauchy::init 0.000299 +TIME@ Exx_Lcao::cal_exx_ions 2.90493 +sizeof_Cs: 174580 +sizeof_Vs: 632144 +sizeof_Cps: 174580 +sizeof_Vps: 11388 +sizeof_Cws: 171296 +sizeof_Vws: 634096 +TIME@ Exx_Lcao::cal_DM 0.000245 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00098 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 0.002878 +TIME@ Hexx_para.Rexx_to_Km2D 0.008337 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.012511 +TIME@ Exx_Lcao::cal_DM 0.00022 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000949 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88444 +TIME@ Exx_Lcao::cal_energy 0.00807 +TIME@ Hexx_para.Rexx_to_Km2D 0.000294 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.009601 +TIME@ Exx_Lcao::cal_DM 0.000232 +TIME@ cauchy.cal_norm_D_max 3.7e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.004007 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88793 +TIME@ Exx_Lcao::cal_energy 0.000359 +TIME@ Hexx_para.Rexx_to_Km2D 0.011705 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.016404 +TIME@ Exx_Lcao::cal_DM 0.000241 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000964 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88903 +TIME@ Exx_Lcao::cal_energy 0.003827 +TIME@ Hexx_para.Rexx_to_Km2D 0.015479 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020577 +TIME@ Exx_Lcao::cal_DM 0.000224 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000955 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88939 +TIME@ Exx_Lcao::cal_energy 0.000485 +TIME@ Hexx_para.Rexx_to_Km2D 0.019206 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020936 +TIME@ Exx_Lcao::cal_DM 0.000242 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000955 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88951 +TIME@ Exx_Lcao::cal_energy 0.003031 +TIME@ Hexx_para.Rexx_to_Km2D 0.016016 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020316 +TIME@ Exx_Lcao::cal_DM 0.000229 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000933 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88955 +TIME@ Exx_Lcao::cal_energy 0.001629 +TIME@ Hexx_para.Rexx_to_Km2D 0.00924 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.012102 +TIME@ Exx_Lcao::cal_DM 0.000298 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000959 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 0.000582 +TIME@ Hexx_para.Rexx_to_Km2D 0.017355 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.019265 +TIME@ Exx_Lcao::cal_DM 0.000198 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000944 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 0.000697 +TIME@ Hexx_para.Rexx_to_Km2D 0.018796 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020702 +TIME@ Exx_Lcao::cal_DM 0.000206 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000938 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000593 +TIME@ Hexx_para.Rexx_to_Km2D 0.018673 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020481 +TIME@ Exx_Lcao::cal_DM 0.000213 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000963 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.009831 +TIME@ Hexx_para.Rexx_to_Km2D 0.00092 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.011994 +TIME@ Exx_Lcao::cal_DM 0.000231 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000963 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000566 +TIME@ Hexx_para.Rexx_to_Km2D 0.01801 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.019841 +TIME@ Exx_Lcao::cal_DM 0.000264 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000935 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.00061 +TIME@ Hexx_para.Rexx_to_Km2D 0.018587 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020466 +TIME@ Exx_Lcao::cal_DM 0.000276 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.000942 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000624 +TIME@ Hexx_para.Rexx_to_Km2D 0.01647 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.018383 +TIME@ Exx_Lcao::cal_DM 0.000238 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00098 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000534 +TIME@ Hexx_para.Rexx_to_Km2D 0.018612 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.020431 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.042668 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 9e-06 1.45449 + 1 1 3e-06 0.097341 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.55195 +TIME@LapackConnector::dsyev 0.000218 +TIME@LapackConnector::dsyev 4.1e-05 +TIME@LapackConnector::dsyev 1.3e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 7e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.44623 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.11503 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.97197 +TIME@ m_abfs_abfs.init_radial 9.7e-05 +TIME@ m_abfslcaos_lcaos.init 0.839806 +TIME@ m_abfslcaos_lcaos.init_radial 0.000279 +TIME@ Exx_Lcao::init 9.41685 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.0006 +TIME@ radial_R_C 8e-06 + 0 0 1e-06 0.817959 + 0 1 2e-06 0.507871 + 1 0 4e-06 0.139111 + 1 1 3e-06 0.087432 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.55257 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.5526 +TIME@ radial_R_V 0.00074 + 0 0 2e-06 0.077461 + 0 1 2.8e-05 0.453219 + 1 0 1.7e-05 0.465201 + 1 1 2e-05 0.17933 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.17542 +TIME@ m_abfs_abfs.init_radial_table 1.17548 +TIME@ init_radial_table_ions 2.72888 +TIME@ Abfs::cal_Vs 0.029398 +TIME@ Abfs::cal_Vps 6.8e-05 +atom_pairs_core 3 +atom_centres_core 3 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.5e-05 +TIME@ Abfs::cal_Cs 0.031195 +TIME@ Abfs::cal_Cps 7e-06 +TIME@ schwarz::init 0.006791 +TIME@ cauchy::init 0.000309 +TIME@ Exx_Lcao::cal_exx_ions 2.88849 +sizeof_Cs: 174580 +sizeof_Vs: 632144 +sizeof_Cps: 174580 +sizeof_Vps: 11388 +sizeof_Cws: 171296 +sizeof_Vws: 634096 +TIME@ Exx_Lcao::cal_DM 0.000553 +TIME@ cauchy.cal_norm_D_max 2.7e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001215 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 7e-06 +E_exx -6.88943 +TIME@ Exx_Lcao::cal_energy 0.000573 +TIME@ Hexx_para.Rexx_to_Km2D 0.020772 +sizeof_Hexx2D 2224 +TIME@ Exx_Lcao::cal_exx_elec 0.023216 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/time_1 b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/time_1 new file mode 100644 index 0000000000000000000000000000000000000000..cc8e52e14f633d13a01ff9c7f8d3b628a9b6431c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/ABACUS/test/test_exx/process/time_1 @@ -0,0 +1,2533 @@ +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 8e-06 1.38142 + 1 1 2e-06 0.087074 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.46859 +TIME@LapackConnector::dsyev 0.000225 +TIME@LapackConnector::dsyev 2e-05 +TIME@LapackConnector::dsyev 1.2e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 0 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0.458232 + 1 0 3e-06 0.128087 + 1 1 3e-06 0.082429 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.44996 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.44999 +TIME@ radial_R_V 0.000704 + 0 0 5e-06 0.178877 + 0 1 2.7e-05 0.462827 + 1 0 1.8e-05 0.466902 + 1 1 3e-06 0.021703 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.13051 +TIME@ m_abfs_abfs.init_radial_table 1.13056 +TIME@ init_radial_table_ions 2.5813 +TIME@ Abfs::cal_Vs 0.068093 +TIME@ Abfs::cal_Vps 0 +atom_pairs_core 0 +atom_centres_core 0 +H_atom_pairs_core 0 +TIME@ Exx_Lcao::allocate_Hexx 1.6e-05 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.041766 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 1e-05 1.39831 + 1 1 1e-06 0.090825 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.48924 +TIME@LapackConnector::dsyev 0.000192 +TIME@LapackConnector::dsyev 2e-05 +TIME@LapackConnector::dsyev 1.1e-05 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 6e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 1e-06 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.3913 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.1045 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.97458 +TIME@ m_abfs_abfs.init_radial 8.5e-05 +TIME@ m_abfslcaos_lcaos.init 0.861986 +TIME@ m_abfslcaos_lcaos.init_radial 0.000275 +TIME@ Exx_Lcao::init 9.3893 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000611 +TIME@ radial_R_C 5e-06 + 0 0 2e-06 0.80674 + 0 1 4e-06 0.482806 + 1 0 4e-06 0.138555 + 1 1 3e-06 0.089027 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.51733 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.51736 +TIME@ radial_R_V 0.0007 + 0 0 5e-06 0.177405 + 0 1 2.9e-05 0.45949 + 1 0 1.8e-05 0.467026 + 1 1 3e-06 0.021947 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.12608 +TIME@ m_abfs_abfs.init_radial_table 1.12614 +TIME@ init_radial_table_ions 2.64426 +TIME@ Abfs::cal_Vs 0.064586 +TIME@ Abfs::cal_Vps 0.000199 +atom_pairs_core 3 +atom_centres_core 2 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.3e-05 +TIME@ Abfs::cal_Cs 0.027066 +TIME@ Abfs::cal_Cps 5e-06 +TIME@ schwarz::init 0.012291 +TIME@ cauchy::init 0.000237 +TIME@ Exx_Lcao::cal_exx_ions 2.74972 +sizeof_Cs: 160424 +sizeof_Vs: 2224420 +sizeof_Cps: 160424 +sizeof_Vps: 39300 +sizeof_Cws: 160384 +sizeof_Vws: 2226472 +TIME@ Exx_Lcao::cal_DM 0.000371 +TIME@ cauchy.cal_norm_D_max 3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001281 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -6.89189 +TIME@ Exx_Lcao::cal_energy 7.3e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.016367 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.0182 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.044528 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 9e-06 1.36778 + 1 1 2e-06 0.092085 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.45999 +TIME@LapackConnector::dsyev 0.000211 +TIME@LapackConnector::dsyev 1.9e-05 +TIME@LapackConnector::dsyev 1.1e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 7e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.34053 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.12185 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.9664 +TIME@ m_abfs_abfs.init_radial 8.7e-05 +TIME@ m_abfslcaos_lcaos.init 0.848835 +TIME@ m_abfslcaos_lcaos.init_radial 0.000272 +TIME@ Exx_Lcao::init 9.33355 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000624 +TIME@ radial_R_C 6e-06 + 0 0 2e-06 0.771125 + 0 1 3e-06 0.507158 + 1 0 4e-06 0.130597 + 1 1 3e-06 0.082065 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.49115 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.49117 +TIME@ radial_R_V 0.000713 + 0 0 4e-06 0.177201 + 0 1 2.8e-05 0.458255 + 1 0 1.7e-05 0.465766 + 1 1 4e-06 0.021778 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.12322 +TIME@ m_abfs_abfs.init_radial_table 1.12328 +TIME@ init_radial_table_ions 2.61522 +TIME@ Abfs::cal_Vs 0.065238 +TIME@ Abfs::cal_Vps 0.000215 +atom_pairs_core 3 +atom_centres_core 2 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.7e-05 +TIME@ Abfs::cal_Cs 0.027413 +TIME@ Abfs::cal_Cps 4e-06 +TIME@ schwarz::init 0.012024 +TIME@ cauchy::init 0.000268 +TIME@ Exx_Lcao::cal_exx_ions 2.72152 +sizeof_Cs: 160424 +sizeof_Vs: 2224420 +sizeof_Cps: 160424 +sizeof_Vps: 39300 +sizeof_Cws: 160384 +sizeof_Vws: 2226472 +TIME@ Exx_Lcao::cal_DM 0.000349 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002217 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -26.4745 +TIME@ Exx_Lcao::cal_energy 7.3e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018064 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02079 +TIME@ Exx_Lcao::cal_DM 0.000359 +TIME@ cauchy.cal_norm_D_max 3.6e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001229 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -26.4835 +TIME@ Exx_Lcao::cal_energy 7.5e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018922 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020671 +TIME@ Exx_Lcao::cal_DM 0.000245 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001162 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -26.4863 +TIME@ Exx_Lcao::cal_energy 0.006975 +TIME@ Hexx_para.Rexx_to_Km2D 0.010229 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.018701 +TIME@ Exx_Lcao::cal_DM 0.000223 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002878 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -26.4872 +TIME@ Exx_Lcao::cal_energy 6.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.017488 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02073 +TIME@ Exx_Lcao::cal_DM 0.000244 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001177 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -26.4875 +TIME@ Exx_Lcao::cal_energy 0.00109 +TIME@ Hexx_para.Rexx_to_Km2D 0.018039 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020624 +TIME@ Exx_Lcao::cal_DM 0.000235 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001195 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -26.4876 +TIME@ Exx_Lcao::cal_energy 7.3e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018979 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020554 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.041591 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 1.1e-05 1.40769 + 1 1 2e-06 0.084005 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.49183 +TIME@LapackConnector::dsyev 0.000207 +TIME@LapackConnector::dsyev 2e-05 +TIME@LapackConnector::dsyev 1.1e-05 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 7e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.36926 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.10165 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.98189 +TIME@ m_abfs_abfs.init_radial 8.7e-05 +TIME@ m_abfslcaos_lcaos.init 0.832091 +TIME@ m_abfslcaos_lcaos.init_radial 0.000269 +TIME@ Exx_Lcao::init 9.3429 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000614 +TIME@ radial_R_C 6e-06 + 0 0 2e-06 0.76481 + 0 1 4e-06 0.489904 + 1 0 4e-06 0.129537 + 1 1 3e-06 0.08124 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.46569 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.46572 +TIME@ radial_R_V 0.000719 + 0 0 5e-06 0.177729 + 0 1 2.9e-05 0.463462 + 1 0 1.7e-05 0.466509 + 1 1 4e-06 0.021889 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.12982 +TIME@ m_abfs_abfs.init_radial_table 1.12988 +TIME@ init_radial_table_ions 2.59638 +TIME@ Abfs::cal_Vs 0.064132 +TIME@ Abfs::cal_Vps 0.000187 +atom_pairs_core 3 +atom_centres_core 2 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.6e-05 +TIME@ Abfs::cal_Cs 0.026797 +TIME@ Abfs::cal_Cps 4e-06 +TIME@ schwarz::init 0.012062 +TIME@ cauchy::init 0.000226 +TIME@ Exx_Lcao::cal_exx_ions 2.70088 +sizeof_Cs: 160424 +sizeof_Vs: 2224420 +sizeof_Cps: 160424 +sizeof_Vps: 39300 +sizeof_Cws: 160384 +sizeof_Vws: 2226472 +TIME@ Exx_Lcao::cal_DM 0.000279 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001349 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 6.9e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018812 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020586 +TIME@ Exx_Lcao::cal_DM 0.000229 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.004231 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88288 +TIME@ Exx_Lcao::cal_energy 6.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.016144 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020752 +TIME@ Exx_Lcao::cal_DM 0.000234 +TIME@ cauchy.cal_norm_D_max 2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001931 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88384 +TIME@ Exx_Lcao::cal_energy 8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018206 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020524 +TIME@ Exx_Lcao::cal_DM 0.000229 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001157 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88393 +TIME@ Exx_Lcao::cal_energy 7e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018963 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02049 +TIME@ Exx_Lcao::cal_DM 0.000209 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001187 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88394 +TIME@ Exx_Lcao::cal_energy 6.4e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018068 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.019601 +TIME@ Exx_Lcao::cal_DM 0.000238 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002959 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88394 +TIME@ Exx_Lcao::cal_energy 7.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019126 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.022467 +TIME@ Exx_Lcao::cal_DM 0.00023 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001202 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88394 +TIME@ Exx_Lcao::cal_energy 7e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018888 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02046 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.043969 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 8e-06 1.34959 + 1 1 2e-06 0.090272 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.43997 +TIME@LapackConnector::dsyev 0.000203 +TIME@LapackConnector::dsyev 1.9e-05 +TIME@LapackConnector::dsyev 1e-05 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +TIME@LapackConnector::dsyev 6e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 1e-06 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.31596 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.09105 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.99285 +TIME@ m_abfs_abfs.init_radial 8.3e-05 +TIME@ m_abfslcaos_lcaos.init 0.834578 +TIME@ m_abfslcaos_lcaos.init_radial 0.000269 +TIME@ Exx_Lcao::init 9.29086 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000623 +TIME@ radial_R_C 5e-06 + 0 0 1e-06 0.756065 + 0 1 4e-06 0.486339 + 1 0 4e-06 0.128503 + 1 1 3e-06 0.081186 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.45228 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.45231 +TIME@ radial_R_V 0.000699 + 0 0 5e-06 0.177248 + 0 1 2.8e-05 0.460088 + 1 0 1.8e-05 0.470233 + 1 1 4e-06 0.021929 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.12971 +TIME@ m_abfs_abfs.init_radial_table 1.12978 +TIME@ init_radial_table_ions 2.58284 +TIME@ Abfs::cal_Vs 0.064405 +TIME@ Abfs::cal_Vps 0.000204 +atom_pairs_core 3 +atom_centres_core 2 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.5e-05 +TIME@ Abfs::cal_Cs 0.026999 +TIME@ Abfs::cal_Cps 4e-06 +TIME@ schwarz::init 0.012124 +TIME@ cauchy::init 0.000228 +TIME@ Exx_Lcao::cal_exx_ions 2.68793 +sizeof_Cs: 160424 +sizeof_Vs: 2224420 +sizeof_Cps: 160424 +sizeof_Vps: 39300 +sizeof_Cws: 160384 +sizeof_Vws: 2226472 +TIME@ Exx_Lcao::cal_DM 0.000287 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001396 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 0.003073 +TIME@ Hexx_para.Rexx_to_Km2D 0.015874 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020712 +TIME@ Exx_Lcao::cal_DM 0.000243 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001214 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88444 +TIME@ Exx_Lcao::cal_energy 7.5e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018984 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020586 +TIME@ Exx_Lcao::cal_DM 0.000292 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001187 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88793 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Exx_Lcao::cal_energy 6.7e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018955 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021152 +TIME@ Exx_Lcao::cal_DM 0.000714 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001157 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88955 +TIME@ Exx_Lcao::cal_energy 0.000899 +TIME@ Hexx_para.Rexx_to_Km2D 0.020196 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.023041 +TIME@ Exx_Lcao::cal_DM 0.000227 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001199 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 0.001943 +TIME@ Hexx_para.Rexx_to_Km2D 0.017027 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020471 +TIME@ Exx_Lcao::cal_DM 0.00023 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.0012 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 6.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.01887 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02044 +TIME@ Exx_Lcao::cal_DM 0.00024 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001172 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 6.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018893 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020442 +TIME@ Exx_Lcao::cal_DM 0.0006 +TIME@ cauchy.cal_norm_D_max 1.9e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001275 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 8.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018791 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020813 +TIME@ Exx_Lcao::cal_DM 0.00023 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001213 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 6.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.017234 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.018816 +TIME@ Exx_Lcao::cal_DM 0.000231 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001351 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 6.8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.01895 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020679 +TIME@ Exx_Lcao::cal_DM 0.000225 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001187 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 6.3e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.01899 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020532 +TIME@ Exx_Lcao::cal_DM 0.000225 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001201 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 6.4e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018959 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020516 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.043268 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 9e-06 1.93636 + 1 1 3e-06 0.110793 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 2.04727 +TIME@LapackConnector::dsyev 0.000183 +TIME@LapackConnector::dsyev 2e-05 +TIME@LapackConnector::dsyev 1.1e-05 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +TIME@LapackConnector::dsyev 6e-06 +TIME@LapackConnector::dsyev 3e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.92369 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.10839 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.95721 +TIME@ m_abfs_abfs.init_radial 9.1e-05 +TIME@ m_abfslcaos_lcaos.init 0.842478 +TIME@ m_abfslcaos_lcaos.init_radial 0.000278 +TIME@ Exx_Lcao::init 9.89455 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000634 +TIME@ radial_R_C 6e-06 + 0 0 1e-06 1.26598 + 0 1 3e-06 0.65188 + 1 0 3e-06 0.217902 + 1 1 3e-06 0.163598 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 2.29956 +TIME@ m_abfslcaos_lcaos.init_radial_table 2.29959 +TIME@ radial_R_V 0.000686 + 0 0 4e-06 0.204543 + 0 1 1.9e-05 0.476666 + 1 0 1.7e-05 0.463664 + 1 1 3e-06 0.021953 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.16704 +TIME@ m_abfs_abfs.init_radial_table 1.1671 +TIME@ init_radial_table_ions 3.46744 +TIME@ Abfs::cal_Vs 0.065643 +TIME@ Abfs::cal_Vps 0.000245 +atom_pairs_core 3 +atom_centres_core 2 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 3e-05 +TIME@ Abfs::cal_Cs 0.027637 +TIME@ Abfs::cal_Cps 5e-06 +TIME@ schwarz::init 0.012703 +TIME@ cauchy::init 0.00024 +TIME@ Exx_Lcao::cal_exx_ions 4.17806 +sizeof_Cs: 160424 +sizeof_Vs: 2224420 +sizeof_Cps: 160424 +sizeof_Vps: 39300 +sizeof_Cws: 160384 +sizeof_Vws: 2226472 +TIME@ Exx_Lcao::cal_DM 0.010689 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001396 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 7.4e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.017537 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.029796 +TIME@ Exx_Lcao::cal_DM 0.000242 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001206 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -9.02854 +TIME@ Exx_Lcao::cal_energy 6.5e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.020933 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.022517 +TIME@ Exx_Lcao::cal_DM 0.000258 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00122 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.66979 +TIME@ Exx_Lcao::cal_energy 5.8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.021297 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.022904 +TIME@ Exx_Lcao::cal_DM 0.000244 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001209 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.75746 +TIME@ Exx_Lcao::cal_energy 0.001654 +TIME@ Hexx_para.Rexx_to_Km2D 0.025504 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.028687 +TIME@ Exx_Lcao::cal_DM 0.000241 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001323 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.8643 +TIME@ Exx_Lcao::cal_energy 6.4e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.026996 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.028695 +TIME@ Exx_Lcao::cal_DM 0.00025 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001238 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.87342 +TIME@ Exx_Lcao::cal_energy 6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019449 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02107 +TIME@ Exx_Lcao::cal_DM 0.000261 +TIME@ cauchy.cal_norm_D_max 2.9e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00155 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88942 +TIME@ Exx_Lcao::cal_energy 6.4e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.023468 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.025454 +TIME@ Exx_Lcao::cal_DM 0.000263 +TIME@ cauchy.cal_norm_D_max 2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001197 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88906 +TIME@ Exx_Lcao::cal_energy 5.7e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.021171 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.022763 +TIME@ Exx_Lcao::cal_DM 0.000247 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002508 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88956 +TIME@ Exx_Lcao::cal_energy 6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.01773 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020617 +TIME@ Exx_Lcao::cal_DM 0.000252 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001211 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.8896 +TIME@ Exx_Lcao::cal_energy 5.7e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019765 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021356 +TIME@ Exx_Lcao::cal_DM 0.000256 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001192 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 5.9e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.020223 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021801 +TIME@ Exx_Lcao::cal_DM 0.000246 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001201 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.001781 +TIME@ Hexx_para.Rexx_to_Km2D 0.020162 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.023461 +TIME@ Exx_Lcao::cal_DM 0.000248 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.003092 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 6.3e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.016986 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020459 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.041534 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 7e-06 1.48693 + 1 1 3e-06 0.09183 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.57887 +TIME@LapackConnector::dsyev 0.00023 +TIME@LapackConnector::dsyev 3.4e-05 +TIME@LapackConnector::dsyev 1.1e-05 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +TIME@LapackConnector::dsyev 6e-06 +TIME@LapackConnector::dsyev 3e-06 +TIME@LapackConnector::dsyev 1e-06 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.45739 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.08366 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.959 +TIME@ m_abfs_abfs.init_radial 8.7e-05 +TIME@ m_abfslcaos_lcaos.init 0.832971 +TIME@ m_abfslcaos_lcaos.init_radial 0.000269 +TIME@ Exx_Lcao::init 9.39045 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000615 +TIME@ radial_R_C 6e-06 + 0 0 2e-06 0.747707 + 0 1 3e-06 0.459397 + 1 0 3e-06 0.124452 + 1 1 3e-06 0.081524 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.41328 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.4133 +TIME@ radial_R_V 0.000725 + 0 0 4e-06 0.179264 + 0 1 2.9e-05 0.46117 + 1 0 1.8e-05 0.468645 + 1 1 3e-06 0.021749 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.13104 +TIME@ m_abfs_abfs.init_radial_table 1.13111 +TIME@ init_radial_table_ions 2.54519 +TIME@ Abfs::cal_Vs 0.064577 +TIME@ Abfs::cal_Vps 0.000221 +atom_pairs_core 3 +atom_centres_core 2 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.9e-05 +TIME@ Abfs::cal_Cs 0.02718 +TIME@ Abfs::cal_Cps 5e-06 +TIME@ schwarz::init 0.012649 +TIME@ cauchy::init 0.000249 +TIME@ Exx_Lcao::cal_exx_ions 2.71921 +sizeof_Cs: 160424 +sizeof_Vs: 2224420 +sizeof_Cps: 160424 +sizeof_Vps: 39300 +sizeof_Cws: 160384 +sizeof_Vws: 2226472 +TIME@ Exx_Lcao::cal_DM 0.000316 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.008089 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 7.3e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.0121 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020653 +TIME@ Exx_Lcao::cal_DM 0.000254 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001168 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -9.02854 +TIME@ Exx_Lcao::cal_energy 6.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018917 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020469 +TIME@ Exx_Lcao::cal_DM 0.000258 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001176 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.66979 +TIME@ Exx_Lcao::cal_energy 5.9e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019492 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021057 +TIME@ Exx_Lcao::cal_DM 0.000263 +TIME@ cauchy.cal_norm_D_max 2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001183 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.75746 +TIME@ Exx_Lcao::cal_energy 5.8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.021189 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.022763 +TIME@ Exx_Lcao::cal_DM 0.000245 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001186 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8643 +TIME@ Exx_Lcao::cal_energy 6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019311 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020873 +TIME@ Exx_Lcao::cal_DM 0.000248 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001177 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.87342 +TIME@ Exx_Lcao::cal_energy 6.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.023962 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.025526 +TIME@ Exx_Lcao::cal_DM 0.000224 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001169 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88942 +TIME@ Exx_Lcao::cal_energy 5.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.020365 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021887 +TIME@ Exx_Lcao::cal_DM 0.000248 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.008079 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88906 +TIME@ Exx_Lcao::cal_energy 5.9e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.020112 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.028566 +TIME@ Exx_Lcao::cal_DM 0.000246 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001184 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88956 +TIME@ Exx_Lcao::cal_energy 5.7e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019631 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02119 +TIME@ Exx_Lcao::cal_DM 0.000257 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001162 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.8896 +TIME@ Exx_Lcao::cal_energy 5.9e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.01898 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020523 +TIME@ Exx_Lcao::cal_DM 0.000251 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001184 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 5.8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018918 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020478 +TIME@ Exx_Lcao::cal_DM 0.000252 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001166 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 5.8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018921 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020465 +TIME@ Exx_Lcao::cal_DM 0.000255 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001193 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.000624 +TIME@ Hexx_para.Rexx_to_Km2D 0.020233 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02238 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.04337 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 8e-06 1.38511 + 1 1 2e-06 0.115408 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.50062 +TIME@LapackConnector::dsyev 0.000208 +TIME@LapackConnector::dsyev 2.1e-05 +TIME@LapackConnector::dsyev 1.2e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 7e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.40529 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.09698 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.97175 +TIME@ m_abfs_abfs.init_radial 8.4e-05 +TIME@ m_abfslcaos_lcaos.init 0.865519 +TIME@ m_abfslcaos_lcaos.init_radial 0.000266 +TIME@ Exx_Lcao::init 9.39529 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000621 +TIME@ radial_R_C 5e-06 + 0 0 2e-06 0.750654 + 0 1 3e-06 0.483637 + 1 0 3e-06 0.126773 + 1 1 3e-06 0.08106 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.44231 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.44233 +TIME@ radial_R_V 0.000709 + 0 0 5e-06 0.179689 + 0 1 2.8e-05 0.458409 + 1 0 1.7e-05 0.469868 + 1 1 3e-06 0.021785 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.12995 +TIME@ m_abfs_abfs.init_radial_table 1.13001 +TIME@ init_radial_table_ions 2.5731 +TIME@ Abfs::cal_Vs 0.064731 +TIME@ Abfs::cal_Vps 0.000237 +atom_pairs_core 3 +atom_centres_core 2 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.8e-05 +TIME@ Abfs::cal_Cs 0.027189 +TIME@ Abfs::cal_Cps 5e-06 +TIME@ schwarz::init 0.01239 +TIME@ cauchy::init 0.00025 +TIME@ Exx_Lcao::cal_exx_ions 2.7654 +sizeof_Cs: 160424 +sizeof_Vs: 2224420 +sizeof_Cps: 160424 +sizeof_Vps: 39300 +sizeof_Cws: 160384 +sizeof_Vws: 2226472 +TIME@ Exx_Lcao::cal_DM 0.000328 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001235 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 6.5e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019283 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020992 +TIME@ Exx_Lcao::cal_DM 0.000261 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001182 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -9.02854 +TIME@ Exx_Lcao::cal_energy 0.002012 +TIME@ Hexx_para.Rexx_to_Km2D 0.018775 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.022303 +TIME@ Exx_Lcao::cal_DM 0.000239 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001193 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.66979 +TIME@ Exx_Lcao::cal_energy 6.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.015504 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.017073 +TIME@ Exx_Lcao::cal_DM 0.000256 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001212 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.75746 +TIME@ Exx_Lcao::cal_energy 6.2e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018953 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020556 +TIME@ Exx_Lcao::cal_DM 0.000244 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001197 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.8643 +TIME@ Exx_Lcao::cal_energy 6.7e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.019955 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021537 +TIME@ Exx_Lcao::cal_DM 0.000244 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001183 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.87342 +TIME@ Exx_Lcao::cal_energy 6.5e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018998 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02056 +TIME@ Exx_Lcao::cal_DM 0.000246 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001301 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88942 +TIME@ Exx_Lcao::cal_energy 6.3e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018846 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02053 +TIME@ Exx_Lcao::cal_DM 0.000257 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001175 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88906 +TIME@ Exx_Lcao::cal_energy 0.006938 +TIME@ Hexx_para.Rexx_to_Km2D 0.013901 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.022344 +TIME@ Exx_Lcao::cal_DM 0.000238 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00118 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88956 +TIME@ Exx_Lcao::cal_energy 0.006972 +TIME@ Hexx_para.Rexx_to_Km2D 0.012058 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.02052 +TIME@ Exx_Lcao::cal_DM 0.000244 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001299 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8896 +TIME@ Exx_Lcao::cal_energy 8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018846 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020545 +TIME@ Exx_Lcao::cal_DM 0.000253 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00117 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 0.00696 +TIME@ Hexx_para.Rexx_to_Km2D 0.015778 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.024236 +TIME@ Exx_Lcao::cal_DM 0.000246 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001265 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 0.006386 +TIME@ Hexx_para.Rexx_to_Km2D 0.013404 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021383 +TIME@ Exx_Lcao::cal_DM 0.000241 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.005348 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 7.4e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.014799 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020533 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.041938 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 1.4e-05 1.45385 + 1 1 2e-06 0.094673 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.54865 +TIME@LapackConnector::dsyev 0.001345 +TIME@LapackConnector::dsyev 2.3e-05 +TIME@LapackConnector::dsyev 1.2e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 1e-06 +TIME@LapackConnector::dsyev 8e-06 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.42007 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.11197 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.95526 +TIME@ m_abfs_abfs.init_radial 8.8e-05 +TIME@ m_abfslcaos_lcaos.init 0.828685 +TIME@ m_abfslcaos_lcaos.init_radial 0.000274 +TIME@ Exx_Lcao::init 9.37392 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000652 +TIME@ radial_R_C 6e-06 + 0 0 2e-06 0.802887 + 0 1 4e-06 0.518317 + 1 0 4e-06 0.138451 + 1 1 3e-06 0.087577 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.54744 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.54746 +TIME@ radial_R_V 0.000713 + 0 0 4e-06 0.176881 + 0 1 2.8e-05 0.463168 + 1 0 1.7e-05 0.469848 + 1 1 3e-06 0.021653 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.13176 +TIME@ m_abfs_abfs.init_radial_table 1.13183 +TIME@ init_radial_table_ions 2.68006 +TIME@ Abfs::cal_Vs 0.07114 +TIME@ Abfs::cal_Vps 0.000236 +atom_pairs_core 3 +atom_centres_core 2 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.7e-05 +TIME@ Abfs::cal_Cs 0.029951 +TIME@ Abfs::cal_Cps 6e-06 +TIME@ schwarz::init 0.013692 +TIME@ cauchy::init 0.000283 +TIME@ Exx_Lcao::cal_exx_ions 2.82942 +sizeof_Cs: 160424 +sizeof_Vs: 2224420 +sizeof_Cps: 160424 +sizeof_Vps: 39300 +sizeof_Cws: 160384 +sizeof_Vws: 2226472 +TIME@ Exx_Lcao::cal_DM 0.001377 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001448 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 7.2e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018714 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021688 +TIME@ Exx_Lcao::cal_DM 0.001843 +TIME@ cauchy.cal_norm_D_max 2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00139 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88444 +TIME@ Exx_Lcao::cal_energy 7.5e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.008357 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.011736 +TIME@ Exx_Lcao::cal_DM 0.000235 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.00138 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88793 +TIME@ Exx_Lcao::cal_energy 7.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018728 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020492 +TIME@ Exx_Lcao::cal_DM 0.00189 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001384 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88903 +TIME@ Exx_Lcao::cal_energy 7.2e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018707 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.022155 +TIME@ Exx_Lcao::cal_DM 0.000345 +TIME@ cauchy.cal_norm_D_max 2.5e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001422 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88939 +TIME@ Exx_Lcao::cal_energy 0.001061 +TIME@ Hexx_para.Rexx_to_Km2D 0.017818 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020716 +TIME@ Exx_Lcao::cal_DM 0.001247 +TIME@ cauchy.cal_norm_D_max 2.2e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002764 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88951 +TIME@ Exx_Lcao::cal_energy 6.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.015326 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.01947 +TIME@ Exx_Lcao::cal_DM 0.001168 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001392 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88955 +TIME@ Exx_Lcao::cal_energy 6.2e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.012164 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.014873 +TIME@ Exx_Lcao::cal_DM 0.000223 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001399 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 6.8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018664 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020435 +TIME@ Exx_Lcao::cal_DM 0.001688 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001379 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 0.003044 +TIME@ Hexx_para.Rexx_to_Km2D 0.01582 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.022005 +TIME@ Exx_Lcao::cal_DM 0.001758 +TIME@ cauchy.cal_norm_D_max 2.4e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.003981 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88957 +TIME@ Exx_Lcao::cal_energy 5.9e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.016156 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.022032 +TIME@ Exx_Lcao::cal_DM 0.001363 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001456 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 3e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 8e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.01635 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.019329 +TIME@ Exx_Lcao::cal_DM 0.001589 +TIME@ cauchy.cal_norm_D_max 2.6e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001106 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 7.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.001118 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.003975 +TIME@ Exx_Lcao::cal_DM 0.000242 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001446 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 7.7e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018715 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020552 +TIME@ Exx_Lcao::cal_DM 0.00113 +TIME@ cauchy.cal_norm_D_max 2.8e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001415 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 8.2e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018709 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021418 +TIME@ Exx_Lcao::cal_DM 0.001424 +TIME@ cauchy.cal_norm_D_max 2.7e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001405 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88958 +TIME@ Exx_Lcao::cal_energy 6.9e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.016326 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.019305 +TIME@ Exx_Abfs::Construct_Orbs::change_orbs 0.040444 +[] +[] +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 7 1 + 1 10 3 + 2 8 5 + 3 3 7 + 4 1 9 +1 + 0 4 1 + 1 3 3 + 2 1 5 + + 0 0 8e-06 1.47141 + 1 1 3e-06 0.095736 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.56727 +TIME@LapackConnector::dsyev 0.000225 +TIME@LapackConnector::dsyev 3.3e-05 +TIME@LapackConnector::dsyev 1.3e-05 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 0 +TIME@LapackConnector::dsyev 7e-06 +TIME@LapackConnector::dsyev 4e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.44575 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.11221 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 4.04815 +TIME@ m_abfs_abfs.init_radial 8.7e-05 +TIME@ m_abfslcaos_lcaos.init 0.839884 +TIME@ m_abfslcaos_lcaos.init_radial 0.00027 +TIME@ Exx_Lcao::init 9.50267 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000665 +TIME@ radial_R_C 6e-06 + 0 0 1e-06 0.809627 + 0 1 4e-06 0.506636 + 1 0 3e-06 0.18151 + 1 1 3e-06 0.087517 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.58548 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.5855 +TIME@ radial_R_V 0.000718 + 0 0 5e-06 0.178246 + 0 1 2.9e-05 0.461331 + 1 0 1.9e-05 0.47099 + 1 1 4e-06 0.021594 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.13238 +TIME@ m_abfs_abfs.init_radial_table 1.13244 +TIME@ init_radial_table_ions 2.7187 +TIME@ Abfs::cal_Vs 0.070776 +TIME@ Abfs::cal_Vps 0.000227 +atom_pairs_core 3 +atom_centres_core 2 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.7e-05 +TIME@ Abfs::cal_Cs 0.030013 +TIME@ Abfs::cal_Cps 6e-06 +TIME@ schwarz::init 0.013834 +TIME@ cauchy::init 0.000281 +TIME@ Exx_Lcao::cal_exx_ions 2.90495 +sizeof_Cs: 160424 +sizeof_Vs: 2224420 +sizeof_Cps: 160424 +sizeof_Vps: 39300 +sizeof_Cws: 160384 +sizeof_Vws: 2226472 +TIME@ Exx_Lcao::cal_DM 0.00063 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.003697 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -7.8727 +TIME@ Exx_Lcao::cal_energy 8.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.016526 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021009 +TIME@ Exx_Lcao::cal_DM 0.000863 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.008954 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88444 +TIME@ Exx_Lcao::cal_energy 6.5e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.000301 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.010257 +TIME@ Exx_Lcao::cal_DM 0.001121 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.004253 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 6e-06 +E_exx -7.88793 +TIME@ Exx_Lcao::cal_energy 9.1e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.011678 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.017232 +TIME@ Exx_Lcao::cal_DM 0.000932 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.004699 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88903 +TIME@ Exx_Lcao::cal_energy 6.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.015373 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021149 +TIME@ Exx_Lcao::cal_DM 0.001129 +TIME@ cauchy.cal_norm_D_max 2.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001371 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88939 +TIME@ Exx_Lcao::cal_energy 7.3e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.018702 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021345 +TIME@ Exx_Lcao::cal_DM 0.001075 +TIME@ cauchy.cal_norm_D_max 3.1e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.003874 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88951 +TIME@ Exx_Lcao::cal_energy 6.6e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.016346 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.021455 +TIME@ Exx_Lcao::cal_DM 0.001396 +TIME@ cauchy.cal_norm_D_max 3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.002455 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 4e-06 +E_exx -7.88955 +TIME@ Exx_Lcao::cal_energy 6.3e-05 +TIME@ Hexx_para.Rexx_to_Km2D 0.001118 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.005113 +TIME@ Exx_Lcao::cal_DM 0.000755 +TIME@ cauchy.cal_norm_D_max 2.3e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 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+TIME@LapackConnector::dsyev 7e-06 +TIME@LapackConnector::dsyev 5e-06 +TIME@LapackConnector::dsyev 0 +0 0 0 2.48306e-06 +0 0 1 0.000231468 +0 0 2 0.000562408 +0 0 3 0.00169989 +0 0 4 0.015632 +0 0 5 0.0944804 +0 0 6 0.558756 +0 1 0 -6.53756e-20 +0 1 1 6.58045e-22 +0 1 2 8.35254e-20 +0 1 3 6.7806e-17 +0 1 4 5.62878e-06 +0 1 5 1.00964e-05 +0 1 6 0.00152844 +0 1 7 0.0118351 +0 1 8 0.0393636 +0 1 9 0.380337 +0 2 0 8.05041e-21 +0 2 1 3.6231e-19 +0 2 2 9.11897e-07 +0 2 3 2.98045e-05 +0 2 4 0.00151012 +0 2 5 0.00956904 +0 2 6 0.0407953 +0 2 7 0.247605 +0 3 0 1.88183e-23 +0 3 1 0.0106119 +0 3 2 0.107086 +0 4 0 0.045708 +eig_value_max: 0.558756 +eig_value_threshold: 5.58756e-05 +1 0 0 0.000163443 +1 0 1 0.00472006 +1 0 2 0.0601941 +1 0 3 0.267196 +1 1 0 2.34309e-18 +1 1 1 0.0100783 +1 1 2 0.11746 +1 2 0 0.0480742 +eig_value_max: 0.267196 +eig_value_threshold: 2.67196e-05 +TIME@ Exx_Abfs::Construct_Orbs::abfs 3.457 +TIME@ Conv_Coulomb_Pot_K::cal_orbs_ccp 1.11689 +Exx_Abfs::Lmax: 4 +0 + 0 2 1 + 1 2 3 + 2 1 5 +1 + 0 2 1 + 1 1 3 + +0 + 0 6 1 + 1 4 3 + 2 4 5 + 3 2 7 + 4 1 9 +1 + 0 4 1 + 1 2 3 + 2 1 5 + +TIME@ m_abfs_abfs.init 3.98347 +TIME@ m_abfs_abfs.init_radial 8.9e-05 +TIME@ m_abfslcaos_lcaos.init 0.84059 +TIME@ m_abfslcaos_lcaos.init_radial 0.000266 +TIME@ Exx_Lcao::init 9.45467 +atom_pairs_core_origin 3 +TIME@ Htime::distribute 0.000606 +TIME@ radial_R_C 6e-06 + 0 0 1e-06 0.859003 + 0 1 4e-06 0.545847 + 1 0 3e-06 0.140352 + 1 1 3e-06 0.083606 +TIME@Exx_Abfs::Matrix_Orbs21::init_radial_table_Rs 1.62899 +TIME@ m_abfslcaos_lcaos.init_radial_table 1.62902 +TIME@ radial_R_V 0.000731 + 0 0 4e-06 0.179387 + 0 1 3.1e-05 0.468401 + 1 0 1.8e-05 0.474248 + 1 1 3e-06 0.021977 +TIME@Exx_Abfs::Matrix_Orbs11::init_radial_table_Rs 1.14421 +TIME@ m_abfs_abfs.init_radial_table 1.14427 +TIME@ init_radial_table_ions 2.77406 +TIME@ Abfs::cal_Vs 0.070041 +TIME@ Abfs::cal_Vps 0.00018 +atom_pairs_core 3 +atom_centres_core 2 +H_atom_pairs_core 9 +TIME@ Exx_Lcao::allocate_Hexx 2.5e-05 +TIME@ Abfs::cal_Cs 0.029443 +TIME@ Abfs::cal_Cps 5e-06 +TIME@ schwarz::init 0.013362 +TIME@ cauchy::init 0.000273 +TIME@ Exx_Lcao::cal_exx_ions 2.88849 +sizeof_Cs: 160424 +sizeof_Vs: 2224420 +sizeof_Cps: 160424 +sizeof_Vps: 39300 +sizeof_Cws: 160384 +sizeof_Vws: 2226472 +TIME@ Exx_Lcao::cal_DM 0.000286 +TIME@ cauchy.cal_norm_D_max 2.8e-05 +sizeof_DM 5204 +TIME@ Exx_Lcao::cal_Hexx 0.001754 +sizeof_HexxR 5204 +TIME@ Exx_Lcao::cal_energy_cal 5e-06 +E_exx -6.88943 +TIME@ Exx_Lcao::cal_energy 0.000104 +TIME@ Hexx_para.Rexx_to_Km2D 0.018308 +sizeof_Hexx2D 2040 +TIME@ Exx_Lcao::cal_exx_elec 0.020567 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/atom.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/atom.npy new file mode 100644 index 0000000000000000000000000000000000000000..6a230754a34b936523b3d5b9f232fa34d7fca78e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.00/atom.npy differ diff --git 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0000000000000000000000000000000000000000..6dc34004157af3b98b95ad421638639e8a7da85d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.02/force.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..8b8f3391d41b64ff6a1c3107f55be9d9f0217091 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.528821 0.63969 0.372867 +H 0.568517 0.587977 0.36801 +H 0.569422 0.687646 0.35752 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..171eb2d59578cf49ba02feddd2547a31f312d816 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4388 2 + 2 -12.9467 2 + 3 -9.30051 2 + 4 -6.77858 2 + 5 1.35157 0 + 6 4.52069 0 + 7 11.0503 0 + 8 11.319 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1e95c8b9f6a69ae840b51dd140c6677027df8141 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:55 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.8069954334 17.9113242282 10.4402890571 0 0 0 0 + tauc_H1 15.9184686019 16.4633684592 10.3042878336 0 0 0 0 + tauc_H2 15.9438195739 19.2540803722 10.0105545672 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0733105422822 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877799106983 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104118731452 (SEC) + + DONE : INIT CHARGE Time : 0.146340237416 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.389765 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108 + + Density error is 0.214319539691 + + Energy Rydberg eV + E_KohnSham -34.1914354427 -465.198344819 + E_Harris -34.3824565737 -467.79732064 + E_Fermi -0.410949351857 -5.59125277466 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125869852073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107358890588 + + Density error is 0.0974998411729 + + Energy Rydberg eV + E_KohnSham -34.2800245371 -466.403661284 + E_Harris -34.2867351489 -466.494963841 + E_Fermi -0.220294076131 -2.99725467103 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116454752163 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100789706527 + + Density error is 0.0623806455493 + + Energy Rydberg eV + E_KohnSham -34.2802053551 -466.406121439 + E_Harris -34.2845384742 -466.46507655 + E_Fermi -0.207725084611 -2.82624476824 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100395859765 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909012141181 + + Density error is 0.00196347237898 + + Energy Rydberg eV + E_KohnSham -34.2802142053 -466.406241852 + E_Harris -34.280214801 -466.406249957 + E_Fermi -0.172025571609 -2.34052797559 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100283692269 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000910282012011 + + Density error is 0.000845664133844 + + Energy Rydberg eV + E_KohnSham -34.2801511904 -466.405384491 + E_Harris -34.280153154 -466.405411207 + E_Fermi -0.171134575553 -2.32840535233 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100122591008 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908990012392 + + Density error is 9.56536296236e-05 + + Energy Rydberg eV + E_KohnSham -34.2801964969 -466.406000917 + E_Harris -34.2801965006 -466.406000968 + E_Fermi -0.171265351916 -2.33018465603 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100093546954 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908889433843 + + Density error is 3.80123239208e-05 + + Energy Rydberg eV + E_KohnSham -34.280182247 -466.405807038 + E_Harris -34.2801822548 -466.405807144 + E_Fermi -0.17115025903 -2.32861873699 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100096194085 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908890200289 + + Density error is 1.03838016825e-05 + + Energy Rydberg eV + E_KohnSham -34.2801843192 -466.405835232 + E_Harris -34.2801843197 -466.405835238 + E_Fermi -0.171198337912 -2.32927288373 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100095319494 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908892351312 + + Density error is 1.57089886855e-06 + + Energy Rydberg eV + E_KohnSham -34.2801831408 -466.405819198 + E_Harris -34.2801831408 -466.405819198 + E_Fermi -0.171188176447 -2.32913462991 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100095211747 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908890667082 + + Density error is 1.17468931449e-07 + + Energy Rydberg eV + E_KohnSham -34.2801832976 -466.405821332 + E_Harris -34.2801832976 -466.405821332 + E_Fermi -0.171186645492 -2.3291138002 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100095233668 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908890911738 + + Density error is 3.00876437745e-08 + + Energy Rydberg eV + E_KohnSham -34.28018333 -466.405821773 + E_Harris -34.28018333 -466.405821773 + E_band -8.00614846975 -108.929238223 + E_one_elec -69.470567637 -945.195563157 + E_Hartree +36.1182809091 +491.414422328 + E_xc -8.22223446435 -111.869239007 + E_Ewald +7.41826939284 +100.930733042 + E_demet -3.92721119006e-82 -5.34324494342e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195170546604 -2.65543151559 + E_Fermi -0.171186671166 -2.32911414951 + + charge density convergence is achieved + final etot is -466.405821773 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4388 2.00000 + 2 -12.9467 2.00000 + 3 -9.30051 2.00000 + 4 -6.77858 2.00000 + 5 1.35157 0.00000 + 6 4.52069 0.00000 + 7 11.0503 0.00000 + 8 11.3190 0.00000 + + EFERMI = -2.329114149506417 eV + OUT.ABACUS/ final etot is -466.4058217730708 eV + correction force for each atom along direction 1 is 0.000194381 + correction force for each atom along direction 2 is 2.95811e-05 + correction force for each atom along direction 3 is 0.000127736 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.42587032 -0.41007815 +0.16055078 + H1 +0.032237608 -0.53208392 +0.041998326 + H2 +0.39363272 +0.94216207 -0.20254910 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4058217730708 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2686 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2619 1 6.3 1.e+02% + Potential init_pot 0.24246 2 0.12 3.9% + PW_Basis recip2real 0.22684 16 0.014 3.6% + PW_Basis gathers_scatterp 0.10734 16 0.0067 1.7% + Potential v_of_rho 0.87626 13 0.067 14.% + XC_Functional v_xc 0.27712 14 0.020 4.4% + H_Hartree_pw v_hartree 0.56632 13 0.044 9.0% + PW_Basis real2recip 0.60447 38 0.016 9.6% + PW_Basis gatherp_scatters 0.26736 38 0.0070 4.3% + ORB_control set_orb_tables 0.90085 1 0.90 14.% + ORB_gen_tables gen_tables 0.90085 1 0.90 14.% + ORB_table_phi init_Table 0.37756 1 0.38 6.0% + ORB_table_phi cal_ST_Phi12_R 0.37337 126 0.0030 6.0% + ORB_table_beta init_Table_Beta 0.15521 1 0.16 2.5% + ORB_table_beta VNL_PhiBeta_R 0.15389 56 0.0027 2.5% + ORB_table_alpha init_Table_Alpha 0.21062 1 0.21 3.4% + ORB_table_alpha S_PhiAlpha_R 0.20891 66 0.0032 3.3% + LOOP_ions opt_ions 4.9016 1 4.9 78.% + ESolver_KS_LCAO Run 4.3753 1 4.4 70.% + HSolverLCAO solve 2.1939 11 0.20 35.% + HamiltLCAO updateHk 1.1487 11 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1194 11 0.10 18.% + Gint_interface cal_gint 0.46261 23 0.020 7.4% + Gint_Gamma distri_vl_value 0.56982 11 0.052 9.1% + Gint_Gamma distri_vl 2.1144 6 0.35 34.% + LCAO_Deepks cal_projected_DM 4.5536 13 0.35 73.% + LCAO_gen_fixedH add_v_delta 1.9856 6 0.33 32.% + LCAO_DESCRIPTOR add_v_delta 1.9857 6 0.33 32.% + ElecStateLCAO psiToRho 1.0292 11 0.094 16.% + Charge mix_rho 0.75521 10 0.076 12.% + LOOP_ions force_stress 0.52614 1 0.53 8.4% + Force_Stress_LCAO getForceStress 0.52612 1 0.53 8.4% + Force_LCAO_gamma ftable_gamma 0.33136 1 0.33 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.11589 1 0.12 1.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:55 2022 + Finish Time : Wed Sep 28 11:09:01 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..047a844f732d7ff07f773e24bca8f23f9cb6f740 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123827 ima = 3.66376e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122621496167 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111741601981 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112236550714 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112494573007 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112431657424 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112466923908 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112464202152 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112466665406 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112466193591 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011246611524 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112466112032 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/STRU new file mode 100644 index 0000000000000000000000000000000000000000..ef0fdb846459320a50467ffe3bb2c0661e2f1dad --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.193004566584 17.911324228270 10.440289057034 0 0 0 +H +0.0 +2 +-12.081531398121 16.463368459223 10.304287833597 0 0 0 +-12.056180426040 19.254080372218 10.010554567137 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/conv new file mode 100644 index 0000000000000000000000000000000000000000..ad4f2b2bd146eb43e6bc53593e024b152bdd6377 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/conv @@ -0,0 +1 @@ +0 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..2cb8a936dc592b32349e8eb13043fb079e320555 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751901375 0.01280041238 1.278740761 1.362529262 1.469910369 0.009067864636 0.01772570692 0.03909643309 +4.530351416e-19 0.001015812892 0.002788337381 0.01305145282 0.04706455327 -3.536362555e-19 2.561316294e-06 6.930688747e-06 +0.001610441586 0.006093655411 + +H atom_index 1 n_descriptor 18 +1.250194345 0.03457708186 0.109744417 0.1496816545 0.3200957756 0.02278743462 0.02826493517 0.03768946599 +3.157578789e-17 5.012019839e-05 0.1030567737 0.1151133379 0.1284990927 -1.585375505e-18 3.696344104e-06 0.01331465747 +0.02683121825 0.03076047275 + +H atom_index 2 n_descriptor 18 +1.265433078 0.03406332417 0.1152238133 0.15692714 0.3249583477 0.02352201859 0.02915254071 0.03726047775 +2.599377134e-17 5.158907974e-05 0.1060575863 0.1165298161 0.1347277205 3.547817607e-18 2.818833008e-06 0.01326797187 +0.02738006007 0.03143222348 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e17b9db61fc20aec53d72b5aeb6fab3088f4e557 Binary files /dev/null and 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0000000000000000000000000000000000000000..01bc9e21f27db810f0e6c62d99a3fafe6d693d3a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:55 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733263 SEC) : SETUP UNITCELL + DONE(0.0877927 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104133 SEC) : INIT PLANEWAVE + DONE(0.146454 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.389806 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651983e+02 0.000000e+00 2.143e-01 4.840e-01 + GE2 -4.664037e+02 -1.205316e+00 9.750e-02 4.451e-01 + GE3 -4.664061e+02 -2.460156e-03 6.238e-02 5.077e-01 + GE4 -4.664062e+02 -1.204132e-04 1.963e-03 3.817e-01 + GE5 -4.664054e+02 8.573619e-04 8.457e-04 3.815e-01 + GE6 -4.664060e+02 -6.164269e-04 9.565e-05 3.579e-01 + GE7 -4.664058e+02 1.938794e-04 3.801e-05 3.733e-01 + GE8 -4.664058e+02 -2.819402e-05 1.038e-05 3.638e-01 + GE9 -4.664058e+02 1.603408e-05 1.571e-06 3.644e-01 + GE10 -4.664058e+02 -2.134258e-06 1.175e-07 3.630e-01 + GE11 -4.664058e+02 -4.408826e-07 3.009e-08 2.993e-01 +E_delta_band = -7.12390160e-02 Ry = -9.69256537e-01 eV +E_delta_NN= -1.95170547e-01 Ry = -2.65543152e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2686 11 0.57 1e+02 % + Run_lcao lcao_line 6.2619 1 6.3 1e+02 % + Potential init_pot 0.24246 2 0.12 3.9 % + PW_Basis recip2real 0.22684 16 0.014 3.6 % + PW_Basis gathers_scatterp 0.10734 16 0.0067 1.7 % + Potential v_of_rho 0.87626 13 0.067 14 % + XC_Functional v_xc 0.27712 14 0.02 4.4 % + H_Hartree_pw v_hartree 0.56632 13 0.044 9 % + PW_Basis real2recip 0.60447 38 0.016 9.6 % + PW_Basis gatherp_scatters 0.26736 38 0.007 4.3 % + ORB_control set_orb_tables 0.90085 1 0.9 14 % + ORB_gen_tables gen_tables 0.90085 1 0.9 14 % + ORB_table_phi init_Table 0.37756 1 0.38 6 % + ORB_table_phi cal_ST_Phi12_R 0.37337 126 0.003 6 % + ORB_table_beta init_Table_Beta 0.15521 1 0.16 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.15389 56 0.0027 2.5 % + ORB_table_alpha init_Table_Alpha 0.21062 1 0.21 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.20891 66 0.0032 3.3 % + LOOP_ions opt_ions 4.9016 1 4.9 78 % + ESolver_KS_LCAO Run 4.3753 1 4.4 70 % + HSolverLCAO solve 2.1939 11 0.2 35 % + HamiltLCAO updateHk 1.1487 11 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1194 11 0.1 18 % + Gint_interface cal_gint 0.46261 23 0.02 7.4 % + Gint_Gamma distri_vl_value 0.56982 11 0.052 9.1 % + Gint_Gamma distri_vl 2.1144 6 0.35 34 % + LCAO_Deepks cal_projected_DM 4.5536 13 0.35 73 % + LCAO_gen_fixedH add_v_delta 1.9856 6 0.33 32 % + LCAO_DESCRIPTOR add_v_delta 1.9857 6 0.33 32 % + ElecStateLCAO psiToRho 1.0292 11 0.094 16 % + Charge mix_rho 0.75521 10 0.076 12 % + LOOP_ions force_stress 0.52614 1 0.53 8.4 % + Force_Stress_LCAO getForceStress 0.52612 1 0.53 8.4 % + Force_LCAO_gamma ftable_gamma 0.33136 1 0.33 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.11589 1 0.12 1.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:55 2022 + FINISH Time : Wed Sep 28 11:09:01 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/0/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9c83c1aab8a48de7e3ff286e2704bb4026ffb582 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.523055 0.662073 0.35009 +H 0.539379 0.603888 0.326146 +H 0.578804 0.69233 0.364444 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9f4e68c96c87e9103d9bafb0469dcd32ca4f1d15 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.322 2 + 2 -13.2246 2 + 3 -9.01356 2 + 4 -6.75137 2 + 5 1.38108 0 + 6 4.54893 0 + 7 11.0599 0 + 8 11.2996 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4ca8ab7dd6edcf78d8b049c825767752c1e71d43 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:34 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.6455302444 18.5380537018 9.80250791029 0 0 0 0 + tauc_H1 15.1026083517 16.9088640449 9.13209143701 0 0 0 0 + tauc_H2 16.2065234609 19.3852358787 10.204437274 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0993758627161 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100234528977 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118284713983 (SEC) + + DONE : INIT CHARGE Time : 0.161508368215 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443853 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000854 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0015 + + Density error is 0.215692592901 + + Energy Rydberg eV + E_KohnSham -34.1912737455 -465.196144816 + E_Harris -34.3844910726 -467.825001417 + E_Fermi -0.409780756123 -5.57535321402 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010359677118 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126763127193 + + Density error is 0.0977927242254 + + Energy Rydberg eV + E_KohnSham -34.2806645031 -466.412368469 + E_Harris -34.2873028109 -466.502687279 + E_Fermi -0.2178803071 -2.96441365855 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000979988660358 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117104330958 + + Density error is 0.0625946131262 + + Energy Rydberg eV + E_KohnSham -34.280868695 -466.415146642 + E_Harris -34.2851374941 -466.473226634 + E_Fermi -0.205243447482 -2.79248036292 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000891002186481 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101061700968 + + Density error is 0.00203603772482 + + Energy Rydberg eV + E_KohnSham -34.2808823152 -466.415331954 + E_Harris -34.2808842781 -466.415358661 + E_Fermi -0.169809282475 -2.31037381496 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000890520577114 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100983048253 + + Density error is 0.000860488779722 + + Energy Rydberg eV + E_KohnSham -34.2808207655 -466.414494528 + E_Harris -34.2808221534 -466.414513411 + E_Fermi -0.168864925195 -2.29752517499 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000889419783735 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100814774871 + + Density error is 0.000171051550833 + + Energy Rydberg eV + E_KohnSham -34.28086216 -466.415057728 + E_Harris -34.2808622297 -466.415058677 + E_Fermi -0.168986865954 -2.29918426413 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000889481131477 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100802794347 + + Density error is 4.05396385444e-05 + + Energy Rydberg eV + E_KohnSham -34.2808465355 -466.414845146 + E_Harris -34.2808465446 -466.41484527 + E_Fermi -0.168829411244 -2.29704198291 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000889437851148 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100803846202 + + Density error is 1.76758155745e-05 + + Energy Rydberg eV + E_KohnSham -34.2808513191 -466.41491023 + E_Harris -34.2808513204 -466.414910248 + E_Fermi -0.168877702766 -2.29769902277 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000889428698698 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100801864819 + + Density error is 2.13427139873e-06 + + Energy Rydberg eV + E_KohnSham -34.2808498065 -466.414889651 + E_Harris -34.2808498065 -466.414889651 + E_Fermi -0.168859204302 -2.29744733825 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000889427497239 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100801245499 + + Density error is 3.74308571564e-07 + + Energy Rydberg eV + E_KohnSham -34.2808500633 -466.414893144 + E_Harris -34.2808500633 -466.414893144 + E_Fermi -0.168857144161 -2.2974193086 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000889428154995 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100801274222 + + Density error is 1.37610574063e-07 + + Energy Rydberg eV + E_KohnSham -34.2808500889 -466.414893493 + E_Harris -34.2808500889 -466.414893493 + E_Fermi -0.168857010359 -2.29741748813 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000889428277519 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100801257129 + + Density error is 1.00357358752e-08 + + Energy Rydberg eV + E_KohnSham -34.2808500916 -466.414893529 + E_Harris -34.2808500916 -466.414893529 + E_band -7.98364972452 -108.62312709 + E_one_elec -69.4438769905 -944.832418282 + E_Hartree +36.1158965126 +491.381980949 + E_xc -8.22178678356 -111.863147998 + E_Ewald +7.39294724599 +100.586207559 + E_demet -4.88002598898e-82 -6.63961598382e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19503541756 -2.65359299062 + E_Fermi -0.168856882425 -2.2974157475 + + charge density convergence is achieved + final etot is -466.414893529 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3220 2.00000 + 2 -13.2246 2.00000 + 3 -9.01356 2.00000 + 4 -6.75137 2.00000 + 5 1.38108 0.00000 + 6 4.54893 0.00000 + 7 11.0599 0.00000 + 8 11.2996 0.00000 + + EFERMI = -2.297415747497181 eV + OUT.ABACUS/ final etot is -466.4148935291349 eV + correction force for each atom along direction 1 is 9.34771e-05 + correction force for each atom along direction 2 is 2.43699e-05 + correction force for each atom along direction 3 is 0.000119993 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.81388052 +0.33996180 +0.12395519 + H1 +0.27470803 -0.48611809 -0.19870244 + H2 +0.53917249 +0.14615628 +0.074747254 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4148935291349 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6697 11 0.70 1.0e+02% + Run_lcao lcao_line 7.6604 1 7.7 1.e+02% + Potential init_pot 0.28478 2 0.14 3.7% + PW_Basis recip2real 0.27156 17 0.016 3.5% + PW_Basis gathers_scatterp 0.12217 17 0.0072 1.6% + Potential v_of_rho 0.84706 14 0.061 11.% + XC_Functional v_xc 0.20445 15 0.014 2.7% + H_Hartree_pw v_hartree 0.60404 14 0.043 7.9% + PW_Basis real2recip 0.70712 41 0.017 9.2% + PW_Basis gatherp_scatters 0.28930 41 0.0071 3.8% + ORB_control set_orb_tables 1.0972 1 1.1 14.% + ORB_gen_tables gen_tables 1.0971 1 1.1 14.% + ORB_table_phi init_Table 0.47450 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46918 126 0.0037 6.1% + ORB_table_beta init_Table_Beta 0.18539 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18383 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24786 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24592 66 0.0037 3.2% + LOOP_ions opt_ions 6.0390 1 6.0 79.% + ESolver_KS_LCAO Run 5.4564 1 5.5 71.% + HSolverLCAO solve 3.1070 12 0.26 41.% + HamiltLCAO updateHk 1.5694 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.5399 12 0.13 20.% + Gint_interface cal_gint 0.92198 25 0.037 12.% + Gint_Gamma distri_vl_value 0.75645 12 0.063 9.9% + Gint_Gamma distri_vl 2.8340 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.6712 14 0.41 74.% + LCAO_gen_fixedH add_v_delta 2.6925 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.6927 6 0.45 35.% + ElecStateLCAO psiToRho 1.5187 12 0.13 20.% + Charge mix_rho 0.88953 11 0.081 12.% + LOOP_ions force_stress 0.58239 1 0.58 7.6% + Force_Stress_LCAO getForceStress 0.58237 1 0.58 7.6% + Force_LCAO_gamma ftable_gamma 0.39047 1 0.39 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.18267 1 0.18 2.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1031. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:34 2022 + Finish Time : Wed Sep 28 11:10:42 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..56be9e5852f3012af4ea1804102c610d412c9dd8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123565 ima = 3.67109e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123165402549 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112350920796 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112812923347 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113058410701 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011300345099 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113036821525 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113028245745 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113031282162 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011303054909 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011303047639 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113030462721 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113030456304 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1e847681d9f3a1ab809374797a9a8642ca47b544 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.354469755630 18.538053701793 9.802507910312 0 0 0 +H +0.0 +2 +-12.897391648318 16.908864044889 9.132091437004 0 0 0 +-11.793476539078 19.385235878668 10.204437274069 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/conv new file mode 100644 index 0000000000000000000000000000000000000000..15ea1183b42238a250bf9f8923d355029c78e1da --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/conv @@ -0,0 +1 @@ +1 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4a7b89a93c134f4f7694429557767df26a4662f5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747211898 0.01270383596 1.281393011 1.370000253 1.469513182 0.008213812153 0.01937038812 0.03896395382 +1.000581898e-19 0.001129387386 0.002548237585 0.01252675572 0.04492898698 3.06476089e-19 1.891427096e-06 5.621567405e-06 +0.001699423865 0.00585573317 + +H atom_index 1 n_descriptor 18 +1.254106577 0.03385054642 0.1097092218 0.1523234722 0.3230130024 0.02227676863 0.02860827341 0.03703050807 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/dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..276509114f24d4fe436573489382b97481a26c09 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..c93da3b007e11513ea490487e3929d96d4c35c65 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:34 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0994001 SEC) : SETUP UNITCELL + DONE(0.100251 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118306 SEC) : INIT PLANEWAVE + DONE(0.161643 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443922 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651961e+02 0.000000e+00 2.157e-01 5.497e-01 + GE2 -4.664124e+02 -1.216224e+00 9.779e-02 5.054e-01 + GE3 -4.664151e+02 -2.778173e-03 6.259e-02 5.697e-01 + GE4 -4.664153e+02 -1.853124e-04 2.036e-03 4.366e-01 + GE5 -4.664145e+02 8.374265e-04 8.605e-04 4.364e-01 + GE6 -4.664151e+02 -5.632002e-04 1.711e-04 4.287e-01 + GE7 -4.664148e+02 2.125815e-04 4.054e-05 4.263e-01 + GE8 -4.664149e+02 -6.508378e-05 1.768e-05 4.200e-01 + GE9 -4.664149e+02 2.057926e-05 2.134e-06 4.208e-01 + GE10 -4.664149e+02 -3.493391e-06 3.743e-07 4.191e-01 + GE11 -4.664149e+02 -3.482634e-07 1.376e-07 4.189e-01 + GE12 -4.664149e+02 -3.650654e-08 1.004e-08 3.649e-01 +E_delta_band = -7.10053415e-02 Ry = -9.66077233e-01 eV +E_delta_NN= -1.95035418e-01 Ry = -2.65359299e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6697 11 0.7 1e+02 % + Run_lcao lcao_line 7.6604 1 7.7 1e+02 % + Potential init_pot 0.28478 2 0.14 3.7 % + PW_Basis recip2real 0.27156 17 0.016 3.5 % + PW_Basis gathers_scatterp 0.12217 17 0.0072 1.6 % + Potential v_of_rho 0.84706 14 0.061 11 % + XC_Functional v_xc 0.20445 15 0.014 2.7 % + H_Hartree_pw v_hartree 0.60404 14 0.043 7.9 % + PW_Basis real2recip 0.70712 41 0.017 9.2 % + PW_Basis gatherp_scatters 0.2893 41 0.0071 3.8 % + ORB_control set_orb_tables 1.0972 1 1.1 14 % + ORB_gen_tables gen_tables 1.0971 1 1.1 14 % + ORB_table_phi init_Table 0.4745 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.46918 126 0.0037 6.1 % + ORB_table_beta init_Table_Beta 0.18539 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18383 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24786 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24592 66 0.0037 3.2 % + LOOP_ions opt_ions 6.039 1 6 79 % + ESolver_KS_LCAO Run 5.4564 1 5.5 71 % + HSolverLCAO solve 3.107 12 0.26 41 % + HamiltLCAO updateHk 1.5694 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.5399 12 0.13 20 % + Gint_interface cal_gint 0.92198 25 0.037 12 % + Gint_Gamma distri_vl_value 0.75645 12 0.063 9.9 % + Gint_Gamma distri_vl 2.834 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.6712 14 0.41 74 % + LCAO_gen_fixedH add_v_delta 2.6925 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.6927 6 0.45 35 % + ElecStateLCAO psiToRho 1.5187 12 0.13 20 % + Charge mix_rho 0.88953 11 0.081 12 % + LOOP_ions force_stress 0.58239 1 0.58 7.6 % + Force_Stress_LCAO getForceStress 0.58237 1 0.58 7.6 % + Force_LCAO_gamma ftable_gamma 0.39047 1 0.39 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.18267 1 0.18 2.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:34 2022 + FINISH Time : Wed Sep 28 11:10:42 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/1/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..7951ba6072042d3e653d742741ff4f0b7187f48a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.529523 0.633037 0.265845 +H 0.506082 0.588903 0.307195 +H 0.500704 0.612009 0.211106 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3c5149cc37bf0eff5c15d4cd6f29fcd6786d4696 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4665 2 + 2 -12.8394 2 + 3 -9.39543 2 + 4 -6.78497 2 + 5 1.3279 0 + 6 4.49527 0 + 7 11.0501 0 + 8 11.3297 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0aaed9ab644b36c515705d8e22793486544fdec1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:28 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.8266320039 17.725038977 7.44365628641 0 0 0 0 + tauc_H1 14.1703041983 16.4892865944 8.60144629222 0 0 0 0 + tauc_H2 14.0197134471 17.1362500878 5.91095451779 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871294213449 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877590176268 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106114424503 (SEC) + + DONE : INIT CHARGE Time : 0.154932208824 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.435857 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 144 4 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000729 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103 + + Density error is 0.214387884651 + + Energy Rydberg eV + E_KohnSham -34.18973999 -465.175277003 + E_Harris -34.3812089349 -467.780345643 + E_Fermi -0.41040337953 -5.58382444007 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0010312085914 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122832785725 + + Density error is 0.0975010589854 + + Energy Rydberg eV + E_KohnSham -34.279235562 -466.392926727 + E_Harris -34.2860195825 -466.485228062 + E_Fermi -0.219778236541 -2.99023631335 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000986506541288 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116775824211 + + Density error is 0.0624566299048 + + Energy Rydberg eV + E_KohnSham -34.2795275814 -466.396899856 + E_Harris -34.2839187185 -466.45664434 + E_Fermi -0.208074176847 -2.83099441177 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00093225531558 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108596889835 + + Density error is 0.00194923961052 + + Energy Rydberg eV + E_KohnSham -34.2795232276 -466.396840619 + E_Harris -34.2795237325 -466.396847489 + E_Fermi -0.172222269312 -2.34320418514 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000935664614256 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108930774334 + + Density error is 0.000914091049702 + + Energy Rydberg eV + E_KohnSham -34.2794567958 -466.395936767 + E_Harris -34.279458919 -466.395965656 + E_Fermi -0.171467778462 -2.33293881049 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000934279631216 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108760784847 + + Density error is 9.48718103329e-05 + + Energy Rydberg eV + E_KohnSham -34.2795027357 -466.396561813 + E_Harris -34.279502739 -466.396561856 + E_Fermi -0.171529712376 -2.33378146461 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000934126522635 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108737994265 + + Density error is 4.13024946666e-05 + + Energy Rydberg eV + E_KohnSham -34.2794890039 -466.396374982 + E_Harris -34.2794890123 -466.396375096 + E_Fermi -0.171418148932 -2.33226356608 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000934100568407 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108736228684 + + Density error is 9.33617077341e-06 + + Energy Rydberg eV + E_KohnSham -34.2794903806 -466.396393712 + E_Harris -34.2794903809 -466.396393716 + E_Fermi -0.17146721221 -2.33293110623 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000934118073204 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108737879702 + + Density error is 2.02122682789e-06 + + Energy Rydberg eV + E_KohnSham -34.2794892792 -466.396378727 + E_Harris -34.2794892792 -466.396378727 + E_Fermi -0.171460667795 -2.3328420649 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000934117789876 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108737738163 + + Density error is 2.04025540712e-07 + + Energy Rydberg eV + E_KohnSham -34.2794894106 -466.396380515 + E_Harris -34.2794894106 -466.396380515 + E_Fermi -0.171458459819 -2.33281202384 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000934118556535 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108737826534 + + Density error is 5.19563975709e-08 + + Energy Rydberg eV + E_KohnSham -34.2794894431 -466.396380957 + E_Harris -34.2794894431 -466.396380957 + E_band -8.00934168911 -108.972684201 + E_one_elec -69.4550798166 -944.98484055 + E_Hartree +36.1077822777 +491.271581121 + E_xc -8.22048200779 -111.845395612 + E_Ewald +7.41224025192 +100.848702371 + E_demet -2.84393447078e-81 -3.86937135412e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195148833961 -2.65513609993 + E_Fermi -0.171458436215 -2.33281170269 + + charge density convergence is achieved + final etot is -466.396380957 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4665 2.00000 + 2 -12.8394 2.00000 + 3 -9.39543 2.00000 + 4 -6.78497 2.00000 + 5 1.32790 0.00000 + 6 4.49527 0.00000 + 7 11.0501 0.00000 + 8 11.3297 0.00000 + + EFERMI = -2.332811702692154 eV + OUT.ABACUS/ final etot is -466.3963809566351 eV + correction force for each atom along direction 1 is 6.24031e-05 + correction force for each atom along direction 2 is -7.29457e-05 + correction force for each atom along direction 3 is -2.29674e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.12988957 +0.24213523 -0.24858070 + H1 -0.096377732 -0.41396823 +0.92186242 + H2 -0.033511839 +0.17183299 -0.67328172 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3963809566351 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.4771 11 0.50 1.0e+02% + Run_lcao lcao_line 5.4669 1 5.5 1.e+02% + Potential init_pot 0.28726 2 0.14 5.2% + PW_Basis recip2real 0.27383 16 0.017 5.0% + PW_Basis gathers_scatterp 0.11999 16 0.0075 2.2% + Potential v_of_rho 0.86287 13 0.066 16.% + XC_Functional v_xc 0.22429 14 0.016 4.1% + H_Hartree_pw v_hartree 0.59930 13 0.046 11.% + PW_Basis real2recip 0.56380 38 0.015 10.% + PW_Basis gatherp_scatters 0.22177 38 0.0058 4.0% + ORB_control set_orb_tables 1.1060 1 1.1 20.% + ORB_gen_tables gen_tables 1.1060 1 1.1 20.% + ORB_table_phi init_Table 0.48003 1 0.48 8.8% + ORB_table_phi cal_ST_Phi12_R 0.47507 126 0.0038 8.7% + ORB_table_beta init_Table_Beta 0.19090 1 0.19 3.5% + ORB_table_beta VNL_PhiBeta_R 0.18938 56 0.0034 3.5% + ORB_table_alpha init_Table_Alpha 0.25388 1 0.25 4.6% + ORB_table_alpha S_PhiAlpha_R 0.25202 66 0.0038 4.6% + LOOP_ions opt_ions 3.8477 1 3.8 70.% + ESolver_KS_LCAO Run 3.3961 1 3.4 62.% + HSolverLCAO solve 1.4337 11 0.13 26.% + HamiltLCAO updateHk 0.80846 11 0.073 15.% + LCAO_Hamilt cal_Hgamma 0.77467 11 0.070 14.% + Gint_interface cal_gint 1.0162 23 0.044 19.% + Gint_Gamma distri_vl 1.6581 6 0.28 30.% + LCAO_Deepks cal_projected_DM 3.6918 13 0.28 67.% + LCAO_gen_fixedH add_v_delta 1.5252 6 0.25 28.% + LCAO_DESCRIPTOR add_v_delta 1.5252 6 0.25 28.% + ElecStateLCAO psiToRho 0.60990 11 0.055 11.% + Charge mix_rho 0.66193 10 0.066 12.% + LOOP_ions force_stress 0.45141 1 0.45 8.2% + Force_Stress_LCAO getForceStress 0.45138 1 0.45 8.2% + Force_LCAO_gamma ftable_gamma 0.24076 1 0.24 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.20699 1 0.21 3.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:28 2022 + Finish Time : Wed Sep 28 11:06:34 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..fa494741093494d79f01b384534b13b55d012bea --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/OUT.ABACUS/warning.log @@ -0,0 +1,73 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123601 ima = 3.6648e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 3 + 3 1 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122609841441 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111545472556 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112096099249 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112363993368 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298738475 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112334449953 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112333296888 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112335670954 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112335247627 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112335162257 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112335152173 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3dc19aa7708fe71c275a94cdaec37c6534463414 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.173367996102 17.725038977005 7.443656286430 0 0 0 +H +0.0 +2 +-13.829695801670 16.489286594428 8.601446292229 0 0 0 +-13.980286552851 17.136250087820 5.910954517792 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/conv new file mode 100644 index 0000000000000000000000000000000000000000..a8dba8b346c7b52f2e8c36223554071080c472f4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/conv @@ -0,0 +1 @@ +10 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a926e085e404cd473bb55f9f914193c4e13f87fa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753354591 0.01282898031 1.277326707 1.358900217 1.469979847 0.009364219774 0.01716004364 0.03913727573 +1.754731537e-18 0.0009634241094 0.00285970559 0.01333009593 0.04745654965 8.207144796e-20 2.801287168e-06 7.391101407e-06 +0.001597191593 0.006147353045 + +H atom_index 1 n_descriptor 18 +1.262547641 0.03436929446 0.115220433 0.1554596095 0.3236957589 0.02371218096 0.0289693329 0.0375265235 +1.253943185e-17 5.224203904e-05 0.1059068781 0.1164641934 0.1334157231 -1.354269291e-18 2.608766785e-06 0.01333139572 +0.02750173384 0.03130661828 + +H atom_index 2 n_descriptor 18 +1.252064215 0.03472003764 0.111419792 0.1504731776 0.3203103134 0.02319543257 0.02835669657 0.0378264589 +-3.182186047e-19 5.123427231e-05 0.1039123664 0.1154067352 0.1291287854 1.346009947e-18 3.20612114e-06 0.01337038764 +0.02712339339 0.03084080516 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..349d45d077c1d51a1e4fb9d30dd007cb448e1f26 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:28 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871513 SEC) : SETUP UNITCELL + DONE(0.0877737 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106136 SEC) : INIT PLANEWAVE + DONE(0.155062 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.435931 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651753e+02 0.000000e+00 2.144e-01 4.246e-01 + GE2 -4.663929e+02 -1.217650e+00 9.750e-02 3.505e-01 + GE3 -4.663969e+02 -3.973129e-03 6.246e-02 4.037e-01 + GE4 -4.663968e+02 5.923716e-05 1.949e-03 2.980e-01 + GE5 -4.663959e+02 9.038513e-04 9.141e-04 2.929e-01 + GE6 -4.663966e+02 -6.250452e-04 9.487e-05 2.708e-01 + GE7 -4.663964e+02 1.868307e-04 4.130e-05 2.719e-01 + GE8 -4.663964e+02 -1.872987e-05 9.336e-06 2.709e-01 + GE9 -4.663964e+02 1.498485e-05 2.021e-06 2.682e-01 + GE10 -4.663964e+02 -1.788436e-06 2.040e-07 2.715e-01 + GE11 -4.663964e+02 -4.413058e-07 5.196e-08 2.110e-01 +E_delta_band = -7.11986856e-02 Ry = -9.68707815e-01 eV +E_delta_NN= -1.95148834e-01 Ry = -2.65513610e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.4771 11 0.5 1e+02 % + Run_lcao lcao_line 5.4669 1 5.5 1e+02 % + Potential init_pot 0.28726 2 0.14 5.2 % + PW_Basis recip2real 0.27383 16 0.017 5 % + PW_Basis gathers_scatterp 0.11999 16 0.0075 2.2 % + Potential v_of_rho 0.86287 13 0.066 16 % + XC_Functional v_xc 0.22429 14 0.016 4.1 % + H_Hartree_pw v_hartree 0.5993 13 0.046 11 % + PW_Basis real2recip 0.5638 38 0.015 10 % + PW_Basis gatherp_scatters 0.22177 38 0.0058 4 % + ORB_control set_orb_tables 1.106 1 1.1 20 % + ORB_gen_tables gen_tables 1.106 1 1.1 20 % + ORB_table_phi init_Table 0.48003 1 0.48 8.8 % + ORB_table_phi cal_ST_Phi12_R 0.47507 126 0.0038 8.7 % + ORB_table_beta init_Table_Beta 0.1909 1 0.19 3.5 % + ORB_table_beta VNL_PhiBeta_R 0.18938 56 0.0034 3.5 % + ORB_table_alpha init_Table_Alpha 0.25388 1 0.25 4.6 % + ORB_table_alpha S_PhiAlpha_R 0.25202 66 0.0038 4.6 % + LOOP_ions opt_ions 3.8477 1 3.8 70 % + ESolver_KS_LCAO Run 3.3961 1 3.4 62 % + HSolverLCAO solve 1.4337 11 0.13 26 % + HamiltLCAO updateHk 0.80846 11 0.073 15 % + LCAO_Hamilt cal_Hgamma 0.77467 11 0.07 14 % + Gint_interface cal_gint 1.0162 23 0.044 19 % + Gint_Gamma distri_vl 1.6581 6 0.28 30 % + LCAO_Deepks cal_projected_DM 3.6918 13 0.28 67 % + LCAO_gen_fixedH add_v_delta 1.5252 6 0.25 28 % + LCAO_DESCRIPTOR add_v_delta 1.5252 6 0.25 28 % + ElecStateLCAO psiToRho 0.6099 11 0.055 11 % + Charge mix_rho 0.66193 10 0.066 12 % + LOOP_ions force_stress 0.45141 1 0.45 8.2 % + Force_Stress_LCAO getForceStress 0.45138 1 0.45 8.2 % + Force_LCAO_gamma ftable_gamma 0.24076 1 0.24 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.20699 1 0.21 3.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:28 2022 + FINISH Time : Wed Sep 28 11:06:34 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/10/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d927bed1ca4feef555f02b49cd12a1b2f2b9c300 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.518307 0.6183 0.252572 +H 0.548527 0.55931 0.254575 +H 0.465513 0.615447 0.212432 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f8b5c2146ee87279e7bb00b8baa1774e560b5cf0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0298 2 + 2 -13.1936 2 + 3 -8.79416 2 + 4 -6.6815 2 + 5 1.18619 0 + 6 4.25563 0 + 7 11.1218 0 + 8 11.3459 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..70039dde1ac88c0b755b46bbaa93bdf4fe5b0a27 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:03 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.5125925115 17.3124108789 7.07202549615 0 0 0 0 + tauc_H1 15.3587641613 15.6606759913 7.1280968529 0 0 0 0 + tauc_H2 13.0343554651 17.2325218682 5.9481004137 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0880615350393 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0884207685266 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106533086147 (SEC) + + DONE : INIT CHARGE Time : 0.149755814529 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.427551 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 144 0 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000504 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00149 + + Density error is 0.214376689146 + + Energy Rydberg eV + E_KohnSham -34.1905483261 -465.186274979 + E_Harris -34.3803352347 -467.768458342 + E_Fermi -0.394933644678 -5.37334789952 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000772358933116 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134486689116 + + Density error is 0.0985969021052 + + Energy Rydberg eV + E_KohnSham -34.279330911 -466.394224017 + E_Harris -34.2861326082 -466.486765855 + E_Fermi -0.20416341397 -2.77778575313 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000748451447702 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125457735272 + + Density error is 0.0633330520629 + + Energy Rydberg eV + E_KohnSham -34.2796093217 -466.398011989 + E_Harris -34.2839782159 -466.457453845 + E_Fermi -0.194560945076 -2.6471374613 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000724493996904 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010949302989 + + Density error is 0.00211391805424 + + Energy Rydberg eV + E_KohnSham -34.2795706389 -466.397485682 + E_Harris -34.2795751082 -466.39754649 + E_Fermi -0.15953152905 -2.17053780573 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000724567365349 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109251667089 + + Density error is 0.000862705341921 + + Energy Rydberg eV + E_KohnSham -34.2795299977 -466.39693273 + E_Harris -34.279530335 -466.39693732 + E_Fermi -0.15896110562 -2.16277679681 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000724247515056 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109050917934 + + Density error is 0.00019936034981 + + Energy Rydberg eV + E_KohnSham -34.2795532515 -466.397249115 + E_Harris -34.2795532766 -466.397249456 + E_Fermi -0.158770015634 -2.16017688417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000724453903178 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109043694128 + + Density error is 3.22206672816e-05 + + Energy Rydberg eV + E_KohnSham -34.2795449151 -466.397135693 + E_Harris -34.2795449198 -466.397135756 + E_Fermi -0.158667644587 -2.15878405462 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000724406358428 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109040168733 + + Density error is 1.6352494393e-05 + + Energy Rydberg eV + E_KohnSham -34.2795489334 -466.397190364 + E_Harris -34.2795489346 -466.397190381 + E_Fermi -0.158698376565 -2.15920218463 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000724413745638 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109038409632 + + Density error is 2.03742218407e-06 + + Energy Rydberg eV + E_KohnSham -34.2795476504 -466.397172907 + E_Harris -34.2795476504 -466.397172907 + E_Fermi -0.158682010906 -2.15897951842 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000724412367849 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109037801928 + + Density error is 5.09776701975e-07 + + Energy Rydberg eV + E_KohnSham -34.2795479269 -466.39717667 + E_Harris -34.2795479269 -466.39717667 + E_Fermi -0.158680344076 -2.15895684003 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000724413182431 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010903784285 + + Density error is 1.69288841471e-07 + + Energy Rydberg eV + E_KohnSham -34.2795479347 -466.397176776 + E_Harris -34.2795479347 -466.397176776 + E_Fermi -0.158680099028 -2.15895350598 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000724413405073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109037829035 + + Density error is 1.02143406742e-08 + + Energy Rydberg eV + E_KohnSham -34.2795479388 -466.397176831 + E_Harris -34.2795479388 -466.397176832 + E_band -7.89361800763 -107.398182739 + E_one_elec -68.9684813955 -938.364329386 + E_Hartree +35.9000264128 +488.444917565 + E_xc -8.18663253142 -111.384849859 + E_Ewald +7.10059094237 +96.6084959834 + E_demet -2.63626964413e-68 -3.58682886246e-67 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194051957637 -2.64021233192 + E_Fermi -0.158679933109 -2.15895124855 + + charge density convergence is achieved + final etot is -466.397176831 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0298 2.00000 + 2 -13.1936 2.00000 + 3 -8.79416 2.00000 + 4 -6.68150 2.00000 + 5 1.18619 0.00000 + 6 4.25563 0.00000 + 7 11.1218 0.00000 + 8 11.3459 0.00000 + + EFERMI = -2.158951248545227 eV + OUT.ABACUS/ final etot is -466.3971768314814 eV + correction force for each atom along direction 1 is -0.000102587 + correction force for each atom along direction 2 is -0.000128309 + correction force for each atom along direction 3 is -0.000171092 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.0095938485 +0.14156559 +0.053617824 + H1 -0.51781823 +0.26145679 -0.29221227 + H2 +0.50822438 -0.40302238 +0.23859445 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3971768314814 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3686 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3588 1 7.4 1.e+02% + Potential init_pot 0.27809 2 0.14 3.8% + PW_Basis recip2real 0.28544 17 0.017 3.9% + PW_Basis gathers_scatterp 0.12860 17 0.0076 1.7% + Potential v_of_rho 1.0524 14 0.075 14.% + XC_Functional v_xc 0.30674 15 0.020 4.2% + H_Hartree_pw v_hartree 0.69836 14 0.050 9.5% + PW_Basis real2recip 0.74287 41 0.018 10.% + PW_Basis gatherp_scatters 0.28192 41 0.0069 3.8% + ORB_control set_orb_tables 1.0976 1 1.1 15.% + ORB_gen_tables gen_tables 1.0976 1 1.1 15.% + ORB_table_phi init_Table 0.47706 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47177 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18453 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18302 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24754 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24557 66 0.0037 3.3% + LOOP_ions opt_ions 5.7541 1 5.8 78.% + ESolver_KS_LCAO Run 5.2175 1 5.2 71.% + HSolverLCAO solve 2.5723 12 0.21 35.% + HamiltLCAO updateHk 1.3333 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.3038 12 0.11 18.% + Gint_interface cal_gint 2.3508 25 0.094 32.% + Gint_Gamma distri_vl 2.7215 6 0.45 37.% + LCAO_Deepks cal_projected_DM 5.6002 14 0.40 76.% + LCAO_gen_fixedH add_v_delta 2.5736 6 0.43 35.% + LCAO_DESCRIPTOR add_v_delta 2.5736 6 0.43 35.% + ElecStateLCAO psiToRho 1.2206 12 0.10 17.% + Charge mix_rho 0.99337 11 0.090 13.% + LOOP_ions force_stress 0.53647 1 0.54 7.3% + Force_Stress_LCAO getForceStress 0.53644 1 0.54 7.3% + Force_LCAO_gamma ftable_gamma 0.32124 1 0.32 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.31300 1 0.31 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:03 2022 + Finish Time : Wed Sep 28 11:04:11 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..923d79896b7b2908fd81ffaba17f5123aa8e7be6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123425 ima = 3.67056e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123820935546 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112810150147 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113388236838 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113582378043 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113554314631 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113571999138 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113565129185 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113567620626 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113566855321 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113566818381 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113566799137 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113566790612 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/STRU new file mode 100644 index 0000000000000000000000000000000000000000..84f643c38554e1cd4d83c83958e36f49d7222633 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.487407488489 17.312410878905 7.072025496135 0 0 0 +H +0.0 +2 +-12.641235838690 15.660675991304 7.128096852928 0 0 0 +-14.965644534903 17.232521868140 5.948100413712 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/conv new file mode 100644 index 0000000000000000000000000000000000000000..829da12b797422047c3461a20bb2cf33e1fc3fca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/conv @@ -0,0 +1 @@ +11 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f3dccc84131d6a093058a6d445d82ef6b1910051 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.744040688 0.01247785069 1.264086193 1.360230071 1.468147734 0.007568032198 0.02004000553 0.03887297337 +-2.074163701e-18 0.001062493168 0.002268438617 0.01183246619 0.04084555143 -1.342061026e-19 1.342078915e-06 4.36164399e-06 +0.001774084544 0.005603956866 + +H atom_index 1 n_descriptor 18 +1.221461309 0.03469087689 0.09870719743 0.1388725321 0.3143355196 0.02044409371 0.02688229286 0.03792633283 +-7.178643876e-17 3.367535164e-05 0.09327960931 0.114250576 0.1189913575 -1.105580008e-17 5.130024872e-06 0.01323896292 +0.02466286339 0.02955340879 + +H atom_index 2 n_descriptor 18 +1.219884618 0.03474550357 0.09820409659 0.1381873482 0.3137869539 0.02037426032 0.0267900962 0.03798728607 +2.972667735e-18 3.355630631e-05 0.09285423557 0.1142093217 0.1183936615 -2.308964519e-18 5.184397935e-06 0.01327088889 +0.02460012477 0.02947537029 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..abc0247436989475cfd122c153731bc300d0e562 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:03 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0880846 SEC) : SETUP UNITCELL + DONE(0.088436 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106554 SEC) : INIT PLANEWAVE + DONE(0.1499 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.427618 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651863e+02 0.000000e+00 2.144e-01 5.300e-01 + GE2 -4.663942e+02 -1.207949e+00 9.860e-02 4.918e-01 + GE3 -4.663980e+02 -3.787972e-03 6.333e-02 5.622e-01 + GE4 -4.663975e+02 5.263071e-04 2.114e-03 4.223e-01 + GE5 -4.663969e+02 5.529516e-04 8.627e-04 4.215e-01 + GE6 -4.663972e+02 -3.163848e-04 1.994e-04 4.145e-01 + GE7 -4.663971e+02 1.134225e-04 3.222e-05 4.012e-01 + GE8 -4.663972e+02 -5.467112e-05 1.635e-05 3.977e-01 + GE9 -4.663972e+02 1.745638e-05 2.037e-06 3.970e-01 + GE10 -4.663972e+02 -3.762900e-06 5.098e-07 3.964e-01 + GE11 -4.663972e+02 -1.061888e-07 1.693e-07 3.971e-01 + GE12 -4.663972e+02 -5.511179e-08 1.021e-08 3.235e-01 +E_delta_band = -6.90005906e-02 Ry = -9.38801197e-01 eV +E_delta_NN= -1.94051958e-01 Ry = -2.64021233e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3686 11 0.67 1e+02 % + Run_lcao lcao_line 7.3588 1 7.4 1e+02 % + Potential init_pot 0.27809 2 0.14 3.8 % + PW_Basis recip2real 0.28544 17 0.017 3.9 % + PW_Basis gathers_scatterp 0.1286 17 0.0076 1.7 % + Potential v_of_rho 1.0524 14 0.075 14 % + XC_Functional v_xc 0.30674 15 0.02 4.2 % + H_Hartree_pw v_hartree 0.69836 14 0.05 9.5 % + PW_Basis real2recip 0.74287 41 0.018 10 % + PW_Basis gatherp_scatters 0.28192 41 0.0069 3.8 % + ORB_control set_orb_tables 1.0976 1 1.1 15 % + ORB_gen_tables gen_tables 1.0976 1 1.1 15 % + ORB_table_phi init_Table 0.47706 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.47177 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18453 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18302 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24754 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24557 66 0.0037 3.3 % + LOOP_ions opt_ions 5.7541 1 5.8 78 % + ESolver_KS_LCAO Run 5.2175 1 5.2 71 % + HSolverLCAO solve 2.5723 12 0.21 35 % + HamiltLCAO updateHk 1.3333 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.3038 12 0.11 18 % + Gint_interface cal_gint 2.3508 25 0.094 32 % + Gint_Gamma distri_vl 2.7215 6 0.45 37 % + LCAO_Deepks cal_projected_DM 5.6002 14 0.4 76 % + LCAO_gen_fixedH add_v_delta 2.5736 6 0.43 35 % + LCAO_DESCRIPTOR add_v_delta 2.5736 6 0.43 35 % + ElecStateLCAO psiToRho 1.2206 12 0.1 17 % + Charge mix_rho 0.99337 11 0.09 13 % + LOOP_ions force_stress 0.53647 1 0.54 7.3 % + Force_Stress_LCAO getForceStress 0.53644 1 0.54 7.3 % + Force_LCAO_gamma ftable_gamma 0.32124 1 0.32 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.313 1 0.31 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:03 2022 + FINISH Time : Wed Sep 28 11:04:11 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/11/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..542fd788878e4ce6da700116861ddfb68bfc7d42 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.51563 0.608944 0.233895 +H 0.527217 0.640785 0.180855 +H 0.451015 0.601358 0.23405 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..02b55ba5f00c64e8bd8a5dbab0b106b07c9ae952 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.555 2 + 2 -13.2631 2 + 3 -9.1583 2 + 4 -6.80272 2 + 5 1.50169 0 + 6 4.79577 0 + 7 11.0107 0 + 8 11.2563 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e0fd6d7ae09bacd3893fca0620134475e6372aa9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:15 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.4376268059 17.0504354086 6.54905841708 0 0 0 0 + tauc_H1 14.762073628 17.9419794533 5.06395000993 0 0 0 0 + tauc_H2 12.6284115409 16.8380119431 6.55340794074 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874341066866 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0986944485198 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.1168072271 (SEC) + + DONE : INIT CHARGE Time : 0.16509350924 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446736 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 0 4 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000677 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0019 + + Density error is 0.218448156873 + + Energy Rydberg eV + E_KohnSham -34.1848318094 -465.108497779 + E_Harris -34.3845327099 -467.825567922 + E_Fermi -0.422221516842 -5.74461844726 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000878680596223 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00149018901708 + + Density error is 0.0973998963287 + + Energy Rydberg eV + E_KohnSham -34.2772780575 -466.366293513 + E_Harris -34.2839154316 -466.45659962 + E_Fermi -0.22807117925 -3.10306758738 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00084078129164 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013596254867 + + Density error is 0.0622600436356 + + Energy Rydberg eV + E_KohnSham -34.2776025245 -466.370708113 + E_Harris -34.2818612984 -466.428651704 + E_Fermi -0.214184228248 -2.9141259259 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000790070515341 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113405057396 + + Density error is 0.00206098914258 + + Energy Rydberg eV + E_KohnSham -34.2776433288 -466.371263283 + E_Harris -34.2776454589 -466.371292264 + E_Fermi -0.178285061736 -2.42569270789 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000792261754191 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113081329991 + + Density error is 0.000961493761409 + + Energy Rydberg eV + E_KohnSham -34.2775611517 -466.370145207 + E_Harris -34.2775637793 -466.370180957 + E_Fermi -0.177120414855 -2.40984687416 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000791238011666 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112891628498 + + Density error is 0.000106143446795 + + Energy Rydberg eV + E_KohnSham -34.2776141288 -466.370865997 + E_Harris -34.2776141424 -466.370866182 + E_Fermi -0.17736900054 -2.41322905591 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000791233599134 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112854965247 + + Density error is 5.48874491752e-05 + + Energy Rydberg eV + E_KohnSham -34.2775972176 -466.370635908 + E_Harris -34.2775972343 -466.370636136 + E_Fermi -0.177219520526 -2.41119527599 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000791184502398 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112862087575 + + Density error is 1.12133775033e-05 + + Energy Rydberg eV + E_KohnSham -34.2776004492 -466.370679877 + E_Harris -34.2776004498 -466.370679884 + E_Fermi -0.177284318608 -2.41207689912 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000791190065817 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112859164388 + + Density error is 1.14709235327e-06 + + Energy Rydberg eV + E_KohnSham -34.2775989053 -466.370658871 + E_Harris -34.2775989053 -466.370658871 + E_Fermi -0.177272046482 -2.41190992828 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000791190959295 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112858920698 + + Density error is 1.00412050089e-07 + + Energy Rydberg eV + E_KohnSham -34.2775990803 -466.370661251 + E_Harris -34.2775990803 -466.370661251 + E_Fermi -0.177271065422 -2.41189658026 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000791191118307 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112858951468 + + Density error is 4.4374330896e-08 + + Energy Rydberg eV + E_KohnSham -34.2775991012 -466.370661537 + E_Harris -34.2775991012 -466.370661537 + E_band -8.05238511979 -109.55832012 + E_one_elec -69.8210299392 -949.963847402 + E_Hartree +36.2887372751 +493.733600166 + E_xc -8.25002787469 -112.247387755 + E_Ewald +7.62796461606 +103.783782921 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195820870366 -2.66427962429 + E_Fermi -0.177271095283 -2.41189698654 + + charge density convergence is achieved + final etot is -466.370661537 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5550 2.00000 + 2 -13.2631 2.00000 + 3 -9.15830 2.00000 + 4 -6.80272 2.00000 + 5 1.50169 0.00000 + 6 4.79577 0.00000 + 7 11.0107 0.00000 + 8 11.2563 0.00000 + + EFERMI = -2.411896986543929 eV + OUT.ABACUS/ final etot is -466.3706615365783 eV + correction force for each atom along direction 1 is -5.14607e-05 + correction force for each atom along direction 2 is 6.36355e-05 + correction force for each atom along direction 3 is -1.18593e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.012573748 -1.1403420 +1.9914116 + H1 +0.54827451 +1.2526170 -2.0707454 + H2 -0.56084826 -0.11227494 +0.079333881 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3706615365783 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5297 11 0.50 1.0e+02% + Run_lcao lcao_line 5.5196 1 5.5 1.e+02% + Potential init_pot 0.28578 2 0.14 5.2% + PW_Basis recip2real 0.27404 16 0.017 5.0% + PW_Basis gathers_scatterp 0.12078 16 0.0075 2.2% + Potential v_of_rho 0.86989 13 0.067 16.% + XC_Functional v_xc 0.23051 14 0.016 4.2% + H_Hartree_pw v_hartree 0.60118 13 0.046 11.% + PW_Basis real2recip 0.55847 38 0.015 10.% + PW_Basis gatherp_scatters 0.21536 38 0.0057 3.9% + ORB_control set_orb_tables 1.1173 1 1.1 20.% + ORB_gen_tables gen_tables 1.1173 1 1.1 20.% + ORB_table_phi init_Table 0.48873 1 0.49 8.8% + ORB_table_phi cal_ST_Phi12_R 0.48374 126 0.0038 8.7% + ORB_table_beta init_Table_Beta 0.19426 1 0.19 3.5% + ORB_table_beta VNL_PhiBeta_R 0.19272 56 0.0034 3.5% + ORB_table_alpha init_Table_Alpha 0.25549 1 0.26 4.6% + ORB_table_alpha S_PhiAlpha_R 0.25362 66 0.0038 4.6% + LOOP_ions opt_ions 3.8788 1 3.9 70.% + ESolver_KS_LCAO Run 3.4321 1 3.4 62.% + HSolverLCAO solve 1.4609 11 0.13 26.% + HamiltLCAO updateHk 0.82082 11 0.075 15.% + LCAO_Hamilt cal_Hgamma 0.78605 11 0.071 14.% + Gint_interface cal_gint 1.2370 23 0.054 22.% + Gint_Gamma distri_vl 1.6813 6 0.28 30.% + LCAO_Deepks cal_projected_DM 3.7492 13 0.29 68.% + LCAO_gen_fixedH add_v_delta 1.5467 6 0.26 28.% + LCAO_DESCRIPTOR add_v_delta 1.5467 6 0.26 28.% + ElecStateLCAO psiToRho 0.62652 11 0.057 11.% + Charge mix_rho 0.66219 10 0.066 12.% + LOOP_ions force_stress 0.44653 1 0.45 8.1% + Force_Stress_LCAO getForceStress 0.44650 1 0.45 8.1% + Force_LCAO_gamma ftable_gamma 0.23745 1 0.24 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.23083 1 0.23 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:15 2022 + Finish Time : Wed Sep 28 11:06:20 2022 + Total Time : 0 h 0 mins 5 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..548a082641ce23a943931b4cb77fdbe088ea7523 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123736 ima = 3.69069e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123020662097 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112043976632 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112485334223 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011278243751 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112706324257 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112747227846 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112742645583 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112746025029 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112745538431 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112745488822 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112745486503 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/STRU new file mode 100644 index 0000000000000000000000000000000000000000..33f56a452ac263b669ade80c6e87c95aed9ad85b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.562373194081 17.050435408610 6.549058417075 0 0 0 +H +0.0 +2 +-13.237926372001 17.941979453335 5.063950009943 0 0 0 +-15.371588459106 16.838011943124 6.553407940737 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/conv new file mode 100644 index 0000000000000000000000000000000000000000..9fe2e3c1870fbc866c2d968a304c8085682d2f5f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/conv @@ -0,0 +1 @@ +12 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..8b8a5d41ca21a5b355ca7f96e73fd90935a44615 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749336122 0.01281877806 1.293173306 1.380627067 1.47061334 0.008734689556 0.01907650965 0.03903393258 +-6.492584443e-19 0.001174644079 0.002765267417 0.01315530017 0.04786682675 3.076284698e-19 2.365702168e-06 6.569744154e-06 +0.001651395084 0.005947730263 + +H atom_index 1 n_descriptor 18 +1.301409289 0.03256186497 0.128340606 0.1754988202 0.3355896149 0.02485464107 0.03123724518 0.03640817751 +3.038324491e-17 5.530112282e-05 0.108367838 0.1250672809 0.1506639544 -1.227045023e-17 1.335964534e-06 0.0137537017 +0.02858432786 0.03282454485 + +H atom_index 2 n_descriptor 18 +1.254544587 0.03406199803 0.1105843587 0.1519533066 0.3220048913 0.02269769784 0.0285570388 0.03717676838 +8.138349076e-18 5.075971695e-05 0.1049287956 0.1150896529 0.1306577845 -3.313180905e-18 3.931584102e-06 0.01318226736 +0.02704510282 0.03099737462 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a56a3f0862c7362e3259954f5175e16fd78d2330 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..1b95722377229c245187d8a1f8f38fdb17656e5c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..c5b4091d0f868f9b9c9febc62eccfc10719bf018 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..e35aabd1f56a8e1fe764fdafe0c3e7d725cd6ef3 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..c251700967bc0f794e88dd7d18823ff40f8eb06e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:15 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874552 SEC) : SETUP UNITCELL + DONE(0.0987109 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116828 SEC) : INIT PLANEWAVE + DONE(0.165216 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446798 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651085e+02 0.000000e+00 2.184e-01 4.300e-01 + GE2 -4.663663e+02 -1.257796e+00 9.740e-02 3.526e-01 + GE3 -4.663707e+02 -4.414600e-03 6.226e-02 4.067e-01 + GE4 -4.663713e+02 -5.551702e-04 2.061e-03 2.972e-01 + GE5 -4.663701e+02 1.118076e-03 9.615e-04 2.976e-01 + GE6 -4.663709e+02 -7.207899e-04 1.061e-04 2.756e-01 + GE7 -4.663706e+02 2.300889e-04 5.489e-05 2.765e-01 + GE8 -4.663707e+02 -4.396903e-05 1.121e-05 2.721e-01 + GE9 -4.663707e+02 2.100578e-05 1.147e-06 2.744e-01 + GE10 -4.663707e+02 -2.379876e-06 1.004e-07 2.743e-01 + GE11 -4.663707e+02 -2.855426e-07 4.437e-08 2.139e-01 +E_delta_band = -7.25776919e-02 Ry = -9.87470158e-01 eV +E_delta_NN= -1.95820870e-01 Ry = -2.66427962e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5297 11 0.5 1e+02 % + Run_lcao lcao_line 5.5196 1 5.5 1e+02 % + Potential init_pot 0.28578 2 0.14 5.2 % + PW_Basis recip2real 0.27404 16 0.017 5 % + PW_Basis gathers_scatterp 0.12078 16 0.0075 2.2 % + Potential v_of_rho 0.86989 13 0.067 16 % + XC_Functional v_xc 0.23051 14 0.016 4.2 % + H_Hartree_pw v_hartree 0.60118 13 0.046 11 % + PW_Basis real2recip 0.55847 38 0.015 10 % + PW_Basis gatherp_scatters 0.21536 38 0.0057 3.9 % + ORB_control set_orb_tables 1.1173 1 1.1 20 % + ORB_gen_tables gen_tables 1.1173 1 1.1 20 % + ORB_table_phi init_Table 0.48873 1 0.49 8.8 % + ORB_table_phi cal_ST_Phi12_R 0.48374 126 0.0038 8.7 % + ORB_table_beta init_Table_Beta 0.19426 1 0.19 3.5 % + ORB_table_beta VNL_PhiBeta_R 0.19272 56 0.0034 3.5 % + ORB_table_alpha init_Table_Alpha 0.25549 1 0.26 4.6 % + ORB_table_alpha S_PhiAlpha_R 0.25362 66 0.0038 4.6 % + LOOP_ions opt_ions 3.8788 1 3.9 70 % + ESolver_KS_LCAO Run 3.4321 1 3.4 62 % + HSolverLCAO solve 1.4609 11 0.13 26 % + HamiltLCAO updateHk 0.82082 11 0.075 15 % + LCAO_Hamilt cal_Hgamma 0.78605 11 0.071 14 % + Gint_interface cal_gint 1.237 23 0.054 22 % + Gint_Gamma distri_vl 1.6813 6 0.28 30 % + LCAO_Deepks cal_projected_DM 3.7492 13 0.29 68 % + LCAO_gen_fixedH add_v_delta 1.5467 6 0.26 28 % + LCAO_DESCRIPTOR add_v_delta 1.5467 6 0.26 28 % + ElecStateLCAO psiToRho 0.62652 11 0.057 11 % + Charge mix_rho 0.66219 10 0.066 12 % + LOOP_ions force_stress 0.44653 1 0.45 8.1 % + Force_Stress_LCAO getForceStress 0.4465 1 0.45 8.1 % + Force_LCAO_gamma ftable_gamma 0.23745 1 0.24 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.23083 1 0.23 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:15 2022 + FINISH Time : Wed Sep 28 11:06:20 2022 + TOTAL Time : 5 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/12/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5327d6f25f1efec7ef7312aa4b103348153a0eaa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.514701 0.618451 0.203999 +H 0.533381 0.631418 0.267775 +H 0.500874 0.556654 0.207733 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..a1e3dd17b548555555f3c36b2c31205ef60ad395 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3603 2 + 2 -12.8805 2 + 3 -9.27421 2 + 4 -6.75868 2 + 5 1.2238 0 + 6 4.42574 0 + 7 11.0686 0 + 8 11.3238 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..df28921c3317886072d38b1e99ba95a7b184d27d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:05 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.4116215738 17.3166232185 5.71196503482 0 0 0 0 + tauc_H1 14.9346799476 17.6797177253 7.49770298328 0 0 0 0 + tauc_H2 14.0244681024 15.5863013325 5.81653661286 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0740457566989 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0821234591745 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0984496954241 (SEC) + + DONE : INIT CHARGE Time : 0.140024772139 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.385992 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00173 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104 + + Density error is 0.213943577038 + + Energy Rydberg eV + E_KohnSham -34.1881210401 -465.153250058 + E_Harris -34.3785610751 -467.744319662 + E_Fermi -0.405863059996 -5.52205022366 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00154357652675 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134497540173 + + Density error is 0.0978355207184 + + Energy Rydberg eV + E_KohnSham -34.2769852783 -466.362310047 + E_Harris -34.2837889512 -466.454878765 + E_Fermi -0.216577025078 -2.94668159694 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00141040794514 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128763234529 + + Density error is 0.0627265582961 + + Energy Rydberg eV + E_KohnSham -34.2772128536 -466.365406368 + E_Harris -34.2816110055 -466.425246294 + E_Fermi -0.205315766231 -2.79346430998 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00117280134091 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121243970729 + + Density error is 0.00195966498411 + + Energy Rydberg eV + E_KohnSham -34.277195474 -466.365169906 + E_Harris -34.27719597 -466.365176655 + E_Fermi -0.169545416836 -2.30678373876 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0011710069617 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121514405697 + + Density error is 0.00082627488395 + + Energy Rydberg eV + E_KohnSham -34.277144307 -466.364473744 + E_Harris -34.2771450825 -466.364484294 + E_Fermi -0.168968625067 -2.29893608414 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116842334085 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121398035332 + + Density error is 0.000114992367701 + + Energy Rydberg eV + E_KohnSham -34.2771756515 -466.364900207 + E_Harris -34.2771756654 -466.364900396 + E_Fermi -0.168878343119 -2.29770773522 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116821641826 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012140495871 + + Density error is 3.92648798019e-05 + + Energy Rydberg eV + E_KohnSham -34.2771656873 -466.364764637 + E_Harris -34.2771656956 -466.36476475 + E_Fermi -0.168779536824 -2.29636340661 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116821293149 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121396911513 + + Density error is 1.29626734756e-05 + + Energy Rydberg eV + E_KohnSham -34.2771687348 -466.364806101 + E_Harris -34.2771687355 -466.36480611 + E_Fermi -0.168817333185 -2.29687765248 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116817972139 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012139689622 + + Density error is 2.00817575879e-06 + + Energy Rydberg eV + E_KohnSham -34.2771673976 -466.364787908 + E_Harris -34.2771673976 -466.364787908 + E_Fermi -0.168803768371 -2.29669309372 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116817561737 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121396876536 + + Density error is 2.34381453465e-07 + + Energy Rydberg eV + E_KohnSham -34.2771675558 -466.36479006 + E_Harris -34.2771675558 -466.36479006 + E_Fermi -0.168802154565 -2.29667113676 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00116817584559 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121396946353 + + Density error is 9.47615670048e-08 + + Energy Rydberg eV + E_KohnSham -34.2771675948 -466.36479059 + E_Harris -34.2771675948 -466.36479059 + E_band -7.97808800738 -108.547456046 + E_one_elec -69.294336401 -942.797814183 + E_Hartree +36.0356958476 +490.290794923 + E_xc -8.20934297667 -111.693841319 + E_Ewald +7.3151260106 +99.5273953322 + E_demet -2.29646833241e-75 -3.12450545973e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194913675831 -2.65193660943 + E_Fermi -0.168802120277 -2.29667067025 + + charge density convergence is achieved + final etot is -466.36479059 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3603 2.00000 + 2 -12.8805 2.00000 + 3 -9.27421 2.00000 + 4 -6.75868 2.00000 + 5 1.22380 0.00000 + 6 4.42574 0.00000 + 7 11.0686 0.00000 + 8 11.3238 0.00000 + + EFERMI = -2.296670670251107 eV + OUT.ABACUS/ final etot is -466.3647905901152 eV + correction force for each atom along direction 1 is 0.000109966 + correction force for each atom along direction 2 is -0.000117598 + correction force for each atom along direction 3 is 2.57774e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.81223586 +2.0413317 +1.3039717 + H1 -0.28659972 +0.012870406 -1.1716066 + H2 -0.52563614 -2.0542021 -0.13236515 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3647905901152 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.4333 11 0.49 1.0e+02% + Run_lcao lcao_line 5.4246 1 5.4 1.e+02% + Potential init_pot 0.24260 2 0.12 4.5% + PW_Basis recip2real 0.25007 16 0.016 4.6% + PW_Basis gathers_scatterp 0.10599 16 0.0066 2.0% + Potential v_of_rho 0.91291 13 0.070 17.% + XC_Functional v_xc 0.27649 14 0.020 5.1% + H_Hartree_pw v_hartree 0.59743 13 0.046 11.% + PW_Basis real2recip 0.60521 38 0.016 11.% + PW_Basis gatherp_scatters 0.22867 38 0.0060 4.2% + ORB_control set_orb_tables 0.90774 1 0.91 17.% + ORB_gen_tables gen_tables 0.90773 1 0.91 17.% + ORB_table_phi init_Table 0.38440 1 0.38 7.1% + ORB_table_phi cal_ST_Phi12_R 0.38013 126 0.0030 7.0% + ORB_table_beta init_Table_Beta 0.15451 1 0.15 2.8% + ORB_table_beta VNL_PhiBeta_R 0.15315 56 0.0027 2.8% + ORB_table_alpha init_Table_Alpha 0.21050 1 0.21 3.9% + ORB_table_alpha S_PhiAlpha_R 0.20883 66 0.0032 3.8% + LOOP_ions opt_ions 4.0609 1 4.1 75.% + ESolver_KS_LCAO Run 3.6393 1 3.6 67.% + HSolverLCAO solve 1.4716 11 0.13 27.% + HamiltLCAO updateHk 0.83019 11 0.075 15.% + LCAO_Hamilt cal_Hgamma 0.80208 11 0.073 15.% + Gint_interface cal_gint 1.2408 23 0.054 23.% + Gint_Gamma distri_vl 1.7693 6 0.29 33.% + LCAO_Deepks cal_projected_DM 3.9400 13 0.30 73.% + LCAO_gen_fixedH add_v_delta 1.6408 6 0.27 30.% + LCAO_DESCRIPTOR add_v_delta 1.6409 6 0.27 30.% + ElecStateLCAO psiToRho 0.62540 11 0.057 12.% + Charge mix_rho 0.76337 10 0.076 14.% + LOOP_ions force_stress 0.42147 1 0.42 7.8% + Force_Stress_LCAO getForceStress 0.42145 1 0.42 7.8% + Force_LCAO_gamma ftable_gamma 0.22842 1 0.23 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.22112 1 0.22 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:05 2022 + Finish Time : Wed Sep 28 11:04:11 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e5e7bcac0327b1c27598ee400f45897b4bdcb5b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123633 ima = 3.68732e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012288069149 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111880220994 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112442142129 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112686886824 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011264329437 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112667272834 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112662480781 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112665334054 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112664821684 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112664721807 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112664714318 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/STRU new file mode 100644 index 0000000000000000000000000000000000000000..637ab36c8b5a128629eddf08dba2f735a5c9ce16 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.588378426196 17.316623218465 5.711965034823 0 0 0 +H +0.0 +2 +-13.065320052388 17.679717725249 7.497702983283 0 0 0 +-13.975531897609 15.586301332517 5.816536612846 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/conv new file mode 100644 index 0000000000000000000000000000000000000000..c52bdb9e6a3ef168a29b44e6b5e4dd888a63b9a4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/conv @@ -0,0 +1 @@ +13 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ed09c2dd8d7b508e2992e328b5827fa19bb2c53e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751994428 0.01268263719 1.264875512 1.36336226 1.469652359 0.009044471934 0.01771573571 0.03913124264 +-1.593141461e-18 0.000979186315 0.002728362675 0.01262863085 0.04615495288 1.503483481e-20 2.320304532e-06 6.551815867e-06 +0.001591693996 0.006008323919 + +H atom_index 1 n_descriptor 18 +1.198577307 0.03624624664 0.09245933936 0.1273344148 0.3021476415 0.02016153774 0.02524884892 0.0396211795 +3.84254175e-17 4.326601469e-05 0.08872014488 0.1089381542 0.1131069261 -8.370836702e-18 6.241714589e-06 0.01431612279 +0.02448949151 0.02818326521 + +H atom_index 2 n_descriptor 18 +1.292796131 0.03316321234 0.1251637046 0.1708367053 0.3333361594 0.02465762597 0.03073679545 0.03679708072 +-7.154636337e-18 5.20901477e-05 0.1077865837 0.1215498928 0.1464855692 3.49441024e-18 1.431097906e-06 0.01355875262 +0.02799502912 0.03250344649 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5276fb65e36a79e1dc25223ee60541c286c36df9 Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..963b0c69572371aa1bcb6b72d720cb0f3e8745c4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:05 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.074064 SEC) : SETUP UNITCELL + DONE(0.0821345 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0984631 SEC) : INIT PLANEWAVE + DONE(0.140133 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.386034 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651533e+02 0.000000e+00 2.139e-01 4.193e-01 + GE2 -4.663623e+02 -1.209060e+00 9.784e-02 3.775e-01 + GE3 -4.663654e+02 -3.096321e-03 6.273e-02 4.412e-01 + GE4 -4.663652e+02 2.364621e-04 1.960e-03 3.125e-01 + GE5 -4.663645e+02 6.961618e-04 8.263e-04 3.140e-01 + GE6 -4.663649e+02 -4.264627e-04 1.150e-04 3.092e-01 + GE7 -4.663648e+02 1.355693e-04 3.926e-05 2.989e-01 + GE8 -4.663648e+02 -4.146366e-05 1.296e-05 2.929e-01 + GE9 -4.663648e+02 1.819346e-05 2.008e-06 2.992e-01 + GE10 -4.663648e+02 -2.152486e-06 2.344e-07 2.943e-01 + GE11 -4.663648e+02 -5.300301e-07 9.476e-08 2.250e-01 +E_delta_band = -7.06036005e-02 Ry = -9.60611266e-01 eV +E_delta_NN= -1.94913676e-01 Ry = -2.65193661e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.4333 11 0.49 1e+02 % + Run_lcao lcao_line 5.4246 1 5.4 1e+02 % + Potential init_pot 0.2426 2 0.12 4.5 % + PW_Basis recip2real 0.25007 16 0.016 4.6 % + PW_Basis gathers_scatterp 0.10599 16 0.0066 2 % + Potential v_of_rho 0.91291 13 0.07 17 % + XC_Functional v_xc 0.27649 14 0.02 5.1 % + H_Hartree_pw v_hartree 0.59743 13 0.046 11 % + PW_Basis real2recip 0.60521 38 0.016 11 % + PW_Basis gatherp_scatters 0.22867 38 0.006 4.2 % + ORB_control set_orb_tables 0.90774 1 0.91 17 % + ORB_gen_tables gen_tables 0.90773 1 0.91 17 % + ORB_table_phi init_Table 0.3844 1 0.38 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.38013 126 0.003 7 % + ORB_table_beta init_Table_Beta 0.15451 1 0.15 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.15315 56 0.0027 2.8 % + ORB_table_alpha init_Table_Alpha 0.2105 1 0.21 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.20883 66 0.0032 3.8 % + LOOP_ions opt_ions 4.0609 1 4.1 75 % + ESolver_KS_LCAO Run 3.6393 1 3.6 67 % + HSolverLCAO solve 1.4716 11 0.13 27 % + HamiltLCAO updateHk 0.83019 11 0.075 15 % + LCAO_Hamilt cal_Hgamma 0.80208 11 0.073 15 % + Gint_interface cal_gint 1.2408 23 0.054 23 % + Gint_Gamma distri_vl 1.7693 6 0.29 33 % + LCAO_Deepks cal_projected_DM 3.94 13 0.3 73 % + LCAO_gen_fixedH add_v_delta 1.6408 6 0.27 30 % + LCAO_DESCRIPTOR add_v_delta 1.6409 6 0.27 30 % + ElecStateLCAO psiToRho 0.6254 11 0.057 12 % + Charge mix_rho 0.76337 10 0.076 14 % + LOOP_ions force_stress 0.42147 1 0.42 7.8 % + Force_Stress_LCAO getForceStress 0.42145 1 0.42 7.8 % + Force_LCAO_gamma ftable_gamma 0.22842 1 0.23 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.22112 1 0.22 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:05 2022 + FINISH Time : Wed Sep 28 11:04:11 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/13/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ad3f71d80bbca8ee2acce268cd71fbff056d92f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.518473 0.630731 0.180012 +H 0.565577 0.626409 0.224595 +H 0.542989 0.664972 0.125733 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..41b45a43adc27f2e9a049bafebac45d24e9e03fd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9947 2 + 2 -13.051 2 + 3 -8.86042 2 + 4 -6.67235 2 + 5 1.07004 0 + 6 4.15521 0 + 7 11.1351 0 + 8 11.3606 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..49a052c10d22a2250c3ee56e3f51433c83d7f7c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:30 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.5172414215 17.6604733134 5.04034723729 0 0 0 0 + tauc_H1 15.8361534687 17.5394515836 6.28864867594 0 0 0 0 + tauc_H2 15.2036911653 18.6192035184 3.52052095981 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0888345618527 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0978088325001 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116017239243 (SEC) + + DONE : INIT CHARGE Time : 0.167198693669 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446142 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 144 0 100 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000932 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000648 + + Density error is 0.214138180762 + + Energy Rydberg eV + E_KohnSham -34.1869491007 -465.137305005 + E_Harris -34.3767132009 -467.719178044 + E_Fermi -0.392546932498 -5.34087501439 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0011899341577 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000794073344361 + + Density error is 0.0990073799712 + + Energy Rydberg eV + E_KohnSham -34.2767975996 -466.359756548 + E_Harris -34.2838008771 -466.455041025 + E_Fermi -0.200666273033 -2.73020470967 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0011379794483 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000764722280953 + + Density error is 0.0637645453843 + + Energy Rydberg eV + E_KohnSham -34.2771988796 -466.365216241 + E_Harris -34.2816758705 -466.426128828 + E_Fermi -0.192884943767 -2.62433429364 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106431867964 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000734726209367 + + Density error is 0.00208368500854 + + Energy Rydberg eV + E_KohnSham -34.2771292297 -466.364268607 + E_Harris -34.2771336991 -466.364329416 + E_Fermi -0.157761702831 -2.14645808469 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106258645838 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000733883866619 + + Density error is 0.000931410980389 + + Energy Rydberg eV + E_KohnSham -34.277088619 -466.36371607 + E_Harris -34.2770889398 -466.363720435 + E_Fermi -0.157409619722 -2.14166774823 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106159958288 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000733563825666 + + Density error is 0.000200039220805 + + Energy Rydberg eV + E_KohnSham -34.2771082079 -466.36398259 + E_Harris -34.2771082372 -466.363982989 + E_Fermi -0.157084909625 -2.13724984072 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106185862253 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000733800972159 + + Density error is 3.16184320204e-05 + + Energy Rydberg eV + E_KohnSham -34.2771013694 -466.363889548 + E_Harris -34.2771013728 -466.363889593 + E_Fermi -0.157029350506 -2.13649392012 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106175917041 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000733731896832 + + Density error is 1.4942047889e-05 + + Energy Rydberg eV + E_KohnSham -34.2771049715 -466.363938556 + E_Harris -34.2771049724 -466.363938568 + E_Fermi -0.157052600689 -2.13681025508 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106176242368 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000733739945454 + + Density error is 3.04792101188e-06 + + Energy Rydberg eV + E_KohnSham -34.2771038547 -466.363923361 + E_Harris -34.2771038547 -466.363923361 + E_Fermi -0.157038870024 -2.13662343981 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106176094036 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000733741032379 + + Density error is 5.73581146196e-07 + + Energy Rydberg eV + E_KohnSham -34.2771040728 -466.363926329 + E_Harris -34.2771040728 -466.363926329 + E_Fermi -0.157036030912 -2.1365848117 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106176139909 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000733741400156 + + Density error is 2.0355128248e-07 + + Energy Rydberg eV + E_KohnSham -34.2771040876 -466.36392653 + E_Harris -34.2771040876 -466.36392653 + E_Fermi -0.157035761933 -2.13658115206 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106176152728 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000733741574517 + + Density error is 1.03966984438e-08 + + Energy Rydberg eV + E_KohnSham -34.2771040909 -466.363926576 + E_Harris -34.2771040909 -466.363926576 + E_band -7.87588946552 -107.156973549 + E_one_elec -68.8165893277 -936.297731782 + E_Hartree +35.8253342928 +487.428679137 + E_xc -8.1750934533 -111.227852647 + E_Ewald +7.01456377012 +95.438036258 + E_demet -5.54826140693e-63 -7.54879691278e-62 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193883241649 -2.63791683314 + E_Fermi -0.15703556174 -2.13657842829 + + charge density convergence is achieved + final etot is -466.363926576 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9947 2.00000 + 2 -13.0510 2.00000 + 3 -8.86042 2.00000 + 4 -6.67235 2.00000 + 5 1.07004 0.00000 + 6 4.15521 0.00000 + 7 11.1351 0.00000 + 8 11.3606 0.00000 + + EFERMI = -2.136578428289992 eV + OUT.ABACUS/ final etot is -466.3639265757647 eV + correction force for each atom along direction 1 is 7.34968e-05 + correction force for each atom along direction 2 is 0.000167064 + correction force for each atom along direction 3 is -1.69391e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.25961569 +0.79320089 -1.8650843 + H1 +0.64482144 +0.14267245 +0.17396848 + H2 -0.38520575 -0.93587334 +1.6911159 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3639265757647 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3108 11 0.57 1.0e+02% + Run_lcao lcao_line 6.3009 1 6.3 1.e+02% + Potential init_pot 0.28343 2 0.14 4.5% + PW_Basis recip2real 0.28409 17 0.017 4.5% + PW_Basis gathers_scatterp 0.12115 17 0.0071 1.9% + Potential v_of_rho 0.95211 14 0.068 15.% + XC_Functional v_xc 0.26496 15 0.018 4.2% + H_Hartree_pw v_hartree 0.64564 14 0.046 10.% + PW_Basis real2recip 0.60335 41 0.015 9.6% + PW_Basis gatherp_scatters 0.22851 41 0.0056 3.6% + ORB_control set_orb_tables 1.1251 1 1.1 18.% + ORB_gen_tables gen_tables 1.1251 1 1.1 18.% + ORB_table_phi init_Table 0.49333 1 0.49 7.8% + ORB_table_phi cal_ST_Phi12_R 0.48836 126 0.0039 7.7% + ORB_table_beta init_Table_Beta 0.19240 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.19090 56 0.0034 3.0% + ORB_table_alpha init_Table_Alpha 0.26075 1 0.26 4.1% + ORB_table_alpha S_PhiAlpha_R 0.25881 66 0.0039 4.1% + LOOP_ions opt_ions 4.6532 1 4.7 74.% + ESolver_KS_LCAO Run 4.1445 1 4.1 66.% + HSolverLCAO solve 1.9811 12 0.17 31.% + HamiltLCAO updateHk 1.0602 12 0.088 17.% + LCAO_Hamilt cal_Hgamma 1.0167 12 0.085 16.% + Gint_interface cal_gint 1.7957 25 0.072 28.% + Gint_Gamma distri_vl 2.1634 6 0.36 34.% + LCAO_Deepks cal_projected_DM 4.5057 14 0.32 71.% + LCAO_gen_fixedH add_v_delta 2.0310 6 0.34 32.% + LCAO_DESCRIPTOR add_v_delta 2.0310 6 0.34 32.% + ElecStateLCAO psiToRho 0.90638 12 0.076 14.% + Charge mix_rho 0.71834 11 0.065 11.% + LOOP_ions force_stress 0.50851 1 0.51 8.1% + Force_Stress_LCAO getForceStress 0.50848 1 0.51 8.1% + Force_LCAO_gamma ftable_gamma 0.29391 1 0.29 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.28713 1 0.29 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:30 2022 + Finish Time : Wed Sep 28 11:05:36 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..52d5e24675de5cf70293a30a48ed9114591e3c0e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123478 ima = 3.68647e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 2 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012396231193 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112647993033 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113336905287 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113541479877 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113518094293 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113533451539 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113527181312 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113529366029 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113528728602 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113528673664 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113528654191 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113528643603 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b6bade324dc0caca8d81f9f5e63a64a3479c324e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.482758578541 17.660473313377 5.040347237295 0 0 0 +H +0.0 +2 +-12.163846531315 17.539451583646 6.288648675960 0 0 0 +-12.796308834667 18.619203518365 3.520520959814 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/conv new file mode 100644 index 0000000000000000000000000000000000000000..e91895e442de4cfa64340864891a3c55947c44d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/conv @@ -0,0 +1 @@ +14 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..75967762bcd8c36f3ea5d05c9a71501c5e07db6c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745814806 0.01240036721 1.252206198 1.356810462 1.468059522 0.007806517755 0.01948369697 0.03895190088 +2.769592006e-18 0.001008104654 0.002293430178 0.01148778683 0.04092141406 -3.735317759e-19 1.344933328e-06 4.440246621e-06 +0.001711571779 0.005632395169 + +H atom_index 1 n_descriptor 18 +1.252516915 0.03376335318 0.1084104219 0.1524568098 0.3239943026 0.02178011778 0.02862959449 0.0370504132 +9.893821021e-19 3.682550421e-05 0.1005025628 0.1151557219 0.1307335263 7.472553959e-18 3.907942675e-06 0.01292492044 +0.02569457957 0.03095623863 + +H atom_index 2 n_descriptor 18 +1.170166013 0.03647713766 0.0830559806 0.1177915992 0.2949425077 0.01813161131 0.02385090737 0.04022717777 +1.452937289e-17 3.053516002e-05 0.07909990469 0.1003714033 0.1123312453 7.277871418e-18 6.467351851e-06 0.01478986905 +0.02238437384 0.02680699753 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4abd6af6f2cb30277795b5c8264c136e9720f49d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:30 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0888589 SEC) : SETUP UNITCELL + DONE(0.0978291 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116039 SEC) : INIT PLANEWAVE + DONE(0.167327 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44621 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651373e+02 0.000000e+00 2.141e-01 4.608e-01 + GE2 -4.663598e+02 -1.222452e+00 9.901e-02 3.886e-01 + GE3 -4.663652e+02 -5.459693e-03 6.376e-02 4.451e-01 + GE4 -4.663643e+02 9.476345e-04 2.084e-03 3.333e-01 + GE5 -4.663637e+02 5.525367e-04 9.314e-04 3.318e-01 + GE6 -4.663640e+02 -2.665201e-04 2.000e-04 3.261e-01 + GE7 -4.663639e+02 9.304255e-05 3.162e-05 3.139e-01 + GE8 -4.663639e+02 -4.900853e-05 1.494e-05 3.062e-01 + GE9 -4.663639e+02 1.519480e-05 3.048e-06 3.107e-01 + GE10 -4.663639e+02 -2.967638e-06 5.736e-07 3.104e-01 + GE11 -4.663639e+02 -2.009971e-07 2.036e-07 3.062e-01 + GE12 -4.663639e+02 -4.588694e-08 1.040e-08 2.493e-01 +E_delta_band = -6.85638687e-02 Ry = -9.32859291e-01 eV +E_delta_NN= -1.93883242e-01 Ry = -2.63791683e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3108 11 0.57 1e+02 % + Run_lcao lcao_line 6.3009 1 6.3 1e+02 % + Potential init_pot 0.28343 2 0.14 4.5 % + PW_Basis recip2real 0.28409 17 0.017 4.5 % + PW_Basis gathers_scatterp 0.12115 17 0.0071 1.9 % + Potential v_of_rho 0.95211 14 0.068 15 % + XC_Functional v_xc 0.26496 15 0.018 4.2 % + H_Hartree_pw v_hartree 0.64564 14 0.046 10 % + PW_Basis real2recip 0.60335 41 0.015 9.6 % + PW_Basis gatherp_scatters 0.22851 41 0.0056 3.6 % + ORB_control set_orb_tables 1.1251 1 1.1 18 % + ORB_gen_tables gen_tables 1.1251 1 1.1 18 % + ORB_table_phi init_Table 0.49333 1 0.49 7.8 % + ORB_table_phi cal_ST_Phi12_R 0.48836 126 0.0039 7.7 % + ORB_table_beta init_Table_Beta 0.1924 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.1909 56 0.0034 3 % + ORB_table_alpha init_Table_Alpha 0.26075 1 0.26 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.25881 66 0.0039 4.1 % + LOOP_ions opt_ions 4.6532 1 4.7 74 % + ESolver_KS_LCAO Run 4.1445 1 4.1 66 % + HSolverLCAO solve 1.9811 12 0.17 31 % + HamiltLCAO updateHk 1.0602 12 0.088 17 % + LCAO_Hamilt cal_Hgamma 1.0167 12 0.085 16 % + Gint_interface cal_gint 1.7957 25 0.072 28 % + Gint_Gamma distri_vl 2.1634 6 0.36 34 % + LCAO_Deepks cal_projected_DM 4.5057 14 0.32 71 % + LCAO_gen_fixedH add_v_delta 2.031 6 0.34 32 % + LCAO_DESCRIPTOR add_v_delta 2.031 6 0.34 32 % + ElecStateLCAO psiToRho 0.90638 12 0.076 14 % + Charge mix_rho 0.71834 11 0.065 11 % + LOOP_ions force_stress 0.50851 1 0.51 8.1 % + Force_Stress_LCAO getForceStress 0.50848 1 0.51 8.1 % + Force_LCAO_gamma ftable_gamma 0.29391 1 0.29 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.28713 1 0.29 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:30 2022 + FINISH Time : Wed Sep 28 11:05:36 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/14/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..594803f3b96b560bfda1e6bc4305185e4c0fede2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.537573 0.641323 0.158285 +H 0.59123 0.657367 0.124548 +H 0.519453 0.696734 0.183045 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..06845b6542d600b22d73fd80c309eb58f0771dff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5182 2 + 2 -13.1443 2 + 3 -9.21483 2 + 4 -6.79474 2 + 5 1.44544 0 + 6 4.70212 0 + 7 11.0243 0 + 8 11.2783 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fd4969c686971e799e5195c4ed1c7a8f780f3efa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.0520369303 17.9570558027 4.4319705246 0 0 0 0 + tauc_H1 16.5544362081 18.4062805488 3.48733010211 0 0 0 0 + tauc_H2 14.5446717813 19.5085469865 5.12526912446 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0742959418902 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0865131214177 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.102461105976 (SEC) + + DONE : INIT CHARGE Time : 0.14399343916 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388493 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00148 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000858 + + Density error is 0.216776047455 + + Energy Rydberg eV + E_KohnSham -34.1878170616 -465.149114219 + E_Harris -34.3837652915 -467.81512666 + E_Fermi -0.417661418643 -5.6825751283 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013677096896 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107649449348 + + Density error is 0.0974424219057 + + Energy Rydberg eV + E_KohnSham -34.2782963028 -466.380147451 + E_Harris -34.2849497069 -466.470671658 + E_Fermi -0.225746142239 -3.07143383597 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125862831856 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102738618974 + + Density error is 0.0622435528133 + + Energy Rydberg eV + E_KohnSham -34.2785389443 -466.383448758 + E_Harris -34.2828132535 -466.441603718 + E_Fermi -0.212022120779 -2.88470894463 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107747030818 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957703110983 + + Density error is 0.00202237813688 + + Energy Rydberg eV + E_KohnSham -34.2785729069 -466.383910842 + E_Harris -34.2785746646 -466.383934757 + E_Fermi -0.176212758944 -2.39749758193 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010760583198 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959692558151 + + Density error is 0.000901976739091 + + Energy Rydberg eV + E_KohnSham -34.2784993962 -466.382910678 + E_Harris -34.2785017324 -466.382942463 + E_Fermi -0.175113527501 -2.38254177089 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107448154532 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000958489190715 + + Density error is 0.000102589633703 + + Energy Rydberg eV + E_KohnSham -34.2785494002 -466.383591017 + E_Harris -34.27854941 -466.383591151 + E_Fermi -0.17533694419 -2.3855815109 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107427310358 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000958465883669 + + Density error is 4.94675988122e-05 + + Energy Rydberg eV + E_KohnSham -34.2785334777 -466.38337438 + E_Harris -34.2785334912 -466.383374564 + E_Fermi -0.175201276156 -2.3837356526 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010742991757 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000958410374054 + + Density error is 9.83365203495e-06 + + Energy Rydberg eV + E_KohnSham -34.2785363545 -466.383413521 + E_Harris -34.278536355 -466.383413528 + E_Fermi -0.175257411407 -2.38449941187 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107428087201 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000958411247597 + + Density error is 5.94971233298e-07 + + Energy Rydberg eV + E_KohnSham -34.2785349195 -466.383393997 + E_Harris -34.2785349195 -466.383393997 + E_Fermi -0.175246407392 -2.38434969456 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107427950472 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000958411978938 + + Density error is 1.44106662237e-07 + + Energy Rydberg eV + E_KohnSham -34.2785351157 -466.383396666 + E_Harris -34.2785351157 -466.383396666 + E_Fermi -0.175246019105 -2.38434441165 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107427981891 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000958412365796 + + Density error is 4.92667516254e-08 + + Energy Rydberg eV + E_KohnSham -34.2785351232 -466.383396769 + E_Harris -34.2785351232 -466.383396769 + E_band -8.03663778659 -109.34406666 + E_one_elec -69.6987607303 -948.300289471 + E_Hartree +36.2290599273 +492.921648195 + E_xc -8.24030596509 -112.115114389 + E_Ewald +7.55495533014 +102.790440625 + E_demet -2.15535326881e-88 -2.93250856587e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195599362081 -2.66126584947 + E_Fermi -0.175246146848 -2.38434614967 + + charge density convergence is achieved + final etot is -466.383396769 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5182 2.00000 + 2 -13.1443 2.00000 + 3 -9.21483 2.00000 + 4 -6.79474 2.00000 + 5 1.44544 0.00000 + 6 4.70212 0.00000 + 7 11.0243 0.00000 + 8 11.2783 0.00000 + + EFERMI = -2.384346149672417 eV + OUT.ABACUS/ final etot is -466.3833967689563 eV + correction force for each atom along direction 1 is 0.000110807 + correction force for each atom along direction 2 is 3.80305e-05 + correction force for each atom along direction 3 is -0.000125846 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.44010231 -1.7046662 -0.68312908 + H1 +0.31248608 -0.078579740 -0.23294501 + H2 -0.75258839 +1.7832459 +0.91607410 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3833967689563 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1429 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1347 1 6.1 1.e+02% + Potential init_pot 0.24379 2 0.12 4.0% + PW_Basis recip2real 0.26127 16 0.016 4.3% + PW_Basis gathers_scatterp 0.10605 16 0.0066 1.7% + Potential v_of_rho 0.91326 13 0.070 15.% + XC_Functional v_xc 0.26755 14 0.019 4.4% + H_Hartree_pw v_hartree 0.60775 13 0.047 9.9% + PW_Basis real2recip 0.59752 38 0.016 9.7% + PW_Basis gatherp_scatters 0.22309 38 0.0059 3.6% + ORB_control set_orb_tables 0.89456 1 0.89 15.% + ORB_gen_tables gen_tables 0.89456 1 0.89 15.% + ORB_table_phi init_Table 0.37475 1 0.37 6.1% + ORB_table_phi cal_ST_Phi12_R 0.37051 126 0.0029 6.0% + ORB_table_beta init_Table_Beta 0.15534 1 0.16 2.5% + ORB_table_beta VNL_PhiBeta_R 0.15406 56 0.0028 2.5% + ORB_table_alpha init_Table_Alpha 0.20656 1 0.21 3.4% + ORB_table_alpha S_PhiAlpha_R 0.20496 66 0.0031 3.3% + LOOP_ions opt_ions 4.7829 1 4.8 78.% + ESolver_KS_LCAO Run 4.2636 1 4.3 69.% + HSolverLCAO solve 2.0984 11 0.19 34.% + HamiltLCAO updateHk 1.1093 11 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.0757 11 0.098 18.% + Gint_interface cal_gint 1.9532 23 0.085 32.% + Gint_Gamma distri_vl 2.0577 6 0.34 33.% + LCAO_Deepks cal_projected_DM 4.6363 13 0.36 75.% + LCAO_gen_fixedH add_v_delta 1.9294 6 0.32 31.% + LCAO_DESCRIPTOR add_v_delta 1.9294 6 0.32 31.% + ElecStateLCAO psiToRho 0.97265 11 0.088 16.% + Charge mix_rho 0.75864 10 0.076 12.% + LOOP_ions force_stress 0.51911 1 0.52 8.5% + Force_Stress_LCAO getForceStress 0.51909 1 0.52 8.5% + Force_LCAO_gamma ftable_gamma 0.32018 1 0.32 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.31267 1 0.31 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:17 2022 + Finish Time : Wed Sep 28 11:09:23 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3ae8961233c1d07b94d08fcb8ae556eb9072ec73 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123788 ima = 3.71396e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122793968909 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111913073642 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112356452933 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112635767765 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112564762301 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112603508464 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112599427128 + charge after normalized = 7.99999999999996 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112602543491 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112602051226 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112602039532 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011260204436 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b96a065f87913cf3c543b97849d41487c31ae3bb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.947963069664 17.957055802686 4.431970524624 0 0 0 +H +0.0 +2 +-11.445563791891 18.406280548753 3.487330102125 0 0 0 +-13.455328218729 19.508546986466 5.125269124467 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/conv new file mode 100644 index 0000000000000000000000000000000000000000..9fdd7f3e706826e95f82ff6b01411d493a76afce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/conv @@ -0,0 +1 @@ +15 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..564950a345306a827bd535b62c636284eb97de65 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750361251 0.0128129894 1.28746783 1.374691216 1.470366091 0.008868099455 0.01856167054 0.03905730229 +2.304136581e-18 0.001115751888 0.002782268388 0.01310475337 0.04769494184 -1.930257104e-19 2.453829373e-06 6.729457833e-06 +0.001631960132 0.006009223085 + +H atom_index 1 n_descriptor 18 +1.248466934 0.034416218 0.1086368084 0.1489962189 0.3198175607 0.02251712823 0.02818542068 0.03751231622 +-3.93317275e-18 5.037419198e-05 0.1032529865 0.1147758877 0.1280360294 9.042148606e-18 4.128361837e-06 0.01326536367 +0.02680553967 0.03070626032 + +H atom_index 2 n_descriptor 18 +1.293585571 0.03294126769 0.1254279096 0.1712438916 0.3333781928 0.02463510071 0.03078446183 0.03657409914 +4.270895194e-17 5.476417018e-05 0.1084419701 0.1225595795 0.1470163009 -3.273092394e-18 1.579777235e-06 0.0135677972 +0.02833896292 0.03254849188 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ae588a2617d2923e6f99bcaf4a133f2e3f642b0e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0743105 SEC) : SETUP UNITCELL + DONE(0.0865261 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.102475 SEC) : INIT PLANEWAVE + DONE(0.144095 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.388537 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651491e+02 0.000000e+00 2.168e-01 4.743e-01 + GE2 -4.663801e+02 -1.231033e+00 9.744e-02 4.356e-01 + GE3 -4.663834e+02 -3.301307e-03 6.224e-02 4.999e-01 + GE4 -4.663839e+02 -4.620839e-04 2.022e-03 3.742e-01 + GE5 -4.663829e+02 1.000164e-03 9.020e-04 3.720e-01 + GE6 -4.663836e+02 -6.803394e-04 1.026e-04 3.533e-01 + GE7 -4.663834e+02 2.166374e-04 4.947e-05 3.561e-01 + GE8 -4.663834e+02 -3.914137e-05 9.834e-06 3.520e-01 + GE9 -4.663834e+02 1.952398e-05 5.950e-07 3.533e-01 + GE10 -4.663834e+02 -2.668701e-06 1.441e-07 3.497e-01 + GE11 -4.663834e+02 -1.028098e-07 4.927e-08 2.842e-01 +E_delta_band = -7.21156768e-02 Ry = -9.81184120e-01 eV +E_delta_NN= -1.95599362e-01 Ry = -2.66126585e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1429 11 0.56 1e+02 % + Run_lcao lcao_line 6.1347 1 6.1 1e+02 % + Potential init_pot 0.24379 2 0.12 4 % + PW_Basis recip2real 0.26127 16 0.016 4.3 % + PW_Basis gathers_scatterp 0.10605 16 0.0066 1.7 % + Potential v_of_rho 0.91326 13 0.07 15 % + XC_Functional v_xc 0.26755 14 0.019 4.4 % + H_Hartree_pw v_hartree 0.60775 13 0.047 9.9 % + PW_Basis real2recip 0.59752 38 0.016 9.7 % + PW_Basis gatherp_scatters 0.22309 38 0.0059 3.6 % + ORB_control set_orb_tables 0.89456 1 0.89 15 % + ORB_gen_tables gen_tables 0.89456 1 0.89 15 % + ORB_table_phi init_Table 0.37475 1 0.37 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.37051 126 0.0029 6 % + ORB_table_beta init_Table_Beta 0.15534 1 0.16 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.15406 56 0.0028 2.5 % + ORB_table_alpha init_Table_Alpha 0.20656 1 0.21 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.20496 66 0.0031 3.3 % + LOOP_ions opt_ions 4.7829 1 4.8 78 % + ESolver_KS_LCAO Run 4.2636 1 4.3 69 % + HSolverLCAO solve 2.0984 11 0.19 34 % + HamiltLCAO updateHk 1.1093 11 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.0757 11 0.098 18 % + Gint_interface cal_gint 1.9532 23 0.085 32 % + Gint_Gamma distri_vl 2.0577 6 0.34 33 % + LCAO_Deepks cal_projected_DM 4.6363 13 0.36 75 % + LCAO_gen_fixedH add_v_delta 1.9294 6 0.32 31 % + LCAO_DESCRIPTOR add_v_delta 1.9294 6 0.32 31 % + ElecStateLCAO psiToRho 0.97265 11 0.088 16 % + Charge mix_rho 0.75864 10 0.076 12 % + LOOP_ions force_stress 0.51911 1 0.52 8.5 % + Force_Stress_LCAO getForceStress 0.51909 1 0.52 8.5 % + Force_LCAO_gamma ftable_gamma 0.32018 1 0.32 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.31267 1 0.31 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:17 2022 + FINISH Time : Wed Sep 28 11:09:23 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/15/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..87fcba04874a4722a1219db2cf0ba4bd9b53ad52 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.549745 0.637682 0.16174 +H 0.56128 0.667121 0.104555 +H 0.492228 0.669505 0.183104 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b2040142a8e5048038d558ee216a6e08502e9e17 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0556 2 + 2 -12.7078 2 + 3 -9.1765 2 + 4 -6.69291 2 + 5 1.00473 0 + 6 4.01759 0 + 7 11.1365 0 + 8 11.3881 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..2b1d076dc279ff360f8994aa071c2e7259c364bb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:49 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.3928724648 17.8551078934 4.52871407108 0 0 0 0 + tauc_H1 15.7158308348 18.6793820178 2.9275525269 0 0 0 0 + tauc_H2 13.7823902526 18.7461398384 5.12692448865 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.100181760443 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.103931840831 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.122118830633 (SEC) + + DONE : INIT CHARGE Time : 0.165273005416 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446963 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000795 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00144 + + Density error is 0.212033321029 + + Energy Rydberg eV + E_KohnSham -34.188307103 -465.155781575 + E_Harris -34.3742321239 -467.685421259 + E_Fermi -0.389382711668 -5.29782358137 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010334733714 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129022730346 + + Density error is 0.098814453893 + + Energy Rydberg eV + E_KohnSham -34.2771842522 -466.365017226 + E_Harris -34.2843511841 -466.462528337 + E_Fermi -0.20006451824 -2.72201741569 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000985902180735 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012045836315 + + Density error is 0.0637312348639 + + Energy Rydberg eV + E_KohnSham -34.2776498662 -466.371352229 + E_Harris -34.2822321798 -466.433697804 + E_Fermi -0.193343564406 -2.63057414755 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000926268764264 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105001880746 + + Density error is 0.00194993317212 + + Energy Rydberg eV + E_KohnSham -34.2775541654 -466.370050153 + E_Harris -34.2775558289 -466.370072786 + E_Fermi -0.157967047333 -2.14925193997 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000926202646033 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104880000225 + + Density error is 0.000953613264135 + + Energy Rydberg eV + E_KohnSham -34.2775162227 -466.369533917 + E_Harris -34.2775166059 -466.36953913 + E_Fermi -0.157903706561 -2.14839014456 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000925433731446 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104643484091 + + Density error is 0.000176069590071 + + Energy Rydberg eV + E_KohnSham -34.2775321312 -466.369750362 + E_Harris -34.2775321463 -466.369750568 + E_Fermi -0.157473644307 -2.1425388474 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000925678874078 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104658370146 + + Density error is 3.22730029739e-05 + + Energy Rydberg eV + E_KohnSham -34.2775272324 -466.369683711 + E_Harris -34.2775272355 -466.369683753 + E_Fermi -0.157451948058 -2.14224365479 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000925594845067 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010465126525 + + Density error is 1.22593095986e-05 + + Energy Rydberg eV + E_KohnSham -34.27753001 -466.369721502 + E_Harris -34.2775300106 -466.36972151 + E_Fermi -0.157466903777 -2.14244713779 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000925596720746 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104649818023 + + Density error is 2.08312460643e-06 + + Energy Rydberg eV + E_KohnSham -34.27752899 -466.369707624 + E_Harris -34.27752899 -466.369707624 + E_Fermi -0.157454916535 -2.14228404299 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000925598040732 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010464956507 + + Density error is 5.23657475805e-07 + + Energy Rydberg eV + E_KohnSham -34.2775291601 -466.369709938 + E_Harris -34.2775291601 -466.369709938 + E_Fermi -0.1574532558 -2.14226144753 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000925598495364 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104649567756 + + Density error is 1.82898955145e-07 + + Energy Rydberg eV + E_KohnSham -34.2775291763 -466.369710158 + E_Harris -34.2775291763 -466.369710158 + E_Fermi -0.157453018737 -2.14225822212 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000925598592542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104649547853 + + Density error is 1.17265811426e-08 + + Energy Rydberg eV + E_KohnSham -34.2775291797 -466.369710206 + E_Harris -34.2775291797 -466.369710206 + E_band -7.88387284102 -107.265592945 + E_one_elec -68.7194306022 -934.975819505 + E_Hartree +35.7668009702 +486.632292426 + E_xc -8.16606569507 -111.105023695 + E_Ewald +6.96662794947 +94.7858359589 + E_demet -9.25281658002e-61 -1.25891028037e-59 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193863873889 -2.63765332125 + E_Fermi -0.157452842662 -2.1422558265 + + charge density convergence is achieved + final etot is -466.369710206 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0556 2.00000 + 2 -12.7078 2.00000 + 3 -9.17650 2.00000 + 4 -6.69291 2.00000 + 5 1.00473 0.00000 + 6 4.01759 0.00000 + 7 11.1365 0.00000 + 8 11.3881 0.00000 + + EFERMI = -2.142255826498923 eV + OUT.ABACUS/ final etot is -466.3697102056749 eV + correction force for each atom along direction 1 is -0.000125523 + correction force for each atom along direction 2 is 0.000181236 + correction force for each atom along direction 3 is 1.99770e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.8147627 +0.81262729 +0.96277861 + H1 +0.15638718 +0.15426576 -0.41663977 + H2 +1.6583755 -0.96689305 -0.54613883 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3697102056749 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.0989 11 0.74 1.0e+02% + Run_lcao lcao_line 8.0885 1 8.1 1.e+02% + Potential init_pot 0.28319 2 0.14 3.5% + PW_Basis recip2real 0.30199 17 0.018 3.7% + PW_Basis gathers_scatterp 0.13047 17 0.0077 1.6% + Potential v_of_rho 1.0862 14 0.078 13.% + XC_Functional v_xc 0.31601 15 0.021 3.9% + H_Hartree_pw v_hartree 0.72533 14 0.052 9.0% + PW_Basis real2recip 0.76033 41 0.019 9.4% + PW_Basis gatherp_scatters 0.29292 41 0.0071 3.6% + ORB_control set_orb_tables 1.0954 1 1.1 14.% + ORB_gen_tables gen_tables 1.0954 1 1.1 14.% + ORB_table_phi init_Table 0.47616 1 0.48 5.9% + ORB_table_phi cal_ST_Phi12_R 0.47093 126 0.0037 5.8% + ORB_table_beta init_Table_Beta 0.18295 1 0.18 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18141 56 0.0032 2.2% + ORB_table_alpha init_Table_Alpha 0.24640 1 0.25 3.0% + ORB_table_alpha S_PhiAlpha_R 0.24446 66 0.0037 3.0% + LOOP_ions opt_ions 6.4690 1 6.5 80.% + ESolver_KS_LCAO Run 5.8818 1 5.9 73.% + HSolverLCAO solve 3.1993 12 0.27 40.% + HamiltLCAO updateHk 1.6189 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.5890 12 0.13 20.% + Gint_interface cal_gint 3.0189 25 0.12 37.% + Gint_Gamma distri_vl 3.0584 6 0.51 38.% + LCAO_Deepks cal_projected_DM 6.2949 14 0.45 78.% + LCAO_gen_fixedH add_v_delta 2.9117 6 0.49 36.% + LCAO_DESCRIPTOR add_v_delta 2.9117 6 0.49 36.% + ElecStateLCAO psiToRho 1.5579 12 0.13 19.% + Charge mix_rho 0.99156 11 0.090 12.% + LOOP_ions force_stress 0.58705 1 0.59 7.2% + Force_Stress_LCAO getForceStress 0.58702 1 0.59 7.2% + Force_LCAO_gamma ftable_gamma 0.36681 1 0.37 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.35864 1 0.36 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:49 2022 + Finish Time : Wed Sep 28 11:06:57 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..71d96231e549569fdaddbc6c5ba35acc28cbb705 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012377 ima = 3.70155e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012342971292 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111936506716 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112716680545 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112930686963 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112911427361 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112923675126 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112919049261 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112921117465 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112920601552 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112920545713 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112920527054 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112920517432 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0fbf651b548c8966b570f9bfdddecc676a26684d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.607127535219 17.855107893390 4.528714071102 0 0 0 +H +0.0 +2 +-12.284169165181 18.679382017822 2.927552526887 0 0 0 +-14.217609747441 18.746139838398 5.126924488648 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/conv new file mode 100644 index 0000000000000000000000000000000000000000..5ee3e21c77d906b92c7bfb134ecf6b8ff8ea3ce3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/conv @@ -0,0 +1 @@ +16 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f4881791224f232b0938d2b4b5060af158fd62cf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751435163 0.01246207267 1.244259179 1.343335803 1.468379238 0.00871754955 0.01753588402 0.03914122347 +4.518265764e-19 0.0008829614358 0.002493890332 0.01169003574 0.04267195585 3.83833939e-19 1.801092177e-06 5.477437362e-06 +0.001584949302 0.005903894724 + +H atom_index 1 n_descriptor 18 +1.25037333 0.03444519753 0.1081605173 0.1501674871 0.3213856022 0.02221562685 0.02832927264 0.03767078982 +-2.456250551e-17 4.234219995e-05 0.09941192593 0.1154467422 0.128698893 -1.200379463e-18 3.747186496e-06 0.0132075616 +0.02582913753 0.03075386301 + +H atom_index 2 n_descriptor 18 +1.167303951 0.03704747518 0.08248343293 0.1154150727 0.2908068966 0.01833642788 0.02346608585 0.04087365502 +8.855585534e-18 3.525089935e-05 0.07824602013 0.09821634029 0.111797203 -8.618391035e-18 6.804639008e-06 0.01526412423 +0.02244263445 0.02645348521 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4ef41c436654a55b3a562e2cde6e818ed22fcda5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:49 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.100204 SEC) : SETUP UNITCELL + DONE(0.10395 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.122141 SEC) : INIT PLANEWAVE + DONE(0.165414 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447034 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651558e+02 0.000000e+00 2.120e-01 5.864e-01 + GE2 -4.663650e+02 -1.209236e+00 9.881e-02 5.456e-01 + GE3 -4.663714e+02 -6.335003e-03 6.373e-02 6.155e-01 + GE4 -4.663701e+02 1.302076e-03 1.950e-03 4.759e-01 + GE5 -4.663695e+02 5.162368e-04 9.536e-04 4.784e-01 + GE6 -4.663698e+02 -2.164452e-04 1.761e-04 4.722e-01 + GE7 -4.663697e+02 6.665111e-05 3.227e-05 4.568e-01 + GE8 -4.663697e+02 -3.779109e-05 1.226e-05 4.510e-01 + GE9 -4.663697e+02 1.387758e-05 2.083e-06 4.521e-01 + GE10 -4.663697e+02 -2.313694e-06 5.237e-07 4.529e-01 + GE11 -4.663697e+02 -2.204384e-07 1.829e-07 4.533e-01 + GE12 -4.663697e+02 -4.739399e-08 1.173e-08 3.782e-01 +E_delta_band = -6.84020718e-02 Ry = -9.30657931e-01 eV +E_delta_NN= -1.93863874e-01 Ry = -2.63765332e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 8.0989 11 0.74 1e+02 % + Run_lcao lcao_line 8.0885 1 8.1 1e+02 % + Potential init_pot 0.28319 2 0.14 3.5 % + PW_Basis recip2real 0.30199 17 0.018 3.7 % + PW_Basis gathers_scatterp 0.13047 17 0.0077 1.6 % + Potential v_of_rho 1.0862 14 0.078 13 % + XC_Functional v_xc 0.31601 15 0.021 3.9 % + H_Hartree_pw v_hartree 0.72533 14 0.052 9 % + PW_Basis real2recip 0.76033 41 0.019 9.4 % + PW_Basis gatherp_scatters 0.29292 41 0.0071 3.6 % + ORB_control set_orb_tables 1.0954 1 1.1 14 % + ORB_gen_tables gen_tables 1.0954 1 1.1 14 % + ORB_table_phi init_Table 0.47616 1 0.48 5.9 % + ORB_table_phi cal_ST_Phi12_R 0.47093 126 0.0037 5.8 % + ORB_table_beta init_Table_Beta 0.18295 1 0.18 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.18141 56 0.0032 2.2 % + ORB_table_alpha init_Table_Alpha 0.2464 1 0.25 3 % + ORB_table_alpha S_PhiAlpha_R 0.24446 66 0.0037 3 % + LOOP_ions opt_ions 6.469 1 6.5 80 % + ESolver_KS_LCAO Run 5.8818 1 5.9 73 % + HSolverLCAO solve 3.1993 12 0.27 40 % + HamiltLCAO updateHk 1.6189 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.589 12 0.13 20 % + Gint_interface cal_gint 3.0189 25 0.12 37 % + Gint_Gamma distri_vl 3.0584 6 0.51 38 % + LCAO_Deepks cal_projected_DM 6.2949 14 0.45 78 % + LCAO_gen_fixedH add_v_delta 2.9117 6 0.49 36 % + LCAO_DESCRIPTOR add_v_delta 2.9117 6 0.49 36 % + ElecStateLCAO psiToRho 1.5579 12 0.13 19 % + Charge mix_rho 0.99156 11 0.09 12 % + LOOP_ions force_stress 0.58705 1 0.59 7.2 % + Force_Stress_LCAO getForceStress 0.58702 1 0.59 7.2 % + Force_LCAO_gamma ftable_gamma 0.36681 1 0.37 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.35864 1 0.36 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:49 2022 + FINISH Time : Wed Sep 28 11:06:57 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/16/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..07788d93e43a0cc21de68641345c800207578ebc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.544741 0.635568 0.166258 +H 0.572023 0.649473 0.109251 +H 0.516831 0.580883 0.155189 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bdcac511c06dec6bfdd84bab911609d68c7d8817 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6687 2 + 2 -13.2601 2 + 3 -9.24079 2 + 4 -6.82693 2 + 5 1.55178 0 + 6 4.9041 0 + 7 10.9883 0 + 8 11.2384 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9f0595822e0736f3179b94fb6068b68ad0876e98 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:19 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.2527562548 17.7959093792 4.65521013331 0 0 0 0 + tauc_H1 16.0166307633 18.1852401379 3.05901610123 0 0 0 0 + tauc_H2 14.4712643096 16.2647270893 4.34530450035 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0848646287821 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0852911929302 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103428390291 (SEC) + + DONE : INIT CHARGE Time : 0.151937691343 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.429185 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00163 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117 + + Density error is 0.218349869949 + + Energy Rydberg eV + E_KohnSham -34.1839537852 -465.096551647 + E_Harris -34.3836291382 -467.813274198 + E_Fermi -0.426764713659 -5.80643181111 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00155209791125 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138341957291 + + Density error is 0.0971341992914 + + Energy Rydberg eV + E_KohnSham -34.2751377265 -466.337172816 + E_Harris -34.2817571775 -466.427235066 + E_Fermi -0.234015064274 -3.18393829197 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00142519499124 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131011661228 + + Density error is 0.0618433832489 + + Energy Rydberg eV + E_KohnSham -34.2753295289 -466.339782421 + E_Harris -34.2795275057 -466.396898826 + E_Fermi -0.218235752763 -2.9692497449 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121638976805 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120024490537 + + Density error is 0.0020833064473 + + Energy Rydberg eV + E_KohnSham -34.2754005084 -466.340748147 + E_Harris -34.2754033409 -466.340786684 + E_Fermi -0.182346848766 -2.48095615556 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121453260153 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012031433814 + + Density error is 0.000931846616985 + + Energy Rydberg eV + E_KohnSham -34.275317759 -466.339622284 + E_Harris -34.2753209822 -466.339666137 + E_Fermi -0.180890980633 -2.46114805342 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121298457014 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120147268123 + + Density error is 0.000104516017206 + + Energy Rydberg eV + E_KohnSham -34.2753771262 -466.340430016 + E_Harris -34.2753771458 -466.340430282 + E_Fermi -0.181322626911 -2.46702090232 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121256458597 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120122358829 + + Density error is 5.78206337624e-05 + + Energy Rydberg eV + E_KohnSham -34.2753580693 -466.340170733 + E_Harris -34.2753580866 -466.340170968 + E_Fermi -0.181169095899 -2.46493200573 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012126346468 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120120119741 + + Density error is 1.07792698561e-05 + + Energy Rydberg eV + E_KohnSham -34.2753611095 -466.340212097 + E_Harris -34.2753611099 -466.340212102 + E_Fermi -0.181236855336 -2.46585392017 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121261806932 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120120577079 + + Density error is 1.99182469619e-06 + + Energy Rydberg eV + E_KohnSham -34.2753596354 -466.340192041 + E_Harris -34.2753596355 -466.340192041 + E_Fermi -0.181226556563 -2.46571379817 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121261324091 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120120515373 + + Density error is 1.24917803353e-07 + + Energy Rydberg eV + E_KohnSham -34.2753597439 -466.340193517 + E_Harris -34.2753597439 -466.340193517 + E_Fermi -0.181224421873 -2.46568475423 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121261375861 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120120564371 + + Density error is 6.59351659696e-08 + + Energy Rydberg eV + E_KohnSham -34.2753597886 -466.340194124 + E_Harris -34.2753597886 -466.340194124 + E_band -8.08433596844 -109.993033717 + E_one_elec -69.9916645166 -952.28544993 + E_Hartree +36.3664203883 +494.790533144 + E_xc -8.26266926747 -112.419382727 + E_Ewald +7.73544057263 +105.246068328 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196175685871 -2.66910713691 + E_Fermi -0.18122457579 -2.46568684838 + + charge density convergence is achieved + final etot is -466.340194124 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6687 2.00000 + 2 -13.2601 2.00000 + 3 -9.24079 2.00000 + 4 -6.82693 2.00000 + 5 1.55178 0.00000 + 6 4.90410 0.00000 + 7 10.9883 0.00000 + 8 11.2384 0.00000 + + EFERMI = -2.465686848377801 eV + OUT.ABACUS/ final etot is -466.3401941243840 eV + correction force for each atom along direction 1 is 0.000107325 + correction force for each atom along direction 2 is -0.000130808 + correction force for each atom along direction 3 is -0.000168997 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.0036007 +2.3168280 +1.0174499 + H1 +0.45420839 +0.38517068 -0.69465974 + H2 -1.4578091 -2.7019987 -0.32279019 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3401941243840 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0803 11 0.55 1.0e+02% + Run_lcao lcao_line 6.0715 1 6.1 1.e+02% + Potential init_pot 0.28300 2 0.14 4.7% + PW_Basis recip2real 0.26871 16 0.017 4.4% + PW_Basis gathers_scatterp 0.11643 16 0.0073 1.9% + Potential v_of_rho 0.86535 13 0.067 14.% + XC_Functional v_xc 0.23551 14 0.017 3.9% + H_Hartree_pw v_hartree 0.59208 13 0.046 9.7% + PW_Basis real2recip 0.55782 38 0.015 9.2% + PW_Basis gatherp_scatters 0.21996 38 0.0058 3.6% + ORB_control set_orb_tables 1.1044 1 1.1 18.% + ORB_gen_tables gen_tables 1.1044 1 1.1 18.% + ORB_table_phi init_Table 0.48492 1 0.48 8.0% + ORB_table_phi cal_ST_Phi12_R 0.48004 126 0.0038 7.9% + ORB_table_beta init_Table_Beta 0.18748 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18603 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25331 1 0.25 4.2% + ORB_table_alpha S_PhiAlpha_R 0.25141 66 0.0038 4.1% + LOOP_ions opt_ions 4.4618 1 4.5 73.% + ESolver_KS_LCAO Run 3.9324 1 3.9 65.% + HSolverLCAO solve 1.9696 11 0.18 32.% + HamiltLCAO updateHk 1.0490 11 0.095 17.% + LCAO_Hamilt cal_Hgamma 1.0150 11 0.092 17.% + Gint_interface cal_gint 1.8271 23 0.079 30.% + Gint_Gamma distri_vl 1.9049 6 0.32 31.% + LCAO_Deepks cal_projected_DM 4.3095 13 0.33 71.% + LCAO_gen_fixedH add_v_delta 1.7718 6 0.30 29.% + LCAO_DESCRIPTOR add_v_delta 1.7718 6 0.30 29.% + ElecStateLCAO psiToRho 0.90724 11 0.082 15.% + Charge mix_rho 0.66198 10 0.066 11.% + LOOP_ions force_stress 0.52921 1 0.53 8.7% + Force_Stress_LCAO getForceStress 0.52918 1 0.53 8.7% + Force_LCAO_gamma ftable_gamma 0.31797 1 0.32 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.31113 1 0.31 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:19 2022 + Finish Time : Wed Sep 28 11:03:25 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d3eea78df64ffcfc1dff7acf67eef6aaea12fe73 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124177 ima = 3.69732e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122656215429 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111913801613 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112274176904 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112578670389 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112493230939 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112539592192 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112535532449 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112538818763 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112538427406 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112538327586 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112538331738 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7dd3d4ca1f0ed20fe74b71e07eecd348a186ae8f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.747243745196 17.795909379256 4.655210133326 0 0 0 +H +0.0 +2 +-11.983369236697 18.185240137930 3.059016101214 0 0 0 +-13.528735690363 16.264727089317 4.345304500363 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/conv new file mode 100644 index 0000000000000000000000000000000000000000..197b75185763b4532c663e0cd150875856c0e154 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/conv @@ -0,0 +1 @@ +17 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..af2db1edbf51e1f731d1d4c24767f145ce0d4d31 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750582345 0.01286688959 1.298493608 1.38468382 1.471115689 0.009033259838 0.01885265649 0.03906994563 +8.215636087e-18 0.001182567817 0.002882270579 0.01352070064 0.04928287745 1.190767851e-18 2.661943653e-06 7.101161352e-06 +0.001626800995 0.005990870985 + +H atom_index 1 n_descriptor 18 +1.263180165 0.03392306547 0.1142781501 0.155835172 0.3241425139 0.02336678077 0.02902661481 0.03706477332 +4.013748675e-18 5.479464819e-05 0.1074149047 0.1161678542 0.1340457081 2.557477014e-18 3.254624632e-06 0.01324663569 +0.02769136196 0.03137158644 + +H atom_index 2 n_descriptor 18 +1.314344751 0.03239074819 0.134432948 0.1823565447 0.3384496942 0.0257574446 0.0319316826 0.03657171358 +-1.272740159e-17 5.98275877e-05 0.107965882 0.1302662597 0.1564255671 -7.875544775e-18 6.341252991e-07 0.01429699972 +0.02927528487 0.03323801999 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..b1d61739c950fe1de1ae2c233cf061be105f2dcc Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:19 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0848873 SEC) : SETUP UNITCELL + DONE(0.085305 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103449 SEC) : INIT PLANEWAVE + DONE(0.152069 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.429244 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650966e+02 0.000000e+00 2.183e-01 4.698e-01 + GE2 -4.663372e+02 -1.240621e+00 9.713e-02 3.918e-01 + GE3 -4.663398e+02 -2.609605e-03 6.184e-02 4.528e-01 + GE4 -4.663407e+02 -9.657258e-04 2.083e-03 3.456e-01 + GE5 -4.663396e+02 1.125863e-03 9.318e-04 3.387e-01 + GE6 -4.663404e+02 -8.077322e-04 1.045e-04 3.216e-01 + GE7 -4.663402e+02 2.592829e-04 5.782e-05 3.302e-01 + GE8 -4.663402e+02 -4.136376e-05 1.078e-05 3.200e-01 + GE9 -4.663402e+02 2.005539e-05 1.992e-06 3.189e-01 + GE10 -4.663402e+02 -1.475498e-06 1.249e-07 3.227e-01 + GE11 -4.663402e+02 -6.076207e-07 6.594e-08 2.587e-01 +E_delta_band = -7.32887205e-02 Ry = -9.97144198e-01 eV +E_delta_NN= -1.96175686e-01 Ry = -2.66910714e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0803 11 0.55 1e+02 % + Run_lcao lcao_line 6.0715 1 6.1 1e+02 % + Potential init_pot 0.283 2 0.14 4.7 % + PW_Basis recip2real 0.26871 16 0.017 4.4 % + PW_Basis gathers_scatterp 0.11643 16 0.0073 1.9 % + Potential v_of_rho 0.86535 13 0.067 14 % + XC_Functional v_xc 0.23551 14 0.017 3.9 % + H_Hartree_pw v_hartree 0.59208 13 0.046 9.7 % + PW_Basis real2recip 0.55782 38 0.015 9.2 % + PW_Basis gatherp_scatters 0.21996 38 0.0058 3.6 % + ORB_control set_orb_tables 1.1044 1 1.1 18 % + ORB_gen_tables gen_tables 1.1044 1 1.1 18 % + ORB_table_phi init_Table 0.48492 1 0.48 8 % + ORB_table_phi cal_ST_Phi12_R 0.48004 126 0.0038 7.9 % + ORB_table_beta init_Table_Beta 0.18748 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18603 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.25331 1 0.25 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.25141 66 0.0038 4.1 % + LOOP_ions opt_ions 4.4618 1 4.5 73 % + ESolver_KS_LCAO Run 3.9324 1 3.9 65 % + HSolverLCAO solve 1.9696 11 0.18 32 % + HamiltLCAO updateHk 1.049 11 0.095 17 % + LCAO_Hamilt cal_Hgamma 1.015 11 0.092 17 % + Gint_interface cal_gint 1.8271 23 0.079 30 % + Gint_Gamma distri_vl 1.9049 6 0.32 31 % + LCAO_Deepks cal_projected_DM 4.3095 13 0.33 71 % + LCAO_gen_fixedH add_v_delta 1.7718 6 0.3 29 % + LCAO_DESCRIPTOR add_v_delta 1.7718 6 0.3 29 % + ElecStateLCAO psiToRho 0.90724 11 0.082 15 % + Charge mix_rho 0.66198 10 0.066 11 % + LOOP_ions force_stress 0.52921 1 0.53 8.7 % + Force_Stress_LCAO getForceStress 0.52918 1 0.53 8.7 % + Force_LCAO_gamma ftable_gamma 0.31797 1 0.32 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.31113 1 0.31 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:19 2022 + FINISH Time : Wed Sep 28 11:03:25 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/17/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d79198e57df45e10b6e1d32681ef9dad31d1e1ce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.523983 0.614056 0.164459 +H 0.565666 0.66255 0.149234 +H 0.558344 0.582744 0.210041 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..933631d7fc491bcde64c8775b6afa0b78843c19a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3767 2 + 2 -12.8751 2 + 3 -9.30665 2 + 4 -6.76558 2 + 5 1.29573 0 + 6 4.42119 0 + 7 11.0656 0 + 8 11.3367 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ec72536e22856e299a52b3f8cc2b01bb95582275 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:41 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.6715183112 17.1935601603 4.60484813937 0 0 0 0 + tauc_H1 15.838651653 18.5513940329 4.17854558654 0 0 0 0 + tauc_H2 15.6336277971 16.3168409594 5.88114571389 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0869018454728 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0878947424225 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105900229542 (SEC) + + DONE : INIT CHARGE Time : 0.160513797115 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.440496 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000943 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000978 + + Density error is 0.213999793227 + + Energy Rydberg eV + E_KohnSham -34.1913641321 -465.19737459 + E_Harris -34.3815407405 -467.78486009 + E_Fermi -0.407018633974 -5.53777261422 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117024783842 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104714430884 + + Density error is 0.0977282510216 + + Energy Rydberg eV + E_KohnSham -34.2803607517 -466.408235719 + E_Harris -34.287144249 -466.500529934 + E_Fermi -0.216330510698 -2.94332759675 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00110645760808 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00099040198572 + + Density error is 0.0626417435868 + + Energy Rydberg eV + E_KohnSham -34.2806264916 -466.411851296 + E_Harris -34.2850178908 -466.471599347 + E_Fermi -0.205115246161 -2.79073609446 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100906292531 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000910505979911 + + Density error is 0.00194827911474 + + Energy Rydberg eV + E_KohnSham -34.2806120174 -466.411654364 + E_Harris -34.2806125278 -466.411661309 + E_Fermi -0.169414215771 -2.30499865669 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010104225286 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000912542362692 + + Density error is 0.000884605940954 + + Energy Rydberg eV + E_KohnSham -34.2805516221 -466.410832644 + E_Harris -34.2805531264 -466.41085311 + E_Fermi -0.168735517933 -2.29576449887 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100890163522 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000911221987908 + + Density error is 0.000101101734364 + + Energy Rydberg eV + E_KohnSham -34.2805923171 -466.411386327 + E_Harris -34.2805923225 -466.411386401 + E_Fermi -0.168739086564 -2.29581305258 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100878755707 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00091117886884 + + Density error is 3.4913242743e-05 + + Energy Rydberg eV + E_KohnSham -34.2805793653 -466.411210109 + E_Harris -34.2805793722 -466.411210204 + E_Fermi -0.168633575884 -2.29437750614 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010087529194 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000911155770693 + + Density error is 1.21817598826e-05 + + Energy Rydberg eV + E_KohnSham -34.2805816683 -466.411241443 + E_Harris -34.2805816689 -466.411241452 + E_Fermi -0.168676100689 -2.2949560858 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100875207495 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000911159634491 + + Density error is 1.88044527249e-06 + + Energy Rydberg eV + E_KohnSham -34.2805804473 -466.411224831 + E_Harris -34.2805804473 -466.411224831 + E_Fermi -0.168663726534 -2.29478772677 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100875222504 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000911158479539 + + Density error is 1.1516032523e-07 + + Energy Rydberg eV + E_KohnSham -34.2805806164 -466.411227132 + E_Harris -34.2805806164 -466.411227132 + E_Fermi -0.168661818199 -2.29476176254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00100875258443 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000911158773641 + + Density error is 4.39336911368e-08 + + Energy Rydberg eV + E_KohnSham -34.2805806542 -466.411227646 + E_Harris -34.2805806542 -466.411227646 + E_band -7.98548265234 -108.648065352 + E_one_elec -69.3347720147 -943.347968931 + E_Hartree +36.0538534194 +490.53784136 + E_xc -8.21183253361 -111.727713479 + E_Ewald +7.33638230177 +99.8166020104 + E_demet -2.75662742013e-78 -3.75058401768e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194920965075 -2.65203578468 + E_Fermi -0.168661847282 -2.29476215824 + + charge density convergence is achieved + final etot is -466.411227646 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3767 2.00000 + 2 -12.8751 2.00000 + 3 -9.30665 2.00000 + 4 -6.76558 2.00000 + 5 1.29573 0.00000 + 6 4.42119 0.00000 + 7 11.0656 0.00000 + 8 11.3367 0.00000 + + EFERMI = -2.294762158235600 eV + OUT.ABACUS/ final etot is -466.4112276462462 eV + correction force for each atom along direction 1 is 3.88039e-05 + correction force for each atom along direction 2 is 7.93717e-05 + correction force for each atom along direction 3 is 3.15197e-07 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.028351998 +0.28949193 -0.25055812 + H1 -0.090028310 +0.23815334 -0.24763310 + H2 +0.11838031 -0.52764528 +0.49819122 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4112276462462 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5633 11 0.60 1.0e+02% + Run_lcao lcao_line 6.5535 1 6.6 1.e+02% + Potential init_pot 0.28263 2 0.14 4.3% + PW_Basis recip2real 0.28366 16 0.018 4.3% + PW_Basis gathers_scatterp 0.12632 16 0.0079 1.9% + Potential v_of_rho 0.96418 13 0.074 15.% + XC_Functional v_xc 0.27728 14 0.020 4.2% + H_Hartree_pw v_hartree 0.64579 13 0.050 9.8% + PW_Basis real2recip 0.65077 38 0.017 9.9% + PW_Basis gatherp_scatters 0.25166 38 0.0066 3.8% + ORB_control set_orb_tables 1.0981 1 1.1 17.% + ORB_gen_tables gen_tables 1.0981 1 1.1 17.% + ORB_table_phi init_Table 0.47710 1 0.48 7.3% + ORB_table_phi cal_ST_Phi12_R 0.47180 126 0.0037 7.2% + ORB_table_beta init_Table_Beta 0.18637 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18476 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25004 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24801 66 0.0038 3.8% + LOOP_ions opt_ions 4.9375 1 4.9 75.% + ESolver_KS_LCAO Run 4.3915 1 4.4 67.% + HSolverLCAO solve 2.1472 11 0.20 33.% + HamiltLCAO updateHk 1.1438 11 0.10 17.% + LCAO_Hamilt cal_Hgamma 1.1161 11 0.10 17.% + Gint_interface cal_gint 1.9657 23 0.085 30.% + Gint_Gamma distri_vl 2.1292 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.7839 13 0.37 73.% + LCAO_gen_fixedH add_v_delta 1.9820 6 0.33 30.% + LCAO_DESCRIPTOR add_v_delta 1.9821 6 0.33 30.% + ElecStateLCAO psiToRho 0.98725 11 0.090 15.% + Charge mix_rho 0.78206 10 0.078 12.% + LOOP_ions force_stress 0.54588 1 0.55 8.3% + Force_Stress_LCAO getForceStress 0.54584 1 0.55 8.3% + Force_LCAO_gamma ftable_gamma 0.33292 1 0.33 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.32509 1 0.33 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:41 2022 + Finish Time : Wed Sep 28 11:14:48 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..cdd6cfbed407465718317cef3a49a1532ad848b6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123705 ima = 3.71001e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122761149812 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111713460899 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112275256562 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112528578198 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112472461843 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112504262366 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112500968003 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112503506427 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112502980425 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112502888317 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112502884167 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/STRU new file mode 100644 index 0000000000000000000000000000000000000000..bf0bd644c1d81b9fe0ef7d6cd906cdbe26d914f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.328481688843 17.193560160276 4.604848139366 0 0 0 +H +0.0 +2 +-12.161348347015 18.551394032885 4.178545586564 0 0 0 +-12.366372202845 16.316840959361 5.881145713908 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/conv new file mode 100644 index 0000000000000000000000000000000000000000..a5ba3576af98e1979de7087648176871473b8b43 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/conv @@ -0,0 +1 @@ +18 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d46533f145f6817269a9ec97186b87f73661a251 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752169863 0.01276478313 1.273239059 1.35731895 1.469627739 0.009068336058 0.01750926207 0.03910910826 +-3.850849686e-19 0.0009784095451 0.002754672893 0.01289700757 0.04640375974 2.314989021e-19 2.49396092e-06 6.805957482e-06 +0.001605124679 0.006095465343 + +H atom_index 1 n_descriptor 18 +1.242498434 0.03487047638 0.1070348256 0.1461489064 0.3176093274 0.02239916152 0.02781519565 0.03798544326 +-6.923305675e-18 4.832586637e-05 0.1006519517 0.1147934113 0.1253900891 -4.847033216e-18 4.057046365e-06 0.01339173674 +0.02641846692 0.03039559788 + +H atom_index 2 n_descriptor 18 +1.256343449 0.03440124461 0.1118970996 0.1525900426 0.3221733317 0.02306862837 0.02862543789 0.03755021215 +-1.528768858e-18 4.964980847e-05 0.1038421752 0.1156430733 0.1309505381 1.813026795e-18 3.277306498e-06 0.01327830195 +0.02693271705 0.03103006464 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d9ca4dd8433d0bf5bd60344b8238cd1cebb5cbe1 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:41 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0869255 SEC) : SETUP UNITCELL + DONE(0.0879118 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.10592 SEC) : INIT PLANEWAVE + DONE(0.160639 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.440559 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651974e+02 0.000000e+00 2.140e-01 5.090e-01 + GE2 -4.664082e+02 -1.210861e+00 9.773e-02 4.497e-01 + GE3 -4.664119e+02 -3.615576e-03 6.264e-02 5.198e-01 + GE4 -4.664117e+02 1.969315e-04 1.948e-03 3.827e-01 + GE5 -4.664108e+02 8.217200e-04 8.846e-04 3.813e-01 + GE6 -4.664114e+02 -5.536829e-04 1.011e-04 3.634e-01 + GE7 -4.664112e+02 1.762182e-04 3.491e-05 3.635e-01 + GE8 -4.664112e+02 -3.133478e-05 1.218e-05 3.559e-01 + GE9 -4.664112e+02 1.661283e-05 1.880e-06 3.557e-01 + GE10 -4.664112e+02 -2.301122e-06 1.152e-07 3.574e-01 + GE11 -4.664112e+02 -5.144659e-07 4.393e-08 2.910e-01 +E_delta_band = -7.07091380e-02 Ry = -9.62047178e-01 eV +E_delta_NN= -1.94920965e-01 Ry = -2.65203578e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5633 11 0.6 1e+02 % + Run_lcao lcao_line 6.5535 1 6.6 1e+02 % + Potential init_pot 0.28263 2 0.14 4.3 % + PW_Basis recip2real 0.28366 16 0.018 4.3 % + PW_Basis gathers_scatterp 0.12632 16 0.0079 1.9 % + Potential v_of_rho 0.96418 13 0.074 15 % + XC_Functional v_xc 0.27728 14 0.02 4.2 % + H_Hartree_pw v_hartree 0.64579 13 0.05 9.8 % + PW_Basis real2recip 0.65077 38 0.017 9.9 % + PW_Basis gatherp_scatters 0.25166 38 0.0066 3.8 % + ORB_control set_orb_tables 1.0981 1 1.1 17 % + ORB_gen_tables gen_tables 1.0981 1 1.1 17 % + ORB_table_phi init_Table 0.4771 1 0.48 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.4718 126 0.0037 7.2 % + ORB_table_beta init_Table_Beta 0.18637 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18476 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25004 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24801 66 0.0038 3.8 % + LOOP_ions opt_ions 4.9375 1 4.9 75 % + ESolver_KS_LCAO Run 4.3915 1 4.4 67 % + HSolverLCAO solve 2.1472 11 0.2 33 % + HamiltLCAO updateHk 1.1438 11 0.1 17 % + LCAO_Hamilt cal_Hgamma 1.1161 11 0.1 17 % + Gint_interface cal_gint 1.9657 23 0.085 30 % + Gint_Gamma distri_vl 2.1292 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.7839 13 0.37 73 % + LCAO_gen_fixedH add_v_delta 1.982 6 0.33 30 % + LCAO_DESCRIPTOR add_v_delta 1.9821 6 0.33 30 % + ElecStateLCAO psiToRho 0.98725 11 0.09 15 % + Charge mix_rho 0.78206 10 0.078 12 % + LOOP_ions force_stress 0.54588 1 0.55 8.3 % + Force_Stress_LCAO getForceStress 0.54584 1 0.55 8.3 % + Force_LCAO_gamma ftable_gamma 0.33292 1 0.33 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.32509 1 0.33 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:41 2022 + FINISH Time : Wed Sep 28 11:14:48 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/18/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3c9d54642be2799584e963ed3cee4ff07b13f146 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.513621 0.600669 0.15401 +H 0.462473 0.643659 0.146471 +H 0.538503 0.621862 0.21364 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..33de89873fb1d96b2174975c93a1009221d3a256 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0148 2 + 2 -12.5639 2 + 3 -9.26753 2 + 4 -6.68827 2 + 5 0.984311 0 + 6 3.87258 0 + 7 11.1503 0 + 8 11.4167 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..687f064b29899d904503d613f858a3778fddd3be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:33 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.3813975937 16.8187405314 4.31229117203 0 0 0 0 + tauc_H1 12.9492403763 18.0224659919 4.10118769823 0 0 0 0 + tauc_H2 15.0780865756 17.4121276831 5.98193190085 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0859207350179 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0952595104416 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.114225798398 (SEC) + + DONE : INIT CHARGE Time : 0.163091138066 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44274 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000693 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000849 + + Density error is 0.210451734841 + + Energy Rydberg eV + E_KohnSham -34.1907211968 -465.188627006 + E_Harris -34.3733769004 -467.673785348 + E_Fermi -0.384720244198 -5.23438745705 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000979497408363 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103499062455 + + Density error is 0.0987231246216 + + Energy Rydberg eV + E_KohnSham -34.2784211284 -466.38184579 + E_Harris -34.2856688497 -466.480456098 + E_Fermi -0.196567034793 -2.67443171214 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000938717196896 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000988084716859 + + Density error is 0.0637519330066 + + Energy Rydberg eV + E_KohnSham -34.2789022943 -466.388392388 + E_Harris -34.283524714 -466.451283635 + E_Fermi -0.190684346595 -2.5943936331 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000896603788137 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000926372329791 + + Density error is 0.00191630037027 + + Energy Rydberg eV + E_KohnSham -34.2787890752 -466.386851963 + E_Harris -34.278790285 -466.386868423 + E_Fermi -0.155437327259 -2.11483333262 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000897044546946 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000925860829991 + + Density error is 0.000950592990036 + + Energy Rydberg eV + E_KohnSham -34.2787575853 -466.386423521 + E_Harris -34.2787579776 -466.386428858 + E_Fermi -0.155513464903 -2.1158692384 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000896581021926 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000925036296187 + + Density error is 0.000172133680549 + + Energy Rydberg eV + E_KohnSham -34.2787697004 -466.386588356 + E_Harris -34.2787697086 -466.386588467 + E_Fermi -0.155017305302 -2.10911864072 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000896790091128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000925209196067 + + Density error is 2.82590562557e-05 + + Energy Rydberg eV + E_KohnSham -34.2787665239 -466.386545137 + E_Harris -34.2787665259 -466.386545164 + E_Fermi -0.155013654744 -2.10906897232 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000896726614824 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000925138222424 + + Density error is 1.09291496597e-05 + + Energy Rydberg eV + E_KohnSham -34.2787686833 -466.386574517 + E_Harris -34.2787686838 -466.386574524 + E_Fermi -0.155024248212 -2.10921310385 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000896729799456 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000925136920743 + + Density error is 1.8062151107e-06 + + Energy Rydberg eV + E_KohnSham -34.2787678034 -466.386562546 + E_Harris -34.2787678035 -466.386562546 + E_Fermi -0.155013466854 -2.10906641595 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000896731201344 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000925138258055 + + Density error is 2.30827925286e-07 + + Energy Rydberg eV + E_KohnSham -34.2787679489 -466.386564525 + E_Harris -34.2787679489 -466.386564525 + E_Fermi -0.155011838681 -2.10904426352 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000896731626562 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000925138775412 + + Density error is 3.53496090564e-08 + + Energy Rydberg eV + E_KohnSham -34.2787679733 -466.386564857 + E_Harris -34.2787679733 -466.386564857 + E_band -7.86942989493 -107.069086583 + E_one_elec -68.5883620256 -933.192540035 + E_Hartree +35.7014143654 +485.742662028 + E_xc -8.15534990631 -110.95922791 + E_Ewald +6.88925563504 +93.7331316152 + E_demet -8.49859949483e-59 -1.1562937815e-57 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193613752954 -2.63425025134 + E_Fermi -0.155011722446 -2.10904268206 + + charge density convergence is achieved + final etot is -466.386564857 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0148 2.00000 + 2 -12.5639 2.00000 + 3 -9.26753 2.00000 + 4 -6.68827 2.00000 + 5 0.984311 0.00000 + 6 3.87258 0.00000 + 7 11.1503 0.00000 + 8 11.4167 0.00000 + + EFERMI = -2.109042682063304 eV + OUT.ABACUS/ final etot is -466.3865648573284 eV + correction force for each atom along direction 1 is 4.49153e-05 + correction force for each atom along direction 2 is 0.000122466 + correction force for each atom along direction 3 is 0.000145196 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.25388381 +1.1874365 +1.2531196 + H1 +0.57869806 -0.62734945 -0.10000481 + H2 -0.32481425 -0.56008709 -1.1531148 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3865648573284 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.7085 11 0.52 1.0e+02% + Run_lcao lcao_line 5.6984 1 5.7 1.e+02% + Potential init_pot 0.28563 2 0.14 5.0% + PW_Basis recip2real 0.27252 16 0.017 4.8% + PW_Basis gathers_scatterp 0.11997 16 0.0075 2.1% + Potential v_of_rho 0.88501 13 0.068 16.% + XC_Functional v_xc 0.25191 14 0.018 4.4% + H_Hartree_pw v_hartree 0.59237 13 0.046 10.% + PW_Basis real2recip 0.55551 38 0.015 9.7% + PW_Basis gatherp_scatters 0.21603 38 0.0057 3.8% + ORB_control set_orb_tables 1.1009 1 1.1 19.% + ORB_gen_tables gen_tables 1.1009 1 1.1 19.% + ORB_table_phi init_Table 0.48250 1 0.48 8.5% + ORB_table_phi cal_ST_Phi12_R 0.47766 126 0.0038 8.4% + ORB_table_beta init_Table_Beta 0.18783 1 0.19 3.3% + ORB_table_beta VNL_PhiBeta_R 0.18637 56 0.0033 3.3% + ORB_table_alpha init_Table_Alpha 0.25108 1 0.25 4.4% + ORB_table_alpha S_PhiAlpha_R 0.24928 66 0.0038 4.4% + LOOP_ions opt_ions 4.0790 1 4.1 71.% + ESolver_KS_LCAO Run 3.5985 1 3.6 63.% + HSolverLCAO solve 1.6300 11 0.15 29.% + HamiltLCAO updateHk 0.89274 11 0.081 16.% + LCAO_Hamilt cal_Hgamma 0.86017 11 0.078 15.% + Gint_interface cal_gint 1.4391 23 0.063 25.% + Gint_Gamma distri_vl 1.7451 6 0.29 31.% + LCAO_Deepks cal_projected_DM 3.9411 13 0.30 69.% + LCAO_gen_fixedH add_v_delta 1.6124 6 0.27 28.% + LCAO_DESCRIPTOR add_v_delta 1.6124 6 0.27 28.% + ElecStateLCAO psiToRho 0.71879 11 0.065 13.% + Charge mix_rho 0.65330 10 0.065 11.% + LOOP_ions force_stress 0.48030 1 0.48 8.4% + Force_Stress_LCAO getForceStress 0.48026 1 0.48 8.4% + Force_LCAO_gamma ftable_gamma 0.27111 1 0.27 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.26445 1 0.26 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:33 2022 + Finish Time : Wed Sep 28 11:09:39 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1818a8e3657ed4bb7b459c49dc4def5f0bbf88cc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.01234 ima = 3.71709e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123332249992 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011180858136 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112630065146 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112830825264 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112817805371 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112826508077 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112823074298 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112824845432 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112824377549 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112824307106 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112824293394 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/STRU new file mode 100644 index 0000000000000000000000000000000000000000..78c9b806c016bc18029ae0e8ec9f44a2bdb10b84 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.618602406311 16.818740531412 4.312291172049 0 0 0 +H +0.0 +2 +-15.050759623706 18.022465991911 4.101187698213 0 0 0 +-12.921913424450 17.412127683051 5.981931900840 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/conv new file mode 100644 index 0000000000000000000000000000000000000000..ad4fd420dacabc7f6da83fcf5e4934b46457a0a0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/conv @@ -0,0 +1 @@ +19 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..29e591d35d7d1329a2d2272742dfc3e188084e75 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752948542 0.01247421157 1.243428871 1.330316938 1.46818925 0.008950236869 0.01683330629 0.03918823045 +-2.643917078e-18 0.000819160967 0.002510259636 0.01182917643 0.04231910274 2.406268402e-19 1.927313917e-06 5.679985248e-06 +0.001569898287 0.005974914057 + +H atom_index 1 n_descriptor 18 +1.209974025 0.03597889936 0.09556484532 0.1321228051 0.306823547 0.0205299027 0.0259250205 0.03932593383 +-5.603127567e-17 3.91750882e-05 0.08895234478 0.112919694 0.1141083008 -3.969300034e-18 5.294998781e-06 0.0139978083 +0.02432089472 0.02874576058 + +H atom_index 2 n_descriptor 18 +1.193319115 0.03649101056 0.0904915412 0.1252902104 0.3004952688 0.01973846685 0.02494509663 0.04000025689 +2.568596195e-17 3.775120091e-05 0.08469486215 0.1069046807 0.1133312901 -5.95326191e-19 5.889764997e-06 0.01447736006 +0.02362691356 0.02785723569 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c9173067683f8e05069c9bb9663cf2711fe99e51 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..d954d8523a0f226c1b47a0dc71372bd9afadbdeb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..f5ccc167d1a85ecc0950bd92932934c46100bbf7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..2396d58cabca11ee91cd9da484efc409acce8075 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..17a9d4c09047a9c2193752e1c173eb19025ce801 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:33 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0859453 SEC) : SETUP UNITCELL + DONE(0.0952775 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.114251 SEC) : INIT PLANEWAVE + DONE(0.163217 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.442806 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651886e+02 0.000000e+00 2.105e-01 4.447e-01 + GE2 -4.663818e+02 -1.193219e+00 9.872e-02 3.629e-01 + GE3 -4.663884e+02 -6.546598e-03 6.375e-02 4.174e-01 + GE4 -4.663869e+02 1.540424e-03 1.916e-03 3.109e-01 + GE5 -4.663864e+02 4.284425e-04 9.506e-04 3.084e-01 + GE6 -4.663866e+02 -1.648347e-04 1.721e-04 3.054e-01 + GE7 -4.663865e+02 4.321903e-05 2.826e-05 2.882e-01 + GE8 -4.663866e+02 -2.938049e-05 1.093e-05 2.883e-01 + GE9 -4.663866e+02 1.197138e-05 1.806e-06 2.907e-01 + GE10 -4.663866e+02 -1.979711e-06 2.308e-07 2.868e-01 + GE11 -4.663866e+02 -3.318714e-07 3.535e-08 2.334e-01 +E_delta_band = -6.78877111e-02 Ry = -9.23659695e-01 eV +E_delta_NN= -1.93613753e-01 Ry = -2.63425025e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.7085 11 0.52 1e+02 % + Run_lcao lcao_line 5.6984 1 5.7 1e+02 % + Potential init_pot 0.28563 2 0.14 5 % + PW_Basis recip2real 0.27252 16 0.017 4.8 % + PW_Basis gathers_scatterp 0.11997 16 0.0075 2.1 % + Potential v_of_rho 0.88501 13 0.068 16 % + XC_Functional v_xc 0.25191 14 0.018 4.4 % + H_Hartree_pw v_hartree 0.59237 13 0.046 10 % + PW_Basis real2recip 0.55551 38 0.015 9.7 % + PW_Basis gatherp_scatters 0.21603 38 0.0057 3.8 % + ORB_control set_orb_tables 1.1009 1 1.1 19 % + ORB_gen_tables gen_tables 1.1009 1 1.1 19 % + ORB_table_phi init_Table 0.4825 1 0.48 8.5 % + ORB_table_phi cal_ST_Phi12_R 0.47766 126 0.0038 8.4 % + ORB_table_beta init_Table_Beta 0.18783 1 0.19 3.3 % + ORB_table_beta VNL_PhiBeta_R 0.18637 56 0.0033 3.3 % + ORB_table_alpha init_Table_Alpha 0.25108 1 0.25 4.4 % + ORB_table_alpha S_PhiAlpha_R 0.24928 66 0.0038 4.4 % + LOOP_ions opt_ions 4.079 1 4.1 71 % + ESolver_KS_LCAO Run 3.5985 1 3.6 63 % + HSolverLCAO solve 1.63 11 0.15 29 % + HamiltLCAO updateHk 0.89274 11 0.081 16 % + LCAO_Hamilt cal_Hgamma 0.86017 11 0.078 15 % + Gint_interface cal_gint 1.4391 23 0.063 25 % + Gint_Gamma distri_vl 1.7451 6 0.29 31 % + LCAO_Deepks cal_projected_DM 3.9411 13 0.3 69 % + LCAO_gen_fixedH add_v_delta 1.6124 6 0.27 28 % + LCAO_DESCRIPTOR add_v_delta 1.6124 6 0.27 28 % + ElecStateLCAO psiToRho 0.71879 11 0.065 13 % + Charge mix_rho 0.6533 10 0.065 11 % + LOOP_ions force_stress 0.4803 1 0.48 8.4 % + Force_Stress_LCAO getForceStress 0.48026 1 0.48 8.4 % + Force_LCAO_gamma ftable_gamma 0.27111 1 0.27 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.26445 1 0.26 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:33 2022 + FINISH Time : Wed Sep 28 11:09:39 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/19/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..7090613aa84218f7400c4d809bfc7c0347b13a5b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.519683 0.678845 0.340891 +H 0.556366 0.646019 0.297784 +H 0.534059 0.73882 0.31788 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..fd5b8506150bdfd129f0920df47ac8170aa93fdb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4397 2 + 2 -12.6094 2 + 3 -9.53811 2 + 4 -6.78 2 + 5 1.22864 0 + 6 4.35183 0 + 7 11.067 0 + 8 11.3633 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0f16d51bbecd429c6d6b1a3cfb8c326846364ec1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:05 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.5511148784 19.0076647037 9.54494103748 0 0 0 0 + tauc_H1 15.5782507172 18.0885286276 8.33795343083 0 0 0 0 + tauc_H2 14.9536416867 20.6869639438 8.90064840609 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101109287398 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101492035744 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119522989615 (SEC) + + DONE : INIT CHARGE Time : 0.162488416927 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443884 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00153 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00084 + + Density error is 0.212221805597 + + Energy Rydberg eV + E_KohnSham -34.190263609 -465.182401204 + E_Harris -34.3773537801 -467.727893571 + E_Fermi -0.405014611021 -5.51050648313 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0014250203976 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113437536269 + + Density error is 0.0973246495213 + + Energy Rydberg eV + E_KohnSham -34.2778389694 -466.373925111 + E_Harris -34.2846905228 -466.467145276 + E_Fermi -0.216599152359 -2.94698265406 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0013071615405 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108963233805 + + Density error is 0.0623945553943 + + Energy Rydberg eV + E_KohnSham -34.2780592089 -466.376921623 + E_Harris -34.2824999612 -466.437341156 + E_Fermi -0.205626470013 -2.7976916518 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109632468481 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104027941121 + + Density error is 0.00191582152355 + + Energy Rydberg eV + E_KohnSham -34.2780339041 -466.376577334 + E_Harris -34.2780343855 -466.376583883 + E_Fermi -0.169815254506 -2.3104550686 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109521676676 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010430497573 + + Density error is 0.000814859229204 + + Energy Rydberg eV + E_KohnSham -34.2779834931 -466.375891456 + E_Harris -34.277984679 -466.375907591 + E_Fermi -0.169323038988 -2.30375813291 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109299217221 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010419549623 + + Density error is 0.000101812508375 + + Energy Rydberg eV + E_KohnSham -34.2780189589 -466.376373993 + E_Harris -34.2780189675 -466.37637411 + E_Fermi -0.1692500975 -2.30276571306 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109255739947 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010418854357 + + Density error is 3.13700034247e-05 + + Energy Rydberg eV + E_KohnSham -34.2780091257 -466.376240205 + E_Harris -34.2780091308 -466.376240275 + E_Fermi -0.169157220488 -2.30150205648 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109257497571 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010418043117 + + Density error is 1.68843052585e-05 + + Energy Rydberg eV + E_KohnSham -34.2780102844 -466.37625597 + E_Harris -34.2780102857 -466.376255988 + E_Fermi -0.169195948209 -2.30202897415 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109255271943 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104182132566 + + Density error is 2.22540864181e-06 + + Energy Rydberg eV + E_KohnSham -34.2780089596 -466.376237946 + E_Harris -34.2780089596 -466.376237946 + E_Fermi -0.169179470303 -2.30180478075 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109255202569 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104182505444 + + Density error is 5.75517500654e-07 + + Energy Rydberg eV + E_KohnSham -34.2780092424 -466.376241793 + E_Harris -34.2780092424 -466.376241793 + E_Fermi -0.169178222395 -2.30178780209 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109255180478 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104182563478 + + Density error is 1.31283019894e-07 + + Energy Rydberg eV + E_KohnSham -34.2780092679 -466.37624214 + E_Harris -34.2780092679 -466.37624214 + E_Fermi -0.16917784425 -2.30178265716 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109255150268 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104182572378 + + Density error is 1.1301652133e-08 + + Energy Rydberg eV + E_KohnSham -34.2780092763 -466.376242255 + E_Harris -34.2780092763 -466.376242255 + E_band -7.99183240232 -108.734458133 + E_one_elec -69.2871673278 -942.700273937 + E_Hartree +36.023471418 +490.124473025 + E_xc -8.20668376843 -111.657660935 + E_Ewald +7.31664824964 +99.5481064568 + E_demet -8.89704666686e-76 -1.21050530041e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194838073808 -2.65090799113 + E_Fermi -0.169177697108 -2.30178065519 + + charge density convergence is achieved + final etot is -466.376242255 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4397 2.00000 + 2 -12.6094 2.00000 + 3 -9.53811 2.00000 + 4 -6.78000 2.00000 + 5 1.22864 0.00000 + 6 4.35183 0.00000 + 7 11.0670 0.00000 + 8 11.3633 0.00000 + + EFERMI = -2.301780655189618 eV + OUT.ABACUS/ final etot is -466.3762422549085 eV + correction force for each atom along direction 1 is 0.000114585 + correction force for each atom along direction 2 is 5.84653e-05 + correction force for each atom along direction 3 is -5.17923e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.23382641 +0.36237870 -0.31799938 + H1 +0.11428167 -0.86984648 -0.072150170 + H2 -0.34810807 +0.50746779 +0.39014955 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3762422549085 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6445 11 0.69 1.0e+02% + Run_lcao lcao_line 7.6345 1 7.6 1.e+02% + Potential init_pot 0.28287 2 0.14 3.7% + PW_Basis recip2real 0.27423 17 0.016 3.6% + PW_Basis gathers_scatterp 0.12473 17 0.0073 1.6% + Potential v_of_rho 0.83530 14 0.060 11.% + XC_Functional v_xc 0.19530 15 0.013 2.6% + H_Hartree_pw v_hartree 0.60156 14 0.043 7.9% + PW_Basis real2recip 0.70636 41 0.017 9.2% + PW_Basis gatherp_scatters 0.28873 41 0.0070 3.8% + ORB_control set_orb_tables 1.1002 1 1.1 14.% + ORB_gen_tables gen_tables 1.1002 1 1.1 14.% + ORB_table_phi init_Table 0.47662 1 0.48 6.2% + ORB_table_phi cal_ST_Phi12_R 0.47135 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18461 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18308 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.25162 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24967 66 0.0038 3.3% + LOOP_ions opt_ions 6.0136 1 6.0 79.% + ESolver_KS_LCAO Run 5.4337 1 5.4 71.% + HSolverLCAO solve 3.0935 12 0.26 40.% + HamiltLCAO updateHk 1.5647 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.5352 12 0.13 20.% + Gint_interface cal_gint 1.2757 25 0.051 17.% + Gint_Gamma distri_vl_value 0.61716 12 0.051 8.1% + Gint_Gamma distri_vl 2.8222 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.6851 14 0.41 74.% + LCAO_gen_fixedH add_v_delta 2.6809 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.6810 6 0.45 35.% + ElecStateLCAO psiToRho 1.5096 12 0.13 20.% + Charge mix_rho 0.89939 11 0.082 12.% + LOOP_ions force_stress 0.57970 1 0.58 7.6% + Force_Stress_LCAO getForceStress 0.57967 1 0.58 7.6% + Force_LCAO_gamma ftable_gamma 0.38476 1 0.38 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.22139 1 0.22 2.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:05 2022 + Finish Time : Wed Sep 28 11:13:13 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..72566d98ea556b601278a3798a855b556496f400 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123988 ima = 3.68362e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122308786478 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111238396192 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111832200382 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112080879732 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112029815874 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112056647296 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011205637088 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112058858494 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112058026191 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112057937521 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112057909776 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112057902953 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a1338c0eb0c0d2e8eff98d74ba287454a15ae15d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.448885121540 19.007664703688 9.544941037462 0 0 0 +H +0.0 +2 +-12.421749282763 18.088528627600 8.337953430816 0 0 0 +-13.046358313309 20.686963943833 8.900648406063 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/conv new file mode 100644 index 0000000000000000000000000000000000000000..8db0d358f38c074733148ce3c41218256a270a2f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/conv @@ -0,0 +1 @@ +2 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b47e241a2f9a7ad2a562deaeaf2af815bb721b68 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755638009 0.01283374258 1.269829658 1.347768687 1.469779245 0.009817547275 0.01613656585 0.03920617379 +-3.127511501e-18 0.0008479843907 0.002918916832 0.01369205463 0.04706701713 9.30889209e-19 3.042788242e-06 7.944389578e-06 +0.001593042994 0.006190125311 + +H atom_index 1 n_descriptor 18 +1.251563273 0.0350632747 0.1132782843 0.1503060817 0.3197920994 0.02370681937 0.02832035139 0.03816392118 +1.792523394e-17 5.005787702e-05 0.1039506459 0.1158198714 0.1288215482 1.70883704e-17 2.447228958e-06 0.01345782842 +0.02734995634 0.03081594595 + +H atom_index 2 n_descriptor 18 +1.242918755 0.03535015993 0.1101857887 0.1462987991 0.3168749263 0.02326787484 0.02781185928 0.03844405844 +-2.734067202e-17 4.926930101e-05 0.1020891884 0.1151369216 0.125360839 -9.166067452e-18 2.911268475e-06 0.01354436419 +0.02702662994 0.03041271093 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0bdeeabaab42e3909e78dd4ff89c2648654b0958 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/dm_eig.npy differ diff --git 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@@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:05 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101132 SEC) : SETUP UNITCELL + DONE(0.101507 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119543 SEC) : INIT PLANEWAVE + DONE(0.16262 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443952 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651824e+02 0.000000e+00 2.122e-01 5.492e-01 + GE2 -4.663739e+02 -1.191524e+00 9.732e-02 5.039e-01 + GE3 -4.663769e+02 -2.996512e-03 6.239e-02 5.669e-01 + GE4 -4.663766e+02 3.442893e-04 1.916e-03 4.319e-01 + GE5 -4.663759e+02 6.858773e-04 8.149e-04 4.328e-01 + GE6 -4.663764e+02 -4.825364e-04 1.018e-04 4.276e-01 + GE7 -4.663762e+02 1.337873e-04 3.137e-05 4.227e-01 + GE8 -4.663763e+02 -1.576499e-05 1.688e-05 4.181e-01 + GE9 -4.663762e+02 1.802465e-05 2.225e-06 4.176e-01 + GE10 -4.663762e+02 -3.847385e-06 5.755e-07 4.166e-01 + GE11 -4.663762e+02 -3.471550e-07 1.313e-07 4.198e-01 + GE12 -4.663762e+02 -1.146577e-07 1.130e-08 3.642e-01 +E_delta_band = -7.05602260e-02 Ry = -9.60021126e-01 eV +E_delta_NN= -1.94838074e-01 Ry = -2.65090799e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6445 11 0.69 1e+02 % + Run_lcao lcao_line 7.6345 1 7.6 1e+02 % + Potential init_pot 0.28287 2 0.14 3.7 % + PW_Basis recip2real 0.27423 17 0.016 3.6 % + PW_Basis gathers_scatterp 0.12473 17 0.0073 1.6 % + Potential v_of_rho 0.8353 14 0.06 11 % + XC_Functional v_xc 0.1953 15 0.013 2.6 % + H_Hartree_pw v_hartree 0.60156 14 0.043 7.9 % + PW_Basis real2recip 0.70636 41 0.017 9.2 % + PW_Basis gatherp_scatters 0.28873 41 0.007 3.8 % + ORB_control set_orb_tables 1.1002 1 1.1 14 % + ORB_gen_tables gen_tables 1.1002 1 1.1 14 % + ORB_table_phi init_Table 0.47662 1 0.48 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.47135 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18461 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18308 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.25162 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24967 66 0.0038 3.3 % + LOOP_ions opt_ions 6.0136 1 6 79 % + ESolver_KS_LCAO Run 5.4337 1 5.4 71 % + HSolverLCAO solve 3.0935 12 0.26 40 % + HamiltLCAO updateHk 1.5647 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.5352 12 0.13 20 % + Gint_interface cal_gint 1.2757 25 0.051 17 % + Gint_Gamma distri_vl_value 0.61716 12 0.051 8.1 % + Gint_Gamma distri_vl 2.8222 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.6851 14 0.41 74 % + LCAO_gen_fixedH add_v_delta 2.6809 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.681 6 0.45 35 % + ElecStateLCAO psiToRho 1.5096 12 0.13 20 % + Charge mix_rho 0.89939 11 0.082 12 % + LOOP_ions force_stress 0.5797 1 0.58 7.6 % + Force_Stress_LCAO getForceStress 0.57967 1 0.58 7.6 % + Force_LCAO_gamma ftable_gamma 0.38476 1 0.38 5 % + Force_LCAO_gamma cal_fvl_dphi 0.22139 1 0.22 2.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:05 2022 + FINISH Time : Wed Sep 28 11:13:13 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/2/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..48514b35fc602ee0a36611b2e2a5a0367e8302f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.493267 0.604961 0.150713 +H 0.439075 0.571443 0.14402 +H 0.477907 0.663449 0.137244 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0ec8c0439ed8e30dfc7aff8654578b2816d9f2ef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.7128 2 + 2 -13.4652 2 + 3 -9.13391 2 + 4 -6.83729 2 + 5 1.64214 0 + 6 5.03819 0 + 7 10.9685 0 + 8 11.2028 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..835b8b44a804f202f90de2f0143fc741da435f69 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:50 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.811463076 16.9389108305 4.21997265551 0 0 0 0 + tauc_H1 12.294104239 16.0004054603 4.03255993205 0 0 0 0 + tauc_H2 13.3813879599 18.5765703828 3.84283409893 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0738303948067 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0885356826286 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104250706367 (SEC) + + DONE : INIT CHARGE Time : 0.145330269792 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388902 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00173 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000704 + + Density error is 0.219824293391 + + Energy Rydberg eV + E_KohnSham -34.1817066156 -465.065977336 + E_Harris -34.3842757896 -467.822072342 + E_Fermi -0.432648001277 -5.88647804568 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00157119605246 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000890690658953 + + Density error is 0.0969925706885 + + Energy Rydberg eV + E_KohnSham -34.2732454174 -466.311426629 + E_Harris -34.2798208455 -466.400889917 + E_Fermi -0.238482217256 -3.24471702636 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00142698510171 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000856688601599 + + Density error is 0.0615810626395 + + Energy Rydberg eV + E_KohnSham -34.273394019 -466.313448457 + E_Harris -34.2775013662 -466.369331784 + E_Fermi -0.221104790999 -3.00828501268 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00119128287151 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000812521682439 + + Density error is 0.00214423577003 + + Energy Rydberg eV + E_KohnSham -34.2734933801 -466.314800335 + E_Harris -34.2734973621 -466.314854513 + E_Fermi -0.185355904916 -2.5218964648 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118677547136 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000815616626279 + + Density error is 0.00097777175043 + + Energy Rydberg eV + E_KohnSham -34.273403728 -466.313580555 + E_Harris -34.2734079957 -466.31363862 + E_Fermi -0.183565819558 -2.49754110403 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118577489818 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00081449171261 + + Density error is 0.00010965229118 + + Energy Rydberg eV + E_KohnSham -34.273470323 -466.314486627 + E_Harris -34.2734703495 -466.314486987 + E_Fermi -0.18418758806 -2.50600069849 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118521036114 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000814510352585 + + Density error is 6.83308069073e-05 + + Energy Rydberg eV + E_KohnSham -34.2734483945 -466.314188274 + E_Harris -34.273448417 -466.31418858 + E_Fermi -0.184005604659 -2.50352468729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118533232902 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00081446358666 + + Density error is 7.18890254523e-06 + + Energy Rydberg eV + E_KohnSham -34.2734519575 -466.314236752 + E_Harris -34.2734519577 -466.314236754 + E_Fermi -0.184081956056 -2.50456350135 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001185326283 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00081447196671 + + Density error is 1.84653983078e-06 + + Energy Rydberg eV + E_KohnSham -34.2734504764 -466.314216599 + E_Harris -34.2734504764 -466.3142166 + E_Fermi -0.184077440737 -2.50450206729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118532043726 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000814472321637 + + Density error is 1.53931243815e-07 + + Energy Rydberg eV + E_KohnSham -34.2734505248 -466.314217258 + E_Harris -34.2734505248 -466.314217258 + E_Fermi -0.184075273808 -2.5044725847 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118532107848 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000814472627052 + + Density error is 3.39278453043e-08 + + Energy Rydberg eV + E_KohnSham -34.2734505645 -466.314217799 + E_Harris -34.2734505645 -466.314217799 + E_band -8.10678793219 -110.298508355 + E_one_elec -70.1729514264 -954.751984876 + E_Hartree +36.4554254716 +496.001509427 + E_xc -8.27719602652 -112.617029424 + E_Ewald +7.84380541008 +106.72044758 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19650648751 -2.67360792411 + E_Fermi -0.184075429041 -2.50447469676 + + charge density convergence is achieved + final etot is -466.314217799 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.7128 2.00000 + 2 -13.4652 2.00000 + 3 -9.13391 2.00000 + 4 -6.83729 2.00000 + 5 1.64214 0.00000 + 6 5.03819 0.00000 + 7 10.9685 0.00000 + 8 11.2028 0.00000 + + EFERMI = -2.504474696756650 eV + OUT.ABACUS/ final etot is -466.3142177991002 eV + correction force for each atom along direction 1 is -0.000132396 + correction force for each atom along direction 2 is 2.70928e-05 + correction force for each atom along direction 3 is -0.000187308 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.9178719 -2.5312915 +0.86206702 + H1 -1.1177651 -0.75980441 -0.12257967 + H2 -0.80010676 +3.2910959 -0.73948735 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3142177991002 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9306 11 0.54 1.0e+02% + Run_lcao lcao_line 5.9231 1 5.9 1.e+02% + Potential init_pot 0.24278 2 0.12 4.1% + PW_Basis recip2real 0.26493 16 0.017 4.5% + PW_Basis gathers_scatterp 0.10649 16 0.0067 1.8% + Potential v_of_rho 0.92309 13 0.071 16.% + XC_Functional v_xc 0.27580 14 0.020 4.7% + H_Hartree_pw v_hartree 0.60991 13 0.047 10.% + PW_Basis real2recip 0.60152 38 0.016 10.% + PW_Basis gatherp_scatters 0.22666 38 0.0060 3.8% + ORB_control set_orb_tables 0.89854 1 0.90 15.% + ORB_gen_tables gen_tables 0.89854 1 0.90 15.% + ORB_table_phi init_Table 0.37442 1 0.37 6.3% + ORB_table_phi cal_ST_Phi12_R 0.37026 126 0.0029 6.2% + ORB_table_beta init_Table_Beta 0.15654 1 0.16 2.6% + ORB_table_beta VNL_PhiBeta_R 0.15518 56 0.0028 2.6% + ORB_table_alpha init_Table_Alpha 0.20974 1 0.21 3.5% + ORB_table_alpha S_PhiAlpha_R 0.20808 66 0.0032 3.5% + LOOP_ions opt_ions 4.5665 1 4.6 77.% + ESolver_KS_LCAO Run 4.0816 1 4.1 69.% + HSolverLCAO solve 1.9030 11 0.17 32.% + HamiltLCAO updateHk 1.0260 11 0.093 17.% + LCAO_Hamilt cal_Hgamma 0.99320 11 0.090 17.% + Gint_interface cal_gint 1.7223 23 0.075 29.% + Gint_Gamma distri_vl 1.9684 6 0.33 33.% + LCAO_Deepks cal_projected_DM 4.4310 13 0.34 75.% + LCAO_gen_fixedH add_v_delta 1.8396 6 0.31 31.% + LCAO_DESCRIPTOR add_v_delta 1.8396 6 0.31 31.% + ElecStateLCAO psiToRho 0.86049 11 0.078 15.% + Charge mix_rho 0.76095 10 0.076 13.% + LOOP_ions force_stress 0.48477 1 0.48 8.2% + Force_Stress_LCAO getForceStress 0.48474 1 0.48 8.2% + Force_LCAO_gamma ftable_gamma 0.28508 1 0.29 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.27761 1 0.28 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:50 2022 + Finish Time : Wed Sep 28 11:03:56 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1b7e96fd4b06726d317e155bb7b8285ad2316c9d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124253 ima = 3.69655e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122769466644 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112204753343 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112486143769 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112800477753 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112705996266 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112757917573 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112752833715 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011275628897 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756069021 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755979976 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755982083 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a46645b094698495d6ed2f3e1a7255337bb1abd1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.188536924042 16.938910830488 4.219972655507 0 0 0 +H +0.0 +2 +-15.705895760988 16.000405460355 4.032559932031 0 0 0 +-14.618612040097 18.576570382745 3.842834098930 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/conv new file mode 100644 index 0000000000000000000000000000000000000000..e693c2adb64a8b0aae79eef5f5c852232d0bcb88 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/conv @@ -0,0 +1 @@ +20 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..41c30d257abcd32837a5331d4e94ebc2f5c6cf60 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748732756 0.01286142971 1.308094461 1.393178009 1.471489948 0.008781278097 0.01977262263 0.03903093103 +-8.285082161e-19 0.001283938874 0.002829112704 0.01357603735 0.04926291834 2.218870933e-19 2.443072007e-06 6.717874344e-06 +0.001663330029 0.00586444236 + +H atom_index 1 n_descriptor 18 +1.27545355 0.03322815457 0.1184662422 0.1620731017 0.3282211827 0.02371192878 0.02976347995 0.03651532533 +1.672738214e-19 5.506390647e-05 0.1087699854 0.1185720849 0.1394958644 2.863609816e-18 2.791633845e-06 0.01323969145 +0.02808574937 0.03190058566 + +H atom_index 2 n_descriptor 18 +1.322091247 0.03191426427 0.1373009272 0.1869127872 0.3404810791 0.02580104322 0.03237390553 0.03644954688 +5.681550368e-18 5.95799578e-05 0.1073607771 0.13328877 0.160320266 -3.202235271e-18 5.542366338e-07 0.01462257003 +0.02944286853 0.03345988777 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..b16c34eebfaa00cbc5e5491f10f3b16aac127ab0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:50 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0738454 SEC) : SETUP UNITCELL + DONE(0.0885468 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104265 SEC) : INIT PLANEWAVE + DONE(0.14545 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.388947 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650660e+02 0.000000e+00 2.198e-01 4.571e-01 + GE2 -4.663114e+02 -1.245449e+00 9.699e-02 4.184e-01 + GE3 -4.663134e+02 -2.021828e-03 6.158e-02 4.796e-01 + GE4 -4.663148e+02 -1.351878e-03 2.144e-03 3.541e-01 + GE5 -4.663136e+02 1.219780e-03 9.778e-04 3.531e-01 + GE6 -4.663145e+02 -9.060718e-04 1.097e-04 3.420e-01 + GE7 -4.663142e+02 2.983528e-04 6.833e-05 3.391e-01 + GE8 -4.663142e+02 -4.847784e-05 7.189e-06 3.394e-01 + GE9 -4.663142e+02 2.015228e-05 1.847e-06 3.389e-01 + GE10 -4.663142e+02 -6.586650e-07 1.539e-07 3.387e-01 + GE11 -4.663142e+02 -5.409850e-07 3.393e-08 2.676e-01 +E_delta_band = -7.39724942e-02 Ry = -1.00644742e+00 eV +E_delta_NN= -1.96506488e-01 Ry = -2.67360792e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9306 11 0.54 1e+02 % + Run_lcao lcao_line 5.9231 1 5.9 1e+02 % + Potential init_pot 0.24278 2 0.12 4.1 % + PW_Basis recip2real 0.26493 16 0.017 4.5 % + PW_Basis gathers_scatterp 0.10649 16 0.0067 1.8 % + Potential v_of_rho 0.92309 13 0.071 16 % + XC_Functional v_xc 0.2758 14 0.02 4.7 % + H_Hartree_pw v_hartree 0.60991 13 0.047 10 % + PW_Basis real2recip 0.60152 38 0.016 10 % + PW_Basis gatherp_scatters 0.22666 38 0.006 3.8 % + ORB_control set_orb_tables 0.89854 1 0.9 15 % + ORB_gen_tables gen_tables 0.89854 1 0.9 15 % + ORB_table_phi init_Table 0.37442 1 0.37 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.37026 126 0.0029 6.2 % + ORB_table_beta init_Table_Beta 0.15654 1 0.16 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.15518 56 0.0028 2.6 % + ORB_table_alpha init_Table_Alpha 0.20974 1 0.21 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.20808 66 0.0032 3.5 % + LOOP_ions opt_ions 4.5665 1 4.6 77 % + ESolver_KS_LCAO Run 4.0816 1 4.1 69 % + HSolverLCAO solve 1.903 11 0.17 32 % + HamiltLCAO updateHk 1.026 11 0.093 17 % + LCAO_Hamilt cal_Hgamma 0.9932 11 0.09 17 % + Gint_interface cal_gint 1.7223 23 0.075 29 % + Gint_Gamma distri_vl 1.9684 6 0.33 33 % + LCAO_Deepks cal_projected_DM 4.431 13 0.34 75 % + LCAO_gen_fixedH add_v_delta 1.8396 6 0.31 31 % + LCAO_DESCRIPTOR add_v_delta 1.8396 6 0.31 31 % + ElecStateLCAO psiToRho 0.86049 11 0.078 15 % + Charge mix_rho 0.76095 10 0.076 13 % + LOOP_ions force_stress 0.48477 1 0.48 8.2 % + Force_Stress_LCAO getForceStress 0.48474 1 0.48 8.2 % + Force_LCAO_gamma ftable_gamma 0.28508 1 0.29 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.27761 1 0.28 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:50 2022 + FINISH Time : Wed Sep 28 11:03:56 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/20/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..96ee5b102f789bd62d3a692dd226d150daaecc78 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.464495 0.624837 0.14643 +H 0.480741 0.580504 0.194171 +H 0.410929 0.594427 0.115058 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..68f50dcec0cd02c7cbaff6b8ab933bc8cce451a8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.889 2 + 2 -12.6139 2 + 3 -9.12595 2 + 4 -6.65741 2 + 5 0.907261 0 + 6 3.77467 0 + 7 11.1733 0 + 8 11.424 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..952ecf2c5396c6b15f3ae6e1502112f201ffefa9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:58 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.0058516256 17.4954238267 4.10002869802 0 0 0 0 + tauc_H1 13.4607532563 16.2541095008 5.43679396153 0 0 0 0 + tauc_H2 11.5060002357 16.6439526233 3.22161892408 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.102091173367 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.102526376982 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.120727277219 (SEC) + + DONE : INIT CHARGE Time : 0.165638291797 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448644 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000706 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00136 + + Density error is 0.210152508927 + + Energy Rydberg eV + E_KohnSham -34.1896476372 -465.174020479 + E_Harris -34.3712514903 -467.644867658 + E_Fermi -0.379585871577 -5.16453073375 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000898115163569 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126898401038 + + Density error is 0.099059673174 + + Energy Rydberg eV + E_KohnSham -34.2768303679 -466.360202382 + E_Harris -34.2841574159 -466.459891985 + E_Fermi -0.191773423281 -2.60921128159 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000857212715528 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011904251599 + + Density error is 0.0640628462838 + + Energy Rydberg eV + E_KohnSham -34.2773024601 -466.366625527 + E_Harris -34.2819459656 -466.42980366 + E_Fermi -0.186666634098 -2.53972985021 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00080889675048 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105052751137 + + Density error is 0.00197968014926 + + Energy Rydberg eV + E_KohnSham -34.2771744092 -466.364883305 + E_Harris -34.277177377 -466.364923683 + E_Fermi -0.151637170046 -2.06312954123 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000808738472115 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104921537413 + + Density error is 0.000924855902518 + + Energy Rydberg eV + E_KohnSham -34.2771535086 -466.364598937 + E_Harris -34.2771538566 -466.364603673 + E_Fermi -0.151751109738 -2.06467977026 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000808260898239 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104708144284 + + Density error is 0.000193717124934 + + Energy Rydberg eV + E_KohnSham -34.2771583713 -466.364665098 + E_Harris -34.2771583698 -466.364665078 + E_Fermi -0.151199887236 -2.05718000336 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000808416095757 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104719256412 + + Density error is 2.45823090016e-05 + + Energy Rydberg eV + E_KohnSham -34.2771584029 -466.364665529 + E_Harris -34.2771584039 -466.364665541 + E_Fermi -0.151218404895 -2.05743194904 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000808370474687 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104712509775 + + Density error is 8.47464514193e-06 + + Energy Rydberg eV + E_KohnSham -34.2771598585 -466.364685332 + E_Harris -34.2771598588 -466.364685337 + E_Fermi -0.151220740495 -2.05746372651 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000808373162443 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104711764519 + + Density error is 1.5163778497e-06 + + Energy Rydberg eV + E_KohnSham -34.277159191 -466.36467625 + E_Harris -34.277159191 -466.36467625 + E_Fermi -0.151212528251 -2.05735199319 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000808373678473 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104711581694 + + Density error is 3.29750013285e-07 + + Energy Rydberg eV + E_KohnSham -34.2771593201 -466.364678008 + E_Harris -34.2771593201 -466.364678008 + E_Fermi -0.151211435514 -2.05733712575 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000808374001581 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104711598245 + + Density error is 4.84536180767e-08 + + Energy Rydberg eV + E_KohnSham -34.2771593301 -466.364678143 + E_Harris -34.27715933 -466.364678143 + E_band -7.83294071504 -106.572625821 + E_one_elec -68.408118764 -930.740204651 + E_Hartree +35.621147446 +484.650574564 + E_xc -8.14262288761 -110.786067937 + E_Ewald +6.7785243885 +92.2265557155 + E_demet -3.1935668574e-54 -4.34507062047e-53 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19329099266 -2.62985887226 + E_Fermi -0.15121121183 -2.05733408238 + + charge density convergence is achieved + final etot is -466.364678143 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.8890 2.00000 + 2 -12.6139 2.00000 + 3 -9.12595 2.00000 + 4 -6.65741 2.00000 + 5 0.907261 0.00000 + 6 3.77467 0.00000 + 7 11.1733 0.00000 + 8 11.4240 0.00000 + + EFERMI = -2.057334082378574 eV + OUT.ABACUS/ final etot is -466.3646781425493 eV + correction force for each atom along direction 1 is -8.77805e-05 + correction force for each atom along direction 2 is -5.74842e-05 + correction force for each atom along direction 3 is 9.92646e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.3502342 -1.4278972 -0.31175943 + H1 -0.19418601 +0.54764220 -0.58697465 + H2 +1.5444202 +0.88025496 +0.89873408 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3646781425493 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6158 11 0.69 1.0e+02% + Run_lcao lcao_line 7.6053 1 7.6 1.e+02% + Potential init_pot 0.28492 2 0.14 3.7% + PW_Basis recip2real 0.28249 16 0.018 3.7% + PW_Basis gathers_scatterp 0.12316 16 0.0077 1.6% + Potential v_of_rho 1.0273 13 0.079 13.% + XC_Functional v_xc 0.30917 14 0.022 4.1% + H_Hartree_pw v_hartree 0.67501 13 0.052 8.9% + PW_Basis real2recip 0.69776 38 0.018 9.2% + PW_Basis gatherp_scatters 0.26593 38 0.0070 3.5% + ORB_control set_orb_tables 1.0997 1 1.1 14.% + ORB_gen_tables gen_tables 1.0997 1 1.1 14.% + ORB_table_phi init_Table 0.47572 1 0.48 6.2% + ORB_table_phi cal_ST_Phi12_R 0.47045 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18476 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18318 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.25002 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24802 66 0.0038 3.3% + LOOP_ions opt_ions 5.9820 1 6.0 79.% + ESolver_KS_LCAO Run 5.3725 1 5.4 71.% + HSolverLCAO solve 2.8941 11 0.26 38.% + HamiltLCAO updateHk 1.4791 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.4515 11 0.13 19.% + Gint_interface cal_gint 2.7505 23 0.12 36.% + Gint_Gamma distri_vl 2.5745 6 0.43 34.% + LCAO_Deepks cal_projected_DM 5.8073 13 0.45 76.% + LCAO_gen_fixedH add_v_delta 2.4281 6 0.40 32.% + LCAO_DESCRIPTOR add_v_delta 2.4282 6 0.40 32.% + ElecStateLCAO psiToRho 1.3932 11 0.13 18.% + Charge mix_rho 0.90720 10 0.091 12.% + LOOP_ions force_stress 0.60932 1 0.61 8.0% + Force_Stress_LCAO getForceStress 0.60929 1 0.61 8.0% + Force_LCAO_gamma ftable_gamma 0.38979 1 0.39 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.38155 1 0.38 5.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:58 2022 + Finish Time : Wed Sep 28 11:07:06 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ec9a8d98d50bf5c37d4e1950228fdd43773dc7e7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123447 ima = 3.68786e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123640231008 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112138176309 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112983741391 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113160576901 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113159555425 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113161885621 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113160079039 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113161371598 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113160980548 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011316094185 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113160923481 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/STRU new file mode 100644 index 0000000000000000000000000000000000000000..efae6b5308e01782b32afa3be596fb42996bcff5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.994148374427 17.495423826745 4.100028698001 0 0 0 +H +0.0 +2 +-14.539246743683 16.254109500759 5.436793961513 0 0 0 +-16.493999764324 16.643952623333 3.221618924096 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/conv new file mode 100644 index 0000000000000000000000000000000000000000..283b6d0422c58d7cd731b47d1161589c8bbced5b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/conv @@ -0,0 +1 @@ +21 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0182c285904dd3476780f0cbacd90a6755807287 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751218431 0.01233304848 1.235662953 1.329625901 1.467705612 0.008552906241 0.01744251206 0.03915171869 +1.242840441e-18 0.0008314822776 0.002368029966 0.01125870776 0.04071552374 2.782657208e-19 1.573229154e-06 4.89562091e-06 +0.001581562449 0.005837793226 + +H atom_index 1 n_descriptor 18 +1.210307065 0.03576252955 0.09457717294 0.1326394775 0.3079752163 0.02015900631 0.02600731745 0.03913979871 +-8.856425256e-18 3.619418644e-05 0.08791569813 0.113360794 0.114272528 -5.845173574e-18 5.406284269e-06 0.01387244584 +0.02393869818 0.02879674088 + +H atom_index 2 n_descriptor 18 +1.166911464 0.03703297349 0.08197610621 0.1154336598 0.291155266 0.01815840729 0.0234698533 0.04090220127 +-4.097945686e-18 3.272378152e-05 0.07701715166 0.09815411709 0.1120063853 1.017174206e-17 6.545968619e-06 0.01523473323 +0.02211464768 0.02643446145 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..2e18178b4474d0f210287ea83a30d38ec139672e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:58 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.102115 SEC) : SETUP UNITCELL + DONE(0.102544 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.120747 SEC) : INIT PLANEWAVE + DONE(0.165772 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448709 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651740e+02 0.000000e+00 2.102e-01 5.834e-01 + GE2 -4.663602e+02 -1.186182e+00 9.906e-02 5.426e-01 + GE3 -4.663666e+02 -6.423144e-03 6.406e-02 6.114e-01 + GE4 -4.663649e+02 1.742222e-03 1.980e-03 4.708e-01 + GE5 -4.663646e+02 2.843679e-04 9.249e-04 4.715e-01 + GE6 -4.663647e+02 -6.616105e-05 1.937e-04 4.630e-01 + GE7 -4.663647e+02 -4.304412e-07 2.458e-05 4.489e-01 + GE8 -4.663647e+02 -1.980396e-05 8.475e-06 4.479e-01 + GE9 -4.663647e+02 9.082116e-06 1.516e-06 4.471e-01 + GE10 -4.663647e+02 -1.757471e-06 3.298e-07 4.482e-01 + GE11 -4.663647e+02 -1.347327e-07 4.845e-08 3.750e-01 +E_delta_band = -6.72014797e-02 Ry = -9.14323038e-01 eV +E_delta_NN= -1.93290993e-01 Ry = -2.62985887e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6158 11 0.69 1e+02 % + Run_lcao lcao_line 7.6053 1 7.6 1e+02 % + Potential init_pot 0.28492 2 0.14 3.7 % + PW_Basis recip2real 0.28249 16 0.018 3.7 % + PW_Basis gathers_scatterp 0.12316 16 0.0077 1.6 % + Potential v_of_rho 1.0273 13 0.079 13 % + XC_Functional v_xc 0.30917 14 0.022 4.1 % + H_Hartree_pw v_hartree 0.67501 13 0.052 8.9 % + PW_Basis real2recip 0.69776 38 0.018 9.2 % + PW_Basis gatherp_scatters 0.26593 38 0.007 3.5 % + ORB_control set_orb_tables 1.0997 1 1.1 14 % + ORB_gen_tables gen_tables 1.0997 1 1.1 14 % + ORB_table_phi init_Table 0.47572 1 0.48 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.47045 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18476 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18318 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.25002 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24802 66 0.0038 3.3 % + LOOP_ions opt_ions 5.982 1 6 79 % + ESolver_KS_LCAO Run 5.3725 1 5.4 71 % + HSolverLCAO solve 2.8941 11 0.26 38 % + HamiltLCAO updateHk 1.4791 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.4515 11 0.13 19 % + Gint_interface cal_gint 2.7505 23 0.12 36 % + Gint_Gamma distri_vl 2.5745 6 0.43 34 % + LCAO_Deepks cal_projected_DM 5.8073 13 0.45 76 % + LCAO_gen_fixedH add_v_delta 2.4281 6 0.4 32 % + LCAO_DESCRIPTOR add_v_delta 2.4282 6 0.4 32 % + ElecStateLCAO psiToRho 1.3932 11 0.13 18 % + Charge mix_rho 0.9072 10 0.091 12 % + LOOP_ions force_stress 0.60932 1 0.61 8 % + Force_Stress_LCAO getForceStress 0.60929 1 0.61 8 % + Force_LCAO_gamma ftable_gamma 0.38979 1 0.39 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.38155 1 0.38 5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:58 2022 + FINISH Time : Wed Sep 28 11:07:06 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/21/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d5f6951ec051c61a8cca9494230c11fb9644d88d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.452833 0.623873 0.141436 +H 0.466448 0.645522 0.202805 +H 0.388325 0.62615 0.141955 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8757cf6feaabc3eda0e73260ee7cd291e18617a1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3593 2 + 2 -12.8721 2 + 3 -9.29334 2 + 4 -6.76126 2 + 5 1.27349 0 + 6 4.40543 0 + 7 11.0692 0 + 8 11.3365 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d20863d8f50a86e439eda7061981c2ae087c5775 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:55 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.6793287927 17.4684364113 3.96022098829 0 0 0 0 + tauc_H1 13.0605529366 18.07460913 5.67852621765 0 0 0 0 + tauc_H2 10.8731000191 17.5322090949 3.97473746979 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0865852059478 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.098164694879 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116314464901 (SEC) + + DONE : INIT CHARGE Time : 0.165485831423 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446526 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000822 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00195 + + Density error is 0.214884089906 + + Energy Rydberg eV + E_KohnSham -34.1887833982 -465.162261903 + E_Harris -34.381002183 -467.77753264 + E_Fermi -0.406714327522 -5.53363231254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012712129383 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00151500642245 + + Density error is 0.0978836191439 + + Energy Rydberg eV + E_KohnSham -34.2796922819 -466.399140721 + E_Harris -34.2865691881 -466.492705829 + E_Fermi -0.214743846405 -2.92173992155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0012193838065 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138432824644 + + Density error is 0.0629517003302 + + Energy Rydberg eV + E_KohnSham -34.2801183358 -466.404937481 + E_Harris -34.2845673119 -466.465468907 + E_Fermi -0.204703370885 -2.78513224384 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115877015474 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114345746971 + + Density error is 0.00195452114156 + + Energy Rydberg eV + E_KohnSham -34.2800890695 -466.404539292 + E_Harris -34.2800897797 -466.404548956 + E_Fermi -0.168900580336 -2.29801028808 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116337368942 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114252317363 + + Density error is 0.00101746717323 + + Energy Rydberg eV + E_KohnSham -34.2800216467 -466.403621959 + E_Harris -34.2800233338 -466.403644912 + E_Fermi -0.168367887243 -2.29076262672 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116179558495 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113940824097 + + Density error is 0.000112527364084 + + Energy Rydberg eV + E_KohnSham -34.2800614037 -466.40416288 + E_Harris -34.2800614122 -466.404162996 + E_Fermi -0.1682755582 -2.28950642565 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116172934317 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113909190077 + + Density error is 3.77857618256e-05 + + Energy Rydberg eV + E_KohnSham -34.2800488332 -466.40399185 + E_Harris -34.2800488408 -466.403991954 + E_Fermi -0.168172105358 -2.28809887752 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116165666216 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113911381079 + + Density error is 1.74984337609e-05 + + Energy Rydberg eV + E_KohnSham -34.280051579 -466.404029209 + E_Harris -34.2800515804 -466.404029227 + E_Fermi -0.168214555065 -2.28867643541 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116167115964 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113908250516 + + Density error is 2.96563495341e-06 + + Energy Rydberg eV + E_KohnSham -34.2800501145 -466.404009283 + E_Harris -34.2800501146 -466.404009284 + E_Fermi -0.168198027357 -2.28845156441 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116167178435 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113907252928 + + Density error is 1.49031020725e-07 + + Energy Rydberg eV + E_KohnSham -34.280050341 -466.404012365 + E_Harris -34.280050341 -466.404012365 + E_Fermi -0.168194731522 -2.28840672229 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116167249123 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113907301065 + + Density error is 5.44486184599e-08 + + Energy Rydberg eV + E_KohnSham -34.2800503988 -466.404013151 + E_Harris -34.2800503988 -466.404013151 + E_band -7.97989235898 -108.572005509 + E_one_elec -69.302915799 -942.91454288 + E_Hartree +36.0392253651 +490.338816472 + E_xc -8.20956689068 -111.696887825 + E_Ewald +7.31749024384 +99.5595623757 + E_demet -4.36504650701e-77 -5.93895045304e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194874181353 -2.65139925948 + E_Fermi -0.168194708442 -2.28840640826 + + charge density convergence is achieved + final etot is -466.404013151 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3593 2.00000 + 2 -12.8721 2.00000 + 3 -9.29334 2.00000 + 4 -6.76126 2.00000 + 5 1.27349 0.00000 + 6 4.40543 0.00000 + 7 11.0692 0.00000 + 8 11.3365 0.00000 + + EFERMI = -2.288406408258947 eV + OUT.ABACUS/ final etot is -466.4040131506353 eV + correction force for each atom along direction 1 is -3.65785e-05 + correction force for each atom along direction 2 is 0.000144083 + correction force for each atom along direction 3 is 1.71322e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.91923384 +0.21398179 +0.65797702 + H1 +0.20229737 -0.15120231 -0.39220600 + H2 -1.1215312 -0.062779484 -0.26577102 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4040131506353 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8635 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8547 1 6.9 1.e+02% + Potential init_pot 0.28373 2 0.14 4.1% + PW_Basis recip2real 0.28700 16 0.018 4.2% + PW_Basis gathers_scatterp 0.12274 16 0.0077 1.8% + Potential v_of_rho 1.0071 13 0.077 15.% + XC_Functional v_xc 0.29793 14 0.021 4.3% + H_Hartree_pw v_hartree 0.66709 13 0.051 9.7% + PW_Basis real2recip 0.65018 38 0.017 9.5% + PW_Basis gatherp_scatters 0.24779 38 0.0065 3.6% + ORB_control set_orb_tables 1.1019 1 1.1 16.% + ORB_gen_tables gen_tables 1.1019 1 1.1 16.% + ORB_table_phi init_Table 0.47923 1 0.48 7.0% + ORB_table_phi cal_ST_Phi12_R 0.47405 126 0.0038 6.9% + ORB_table_beta init_Table_Beta 0.18581 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18425 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.25053 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.24858 66 0.0038 3.6% + LOOP_ions opt_ions 5.2200 1 5.2 76.% + ESolver_KS_LCAO Run 4.6395 1 4.6 68.% + HSolverLCAO solve 2.3400 11 0.21 34.% + HamiltLCAO updateHk 1.2373 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2045 11 0.11 18.% + Gint_interface cal_gint 2.1817 23 0.095 32.% + Gint_Gamma distri_vl 2.2370 6 0.37 33.% + LCAO_Deepks cal_projected_DM 5.0596 13 0.39 74.% + LCAO_gen_fixedH add_v_delta 2.0922 6 0.35 30.% + LCAO_DESCRIPTOR add_v_delta 2.0923 6 0.35 30.% + ElecStateLCAO psiToRho 1.0861 11 0.099 16.% + Charge mix_rho 0.77787 10 0.078 11.% + LOOP_ions force_stress 0.58033 1 0.58 8.5% + Force_Stress_LCAO getForceStress 0.58030 1 0.58 8.5% + Force_LCAO_gamma ftable_gamma 0.35996 1 0.36 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.35205 1 0.35 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:55 2022 + Finish Time : Wed Sep 28 11:08:02 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1be9a83b57a17cf536af786c8dacb8f168287df6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123573 ima = 3.69394e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123018482704 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111691246559 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112319890113 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011258680285 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112529720291 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112561059952 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112557167159 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112560106486 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112559355707 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112559210119 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112559201939 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4f237c578c803c409207f8757037f7179f7941f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.320671207297 17.468436411366 3.960220988271 0 0 0 +H +0.0 +2 +-14.939447063406 18.074609130033 5.678526217665 0 0 0 +-17.126899980903 17.532209094890 3.974737469785 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/conv new file mode 100644 index 0000000000000000000000000000000000000000..76824d2c1ec8e7dc2c003642ff0dac76c81a6ce4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/conv @@ -0,0 +1 @@ +22 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d28be6e723fb023ca679dd8f7b8d28341d90c50c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752056284 0.01274021857 1.270670703 1.357864071 1.469580794 0.009039431959 0.01755623677 0.03911397576 +-3.058279332e-18 0.0009760124848 0.002737240891 0.0127952999 0.04619304618 3.34723598e-19 2.427600285e-06 6.695110511e-06 +0.001602968056 0.006073706119 + +H atom_index 1 n_descriptor 18 +1.225833476 0.03540904403 0.1012838492 0.1387463693 0.3119657068 0.02154232754 0.02684154217 0.0385685501 +-3.089400956e-17 4.627564705e-05 0.0961465197 0.1141534182 0.118948114 9.483840003e-18 4.972077753e-06 0.01364904927 +0.02569836757 0.02958821477 + +H atom_index 2 n_descriptor 18 +1.26848319 0.03397093331 0.1161418611 0.1584656196 0.3260829517 0.02359531847 0.02933510536 0.03721630551 +-1.414843766e-17 5.031844374e-05 0.1058620747 0.1168815641 0.1359842044 -1.760405001e-18 2.631060203e-06 0.01326384919 +0.02729098423 0.03155408438 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..453eee29b91831ccdf63d55e44e090375ee34545 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:55 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0866071 SEC) : SETUP UNITCELL + DONE(0.0981817 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116334 SEC) : INIT PLANEWAVE + DONE(0.16562 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44659 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651623e+02 0.000000e+00 2.149e-01 5.293e-01 + GE2 -4.663991e+02 -1.236879e+00 9.788e-02 4.702e-01 + GE3 -4.664049e+02 -5.796760e-03 6.295e-02 5.363e-01 + GE4 -4.664045e+02 3.981882e-04 1.955e-03 4.010e-01 + GE5 -4.664036e+02 9.173334e-04 1.017e-03 4.001e-01 + GE6 -4.664042e+02 -5.409207e-04 1.125e-04 3.937e-01 + GE7 -4.664040e+02 1.710296e-04 3.779e-05 3.840e-01 + GE8 -4.664040e+02 -3.735882e-05 1.750e-05 3.798e-01 + GE9 -4.664040e+02 1.992576e-05 2.966e-06 3.830e-01 + GE10 -4.664040e+02 -3.081435e-06 1.490e-07 3.829e-01 + GE11 -4.664040e+02 -7.860350e-07 5.445e-08 3.170e-01 +E_delta_band = -7.05908633e-02 Ry = -9.60437967e-01 eV +E_delta_NN= -1.94874181e-01 Ry = -2.65139926e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8635 11 0.62 1e+02 % + Run_lcao lcao_line 6.8547 1 6.9 1e+02 % + Potential init_pot 0.28373 2 0.14 4.1 % + PW_Basis recip2real 0.287 16 0.018 4.2 % + PW_Basis gathers_scatterp 0.12274 16 0.0077 1.8 % + Potential v_of_rho 1.0071 13 0.077 15 % + XC_Functional v_xc 0.29793 14 0.021 4.3 % + H_Hartree_pw v_hartree 0.66709 13 0.051 9.7 % + PW_Basis real2recip 0.65018 38 0.017 9.5 % + PW_Basis gatherp_scatters 0.24779 38 0.0065 3.6 % + ORB_control set_orb_tables 1.1019 1 1.1 16 % + ORB_gen_tables gen_tables 1.1019 1 1.1 16 % + ORB_table_phi init_Table 0.47923 1 0.48 7 % + ORB_table_phi cal_ST_Phi12_R 0.47405 126 0.0038 6.9 % + ORB_table_beta init_Table_Beta 0.18581 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18425 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.25053 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.24858 66 0.0038 3.6 % + LOOP_ions opt_ions 5.22 1 5.2 76 % + ESolver_KS_LCAO Run 4.6395 1 4.6 68 % + HSolverLCAO solve 2.34 11 0.21 34 % + HamiltLCAO updateHk 1.2373 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.2045 11 0.11 18 % + Gint_interface cal_gint 2.1817 23 0.095 32 % + Gint_Gamma distri_vl 2.237 6 0.37 33 % + LCAO_Deepks cal_projected_DM 5.0596 13 0.39 74 % + LCAO_gen_fixedH add_v_delta 2.0922 6 0.35 30 % + LCAO_DESCRIPTOR add_v_delta 2.0923 6 0.35 30 % + ElecStateLCAO psiToRho 1.0861 11 0.099 16 % + Charge mix_rho 0.77787 10 0.078 11 % + LOOP_ions force_stress 0.58033 1 0.58 8.5 % + Force_Stress_LCAO getForceStress 0.5803 1 0.58 8.5 % + Force_LCAO_gamma ftable_gamma 0.35996 1 0.36 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.35205 1 0.35 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:55 2022 + FINISH Time : Wed Sep 28 11:08:02 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/22/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..8110cccd2b6c7bacc5da28f495dafe033b3e687c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.44467 0.625423 0.129276 +H 0.489482 0.666577 0.115123 +H 0.388451 0.656741 0.126558 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..899e15ff3c934500481dadf57d2412a1d3cb0a03 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5887 2 + 2 -13.5035 2 + 3 -9.01679 2 + 4 -6.81009 2 + 5 1.59563 0 + 6 4.93983 0 + 7 10.9919 0 + 8 11.218 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9145e533b6c9b7c608667c2e8d17033e6789dbc8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:31 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.4507542694 17.511855742 3.61971758038 0 0 0 0 + tauc_H1 13.7054855543 18.6641459822 3.22344108838 0 0 0 0 + tauc_H2 10.8766290692 18.3887553507 3.54362922157 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0949896706997 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.108009625243 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.127172333504 (SEC) + + DONE : INIT CHARGE Time : 0.170261745048 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.452418 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000775 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00163 + + Density error is 0.219806609448 + + Energy Rydberg eV + E_KohnSham -34.1828295564 -465.08125573 + E_Harris -34.3852653737 -467.835536325 + E_Fermi -0.427017752352 -5.80987457914 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000946814941272 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138158850051 + + Density error is 0.0973358007844 + + Energy Rydberg eV + E_KohnSham -34.2752527998 -466.338738468 + E_Harris -34.2817983135 -466.42779475 + E_Fermi -0.232599643337 -3.16468050215 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000899892145658 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126753004393 + + Density error is 0.0619852528043 + + Energy Rydberg eV + E_KohnSham -34.2755254179 -466.342447627 + E_Harris -34.2796678803 -466.39880872 + E_Fermi -0.216858903809 -2.95051675384 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000834430266151 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107351468774 + + Density error is 0.00212334498913 + + Energy Rydberg eV + E_KohnSham -34.2755981532 -466.343437242 + E_Harris -34.2756013611 -466.343480887 + E_Fermi -0.181152288846 -2.46470333404 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000835970529586 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010692788537 + + Density error is 0.000940261981467 + + Energy Rydberg eV + E_KohnSham -34.2755130816 -466.342279783 + E_Harris -34.2755161905 -466.342322082 + E_Fermi -0.179647494105 -2.44422955126 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000834933752029 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106803144319 + + Density error is 0.000148653274102 + + Energy Rydberg eV + E_KohnSham -34.2755718393 -466.343079223 + E_Harris -34.2755719105 -466.343080192 + E_Fermi -0.180107924131 -2.45049402313 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000835076279914 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106768148198 + + Density error is 5.38104193289e-05 + + Energy Rydberg eV + E_KohnSham -34.2755509022 -466.342794359 + E_Harris -34.2755509179 -466.342794573 + E_Fermi -0.179910381179 -2.44780631339 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000835026095217 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106771953389 + + Density error is 1.50240158445e-05 + + Energy Rydberg eV + E_KohnSham -34.2755555979 -466.342858247 + E_Harris -34.2755555987 -466.342858259 + E_Fermi -0.179974944559 -2.44868474324 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000835019497661 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106768506647 + + Density error is 2.20750247149e-06 + + Energy Rydberg eV + E_KohnSham -34.275554057 -466.342837282 + E_Harris -34.275554057 -466.342837282 + E_Fermi -0.179959459858 -2.44847406308 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000835020908328 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106768135343 + + Density error is 1.41037642012e-07 + + Energy Rydberg eV + E_KohnSham -34.2755542105 -466.342839371 + E_Harris -34.2755542105 -466.342839371 + E_Fermi -0.17995705283 -2.44844131377 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000835021100214 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106768179972 + + Density error is 6.29934120426e-08 + + Energy Rydberg eV + E_KohnSham -34.2755542546 -466.34283997 + E_Harris -34.2755542546 -466.34283997 + E_band -8.07294814787 -109.83809447 + E_one_elec -70.0058874245 -952.47896252 + E_Hartree +36.3806991343 +494.98480545 + E_xc -8.26489680593 -112.449689943 + E_Ewald +7.7374176387 +105.272967692 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196130701767 -2.66849509677 + E_Fermi -0.179957124235 -2.44844228529 + + charge density convergence is achieved + final etot is -466.34283997 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5887 2.00000 + 2 -13.5035 2.00000 + 3 -9.01679 2.00000 + 4 -6.81009 2.00000 + 5 1.59563 0.00000 + 6 4.93983 0.00000 + 7 10.9919 0.00000 + 8 11.2180 0.00000 + + EFERMI = -2.448442285285765 eV + OUT.ABACUS/ final etot is -466.3428399700702 eV + correction force for each atom along direction 1 is 1.06790e-05 + correction force for each atom along direction 2 is 4.97472e-05 + correction force for each atom along direction 3 is 6.15281e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.1469418 -2.5749947 +0.73899793 + H1 +1.9676459 +1.9803350 -0.66490953 + H2 -0.82070416 +0.59465969 -0.074088406 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3428399700702 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6150 11 0.69 1.0e+02% + Run_lcao lcao_line 7.6051 1 7.6 1.e+02% + Potential init_pot 0.28391 2 0.14 3.7% + PW_Basis recip2real 0.28222 16 0.018 3.7% + PW_Basis gathers_scatterp 0.12383 16 0.0077 1.6% + Potential v_of_rho 1.0190 13 0.078 13.% + XC_Functional v_xc 0.30396 14 0.022 4.0% + H_Hartree_pw v_hartree 0.67165 13 0.052 8.8% + PW_Basis real2recip 0.69805 38 0.018 9.2% + PW_Basis gatherp_scatters 0.26482 38 0.0070 3.5% + ORB_control set_orb_tables 1.0993 1 1.1 14.% + ORB_gen_tables gen_tables 1.0993 1 1.1 14.% + ORB_table_phi init_Table 0.47636 1 0.48 6.3% + ORB_table_phi cal_ST_Phi12_R 0.47116 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18404 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18242 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24919 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24723 66 0.0037 3.2% + LOOP_ions opt_ions 5.9776 1 6.0 78.% + ESolver_KS_LCAO Run 5.3619 1 5.4 70.% + HSolverLCAO solve 2.8899 11 0.26 38.% + HamiltLCAO updateHk 1.4754 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.4479 11 0.13 19.% + Gint_interface cal_gint 2.7556 23 0.12 36.% + Gint_Gamma distri_vl 2.5737 6 0.43 34.% + LCAO_Deepks cal_projected_DM 5.8034 13 0.45 76.% + LCAO_gen_fixedH add_v_delta 2.4261 6 0.40 32.% + LCAO_DESCRIPTOR add_v_delta 2.4261 6 0.40 32.% + ElecStateLCAO psiToRho 1.3975 11 0.13 18.% + Charge mix_rho 0.90559 10 0.091 12.% + LOOP_ions force_stress 0.61543 1 0.62 8.1% + Force_Stress_LCAO getForceStress 0.61540 1 0.62 8.1% + Force_LCAO_gamma ftable_gamma 0.39635 1 0.40 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.38808 1 0.39 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:31 2022 + Finish Time : Wed Sep 28 11:03:39 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4f2979498b8ea2c18354dfd0f94601531ad23659 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124055 ima = 3.65888e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123098197725 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112331386751 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112674706315 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011297364924 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112892167447 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112939076938 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112930945047 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112934309511 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011293380566 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112933701035 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112933699175 + charge after normalized = 7.99999999999997 + charge before normalized = 7.99999999999997 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/STRU new file mode 100644 index 0000000000000000000000000000000000000000..fa244de5aa849d7428daa65a7766b3cdb35a1126 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.549245730546 17.511855742028 3.619717580373 0 0 0 +H +0.0 +2 +-14.294514445641 18.664145982267 3.223441088354 0 0 0 +-17.123370930782 18.388755350750 3.543629221561 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/conv new file mode 100644 index 0000000000000000000000000000000000000000..45f3109f6cb40d2bef132687b8c3a292288244c8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/conv @@ -0,0 +1 @@ +23 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..bd3f033b6b246a1cd634658d7671372eb0609dd3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746789403 0.01281057896 1.3035677 1.390302953 1.470917261 0.008386920233 0.02021171015 0.03896635883 +3.096521879e-18 0.001281737132 0.002682038165 0.01326431534 0.04746055164 4.888506204e-20 2.095548626e-06 6.077692803e-06 +0.001712017916 0.005776665447 + +H atom_index 1 n_descriptor 18 +1.309322054 0.03197274723 0.131436325 0.1802433909 0.3380374317 0.02487876449 0.03172279116 0.03614230455 +-2.968846741e-17 5.365948813e-05 0.1079537454 0.1280375241 0.1547326339 2.478846037e-18 1.211652733e-06 0.01395855158 +0.02877128251 0.03309230286 + +H atom_index 2 n_descriptor 18 +1.266213318 0.03330390728 0.1146944612 0.1580051607 0.3263197769 0.02299598783 0.02929176262 0.03652463104 +-3.609573462e-17 4.9634023e-05 0.1073425775 0.1163749421 0.1359562802 8.378400406e-19 3.471851888e-06 0.01306129006 +0.02743009075 0.03154054448 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a13c2566847054a523b62b44fe334f7a875e496c Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..f952710c30b9a711e531536cb595e541871f34b0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..9da0fa1c7ac1c1e01bc84d1ac52f8512dd485d05 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..76dc8c88c80159820efe8673568ca5a2ae1b583d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:31 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0950147 SEC) : SETUP UNITCELL + DONE(0.108028 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.127196 SEC) : INIT PLANEWAVE + DONE(0.170402 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.452483 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650813e+02 0.000000e+00 2.198e-01 5.793e-01 + GE2 -4.663387e+02 -1.257483e+00 9.734e-02 5.433e-01 + GE3 -4.663424e+02 -3.709158e-03 6.199e-02 6.117e-01 + GE4 -4.663434e+02 -9.896149e-04 2.123e-03 4.700e-01 + GE5 -4.663423e+02 1.157459e-03 9.403e-04 4.676e-01 + GE6 -4.663431e+02 -7.994403e-04 1.487e-04 4.556e-01 + GE7 -4.663428e+02 2.848639e-04 5.381e-05 4.548e-01 + GE8 -4.663429e+02 -6.388783e-05 1.502e-05 4.468e-01 + GE9 -4.663428e+02 2.096505e-05 2.208e-06 4.483e-01 + GE10 -4.663428e+02 -2.088684e-06 1.410e-07 4.466e-01 + GE11 -4.663428e+02 -5.992195e-07 6.299e-08 3.757e-01 +E_delta_band = -7.32439047e-02 Ry = -9.96534448e-01 eV +E_delta_NN= -1.96130702e-01 Ry = -2.66849510e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.615 11 0.69 1e+02 % + Run_lcao lcao_line 7.6051 1 7.6 1e+02 % + Potential init_pot 0.28391 2 0.14 3.7 % + PW_Basis recip2real 0.28222 16 0.018 3.7 % + PW_Basis gathers_scatterp 0.12383 16 0.0077 1.6 % + Potential v_of_rho 1.019 13 0.078 13 % + XC_Functional v_xc 0.30396 14 0.022 4 % + H_Hartree_pw v_hartree 0.67165 13 0.052 8.8 % + PW_Basis real2recip 0.69805 38 0.018 9.2 % + PW_Basis gatherp_scatters 0.26482 38 0.007 3.5 % + ORB_control set_orb_tables 1.0993 1 1.1 14 % + ORB_gen_tables gen_tables 1.0993 1 1.1 14 % + ORB_table_phi init_Table 0.47636 1 0.48 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.47116 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18404 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18242 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24919 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24723 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9776 1 6 78 % + ESolver_KS_LCAO Run 5.3619 1 5.4 70 % + HSolverLCAO solve 2.8899 11 0.26 38 % + HamiltLCAO updateHk 1.4754 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.4479 11 0.13 19 % + Gint_interface cal_gint 2.7556 23 0.12 36 % + Gint_Gamma distri_vl 2.5737 6 0.43 34 % + LCAO_Deepks cal_projected_DM 5.8034 13 0.45 76 % + LCAO_gen_fixedH add_v_delta 2.4261 6 0.4 32 % + LCAO_DESCRIPTOR add_v_delta 2.4261 6 0.4 32 % + ElecStateLCAO psiToRho 1.3975 11 0.13 18 % + Charge mix_rho 0.90559 10 0.091 12 % + LOOP_ions force_stress 0.61543 1 0.62 8.1 % + Force_Stress_LCAO getForceStress 0.6154 1 0.62 8.1 % + Force_LCAO_gamma ftable_gamma 0.39635 1 0.4 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.38808 1 0.39 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:31 2022 + FINISH Time : Wed Sep 28 11:03:39 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/23/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..cc4c227398fd0edf19e0ccb841b5c7d336526701 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.428233 0.636309 0.11047 +H 0.427927 0.615091 0.0467266 +H 0.370855 0.667822 0.111935 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b6da1c81ad7218fb24b943e1268d1703398bde38 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2398 2 + 2 -12.7119 2 + 3 -9.32324 2 + 4 -6.73614 2 + 5 1.15637 0 + 6 4.196 0 + 7 11.1003 0 + 8 11.3721 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0bd08242919b0262119b7f21d628ab70476bf485 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:38 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.9905335308 17.8166534638 3.09314951213 0 0 0 0 + tauc_H1 11.9819697629 17.2225466664 1.30834452603 0 0 0 0 + tauc_H2 10.3839443679 18.6990174961 3.13417185446 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0739123197069 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0886101605607 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104890209334 (SEC) + + DONE : INIT CHARGE Time : 0.147403373647 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.389282 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00164 + + Density error is 0.212757952303 + + Energy Rydberg eV + E_KohnSham -34.1903383561 -465.18341819 + E_Harris -34.3781452318 -467.738661824 + E_Fermi -0.398170905884 -5.41739309784 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00132702593558 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00141157594717 + + Density error is 0.0981743066377 + + Energy Rydberg eV + E_KohnSham -34.2796512385 -466.398582297 + E_Harris -34.2866483471 -466.493782843 + E_Fermi -0.207973187229 -2.82962037753 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00125827122093 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130548252547 + + Density error is 0.0632251992467 + + Energy Rydberg eV + E_KohnSham -34.2800696091 -466.404274521 + E_Harris -34.2845853576 -466.465714431 + E_Fermi -0.199464388386 -2.71385223013 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115690406692 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111640723802 + + Density error is 0.00191743961552 + + Energy Rydberg eV + E_KohnSham -34.2800076405 -466.403431394 + E_Harris -34.2800081003 -466.40343765 + E_Fermi -0.163843975902 -2.22921165524 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115908602368 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111682382347 + + Density error is 0.000977246267474 + + Energy Rydberg eV + E_KohnSham -34.2799544843 -466.402708167 + E_Harris -34.2799554892 -466.40272184 + E_Fermi -0.163575833835 -2.22556339526 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115729575312 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111404908344 + + Density error is 0.000122228142764 + + Energy Rydberg eV + E_KohnSham -34.2799844256 -466.403115539 + E_Harris -34.2799844358 -466.403115678 + E_Fermi -0.163325741068 -2.22216070859 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115732053539 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111396563582 + + Density error is 3.28764501054e-05 + + Energy Rydberg eV + E_KohnSham -34.2799747531 -466.402983938 + E_Harris -34.2799747581 -466.402984006 + E_Fermi -0.163250210983 -2.22113306907 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115725655218 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111394620675 + + Density error is 1.40853115636e-05 + + Energy Rydberg eV + E_KohnSham -34.2799774278 -466.403020329 + E_Harris -34.2799774286 -466.40302034 + E_Fermi -0.16328033585 -2.22154293891 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115725469048 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111392669667 + + Density error is 2.48396249949e-06 + + Energy Rydberg eV + E_KohnSham -34.2799762202 -466.4030039 + E_Harris -34.2799762203 -466.4030039 + E_Fermi -0.163266727635 -2.22135778965 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115725243533 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111392000852 + + Density error is 2.72254460206e-07 + + Energy Rydberg eV + E_KohnSham -34.2799763977 -466.403006314 + E_Harris -34.2799763977 -466.403006314 + E_Fermi -0.163264183509 -2.22132317503 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115725319016 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111392041143 + + Density error is 1.00682729133e-07 + + Energy Rydberg eV + E_KohnSham -34.2799764393 -466.40300688 + E_Harris -34.2799764393 -466.40300688 + E_Fermi -0.163264115868 -2.22132225473 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00115725334161 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011139203046 + + Density error is 1.07693777935e-08 + + Energy Rydberg eV + E_KohnSham -34.2799764417 -466.403006913 + E_Harris -34.2799764417 -466.403006913 + E_band -7.93947416416 -108.022087756 + E_one_elec -69.0270613792 -939.161350953 + E_Hartree +35.9074843815 +488.546388434 + E_xc -8.18831321065 -111.407716673 + E_Ewald +7.15275747294 +97.3182580441 + E_demet -1.3722082913e-69 -1.86698516045e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194382204728 -2.6447055741 + E_Fermi -0.163264039384 -2.22132121412 + + charge density convergence is achieved + final etot is -466.403006913 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2398 2.00000 + 2 -12.7119 2.00000 + 3 -9.32324 2.00000 + 4 -6.73614 2.00000 + 5 1.15637 0.00000 + 6 4.19600 0.00000 + 7 11.1003 0.00000 + 8 11.3721 0.00000 + + EFERMI = -2.221321214115055 eV + OUT.ABACUS/ final etot is -466.4030069126299 eV + correction force for each atom along direction 1 is -8.90821e-06 + correction force for each atom along direction 2 is -2.13073e-05 + correction force for each atom along direction 3 is -0.000111856 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.019400174 -0.38807536 -1.1271906 + H1 +0.28614054 +0.11426776 +0.80323991 + H2 -0.30554071 +0.27380760 +0.32395068 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4030069126299 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9778 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9700 1 7.0 1.e+02% + Potential init_pot 0.24218 2 0.12 3.5% + PW_Basis recip2real 0.28003 17 0.016 4.0% + PW_Basis gathers_scatterp 0.11031 17 0.0065 1.6% + Potential v_of_rho 0.98853 14 0.071 14.% + XC_Functional v_xc 0.29400 15 0.020 4.2% + H_Hartree_pw v_hartree 0.65494 14 0.047 9.4% + PW_Basis real2recip 0.64746 41 0.016 9.3% + PW_Basis gatherp_scatters 0.23794 41 0.0058 3.4% + ORB_control set_orb_tables 0.89510 1 0.90 13.% + ORB_gen_tables gen_tables 0.89510 1 0.90 13.% + ORB_table_phi init_Table 0.37489 1 0.37 5.4% + ORB_table_phi cal_ST_Phi12_R 0.37074 126 0.0029 5.3% + ORB_table_beta init_Table_Beta 0.15394 1 0.15 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15265 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20855 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20693 66 0.0031 3.0% + LOOP_ions opt_ions 5.6170 1 5.6 80.% + ESolver_KS_LCAO Run 5.0530 1 5.1 72.% + HSolverLCAO solve 2.6858 12 0.22 38.% + HamiltLCAO updateHk 1.3758 12 0.11 20.% + LCAO_Hamilt cal_Hgamma 1.3405 12 0.11 19.% + Gint_interface cal_gint 2.5713 25 0.10 37.% + Gint_Gamma distri_vl 2.6275 6 0.44 38.% + LCAO_Deepks cal_projected_DM 5.4655 14 0.39 78.% + LCAO_gen_fixedH add_v_delta 2.4984 6 0.42 36.% + LCAO_DESCRIPTOR add_v_delta 2.4984 6 0.42 36.% + ElecStateLCAO psiToRho 1.2932 12 0.11 19.% + Charge mix_rho 0.82653 11 0.075 12.% + LOOP_ions force_stress 0.56390 1 0.56 8.1% + Force_Stress_LCAO getForceStress 0.56387 1 0.56 8.1% + Force_LCAO_gamma ftable_gamma 0.36533 1 0.37 5.2% + Force_LCAO_gamma cal_fvl_dphi 0.35777 1 0.36 5.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:38 2022 + Finish Time : Wed Sep 28 11:13:45 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..0c08fb7ed7c308c278521c0abafa1b62f5808162 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123711 ima = 3.66916e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123006442912 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111607850329 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112309625603 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112551255307 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112510368941 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112534046837 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112529751477 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112532230538 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112531645663 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112531535773 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112531524945 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112531520707 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d97008a9a5fd8b4ad1ad332e81e2232b44a61514 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.009466469222 17.816653463797 3.093149512154 0 0 0 +H +0.0 +2 +-16.018030237098 17.222546666466 1.308344526017 0 0 0 +-17.616055632088 18.699017496042 3.134171854484 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/conv new file mode 100644 index 0000000000000000000000000000000000000000..bf99cbe4ab7af81d3b656381f8aa819ddacc2421 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/conv @@ -0,0 +1 @@ +24 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..458e7375da2e0c88b160f3fe7305f5f17c5d4a27 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752944442 0.01266248753 1.259705824 1.346211931 1.469044023 0.009113718218 0.01703522822 0.03914948344 +2.793230882e-18 0.0008952446679 0.002679190464 0.01253548376 0.04490140314 -6.84753346e-19 2.32103887e-06 6.504402707e-06 +0.001587259662 0.0060714455 + +H atom_index 1 n_descriptor 18 +1.211270066 0.03597789101 0.0967144592 0.1325153544 0.3067094509 0.02085743257 0.02597976987 0.03925991121 +3.671706851e-17 4.309995064e-05 0.09132834683 0.1133791338 0.1138120003 -1.153232051e-18 5.389696716e-06 0.01400729319 +0.02490232209 0.0288246882 + +H atom_index 2 n_descriptor 18 +1.248773267 0.03473257465 0.109169418 0.1490846551 0.3198751578 0.02267204869 0.02818477149 0.03788639929 +-4.057078706e-17 4.654154229e-05 0.1008635708 0.1153640623 0.1278065448 2.207648494e-18 3.521249854e-06 0.01333151161 +0.02637658273 0.03067157846 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..dd408925f8de9663c1a76a4e59350acd55608a1c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:38 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0739283 SEC) : SETUP UNITCELL + DONE(0.0886237 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104902 SEC) : INIT PLANEWAVE + DONE(0.147504 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.389347 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651834e+02 0.000000e+00 2.128e-01 5.025e-01 + GE2 -4.663986e+02 -1.215164e+00 9.817e-02 4.726e-01 + GE3 -4.664043e+02 -5.692224e-03 6.323e-02 5.344e-01 + GE4 -4.664034e+02 8.431272e-04 1.917e-03 4.103e-01 + GE5 -4.664027e+02 7.232268e-04 9.772e-04 4.073e-01 + GE6 -4.664031e+02 -4.073724e-04 1.222e-04 4.062e-01 + GE7 -4.664030e+02 1.316015e-04 3.288e-05 3.933e-01 + GE8 -4.664030e+02 -3.639138e-05 1.409e-05 3.917e-01 + GE9 -4.664030e+02 1.642927e-05 2.484e-06 3.884e-01 + GE10 -4.664030e+02 -2.414020e-06 2.723e-07 3.844e-01 + GE11 -4.664030e+02 -5.658259e-07 1.007e-07 3.874e-01 + GE12 -4.664030e+02 -3.292060e-08 1.077e-08 3.207e-01 +E_delta_band = -6.95384985e-02 Ry = -9.46119810e-01 eV +E_delta_NN= -1.94382205e-01 Ry = -2.64470557e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9778 11 0.63 1e+02 % + Run_lcao lcao_line 6.97 1 7 1e+02 % + Potential init_pot 0.24218 2 0.12 3.5 % + PW_Basis recip2real 0.28003 17 0.016 4 % + PW_Basis gathers_scatterp 0.11031 17 0.0065 1.6 % + Potential v_of_rho 0.98853 14 0.071 14 % + XC_Functional v_xc 0.294 15 0.02 4.2 % + H_Hartree_pw v_hartree 0.65494 14 0.047 9.4 % + PW_Basis real2recip 0.64746 41 0.016 9.3 % + PW_Basis gatherp_scatters 0.23794 41 0.0058 3.4 % + ORB_control set_orb_tables 0.8951 1 0.9 13 % + ORB_gen_tables gen_tables 0.8951 1 0.9 13 % + ORB_table_phi init_Table 0.37489 1 0.37 5.4 % + ORB_table_phi cal_ST_Phi12_R 0.37074 126 0.0029 5.3 % + ORB_table_beta init_Table_Beta 0.15394 1 0.15 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15265 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20855 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20693 66 0.0031 3 % + LOOP_ions opt_ions 5.617 1 5.6 80 % + ESolver_KS_LCAO Run 5.053 1 5.1 72 % + HSolverLCAO solve 2.6858 12 0.22 38 % + HamiltLCAO updateHk 1.3758 12 0.11 20 % + LCAO_Hamilt cal_Hgamma 1.3405 12 0.11 19 % + Gint_interface cal_gint 2.5713 25 0.1 37 % + Gint_Gamma distri_vl 2.6275 6 0.44 38 % + LCAO_Deepks cal_projected_DM 5.4655 14 0.39 78 % + LCAO_gen_fixedH add_v_delta 2.4984 6 0.42 36 % + LCAO_DESCRIPTOR add_v_delta 2.4984 6 0.42 36 % + ElecStateLCAO psiToRho 1.2932 12 0.11 19 % + Charge mix_rho 0.82653 11 0.075 12 % + LOOP_ions force_stress 0.5639 1 0.56 8.1 % + Force_Stress_LCAO getForceStress 0.56387 1 0.56 8.1 % + Force_LCAO_gamma ftable_gamma 0.36533 1 0.37 5.2 % + Force_LCAO_gamma cal_fvl_dphi 0.35777 1 0.36 5.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:38 2022 + FINISH Time : Wed Sep 28 11:13:45 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/24/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..846b26b9d19c0a5c5a3cc29cc501bbfa530d3eb4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.410267 0.643939 0.0937871 +H 0.367311 0.615006 0.054253 +H 0.392408 0.70497 0.101874 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..03e4042e5bc43559b4b4f6d4205d6b062298f35f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3503 2 + 2 -13.3769 2 + 3 -8.92351 2 + 4 -6.75692 2 + 5 1.43795 0 + 6 4.65607 0 + 7 11.0467 0 + 8 11.2748 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b889cf5c003a4e0433019cc55fb025fa5a2559a5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:51 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.4874747338 18.0302821477 2.62603815023 0 0 0 0 + tauc_H1 10.2847161124 17.2201748416 1.51908325437 0 0 0 0 + tauc_H2 10.9874262886 19.7391479764 2.85247101717 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0861338077623 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0980455848988 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116343896278 (SEC) + + DONE : INIT CHARGE Time : 0.166710065764 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.444289 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00166 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783 + + Density error is 0.216752578807 + + Energy Rydberg eV + E_KohnSham -34.1896778817 -465.174431976 + E_Harris -34.385003553 -467.831974072 + E_Fermi -0.413194695136 -5.62180223722 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00150140670766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000984082658773 + + Density error is 0.0977025890753 + + Energy Rydberg eV + E_KohnSham -34.2793283045 -466.394188554 + E_Harris -34.2858978033 -466.483571171 + E_Fermi -0.220988154849 -3.00669809645 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00137431418772 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000948474021007 + + Density error is 0.0624099101584 + + Energy Rydberg eV + E_KohnSham -34.279493445 -466.396435406 + E_Harris -34.2836938403 -466.453584715 + E_Fermi -0.207200485358 -2.81910722924 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011531579472 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000903311987164 + + Density error is 0.00207956778933 + + Energy Rydberg eV + E_KohnSham -34.2795275739 -466.396899753 + E_Harris -34.2795303548 -466.396937589 + E_Fermi -0.171845031087 -2.33807159577 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114894596561 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904522041205 + + Density error is 0.000856655494172 + + Energy Rydberg eV + E_KohnSham -34.2794627612 -466.396017931 + E_Harris -34.2794643965 -466.396040181 + E_Fermi -0.170706081526 -2.322575392 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114722982456 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000903726008923 + + Density error is 0.000193525368587 + + Energy Rydberg eV + E_KohnSham -34.2795079072 -466.396632173 + E_Harris -34.2795080189 -466.396633693 + E_Fermi -0.170941159581 -2.32577379302 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114691323073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000904026793822 + + Density error is 4.35263162791e-05 + + Energy Rydberg eV + E_KohnSham -34.2794901942 -466.396391176 + E_Harris -34.2794902047 -466.396391318 + E_Fermi -0.170746008067 -2.32311862047 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114694514643 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000903958719335 + + Density error is 1.71788685818e-05 + + Energy Rydberg eV + E_KohnSham -34.2794957145 -466.396466284 + E_Harris -34.2794957157 -466.3964663 + E_Fermi -0.170798603129 -2.32383421299 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114689661373 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000903956946329 + + Density error is 1.54746274015e-06 + + Energy Rydberg eV + E_KohnSham -34.279494204 -466.396445732 + E_Harris -34.279494204 -466.396445733 + E_Fermi -0.170779670786 -2.32357662526 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114689272156 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000903957970353 + + Density error is 1.9798682186e-07 + + Energy Rydberg eV + E_KohnSham -34.2794944458 -466.396449022 + E_Harris -34.2794944458 -466.396449022 + E_Fermi -0.170778289987 -2.32355783851 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114689304683 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000903958292594 + + Density error is 6.84076203129e-08 + + Energy Rydberg eV + E_KohnSham -34.2794944665 -466.396449304 + E_Harris -34.2794944665 -466.396449304 + E_band -7.99776698352 -108.815202252 + E_one_elec -69.5719686875 -946.575195228 + E_Hartree +36.1796365906 +492.249209201 + E_xc -8.23201733222 -112.002341753 + E_Ewald +7.46863671634 +101.616015634 + E_demet -1.16544311575e-85 -1.58566670691e-84 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195235912152 -2.65632085949 + E_Fermi -0.170778256098 -2.32355737744 + + charge density convergence is achieved + final etot is -466.396449304 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3503 2.00000 + 2 -13.3769 2.00000 + 3 -8.92351 2.00000 + 4 -6.75692 2.00000 + 5 1.43795 0.00000 + 6 4.65607 0.00000 + 7 11.0467 0.00000 + 8 11.2748 0.00000 + + EFERMI = -2.323557377437100 eV + OUT.ABACUS/ final etot is -466.3964493038513 eV + correction force for each atom along direction 1 is -0.000120016 + correction force for each atom along direction 2 is 3.63940e-05 + correction force for each atom along direction 3 is -2.82163e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.95628845 -1.2311453 +0.25255811 + H1 -0.39010342 +0.053100428 -0.25385431 + H2 -0.56618504 +1.1780448 +0.0012962039 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3964493038513 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5449 11 0.59 1.0e+02% + Run_lcao lcao_line 6.5353 1 6.5 1.e+02% + Potential init_pot 0.28456 2 0.14 4.3% + PW_Basis recip2real 0.26623 16 0.017 4.1% + PW_Basis gathers_scatterp 0.11316 16 0.0071 1.7% + Potential v_of_rho 0.88777 13 0.068 14.% + XC_Functional v_xc 0.25774 14 0.018 3.9% + H_Hartree_pw v_hartree 0.59306 13 0.046 9.1% + PW_Basis real2recip 0.55683 38 0.015 8.5% + PW_Basis gatherp_scatters 0.21531 38 0.0057 3.3% + ORB_control set_orb_tables 1.1146 1 1.1 17.% + ORB_gen_tables gen_tables 1.1146 1 1.1 17.% + ORB_table_phi init_Table 0.48739 1 0.49 7.4% + ORB_table_phi cal_ST_Phi12_R 0.48253 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.19016 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18864 56 0.0034 2.9% + ORB_table_alpha init_Table_Alpha 0.25717 1 0.26 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25527 66 0.0039 3.9% + LOOP_ions opt_ions 4.8993 1 4.9 75.% + ESolver_KS_LCAO Run 4.3180 1 4.3 66.% + HSolverLCAO solve 2.3339 11 0.21 36.% + HamiltLCAO updateHk 1.2156 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.1757 11 0.11 18.% + Gint_interface cal_gint 2.2313 23 0.097 34.% + Gint_Gamma distri_vl 2.0814 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.7315 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9493 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9493 6 0.32 30.% + ElecStateLCAO psiToRho 1.1041 11 0.10 17.% + Charge mix_rho 0.65835 10 0.066 10.% + LOOP_ions force_stress 0.58114 1 0.58 8.9% + Force_Stress_LCAO getForceStress 0.58111 1 0.58 8.9% + Force_LCAO_gamma ftable_gamma 0.36689 1 0.37 5.6% + Force_LCAO_gamma cal_fvl_dphi 0.36017 1 0.36 5.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:51 2022 + Finish Time : Wed Sep 28 11:08:57 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c964d92f05ef11b5a8c28be043b5ac8eea36cc2c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123994 ima = 3.7037e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123239378134 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112545740668 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112945789578 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113192888809 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113133057869 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113169888433 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113159608458 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113162697907 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113162027059 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113161972817 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113161964841 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8df5581db3d25df6fa9f441d8dc2ad6085b8c056 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.512525266174 18.030282147661 2.626038150214 0 0 0 +H +0.0 +2 +-17.715283887607 17.220174841538 1.519083254365 0 0 0 +-17.012573711458 19.739147976422 2.852471017177 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/conv new file mode 100644 index 0000000000000000000000000000000000000000..b198e13f3172506ea257e6ab75fe165e5d2947ee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/conv @@ -0,0 +1 @@ +25 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e387c70b542d4eaec81c6931a4f0d48374c58f4c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745470265 0.01270721846 1.287809738 1.377351675 1.469713811 0.007995277723 0.02009978481 0.03891646613 +-1.693242255e-18 0.00119083207 0.002502863891 0.01266419994 0.04468957326 7.330899795e-19 1.762146254e-06 5.368549028e-06 +0.001746132091 0.005741704687 + +H atom_index 1 n_descriptor 18 +1.248727783 0.03382052414 0.1080846874 0.1502306614 0.3218969203 0.0219455845 0.02835090122 0.0369729424 +-4.429394292e-18 4.253176475e-05 0.1023788736 0.1147238029 0.1290923852 4.876196044e-20 4.350442728e-06 0.01298691767 +0.0263035409 0.03079590427 + +H atom_index 2 n_descriptor 18 +1.272235672 0.03300524086 0.1164521631 0.1614654944 0.3289668661 0.02297661568 0.02970091473 0.03638204348 +-5.617676673e-17 4.45881163e-05 0.106866942 0.1169569285 0.1387319579 8.597823376e-18 3.125306531e-06 0.01300563492 +0.02713515827 0.03178784949 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..620fa579a377e487c8853ea6da5d0af8f2ef2d9b Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..a1c0ef1bcc5b648aa537b0f9253da8e4c46b7ee4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..a54f5cec6f7ff75f622c580ca52624dba06f76e1 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..c61b1d5a9a502eeae628cb18a1ac9938ea8f192f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:51 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0861566 SEC) : SETUP UNITCELL + DONE(0.0980628 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116361 SEC) : INIT PLANEWAVE + DONE(0.166845 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44435 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651744e+02 0.000000e+00 2.168e-01 5.054e-01 + GE2 -4.663942e+02 -1.219757e+00 9.770e-02 4.366e-01 + GE3 -4.663964e+02 -2.246852e-03 6.241e-02 4.871e-01 + GE4 -4.663969e+02 -4.643467e-04 2.080e-03 3.768e-01 + GE5 -4.663960e+02 8.818219e-04 8.567e-04 3.794e-01 + GE6 -4.663966e+02 -6.142426e-04 1.935e-04 3.644e-01 + GE7 -4.663964e+02 2.409976e-04 4.353e-05 3.642e-01 + GE8 -4.663965e+02 -7.510858e-05 1.718e-05 3.504e-01 + GE9 -4.663964e+02 2.055187e-05 1.547e-06 3.504e-01 + GE10 -4.663964e+02 -3.289996e-06 1.980e-07 3.473e-01 + GE11 -4.663964e+02 -2.814253e-07 6.841e-08 2.946e-01 +E_delta_band = -7.14541585e-02 Ry = -9.72183701e-01 eV +E_delta_NN= -1.95235912e-01 Ry = -2.65632086e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5449 11 0.59 1e+02 % + Run_lcao lcao_line 6.5353 1 6.5 1e+02 % + Potential init_pot 0.28456 2 0.14 4.3 % + PW_Basis recip2real 0.26623 16 0.017 4.1 % + PW_Basis gathers_scatterp 0.11316 16 0.0071 1.7 % + Potential v_of_rho 0.88777 13 0.068 14 % + XC_Functional v_xc 0.25774 14 0.018 3.9 % + H_Hartree_pw v_hartree 0.59306 13 0.046 9.1 % + PW_Basis real2recip 0.55683 38 0.015 8.5 % + PW_Basis gatherp_scatters 0.21531 38 0.0057 3.3 % + ORB_control set_orb_tables 1.1146 1 1.1 17 % + ORB_gen_tables gen_tables 1.1146 1 1.1 17 % + ORB_table_phi init_Table 0.48739 1 0.49 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.48253 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.19016 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18864 56 0.0034 2.9 % + ORB_table_alpha init_Table_Alpha 0.25717 1 0.26 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25527 66 0.0039 3.9 % + LOOP_ions opt_ions 4.8993 1 4.9 75 % + ESolver_KS_LCAO Run 4.318 1 4.3 66 % + HSolverLCAO solve 2.3339 11 0.21 36 % + HamiltLCAO updateHk 1.2156 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.1757 11 0.11 18 % + Gint_interface cal_gint 2.2313 23 0.097 34 % + Gint_Gamma distri_vl 2.0814 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.7315 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9493 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.9493 6 0.32 30 % + ElecStateLCAO psiToRho 1.1041 11 0.1 17 % + Charge mix_rho 0.65835 10 0.066 10 % + LOOP_ions force_stress 0.58114 1 0.58 8.9 % + Force_Stress_LCAO getForceStress 0.58111 1 0.58 8.9 % + Force_LCAO_gamma ftable_gamma 0.36689 1 0.37 5.6 % + Force_LCAO_gamma cal_fvl_dphi 0.36017 1 0.36 5.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:51 2022 + FINISH Time : Wed Sep 28 11:08:57 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/25/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9407ff749a911aa5f4d0742864ccce1cfe7be334 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.387671 0.634039 0.0760164 +H 0.323739 0.651342 0.0723584 +H 0.41572 0.69711 0.0794588 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..16c0c0d3d9c65bbfb8df35b751af22d2a3a301e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0314 2 + 2 -12.4894 2 + 3 -9.33037 2 + 4 -6.692 2 + 5 0.939196 0 + 6 3.85894 0 + 7 11.1504 0 + 8 11.4173 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0101c80f7afd10ee8c59ebe19ea76cc3e4190372 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:20 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 10.8547933401 17.7530839851 2.12846035081 0 0 0 0 + tauc_H1 9.06468189065 18.2375773673 2.02603419982 0 0 0 0 + tauc_H2 11.6401659419 19.5190785228 2.22484697621 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0864404049357 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0951425804549 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11358268457 (SEC) + + DONE : INIT CHARGE Time : 0.162895217853 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446158 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00135 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000747 + + Density error is 0.209900202169 + + Energy Rydberg eV + E_KohnSham -34.1894925193 -465.171909991 + E_Harris -34.3711728788 -467.643798095 + E_Fermi -0.384490272454 -5.23125853095 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121121410791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000885730285651 + + Density error is 0.0985733459013 + + Energy Rydberg eV + E_KohnSham -34.2765811489 -466.356811585 + E_Harris -34.2838423449 -466.455605224 + E_Fermi -0.197076285119 -2.68136041829 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112128743695 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00084556827089 + + Density error is 0.0637029163941 + + Energy Rydberg eV + E_KohnSham -34.277024643 -466.362845631 + E_Harris -34.2816621066 -466.42594156 + E_Fermi -0.191134480393 -2.60051801762 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00095058070804 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000789631571356 + + Density error is 0.00190492322589 + + Energy Rydberg eV + E_KohnSham -34.2769075691 -466.361252759 + E_Harris -34.2769086677 -466.361267706 + E_Fermi -0.155818503896 -2.12001950682 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00094957424364 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000788103388441 + + Density error is 0.000913043150216 + + Energy Rydberg eV + E_KohnSham -34.2768839567 -466.360931496 + E_Harris -34.276884227 -466.360935173 + E_Fermi -0.155973861259 -2.12213325219 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947268747581 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787427682677 + + Density error is 0.000166599836062 + + Energy Rydberg eV + E_KohnSham -34.2768905829 -466.361021649 + E_Harris -34.2768905736 -466.361021524 + E_Fermi -0.155471804775 -2.11530242328 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947295616536 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787503218215 + + Density error is 2.59818943626e-05 + + Energy Rydberg eV + E_KohnSham -34.2768901406 -466.361015633 + E_Harris -34.2768901412 -466.36101564 + E_Fermi -0.155446420782 -2.11495705634 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947248407977 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787457074886 + + Density error is 8.22566953622e-06 + + Energy Rydberg eV + E_KohnSham -34.2768914103 -466.361032907 + E_Harris -34.2768914106 -466.361032911 + E_Fermi -0.155451901245 -2.11503162187 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947244688361 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00078745972664 + + Density error is 2.56959947841e-06 + + Energy Rydberg eV + E_KohnSham -34.2768907873 -466.361024431 + E_Harris -34.2768907873 -466.361024432 + E_Fermi -0.155445253792 -2.11494117863 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947238870144 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787458049717 + + Density error is 4.87764320279e-07 + + Energy Rydberg eV + E_KohnSham -34.2768909212 -466.361026253 + E_Harris -34.2768909212 -466.361026253 + E_Fermi -0.155443204303 -2.1149132939 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00094723849935 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787458546324 + + Density error is 1.89383431396e-07 + + Energy Rydberg eV + E_KohnSham -34.2768909252 -466.361026307 + E_Harris -34.2768909252 -466.361026307 + E_Fermi -0.155442974999 -2.11491017406 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000947238133961 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00078745878836 + + Density error is 1.15547283952e-08 + + Energy Rydberg eV + E_KohnSham -34.2768909283 -466.361026349 + E_Harris -34.2768909283 -466.361026349 + E_band -7.87070836405 -107.086481047 + E_one_elec -68.5662415295 -932.891575246 + E_Hartree +35.6884369481 +485.566095208 + E_xc -8.15341289322 -110.932873495 + E_Ewald +6.88007633755 +93.6082408656 + E_demet -2.21068189802e-57 -3.00778702785e-56 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193615325424 -2.63427164589 + E_Fermi -0.155442811841 -2.11490795417 + + charge density convergence is achieved + final etot is -466.361026349 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0314 2.00000 + 2 -12.4894 2.00000 + 3 -9.33037 2.00000 + 4 -6.69200 2.00000 + 5 0.939196 0.00000 + 6 3.85894 0.00000 + 7 11.1504 0.00000 + 8 11.4173 0.00000 + + EFERMI = -2.114907954174513 eV + OUT.ABACUS/ final etot is -466.3610263489481 eV + correction force for each atom along direction 1 is -2.70685e-05 + correction force for each atom along direction 2 is 4.73695e-05 + correction force for each atom along direction 3 is 0.000162335 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.39355359 +2.2008262 +0.090706788 + H1 +0.096744169 -0.35313468 -0.0070867893 + H2 -0.49029776 -1.8476915 -0.083619999 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3610263489481 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.8190 11 0.71 1.0e+02% + Run_lcao lcao_line 7.8097 1 7.8 1.e+02% + Potential init_pot 0.28334 2 0.14 3.6% + PW_Basis recip2real 0.30547 17 0.018 3.9% + PW_Basis gathers_scatterp 0.12777 17 0.0075 1.6% + Potential v_of_rho 1.0654 14 0.076 14.% + XC_Functional v_xc 0.30336 15 0.020 3.9% + H_Hartree_pw v_hartree 0.71694 14 0.051 9.2% + PW_Basis real2recip 0.69555 41 0.017 8.9% + PW_Basis gatherp_scatters 0.26554 41 0.0065 3.4% + ORB_control set_orb_tables 1.0965 1 1.1 14.% + ORB_gen_tables gen_tables 1.0965 1 1.1 14.% + ORB_table_phi init_Table 0.47497 1 0.47 6.1% + ORB_table_phi cal_ST_Phi12_R 0.46982 126 0.0037 6.0% + ORB_table_beta init_Table_Beta 0.18573 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18414 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24946 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24747 66 0.0037 3.2% + LOOP_ions opt_ions 6.1881 1 6.2 79.% + ESolver_KS_LCAO Run 5.5743 1 5.6 71.% + HSolverLCAO solve 3.0982 12 0.26 40.% + HamiltLCAO updateHk 1.5687 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.5299 12 0.13 20.% + Gint_interface cal_gint 2.9543 25 0.12 38.% + Gint_Gamma distri_vl 2.8994 6 0.48 37.% + LCAO_Deepks cal_projected_DM 6.0117 14 0.43 77.% + LCAO_gen_fixedH add_v_delta 2.7532 6 0.46 35.% + LCAO_DESCRIPTOR add_v_delta 2.7533 6 0.46 35.% + ElecStateLCAO psiToRho 1.5128 12 0.13 19.% + Charge mix_rho 0.84968 11 0.077 11.% + LOOP_ions force_stress 0.61359 1 0.61 7.8% + Force_Stress_LCAO getForceStress 0.61355 1 0.61 7.8% + Force_LCAO_gamma ftable_gamma 0.39276 1 0.39 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.38485 1 0.38 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:20 2022 + Finish Time : Wed Sep 28 11:10:28 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8001c04c76721b0f277da460c776b1d66d3f90df --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123726 ima = 3.66887e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123178895235 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111683124091 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112510942209 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112706720169 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112700871795 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112704435433 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011270291942 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112704091191 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112703703335 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112703680309 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112703662845 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112703653831 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/STRU new file mode 100644 index 0000000000000000000000000000000000000000..60a3a2d96de124c9809ead4892bbb2e9ed479b33 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-17.145206659838 17.753083985169 2.128460350819 0 0 0 +H +0.0 +2 +-18.935318109371 18.237577367365 2.026034199840 0 0 0 +-16.359834058139 19.519078522755 2.224846976220 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/conv new file mode 100644 index 0000000000000000000000000000000000000000..70696c11f83cd15c9f82a5df24cb2452d8b5067d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/conv @@ -0,0 +1 @@ +26 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..49b5af2d644df7d0a67ecc384fc693b856f8c9f9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75406011 0.01246711148 1.239392603 1.329877207 1.46830599 0.009184015822 0.01648056337 0.0392355189 +1.191789654e-19 0.0007866197424 0.002549823812 0.01193074699 0.04252351354 -8.125949965e-21 2.005380488e-06 5.910386478e-06 +0.001553903694 0.0059780892 + +H atom_index 1 n_descriptor 18 +1.230685166 0.0354138947 0.1027737203 0.1409591766 0.3140081016 0.0216942013 0.02712628791 0.03863536715 +9.203407803e-18 4.129084094e-05 0.09439628436 0.114948562 0.1206136515 -2.732344518e-19 4.174610948e-06 0.01358030031 +0.025240408 0.02978858919 + +H atom_index 2 n_descriptor 18 +1.169919284 0.03723715805 0.08421753131 0.1160879175 0.290791229 0.01878327249 0.02355374888 0.04104342847 +-2.853559958e-17 3.612861008e-05 0.07905627539 0.09872444365 0.1118750429 9.110294445e-18 6.36117045e-06 0.01531417476 +0.02270920986 0.02654181211 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9b02826e2f5e79c43408e07498d115160e8f7295 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:20 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0864642 SEC) : SETUP UNITCELL + DONE(0.0951605 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.113603 SEC) : INIT PLANEWAVE + DONE(0.163978 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44623 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651719e+02 0.000000e+00 2.099e-01 5.726e-01 + GE2 -4.663568e+02 -1.184902e+00 9.857e-02 5.167e-01 + GE3 -4.663628e+02 -6.034046e-03 6.370e-02 5.844e-01 + GE4 -4.663613e+02 1.592872e-03 1.905e-03 4.464e-01 + GE5 -4.663609e+02 3.212623e-04 9.130e-04 4.467e-01 + GE6 -4.663610e+02 -9.015312e-05 1.666e-04 4.465e-01 + GE7 -4.663610e+02 6.016737e-06 2.598e-05 4.223e-01 + GE8 -4.663610e+02 -1.727458e-05 8.226e-06 4.275e-01 + GE9 -4.663610e+02 8.475860e-06 2.570e-06 4.312e-01 + GE10 -4.663610e+02 -1.821323e-06 4.878e-07 4.276e-01 + GE11 -4.663610e+02 -5.399550e-08 1.894e-07 4.277e-01 + GE12 -4.663610e+02 -4.216585e-08 1.155e-08 3.621e-01 +E_delta_band = -6.78655343e-02 Ry = -9.23357964e-01 eV +E_delta_NN= -1.93615325e-01 Ry = -2.63427165e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.819 11 0.71 1e+02 % + Run_lcao lcao_line 7.8097 1 7.8 1e+02 % + Potential init_pot 0.28334 2 0.14 3.6 % + PW_Basis recip2real 0.30547 17 0.018 3.9 % + PW_Basis gathers_scatterp 0.12777 17 0.0075 1.6 % + Potential v_of_rho 1.0654 14 0.076 14 % + XC_Functional v_xc 0.30336 15 0.02 3.9 % + H_Hartree_pw v_hartree 0.71694 14 0.051 9.2 % + PW_Basis real2recip 0.69555 41 0.017 8.9 % + PW_Basis gatherp_scatters 0.26554 41 0.0065 3.4 % + ORB_control set_orb_tables 1.0965 1 1.1 14 % + ORB_gen_tables gen_tables 1.0965 1 1.1 14 % + ORB_table_phi init_Table 0.47497 1 0.47 6.1 % + ORB_table_phi cal_ST_Phi12_R 0.46982 126 0.0037 6 % + ORB_table_beta init_Table_Beta 0.18573 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18414 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24946 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24747 66 0.0037 3.2 % + LOOP_ions opt_ions 6.1881 1 6.2 79 % + ESolver_KS_LCAO Run 5.5743 1 5.6 71 % + HSolverLCAO solve 3.0982 12 0.26 40 % + HamiltLCAO updateHk 1.5687 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.5299 12 0.13 20 % + Gint_interface cal_gint 2.9543 25 0.12 38 % + Gint_Gamma distri_vl 2.8994 6 0.48 37 % + LCAO_Deepks cal_projected_DM 6.0117 14 0.43 77 % + LCAO_gen_fixedH add_v_delta 2.7532 6 0.46 35 % + LCAO_DESCRIPTOR add_v_delta 2.7533 6 0.46 35 % + ElecStateLCAO psiToRho 1.5128 12 0.13 19 % + Charge mix_rho 0.84968 11 0.077 11 % + LOOP_ions force_stress 0.61359 1 0.61 7.8 % + Force_Stress_LCAO getForceStress 0.61355 1 0.61 7.8 % + Force_LCAO_gamma ftable_gamma 0.39276 1 0.39 5 % + Force_LCAO_gamma cal_fvl_dphi 0.38485 1 0.38 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:20 2022 + FINISH Time : Wed Sep 28 11:10:28 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/26/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..dc600ce067687ef8160095591b3e7c27f5386b1f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.370532 0.640744 0.0545113 +H 0.322399 0.626491 0.0984582 +H 0.40788 0.687277 0.0808896 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..16b33234ff3d5f9c8756bc4a8c6e77661f223576 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.143 2 + 2 -13.1302 2 + 3 -8.93698 2 + 4 -6.70969 2 + 5 1.23647 0 + 6 4.32831 0 + 7 11.1008 0 + 8 11.3362 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..012751ec028e8baff3c1ea293aef5e62b8ff80c1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:54 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 10.3749055569 17.9408408521 1.52631551177 0 0 0 0 + tauc_H1 9.02716993056 17.5417607358 2.75682907709 0 0 0 0 + tauc_H2 11.4206488336 19.2437476633 2.26490951513 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105188061713 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105558376015 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123606845072 (SEC) + + DONE : INIT CHARGE Time : 0.16688873268 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451089 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00129 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114 + + Density error is 0.214790815433 + + Energy Rydberg eV + E_KohnSham -34.1906357507 -465.187464453 + E_Harris -34.381704737 -467.787091377 + E_Fermi -0.399522353959 -5.43578049221 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00137505308339 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119369727126 + + Density error is 0.098428852759 + + Energy Rydberg eV + E_KohnSham -34.2802874184 -466.407237968 + E_Harris -34.2870835813 -466.499704509 + E_Fermi -0.208312223946 -2.83423320872 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00129087885488 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112504580053 + + Density error is 0.0632130757406 + + Energy Rydberg eV + E_KohnSham -34.2806136833 -466.41167703 + E_Harris -34.2849908561 -466.471231521 + E_Fermi -0.19835634324 -2.6987765025 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114844680736 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101106653077 + + Density error is 0.00204623440196 + + Energy Rydberg eV + E_KohnSham -34.2805814105 -466.411237935 + E_Harris -34.2805844362 -466.411279103 + E_Fermi -0.163062728356 -2.21858223707 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.001147426594 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100955308469 + + Density error is 0.000900365115134 + + Energy Rydberg eV + E_KohnSham -34.2805304528 -466.410544621 + E_Harris -34.2805310787 -466.410553137 + E_Fermi -0.162481158148 -2.21066956845 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011455874828 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100810505888 + + Density error is 0.000188158378776 + + Energy Rydberg eV + E_KohnSham -34.2805592908 -466.410936981 + E_Harris -34.2805593417 -466.410937675 + E_Fermi -0.162337533149 -2.2087154501 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114569260184 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100822868991 + + Density error is 3.68583457121e-05 + + Energy Rydberg eV + E_KohnSham -34.2805484712 -466.410789773 + E_Harris -34.2805484778 -466.410789864 + E_Fermi -0.162225955115 -2.20719735306 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114563969901 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100817347284 + + Density error is 1.60872261757e-05 + + Energy Rydberg eV + E_KohnSham -34.2805529682 -466.410850959 + E_Harris -34.2805529693 -466.410850973 + E_Fermi -0.162261907452 -2.2076865097 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114561848123 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100815561073 + + Density error is 1.63040821421e-06 + + Energy Rydberg eV + E_KohnSham -34.2805516147 -466.410832542 + E_Harris -34.2805516147 -466.410832543 + E_Fermi -0.162244706324 -2.20745247635 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114561644872 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100815510507 + + Density error is 1.8298831482e-07 + + Energy Rydberg eV + E_KohnSham -34.2805518426 -466.410835644 + E_Harris -34.2805518426 -466.410835644 + E_Fermi -0.162243281618 -2.20743309222 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00114561702612 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100815569839 + + Density error is 3.20782619395e-08 + + Energy Rydberg eV + E_KohnSham -34.280551867 -466.410835976 + E_Harris -34.280551867 -466.410835976 + E_band -7.92607094424 -107.839727594 + E_one_elec -69.1083876306 -940.267851369 + E_Hartree +35.9603594651 +489.265790853 + E_xc -8.19665023858 -111.521147758 + E_Ewald +7.18886440117 +97.8095180053 + E_demet -3.07957971537e-72 -4.18998315743e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194395395547 -2.6448850444 + E_Fermi -0.162243224959 -2.20743232133 + + charge density convergence is achieved + final etot is -466.410835976 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1430 2.00000 + 2 -13.1302 2.00000 + 3 -8.93698 2.00000 + 4 -6.70969 2.00000 + 5 1.23647 0.00000 + 6 4.32831 0.00000 + 7 11.1008 0.00000 + 8 11.3362 0.00000 + + EFERMI = -2.207432321332049 eV + OUT.ABACUS/ final etot is -466.4108359756044 eV + correction force for each atom along direction 1 is -5.57511e-05 + correction force for each atom along direction 2 is 2.19278e-05 + correction force for each atom along direction 3 is 7.66993e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.68027453 -0.59399849 -0.050003864 + H1 +0.60367653 +0.31903604 -0.31127244 + H2 +0.076598002 +0.27496246 +0.36127631 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4108359756044 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7784 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7689 1 6.8 1.e+02% + Potential init_pot 0.28674 2 0.14 4.2% + PW_Basis recip2real 0.28471 16 0.018 4.2% + PW_Basis gathers_scatterp 0.12621 16 0.0079 1.9% + Potential v_of_rho 1.0293 13 0.079 15.% + XC_Functional v_xc 0.31267 14 0.022 4.6% + H_Hartree_pw v_hartree 0.67250 13 0.052 9.9% + PW_Basis real2recip 0.70054 38 0.018 10.% + PW_Basis gatherp_scatters 0.26721 38 0.0070 3.9% + ORB_control set_orb_tables 1.0950 1 1.1 16.% + ORB_gen_tables gen_tables 1.0950 1 1.1 16.% + ORB_table_phi init_Table 0.47429 1 0.47 7.0% + ORB_table_phi cal_ST_Phi12_R 0.46907 126 0.0037 6.9% + ORB_table_beta init_Table_Beta 0.18512 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18357 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24586 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24387 66 0.0037 3.6% + LOOP_ions opt_ions 5.1469 1 5.1 76.% + ESolver_KS_LCAO Run 4.5918 1 4.6 68.% + HSolverLCAO solve 2.1160 11 0.19 31.% + HamiltLCAO updateHk 1.1401 11 0.10 17.% + LCAO_Hamilt cal_Hgamma 1.1127 11 0.10 16.% + Gint_interface cal_gint 1.9187 23 0.083 28.% + Gint_Gamma distri_vl 2.2198 6 0.37 33.% + LCAO_Deepks cal_projected_DM 4.9940 13 0.38 74.% + LCAO_gen_fixedH add_v_delta 2.0727 6 0.35 31.% + LCAO_DESCRIPTOR add_v_delta 2.0728 6 0.35 31.% + ElecStateLCAO psiToRho 0.95882 11 0.087 14.% + Charge mix_rho 0.90309 10 0.090 13.% + LOOP_ions force_stress 0.55489 1 0.55 8.2% + Force_Stress_LCAO getForceStress 0.55486 1 0.55 8.2% + Force_LCAO_gamma ftable_gamma 0.33233 1 0.33 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.32419 1 0.32 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:54 2022 + Finish Time : Wed Sep 28 11:15:01 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e9b8e8bdbd701ec67ffda0df81f400b5bbab7192 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123444 ima = 3.64116e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001235939625 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112511002866 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113093486148 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113315625439 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113278443328 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113301357229 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113293324731 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113296071641 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113295406072 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113295340162 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113295330255 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0b42c5482e3249a914a2e319828c6a7cee2ba582 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-17.625094443098 17.940840852149 1.526315511766 0 0 0 +H +0.0 +2 +-18.972830069430 17.541760735806 2.756829077094 0 0 0 +-16.579351166402 19.243747663275 2.264909515125 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/conv new file mode 100644 index 0000000000000000000000000000000000000000..67b96e55855ceadff49034dd726fc29ed51ae9b1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/conv @@ -0,0 +1 @@ +27 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..86caf5286f8f606ffbe71cd9d4a7c24159cadda9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746423256 0.01256732369 1.267402326 1.361325222 1.468681435 0.007970785169 0.01937605695 0.03894735872 +7.312546841e-18 0.001064258254 0.002410331922 0.01200646645 0.04277648736 5.431929647e-19 1.606218523e-06 4.998075747e-06 +0.001710961823 0.005769478817 + +H atom_index 1 n_descriptor 18 +1.21512292 0.03513450256 0.09645258337 0.135335913 0.3108174814 0.02030495697 0.02639709006 0.03838226772 +4.313465731e-17 3.725263559e-05 0.09175416698 0.1139898412 0.1159587643 -1.768755962e-17 5.655995341e-06 0.01353165075 +0.02457975341 0.02916098 + +H atom_index 2 n_descriptor 18 +1.248114067 0.03398806267 0.1072273221 0.1499445015 0.3218698579 0.02178549541 0.02831571124 0.03719487187 +3.914213686e-17 4.000826661e-05 0.1004249432 0.1149141884 0.1286681353 1.127438858e-18 4.245983153e-06 0.01301313452 +0.02585989395 0.03073868894 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0298c34ef5ad6c10eaab00d7a831641544fed7a9 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:54 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105212 SEC) : SETUP UNITCELL + DONE(0.105572 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123628 SEC) : INIT PLANEWAVE + DONE(0.167032 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451151 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651875e+02 0.000000e+00 2.148e-01 5.200e-01 + GE2 -4.664072e+02 -1.219774e+00 9.843e-02 4.687e-01 + GE3 -4.664117e+02 -4.439062e-03 6.321e-02 5.407e-01 + GE4 -4.664112e+02 4.390946e-04 2.046e-03 3.999e-01 + GE5 -4.664105e+02 6.933146e-04 9.004e-04 3.993e-01 + GE6 -4.664109e+02 -3.923604e-04 1.882e-04 3.904e-01 + GE7 -4.664108e+02 1.472080e-04 3.686e-05 3.824e-01 + GE8 -4.664109e+02 -6.118546e-05 1.609e-05 3.762e-01 + GE9 -4.664108e+02 1.841615e-05 1.630e-06 3.763e-01 + GE10 -4.664108e+02 -3.101302e-06 1.830e-07 3.756e-01 + GE11 -4.664108e+02 -3.319114e-07 3.208e-08 2.999e-01 +E_delta_band = -6.96575315e-02 Ry = -9.47739337e-01 eV +E_delta_NN= -1.94395396e-01 Ry = -2.64488504e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7784 11 0.62 1e+02 % + Run_lcao lcao_line 6.7689 1 6.8 1e+02 % + Potential init_pot 0.28674 2 0.14 4.2 % + PW_Basis recip2real 0.28471 16 0.018 4.2 % + PW_Basis gathers_scatterp 0.12621 16 0.0079 1.9 % + Potential v_of_rho 1.0293 13 0.079 15 % + XC_Functional v_xc 0.31267 14 0.022 4.6 % + H_Hartree_pw v_hartree 0.6725 13 0.052 9.9 % + PW_Basis real2recip 0.70054 38 0.018 10 % + PW_Basis gatherp_scatters 0.26721 38 0.007 3.9 % + ORB_control set_orb_tables 1.095 1 1.1 16 % + ORB_gen_tables gen_tables 1.095 1 1.1 16 % + ORB_table_phi init_Table 0.47429 1 0.47 7 % + ORB_table_phi cal_ST_Phi12_R 0.46907 126 0.0037 6.9 % + ORB_table_beta init_Table_Beta 0.18512 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18357 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24586 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24387 66 0.0037 3.6 % + LOOP_ions opt_ions 5.1469 1 5.1 76 % + ESolver_KS_LCAO Run 4.5918 1 4.6 68 % + HSolverLCAO solve 2.116 11 0.19 31 % + HamiltLCAO updateHk 1.1401 11 0.1 17 % + LCAO_Hamilt cal_Hgamma 1.1127 11 0.1 16 % + Gint_interface cal_gint 1.9187 23 0.083 28 % + Gint_Gamma distri_vl 2.2198 6 0.37 33 % + LCAO_Deepks cal_projected_DM 4.994 13 0.38 74 % + LCAO_gen_fixedH add_v_delta 2.0727 6 0.35 31 % + LCAO_DESCRIPTOR add_v_delta 2.0728 6 0.35 31 % + ElecStateLCAO psiToRho 0.95882 11 0.087 14 % + Charge mix_rho 0.90309 10 0.09 13 % + LOOP_ions force_stress 0.55489 1 0.55 8.2 % + Force_Stress_LCAO getForceStress 0.55486 1 0.55 8.2 % + Force_LCAO_gamma ftable_gamma 0.33233 1 0.33 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.32419 1 0.32 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:54 2022 + FINISH Time : Wed Sep 28 11:15:01 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/27/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..455166f854ce6936216d4366ddd9dbece2dd339e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.360763 0.654315 0.0518043 +H 0.380044 0.608989 0.0938128 +H 0.41734 0.67121 0.0267412 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..26c6813382d0179cd684c1c2446dd32d602529aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5592 2 + 2 -12.9914 2 + 3 -9.35358 2 + 4 -6.80435 2 + 5 1.4261 0 + 6 4.66569 0 + 7 11.0242 0 + 8 11.2964 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7cc33760bca1548675c87d943062dd312132e57e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:24 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 10.1013707343 18.3208336768 1.4505214587 0 0 0 0 + tauc_H1 10.6412330508 17.051695852 2.62675710557 0 0 0 0 + tauc_H2 11.6855333024 18.7938897473 0.748752518091 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0733678145102 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0887721935296 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104455908647 (SEC) + + DONE : INIT CHARGE Time : 0.146755529025 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.389262 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 81 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000792 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00162 + + Density error is 0.216182373286 + + Energy Rydberg eV + E_KohnSham -34.1877708793 -465.148485877 + E_Harris -34.3828755408 -467.803020979 + E_Fermi -0.417951907434 -5.68652743107 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115103682583 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134146418246 + + Density error is 0.0973752434769 + + Energy Rydberg eV + E_KohnSham -34.2784081199 -466.3816688 + E_Harris -34.2851193939 -466.472980368 + E_Fermi -0.225493590755 -3.06799769675 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00109902435015 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123209363794 + + Density error is 0.0622727519844 + + Energy Rydberg eV + E_KohnSham -34.2786866241 -466.385458045 + E_Harris -34.2830135574 -466.444328992 + E_Fermi -0.212373256888 -2.88948639649 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00102902140089 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104911180045 + + Density error is 0.0020026398484 + + Energy Rydberg eV + E_KohnSham -34.2787095211 -466.385769574 + E_Harris -34.2787113859 -466.385794946 + E_Fermi -0.176433367301 -2.40049911262 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103328549384 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104871333089 + + Density error is 0.00093610054765 + + Energy Rydberg eV + E_KohnSham -34.2786341215 -466.38474371 + E_Harris -34.2786366032 -466.384777474 + E_Fermi -0.175428958291 -2.38683342697 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103153552872 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104686098672 + + Density error is 0.000100577666525 + + Energy Rydberg eV + E_KohnSham -34.2786862632 -466.385453134 + E_Harris -34.2786862724 -466.385453259 + E_Fermi -0.175624618808 -2.38949552487 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0010312165386 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104651307207 + + Density error is 4.44879478094e-05 + + Energy Rydberg eV + E_KohnSham -34.2786704046 -466.385237366 + E_Harris -34.2786704157 -466.385237517 + E_Fermi -0.175507314489 -2.38789951773 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0010311904868 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010465797936 + + Density error is 1.79093673615e-05 + + Energy Rydberg eV + E_KohnSham -34.2786723773 -466.385264207 + E_Harris -34.2786723788 -466.385264226 + E_Fermi -0.175567676868 -2.38872079003 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103120399674 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104655727542 + + Density error is 2.06003499451e-06 + + Energy Rydberg eV + E_KohnSham -34.2786708248 -466.385243083 + E_Harris -34.2786708248 -466.385243083 + E_Fermi -0.175548433314 -2.38845896804 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103120667714 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104655375089 + + Density error is 4.89318838918e-07 + + Energy Rydberg eV + E_KohnSham -34.2786711075 -466.38524693 + E_Harris -34.2786711075 -466.38524693 + E_Fermi -0.175547166145 -2.38844172732 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103120765444 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104655378353 + + Density error is 1.32317471958e-07 + + Energy Rydberg eV + E_KohnSham -34.278671131 -466.385247249 + E_Harris -34.278671131 -466.385247249 + E_Fermi -0.175546861981 -2.38843758896 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00103120769438 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104655351538 + + Density error is 1.03385424231e-08 + + Energy Rydberg eV + E_KohnSham -34.2786711369 -466.385247331 + E_Harris -34.2786711369 -466.385247331 + E_band -8.04201594645 -109.417240279 + E_one_elec -69.6813707654 -948.06368686 + E_Hartree +36.2161800364 +492.746408289 + E_xc -8.23804764307 -112.084388341 + E_Ewald +7.54805766666 +102.696593099 + E_demet -6.21730366325e-88 -8.45907560165e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195571109355 -2.66088145142 + E_Fermi -0.175546712106 -2.3884355498 + + charge density convergence is achieved + final etot is -466.385247331 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5592 2.00000 + 2 -12.9914 2.00000 + 3 -9.35358 2.00000 + 4 -6.80435 2.00000 + 5 1.42610 0.00000 + 6 4.66569 0.00000 + 7 11.0242 0.00000 + 8 11.2964 0.00000 + + EFERMI = -2.388435549802641 eV + OUT.ABACUS/ final etot is -466.3852473305523 eV + correction force for each atom along direction 1 is 3.93616e-05 + correction force for each atom along direction 2 is 4.49592e-05 + correction force for each atom along direction 3 is 9.23837e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0170078 +0.078713163 +0.079289821 + H1 -0.093764714 -0.73336975 +0.73598840 + H2 +1.1107725 +0.65465658 -0.81527822 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3852473305523 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0398 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0321 1 7.0 1.e+02% + Potential init_pot 0.24040 2 0.12 3.4% + PW_Basis recip2real 0.27470 17 0.016 3.9% + PW_Basis gathers_scatterp 0.11000 17 0.0065 1.6% + Potential v_of_rho 0.97856 14 0.070 14.% + XC_Functional v_xc 0.28233 15 0.019 4.0% + H_Hartree_pw v_hartree 0.65473 14 0.047 9.3% + PW_Basis real2recip 0.64248 41 0.016 9.1% + PW_Basis gatherp_scatters 0.23793 41 0.0058 3.4% + ORB_control set_orb_tables 0.89581 1 0.90 13.% + ORB_gen_tables gen_tables 0.89581 1 0.90 13.% + ORB_table_phi init_Table 0.37506 1 0.38 5.3% + ORB_table_phi cal_ST_Phi12_R 0.37085 126 0.0029 5.3% + ORB_table_beta init_Table_Beta 0.15381 1 0.15 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15249 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20938 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20762 66 0.0031 2.9% + LOOP_ions opt_ions 5.6785 1 5.7 81.% + ESolver_KS_LCAO Run 5.1288 1 5.1 73.% + HSolverLCAO solve 2.7784 12 0.23 39.% + HamiltLCAO updateHk 1.4121 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3756 12 0.11 20.% + Gint_interface cal_gint 2.6529 25 0.11 38.% + Gint_Gamma distri_vl 2.6764 6 0.45 38.% + LCAO_Deepks cal_projected_DM 5.5270 14 0.39 79.% + LCAO_gen_fixedH add_v_delta 2.5483 6 0.42 36.% + LCAO_DESCRIPTOR add_v_delta 2.5483 6 0.42 36.% + ElecStateLCAO psiToRho 1.3483 12 0.11 19.% + Charge mix_rho 0.83011 11 0.075 12.% + LOOP_ions force_stress 0.54960 1 0.55 7.8% + Force_Stress_LCAO getForceStress 0.54958 1 0.55 7.8% + Force_LCAO_gamma ftable_gamma 0.35222 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.34502 1 0.35 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:24 2022 + Finish Time : Wed Sep 28 11:13:31 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..cb20aeec101dfda5bfc3f9f4b125b504aff6ecd4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124073 ima = 3.66274e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122582225829 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111554941398 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112044312701 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112332750126 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112257166061 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112297946233 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112296257986 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112299318562 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298505216 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298429696 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298408762 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298402219 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/STRU new file mode 100644 index 0000000000000000000000000000000000000000..eaf29dad893eea73ea3537c86539af5016853161 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-17.898629265673 18.320833676766 1.450521458710 0 0 0 +H +0.0 +2 +-17.358766949223 17.051695851967 2.626757105589 0 0 0 +-16.314466697632 18.793889747273 0.748752518105 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/conv new file mode 100644 index 0000000000000000000000000000000000000000..513fc20133af6fa2ac79545232b5744d7bf44b7c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/conv @@ -0,0 +1 @@ +28 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ec8cc34f1c5aa1e7528165b285469058b9a83de1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752487916 0.0128676431 1.28669886 1.368553164 1.470435034 0.009270966804 0.01771113561 0.0391080352 +-5.626976042e-19 0.001042605481 0.002891883422 0.01347197391 0.04842286226 -2.930221146e-19 2.83554364e-06 7.419883562e-06 +0.001605830012 0.006121349043 + +H atom_index 1 n_descriptor 18 +1.264498203 0.0341840886 0.1155724935 0.1563783261 0.3242861741 0.02371299645 0.02908467923 0.03734278587 +-2.022184094e-17 5.40656832e-05 0.106925093 0.1165979885 0.1343212779 -1.105952896e-17 2.727563208e-06 0.01331580516 +0.02769787016 0.03140286043 + +H atom_index 2 n_descriptor 18 +1.27753555 0.0337585618 0.1204773739 0.1628140268 0.3282695957 0.02434776984 0.02983976904 0.03705540932 +7.439076774e-18 5.5341935e-05 0.1082281026 0.1190587826 0.1398132908 -3.58927136e-18 1.990324986e-06 0.01338960718 +0.02814189043 0.0319418658 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fdaed23a97286fb9264271745053401a5023783f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:24 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733836 SEC) : SETUP UNITCELL + DONE(0.0887848 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104469 SEC) : INIT PLANEWAVE + DONE(0.146866 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.389304 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651485e+02 0.000000e+00 2.162e-01 5.083e-01 + GE2 -4.663817e+02 -1.233183e+00 9.738e-02 4.822e-01 + GE3 -4.663855e+02 -3.789245e-03 6.227e-02 5.403e-01 + GE4 -4.663858e+02 -3.115289e-04 2.003e-03 4.144e-01 + GE5 -4.663847e+02 1.025864e-03 9.361e-04 4.146e-01 + GE6 -4.663855e+02 -7.094236e-04 1.006e-04 3.962e-01 + GE7 -4.663852e+02 2.157674e-04 4.449e-05 4.086e-01 + GE8 -4.663853e+02 -2.684042e-05 1.791e-05 3.947e-01 + GE9 -4.663852e+02 2.112327e-05 2.060e-06 3.973e-01 + GE10 -4.663852e+02 -3.847208e-06 4.893e-07 3.949e-01 + GE11 -4.663852e+02 -3.188106e-07 1.323e-07 3.969e-01 + GE12 -4.663852e+02 -8.126403e-08 1.034e-08 3.268e-01 +E_delta_band = -7.20806779e-02 Ry = -9.80707935e-01 eV +E_delta_NN= -1.95571109e-01 Ry = -2.66088145e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0398 11 0.64 1e+02 % + Run_lcao lcao_line 7.0321 1 7 1e+02 % + Potential init_pot 0.2404 2 0.12 3.4 % + PW_Basis recip2real 0.2747 17 0.016 3.9 % + PW_Basis gathers_scatterp 0.11 17 0.0065 1.6 % + Potential v_of_rho 0.97856 14 0.07 14 % + XC_Functional v_xc 0.28233 15 0.019 4 % + H_Hartree_pw v_hartree 0.65473 14 0.047 9.3 % + PW_Basis real2recip 0.64248 41 0.016 9.1 % + PW_Basis gatherp_scatters 0.23793 41 0.0058 3.4 % + ORB_control set_orb_tables 0.89581 1 0.9 13 % + ORB_gen_tables gen_tables 0.89581 1 0.9 13 % + ORB_table_phi init_Table 0.37506 1 0.38 5.3 % + ORB_table_phi cal_ST_Phi12_R 0.37085 126 0.0029 5.3 % + ORB_table_beta init_Table_Beta 0.15381 1 0.15 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15249 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20938 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20762 66 0.0031 2.9 % + LOOP_ions opt_ions 5.6785 1 5.7 81 % + ESolver_KS_LCAO Run 5.1288 1 5.1 73 % + HSolverLCAO solve 2.7784 12 0.23 39 % + HamiltLCAO updateHk 1.4121 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.3756 12 0.11 20 % + Gint_interface cal_gint 2.6529 25 0.11 38 % + Gint_Gamma distri_vl 2.6764 6 0.45 38 % + LCAO_Deepks cal_projected_DM 5.527 14 0.39 79 % + LCAO_gen_fixedH add_v_delta 2.5483 6 0.42 36 % + LCAO_DESCRIPTOR add_v_delta 2.5483 6 0.42 36 % + ElecStateLCAO psiToRho 1.3483 12 0.11 19 % + Charge mix_rho 0.83011 11 0.075 12 % + LOOP_ions force_stress 0.5496 1 0.55 7.8 % + Force_Stress_LCAO getForceStress 0.54958 1 0.55 7.8 % + Force_LCAO_gamma ftable_gamma 0.35222 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.34502 1 0.35 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:24 2022 + FINISH Time : Wed Sep 28 11:13:31 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/28/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..7d66a778fe496759e36b79bba49235645e5375eb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.369442 0.668474 0.0616113 +H 0.425794 0.633897 0.0456914 +H 0.347902 0.698949 0.00426919 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8b7c7d6f4c8283909941f218702a9006038114b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.7947 2 + 2 -12.7944 2 + 3 -8.90526 2 + 4 -6.63071 2 + 5 0.908873 0 + 6 3.78475 0 + 7 11.1861 0 + 8 11.4202 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..8eeccf9fca2722b6a029bba1ad081c39f5ddb5ce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:10 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 10.3443658192 18.7172787718 1.72511671261 0 0 0 0 + tauc_H1 11.9222255112 17.7491092919 1.27935886494 0 0 0 0 + tauc_H2 9.74125957977 19.5705770233 0.119537352693 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0730867482572 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0733769223082 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.089618975275 (SEC) + + DONE : INIT CHARGE Time : 0.130877308518 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374751 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 81 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000886 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000756 + + Density error is 0.211180987515 + + Energy Rydberg eV + E_KohnSham -34.1885610845 -465.15923717 + E_Harris -34.3717772309 -467.652020727 + E_Fermi -0.37820335722 -5.14572066092 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113893755232 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00092401347992 + + Density error is 0.0994658902017 + + Energy Rydberg eV + E_KohnSham -34.2763558277 -466.353745933 + E_Harris -34.2836740288 -466.453315167 + E_Fermi -0.189069664173 -2.5724247517 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108843946791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000886599288369 + + Density error is 0.0643424366141 + + Energy Rydberg eV + E_KohnSham -34.2768206076 -466.360069587 + E_Harris -34.2814409276 -466.422932265 + E_Fermi -0.184117585439 -2.50504826397 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00101597250597 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000837069606108 + + Density error is 0.00207981534187 + + Energy Rydberg eV + E_KohnSham -34.2766968129 -466.358385273 + E_Harris -34.2767023107 -466.358460075 + E_Fermi -0.149322336743 -2.03163461838 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00101387977854 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834834443829 + + Density error is 0.000937812553461 + + Energy Rydberg eV + E_KohnSham -34.2766752127 -466.358091388 + E_Harris -34.2766753765 -466.358093617 + E_Fermi -0.149308733455 -2.03144953615 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00101289169213 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834218195531 + + Density error is 0.000208799543133 + + Energy Rydberg eV + E_KohnSham -34.276681955 -466.358183122 + E_Harris -34.2766819626 -466.358183225 + E_Fermi -0.148767689537 -2.024088256 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00101308116107 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834377452556 + + Density error is 2.5662165253e-05 + + Energy Rydberg eV + E_KohnSham -34.2766809991 -466.358170116 + E_Harris -34.2766810004 -466.358170133 + E_Fermi -0.148792101591 -2.02442039903 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00101300885312 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834319968304 + + Density error is 1.00602938705e-05 + + Energy Rydberg eV + E_KohnSham -34.2766828487 -466.358195281 + E_Harris -34.2766828491 -466.358195287 + E_Fermi -0.148798753961 -2.02451090917 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00101300540425 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834318218164 + + Density error is 1.73899397846e-06 + + Energy Rydberg eV + E_KohnSham -34.2766821067 -466.358185185 + E_Harris -34.2766821067 -466.358185185 + E_Fermi -0.148788853954 -2.02437621266 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00101300535764 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834318743684 + + Density error is 4.08770194639e-07 + + Energy Rydberg eV + E_KohnSham -34.2766822487 -466.358187118 + E_Harris -34.2766822487 -466.358187118 + E_Fermi -0.148787501636 -2.02435781343 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00101300579256 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834319197576 + + Density error is 1.0791309746e-07 + + Energy Rydberg eV + E_KohnSham -34.2766822578 -466.358187242 + E_Harris -34.2766822578 -466.358187242 + E_Fermi -0.148787265086 -2.024354595 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00101300579009 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834319239947 + + Density error is 1.04592526781e-08 + + Energy Rydberg eV + E_KohnSham -34.276682263 -466.358187312 + E_Harris -34.276682263 -466.358187312 + E_band -7.80924519403 -106.250231718 + E_one_elec -68.3608495203 -930.097073596 + E_Hartree +35.6077381818 +484.468132165 + E_xc -8.14015767861 -110.752527047 + E_Ewald +6.74280198661 +91.7405275036 + E_demet -3.88473556273e-53 -5.28545388764e-52 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193098934886 -2.62724579218 + E_Fermi -0.14878717128 -2.02435331872 + + charge density convergence is achieved + final etot is -466.358187312 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.7947 2.00000 + 2 -12.7944 2.00000 + 3 -8.90526 2.00000 + 4 -6.63071 2.00000 + 5 0.908873 0.00000 + 6 3.78475 0.00000 + 7 11.1861 0.00000 + 8 11.4202 0.00000 + + EFERMI = -2.024353318716007 eV + OUT.ABACUS/ final etot is -466.3581873121616 eV + correction force for each atom along direction 1 is -9.12474e-06 + correction force for each atom along direction 2 is 3.30702e-05 + correction force for each atom along direction 3 is -4.27513e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.46598404 +0.042268079 -1.3351584 + H1 -1.2320880 +0.83448454 +0.057823059 + H2 +0.76610391 -0.87675262 +1.2773353 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3581873121616 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9136 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9060 1 6.9 1.e+02% + Potential init_pot 0.24391 2 0.12 3.5% + PW_Basis recip2real 0.28573 17 0.017 4.1% + PW_Basis gathers_scatterp 0.11623 17 0.0068 1.7% + Potential v_of_rho 0.99456 14 0.071 14.% + XC_Functional v_xc 0.28595 15 0.019 4.1% + H_Hartree_pw v_hartree 0.66693 14 0.048 9.6% + PW_Basis real2recip 0.64544 41 0.016 9.3% + PW_Basis gatherp_scatters 0.24299 41 0.0059 3.5% + ORB_control set_orb_tables 0.89564 1 0.90 13.% + ORB_gen_tables gen_tables 0.89564 1 0.90 13.% + ORB_table_phi init_Table 0.37439 1 0.37 5.4% + ORB_table_phi cal_ST_Phi12_R 0.37017 126 0.0029 5.4% + ORB_table_beta init_Table_Beta 0.15533 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15407 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.20748 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20589 66 0.0031 3.0% + LOOP_ions opt_ions 5.5650 1 5.6 80.% + ESolver_KS_LCAO Run 5.0207 1 5.0 73.% + HSolverLCAO solve 2.6626 12 0.22 39.% + HamiltLCAO updateHk 1.3608 12 0.11 20.% + LCAO_Hamilt cal_Hgamma 1.3255 12 0.11 19.% + Gint_interface cal_gint 2.5275 25 0.10 37.% + Gint_Gamma distri_vl 2.6078 6 0.43 38.% + LCAO_Deepks cal_projected_DM 5.4177 14 0.39 78.% + LCAO_gen_fixedH add_v_delta 2.4802 6 0.41 36.% + LCAO_DESCRIPTOR add_v_delta 2.4802 6 0.41 36.% + ElecStateLCAO psiToRho 1.2825 12 0.11 19.% + Charge mix_rho 0.82988 11 0.075 12.% + LOOP_ions force_stress 0.54414 1 0.54 7.9% + Force_Stress_LCAO getForceStress 0.54412 1 0.54 7.9% + Force_LCAO_gamma ftable_gamma 0.34660 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.33903 1 0.34 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:10 2022 + Finish Time : Wed Sep 28 11:07:17 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b10e6928734fb867039b4c9bfe8ea7841f9a64c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123453 ima = 3.67198e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124076218504 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112561808427 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113392492683 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113558830242 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113556315457 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113560490537 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113557883964 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113559345223 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113558918274 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113558879592 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113558860945 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011355885592 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4561e28d17c5b0a5be04f796980eeaca36d3e4e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-17.655634180763 18.717278771851 1.725116712628 0 0 0 +H +0.0 +2 +-16.077774488830 17.749109291896 1.279358864912 0 0 0 +-18.258740420250 19.570577023328 0.119537352695 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/conv new file mode 100644 index 0000000000000000000000000000000000000000..df12c43894b0c8446b2a7dca09df1fa7cde387f1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/conv @@ -0,0 +1 @@ +29 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f47cfe28abe9f35835dc4c1b48d62fe61333b3ab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747572611 0.0122451924 1.236639894 1.33453669 1.467215897 0.007903370802 0.01864220612 0.03902529009 +-3.433258622e-18 0.0008881240122 0.002209168096 0.01097441721 0.03903374976 9.629871255e-20 1.248755497e-06 4.09016594e-06 +0.001658982821 0.005651960569 + +H atom_index 1 n_descriptor 18 +1.187517902 0.03614219375 0.08737565526 0.1242659138 0.301248096 0.01880738757 0.02481827236 0.03974482087 +3.114849209e-17 3.051306871e-05 0.08194330018 0.1059840063 0.1134314678 -2.243395597e-20 5.919123289e-06 0.01430633193 +0.02278171694 0.02769609871 + +H atom_index 2 n_descriptor 18 +1.178425302 0.0364107657 0.08480252179 0.1207165539 0.2977519824 0.01840166909 0.02429010161 0.04012281463 +-1.711420144e-17 2.985241495e-05 0.07965792377 0.1028417614 0.1129733264 -3.969232373e-18 6.094133025e-06 0.01460031971 +0.02239981109 0.02720100359 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ed512cea9bf1ed0ae1e007acb67070019fb7172e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:10 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.073102 SEC) : SETUP UNITCELL + DONE(0.0733857 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0896331 SEC) : INIT PLANEWAVE + DONE(0.130981 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374793 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651592e+02 0.000000e+00 2.112e-01 4.982e-01 + GE2 -4.663537e+02 -1.194509e+00 9.947e-02 4.721e-01 + GE3 -4.663601e+02 -6.323654e-03 6.434e-02 5.299e-01 + GE4 -4.663584e+02 1.684313e-03 2.080e-03 4.071e-01 + GE5 -4.663581e+02 2.938850e-04 9.378e-04 4.071e-01 + GE6 -4.663582e+02 -9.173320e-05 2.088e-04 4.034e-01 + GE7 -4.663582e+02 1.300536e-05 2.566e-05 3.835e-01 + GE8 -4.663582e+02 -2.516496e-05 1.006e-05 3.878e-01 + GE9 -4.663582e+02 1.009583e-05 1.739e-06 3.874e-01 + GE10 -4.663582e+02 -1.932933e-06 4.088e-07 3.856e-01 + GE11 -4.663582e+02 -1.233222e-07 1.079e-07 3.839e-01 + GE12 -4.663582e+02 -7.058993e-08 1.046e-08 3.210e-01 +E_delta_band = -6.68837024e-02 Ry = -9.09999455e-01 eV +E_delta_NN= -1.93098935e-01 Ry = -2.62724579e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9136 11 0.63 1e+02 % + Run_lcao lcao_line 6.906 1 6.9 1e+02 % + Potential init_pot 0.24391 2 0.12 3.5 % + PW_Basis recip2real 0.28573 17 0.017 4.1 % + PW_Basis gathers_scatterp 0.11623 17 0.0068 1.7 % + Potential v_of_rho 0.99456 14 0.071 14 % + XC_Functional v_xc 0.28595 15 0.019 4.1 % + H_Hartree_pw v_hartree 0.66693 14 0.048 9.6 % + PW_Basis real2recip 0.64544 41 0.016 9.3 % + PW_Basis gatherp_scatters 0.24299 41 0.0059 3.5 % + ORB_control set_orb_tables 0.89564 1 0.9 13 % + ORB_gen_tables gen_tables 0.89564 1 0.9 13 % + ORB_table_phi init_Table 0.37439 1 0.37 5.4 % + ORB_table_phi cal_ST_Phi12_R 0.37017 126 0.0029 5.4 % + ORB_table_beta init_Table_Beta 0.15533 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15407 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.20748 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20589 66 0.0031 3 % + LOOP_ions opt_ions 5.565 1 5.6 80 % + ESolver_KS_LCAO Run 5.0207 1 5 73 % + HSolverLCAO solve 2.6626 12 0.22 39 % + HamiltLCAO updateHk 1.3608 12 0.11 20 % + LCAO_Hamilt cal_Hgamma 1.3255 12 0.11 19 % + Gint_interface cal_gint 2.5275 25 0.1 37 % + Gint_Gamma distri_vl 2.6078 6 0.43 38 % + LCAO_Deepks cal_projected_DM 5.4177 14 0.39 78 % + LCAO_gen_fixedH add_v_delta 2.4802 6 0.41 36 % + LCAO_DESCRIPTOR add_v_delta 2.4802 6 0.41 36 % + ElecStateLCAO psiToRho 1.2825 12 0.11 19 % + Charge mix_rho 0.82988 11 0.075 12 % + LOOP_ions force_stress 0.54414 1 0.54 7.9 % + Force_Stress_LCAO getForceStress 0.54412 1 0.54 7.9 % + Force_LCAO_gamma ftable_gamma 0.3466 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.33903 1 0.34 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:10 2022 + FINISH Time : Wed Sep 28 11:07:17 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/29/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..8b72fd17fba510a3746868698a9dbe7d4f7c568b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.518329 0.703007 0.31994 +H 0.569758 0.6702 0.29983 +H 0.491826 0.736268 0.271857 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b3228dab70dba19a45204909b2a30e9dd055f693 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3659 2 + 2 -13.5672 2 + 3 -8.7986 2 + 4 -6.75997 2 + 5 1.5041 0 + 6 4.76775 0 + 7 11.034 0 + 8 11.2466 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3423d2ab114ba13ebd22efd044005cf31fcc02aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:20 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.513210942 19.6841921218 8.95832131331 0 0 0 0 + tauc_H1 15.9532129942 18.7655860641 8.39524743435 0 0 0 0 + tauc_H2 13.7711312667 20.615492912 7.61198949102 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0866118948337 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.098158981786 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116477334242 (SEC) + + DONE : INIT CHARGE Time : 0.165353232354 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448682 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00157 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000953 + + Density error is 0.218851454843 + + Energy Rydberg eV + E_KohnSham -34.1857089571 -465.120431987 + E_Harris -34.3854846594 -467.838519859 + E_Fermi -0.417150071853 -5.6756178983 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00143635736275 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110034410794 + + Density error is 0.0977704230048 + + Energy Rydberg eV + E_KohnSham -34.2774232897 -466.368269498 + E_Harris -34.2839455482 -466.457009377 + E_Fermi -0.223094401222 -3.03535504851 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00133431121745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104663425098 + + Density error is 0.062444888252 + + Energy Rydberg eV + E_KohnSham -34.2776939988 -466.371952684 + E_Harris -34.2818480253 -466.428471114 + E_Fermi -0.20900513021 -2.84366068209 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116326046211 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000962407917205 + + Density error is 0.00214633689592 + + Energy Rydberg eV + E_KohnSham -34.2777372588 -466.372541267 + E_Harris -34.2777409302 -466.372591218 + E_Fermi -0.173654202141 -2.36268663076 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116078775762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00096167858205 + + Density error is 0.000901354529181 + + Energy Rydberg eV + E_KohnSham -34.2776646742 -466.371553702 + E_Harris -34.2776665182 -466.371578791 + E_Fermi -0.172413592623 -2.34580727233 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115919545143 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00096063773509 + + Density error is 0.000224554124544 + + Energy Rydberg eV + E_KohnSham -34.2777127835 -466.372208264 + E_Harris -34.2777129525 -466.372210563 + E_Fermi -0.172697788173 -2.34967395114 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115904515289 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00096080037319 + + Density error is 4.59252675488e-05 + + Energy Rydberg eV + E_KohnSham -34.2776932901 -466.371943041 + E_Harris -34.2776933016 -466.371943199 + E_Fermi -0.172468682604 -2.34655680997 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115904464363 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000960748674427 + + Density error is 1.94579371685e-05 + + Energy Rydberg eV + E_KohnSham -34.2776996601 -466.37202971 + E_Harris -34.2776996616 -466.372029731 + E_Fermi -0.172526134642 -2.34733848504 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115900709282 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000960732857675 + + Density error is 1.53773533093e-06 + + Energy Rydberg eV + E_KohnSham -34.2776980718 -466.3720081 + E_Harris -34.2776980718 -466.3720081 + E_Fermi -0.172504651854 -2.34704619673 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115900419882 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000960733764187 + + Density error is 1.53630469723e-07 + + Energy Rydberg eV + E_KohnSham -34.27769834 -466.372011749 + E_Harris -34.27769834 -466.372011749 + E_Fermi -0.172503220712 -2.34702672503 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00115900477866 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009607342306 + + Density error is 3.20503398511e-08 + + Energy Rydberg eV + E_KohnSham -34.2776983622 -466.372012051 + E_Harris -34.2776983622 -466.372012051 + E_band -8.01012630517 -108.98335945 + E_one_elec -69.7055171326 -948.392215039 + E_Hartree +36.2473397897 +493.170358483 + E_xc -8.2427886471 -112.14889301 + E_Ewald +7.54679430775 +102.679404219 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195410073618 -2.65869044781 + E_Fermi -0.172503198413 -2.34702642164 + + charge density convergence is achieved + final etot is -466.372012051 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3659 2.00000 + 2 -13.5672 2.00000 + 3 -8.79860 2.00000 + 4 -6.75997 2.00000 + 5 1.50410 0.00000 + 6 4.76775 0.00000 + 7 11.0340 0.00000 + 8 11.2466 0.00000 + + EFERMI = -2.347026421637870 eV + OUT.ABACUS/ final etot is -466.3720120510324 eV + correction force for each atom along direction 1 is -2.30005e-05 + correction force for each atom along direction 2 is 7.42877e-06 + correction force for each atom along direction 3 is -4.39887e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.65943910 -0.029979510 +1.8639413 + H1 +0.80988991 -0.39485951 -0.74911213 + H2 -0.15045081 +0.42483902 -1.1148292 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3720120510324 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.7946 11 0.53 1.0e+02% + Run_lcao lcao_line 5.7848 1 5.8 1.e+02% + Potential init_pot 0.28906 2 0.14 5.0% + PW_Basis recip2real 0.25889 16 0.016 4.5% + PW_Basis gathers_scatterp 0.11198 16 0.0070 1.9% + Potential v_of_rho 0.87263 13 0.067 15.% + XC_Functional v_xc 0.25536 14 0.018 4.4% + H_Hartree_pw v_hartree 0.58112 13 0.045 10.% + PW_Basis real2recip 0.55551 38 0.015 9.6% + PW_Basis gatherp_scatters 0.21906 38 0.0058 3.8% + ORB_control set_orb_tables 1.1097 1 1.1 19.% + ORB_gen_tables gen_tables 1.1097 1 1.1 19.% + ORB_table_phi init_Table 0.48883 1 0.49 8.4% + ORB_table_phi cal_ST_Phi12_R 0.48382 126 0.0038 8.3% + ORB_table_beta init_Table_Beta 0.18649 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18502 56 0.0033 3.2% + ORB_table_alpha init_Table_Alpha 0.25363 1 0.25 4.4% + ORB_table_alpha S_PhiAlpha_R 0.25179 66 0.0038 4.3% + LOOP_ions opt_ions 4.1494 1 4.1 72.% + ESolver_KS_LCAO Run 3.6589 1 3.7 63.% + HSolverLCAO solve 1.7002 11 0.15 29.% + HamiltLCAO updateHk 0.92590 11 0.084 16.% + LCAO_Hamilt cal_Hgamma 0.89449 11 0.081 15.% + Gint_interface cal_gint 0.78442 23 0.034 14.% + Gint_Gamma distri_vl_value 0.26299 11 0.024 4.5% + Gint_Gamma distri_vl 1.7806 6 0.30 31.% + LCAO_Deepks cal_projected_DM 3.9103 13 0.30 67.% + LCAO_gen_fixedH add_v_delta 1.6476 6 0.27 28.% + LCAO_DESCRIPTOR add_v_delta 1.6476 6 0.27 28.% + ElecStateLCAO psiToRho 0.75702 11 0.069 13.% + Charge mix_rho 0.64928 10 0.065 11.% + LOOP_ions force_stress 0.49033 1 0.49 8.5% + Force_Stress_LCAO getForceStress 0.49030 1 0.49 8.5% + Force_LCAO_gamma ftable_gamma 0.27909 1 0.28 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.17282 1 0.17 3.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:20 2022 + Finish Time : Wed Sep 28 11:13:26 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..862e4570a8b5ec9f8a127252b258c1460d5eab37 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123694 ima = 3.65661e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123597951038 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112853736539 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113239210556 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011350174065 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113438048945 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113477443142 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113465381218 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113468588962 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113467847854 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113467790828 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113467783026 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/STRU new file mode 100644 index 0000000000000000000000000000000000000000..97a7cbeaec83626d13625ecb686706308ecf2d51 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.486789058040 19.684192121748 8.958321313305 0 0 0 +H +0.0 +2 +-12.046787005844 18.765586064138 8.395247434364 0 0 0 +-14.228868733235 20.615492911975 7.611989491001 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/conv new file mode 100644 index 0000000000000000000000000000000000000000..57fe534564c694257d2bf5413ba64ea8cf8348e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/conv @@ -0,0 +1 @@ +3 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..17fa998216cfd5b0a79435a21ea2f7bd565c2029 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742957161 0.0127069941 1.296199053 1.384892991 1.469879622 0.007690790272 0.02106898518 0.03884638997 +5.914132234e-18 0.001253913617 0.002421117895 0.01292840483 0.04391753059 7.125069099e-19 1.587741553e-06 4.993169058e-06 +0.001821035837 0.005566815172 + +H atom_index 1 n_descriptor 18 +1.266471833 0.03289184438 0.115104388 0.1593800151 0.328108252 0.0226362763 0.02945796819 0.03622020006 +4.071238409e-17 4.119994312e-05 0.1065885186 0.1162997633 0.1369967978 4.197349524e-18 3.393597772e-06 0.01285319192 +0.02700205145 0.03161249044 + +H atom_index 2 n_descriptor 18 +1.267331792 0.03286184058 0.1154186773 0.1598012699 0.3283577805 0.02267267183 0.02950724058 0.03620182078 +-3.315447389e-18 4.127074867e-05 0.1067093767 0.1164237873 0.1373567571 -1.635132387e-17 3.350590355e-06 0.01285840786 +0.02703137922 0.03164729506 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e86d2a697cacdce3d492433da54cf46338d78481 Binary files /dev/null and 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0000000000000000000000000000000000000000..f70e01ea7f455f3cfda4fb65e1bd932005b1f732 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:20 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0866362 SEC) : SETUP UNITCELL + DONE(0.098175 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116496 SEC) : INIT PLANEWAVE + DONE(0.165472 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448756 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651204e+02 0.000000e+00 2.189e-01 4.470e-01 + GE2 -4.663683e+02 -1.247838e+00 9.777e-02 3.725e-01 + GE3 -4.663720e+02 -3.683186e-03 6.244e-02 4.315e-01 + GE4 -4.663725e+02 -5.885826e-04 2.146e-03 3.170e-01 + GE5 -4.663716e+02 9.875645e-04 9.014e-04 3.123e-01 + GE6 -4.663722e+02 -6.545614e-04 2.246e-04 3.080e-01 + GE7 -4.663719e+02 2.652223e-04 4.593e-05 3.021e-01 + GE8 -4.663720e+02 -8.666895e-05 1.946e-05 2.917e-01 + GE9 -4.663720e+02 2.161025e-05 1.538e-06 2.901e-01 + GE10 -4.663720e+02 -3.648986e-06 1.536e-07 2.918e-01 + GE11 -4.663720e+02 -3.020964e-07 3.205e-08 2.329e-01 +E_delta_band = -7.18833936e-02 Ry = -9.78023745e-01 eV +E_delta_NN= -1.95410074e-01 Ry = -2.65869045e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.7946 11 0.53 1e+02 % + Run_lcao lcao_line 5.7848 1 5.8 1e+02 % + Potential init_pot 0.28906 2 0.14 5 % + PW_Basis recip2real 0.25889 16 0.016 4.5 % + PW_Basis gathers_scatterp 0.11198 16 0.007 1.9 % + Potential v_of_rho 0.87263 13 0.067 15 % + XC_Functional v_xc 0.25536 14 0.018 4.4 % + H_Hartree_pw v_hartree 0.58112 13 0.045 10 % + PW_Basis real2recip 0.55551 38 0.015 9.6 % + PW_Basis gatherp_scatters 0.21906 38 0.0058 3.8 % + ORB_control set_orb_tables 1.1097 1 1.1 19 % + ORB_gen_tables gen_tables 1.1097 1 1.1 19 % + ORB_table_phi init_Table 0.48883 1 0.49 8.4 % + ORB_table_phi cal_ST_Phi12_R 0.48382 126 0.0038 8.3 % + ORB_table_beta init_Table_Beta 0.18649 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18502 56 0.0033 3.2 % + ORB_table_alpha init_Table_Alpha 0.25363 1 0.25 4.4 % + ORB_table_alpha S_PhiAlpha_R 0.25179 66 0.0038 4.3 % + LOOP_ions opt_ions 4.1494 1 4.1 72 % + ESolver_KS_LCAO Run 3.6589 1 3.7 63 % + HSolverLCAO solve 1.7002 11 0.15 29 % + HamiltLCAO updateHk 0.9259 11 0.084 16 % + LCAO_Hamilt cal_Hgamma 0.89449 11 0.081 15 % + Gint_interface cal_gint 0.78442 23 0.034 14 % + Gint_Gamma distri_vl_value 0.26299 11 0.024 4.5 % + Gint_Gamma distri_vl 1.7806 6 0.3 31 % + LCAO_Deepks cal_projected_DM 3.9103 13 0.3 67 % + LCAO_gen_fixedH add_v_delta 1.6476 6 0.27 28 % + LCAO_DESCRIPTOR add_v_delta 1.6476 6 0.27 28 % + ElecStateLCAO psiToRho 0.75702 11 0.069 13 % + Charge mix_rho 0.64928 10 0.065 11 % + LOOP_ions force_stress 0.49033 1 0.49 8.5 % + Force_Stress_LCAO getForceStress 0.4903 1 0.49 8.5 % + Force_LCAO_gamma ftable_gamma 0.27909 1 0.28 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.17282 1 0.17 3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:20 2022 + FINISH Time : Wed Sep 28 11:13:26 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/3/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..25f3bd3d86a09603ff9575e20457aa4da2dfdb4d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.385882 0.681498 0.0720951 +H 0.417611 0.72032 0.0312618 +H 0.327784 0.698454 0.0544824 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ed5e173e97f26a4db84af455d14e46df7650e0bc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.754 2 + 2 -12.8829 2 + 3 -9.55305 2 + 4 -6.84373 2 + 5 1.46258 0 + 6 4.81458 0 + 7 10.9927 0 + 8 11.2822 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1ed08d7aee32f7b7f118c94be236fb893c29972b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:34 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 10.8047039772 19.0819510142 2.01866404911 0 0 0 0 + tauc_H1 11.6931058926 20.1689524505 0.875329194925 0 0 0 0 + tauc_H2 9.17794891168 19.5567258609 1.52550747923 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0873637387665 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877729090193 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105937197253 (SEC) + + DONE : INIT CHARGE Time : 0.155270935359 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437842 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000815 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00184 + + Density error is 0.217180851948 + + Energy Rydberg eV + E_KohnSham -34.1816161262 -465.064746166 + E_Harris -34.3796185986 -467.758708008 + E_Fermi -0.425466264167 -5.78876549945 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00118985519537 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00152158011922 + + Density error is 0.09702791657 + + Energy Rydberg eV + E_KohnSham -34.2733396972 -466.312709371 + E_Harris -34.2801040181 -466.404742678 + E_Fermi -0.232823370836 -3.16772447093 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00113551870545 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138604670879 + + Density error is 0.0619586921843 + + Energy Rydberg eV + E_KohnSham -34.2736481337 -466.316905865 + E_Harris -34.2779945961 -466.37604252 + E_Fermi -0.218773240031 -2.97656263434 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106591487475 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115564581784 + + Density error is 0.00206512274345 + + Energy Rydberg eV + E_KohnSham -34.2736895726 -466.317469671 + E_Harris -34.273692865 -466.317514466 + E_Fermi -0.182470726653 -2.48264160068 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00107169729913 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115500301784 + + Density error is 0.000949819738993 + + Energy Rydberg eV + E_KohnSham -34.2736124201 -466.316419957 + E_Harris -34.273614787 -466.316452161 + E_Fermi -0.181493077194 -2.46933999739 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106980913458 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115243718995 + + Density error is 0.000162669975889 + + Energy Rydberg eV + E_KohnSham -34.2736646738 -466.317130905 + E_Harris -34.2736647616 -466.3171321 + E_Fermi -0.181701635595 -2.47217758001 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106980965646 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115201182894 + + Density error is 4.51487418189e-05 + + Energy Rydberg eV + E_KohnSham -34.2736457049 -466.316872819 + E_Harris -34.273645715 -466.316872957 + E_Fermi -0.181536200769 -2.46992672373 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106973584128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115204111244 + + Density error is 2.39318196933e-05 + + Energy Rydberg eV + E_KohnSham -34.2736502984 -466.316935318 + E_Harris -34.2736503007 -466.316935348 + E_Fermi -0.181591319417 -2.47067665141 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106973177431 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115197593916 + + Density error is 2.06344701834e-06 + + Energy Rydberg eV + E_KohnSham -34.2736485862 -466.316912023 + E_Harris -34.2736485863 -466.316912023 + E_Fermi -0.181564773625 -2.47031547738 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106973248847 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115197325101 + + Density error is 5.24636311394e-07 + + Energy Rydberg eV + E_KohnSham -34.2736488957 -466.316916233 + E_Harris -34.2736488957 -466.316916233 + E_Fermi -0.181563359517 -2.47029623746 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106973367765 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115197315123 + + Density error is 1.63474624957e-07 + + Energy Rydberg eV + E_KohnSham -34.27364892 -466.316916564 + E_Harris -34.27364892 -466.316916564 + E_Fermi -0.181563107874 -2.47029281368 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106973385822 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115197278921 + + Density error is 1.0891183457e-08 + + Energy Rydberg eV + E_KohnSham -34.2736489244 -466.316916623 + E_Harris -34.2736489244 -466.316916623 + E_band -8.08979854281 -110.067355854 + E_one_elec -69.9165670348 -951.263696273 + E_Hartree +36.321003556 +494.17260544 + E_xc -8.25489775026 -112.313645811 + E_Ewald +7.69981045615 +104.761295724 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196023710875 -2.667039411 + E_Fermi -0.181562927214 -2.47029035567 + + charge density convergence is achieved + final etot is -466.316916623 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.7540 2.00000 + 2 -12.8829 2.00000 + 3 -9.55305 2.00000 + 4 -6.84373 2.00000 + 5 1.46258 0.00000 + 6 4.81458 0.00000 + 7 10.9927 0.00000 + 8 11.2822 0.00000 + + EFERMI = -2.470290355665553 eV + OUT.ABACUS/ final etot is -466.3169166230643 eV + correction force for each atom along direction 1 is -7.94275e-05 + correction force for each atom along direction 2 is -3.04381e-05 + correction force for each atom along direction 3 is -0.000172668 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.4941111 -0.64687180 +0.66368087 + H1 +1.2113113 +0.42981913 -0.44947047 + H2 -2.7054225 +0.21705268 -0.21421039 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3169166230643 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6699 11 0.70 1.0e+02% + Run_lcao lcao_line 7.6598 1 7.7 1.e+02% + Potential init_pot 0.28467 2 0.14 3.7% + PW_Basis recip2real 0.30832 17 0.018 4.0% + PW_Basis gathers_scatterp 0.13054 17 0.0077 1.7% + Potential v_of_rho 1.0817 14 0.077 14.% + XC_Functional v_xc 0.31293 15 0.021 4.1% + H_Hartree_pw v_hartree 0.72456 14 0.052 9.4% + PW_Basis real2recip 0.69667 41 0.017 9.1% + PW_Basis gatherp_scatters 0.26373 41 0.0064 3.4% + ORB_control set_orb_tables 1.1014 1 1.1 14.% + ORB_gen_tables gen_tables 1.1014 1 1.1 14.% + ORB_table_phi init_Table 0.47742 1 0.48 6.2% + ORB_table_phi cal_ST_Phi12_R 0.47222 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18663 1 0.19 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18508 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24925 1 0.25 3.2% + ORB_table_alpha S_PhiAlpha_R 0.24728 66 0.0037 3.2% + LOOP_ions opt_ions 6.0426 1 6.0 79.% + ESolver_KS_LCAO Run 5.4438 1 5.4 71.% + HSolverLCAO solve 2.9608 12 0.25 39.% + HamiltLCAO updateHk 1.5186 12 0.13 20.% + LCAO_Hamilt cal_Hgamma 1.4818 12 0.12 19.% + Gint_interface cal_gint 2.8065 25 0.11 37.% + Gint_Gamma distri_vl 2.8372 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.8708 14 0.42 77.% + LCAO_gen_fixedH add_v_delta 2.6923 6 0.45 35.% + LCAO_DESCRIPTOR add_v_delta 2.6924 6 0.45 35.% + ElecStateLCAO psiToRho 1.4245 12 0.12 19.% + Charge mix_rho 0.84792 11 0.077 11.% + LOOP_ions force_stress 0.59860 1 0.60 7.8% + Force_Stress_LCAO getForceStress 0.59856 1 0.60 7.8% + Force_LCAO_gamma ftable_gamma 0.37859 1 0.38 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.37077 1 0.37 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:34 2022 + Finish Time : Wed Sep 28 11:12:42 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d4319afa7daa0b652ebf33ef409d7ec837c7a5f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124245 ima = 3.662e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122306909568 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111203356191 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111682611833 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112002330574 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111924097599 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111967964619 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111960503572 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111963842353 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111962959664 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111962883841 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111962865209 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111962856828 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4a6d97cb39ab9ab7e8737a8c19abee150c8330ed --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-17.195296022821 19.081951014188 2.018664049124 0 0 0 +H +0.0 +2 +-16.306894107359 20.168952450436 0.875329194911 0 0 0 +-18.822051088299 19.556725860904 1.525507479237 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/conv new file mode 100644 index 0000000000000000000000000000000000000000..3e63a8a7995e00081393d748f8a10dd58a4816fb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/conv @@ -0,0 +1 @@ +30 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..13d793afefabc1b8f2239a4d150339659cc9adcf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755255534 0.01296787615 1.29281651 1.372232884 1.471184621 0.009984144815 0.01691758288 0.03918094181 +-1.220143491e-18 0.0009858537327 0.003133945683 0.01452393688 0.05053241869 -9.025136053e-19 3.592541976e-06 8.769562293e-06 +0.001592169228 0.006188058504 + +H atom_index 1 n_descriptor 18 +1.26774869 0.03453205712 0.1197246685 0.1579786851 0.3245221378 0.0247253705 0.02926139607 0.03767709161 +-4.896315646e-17 5.783343213e-05 0.1089388899 0.1184332094 0.1356639673 -6.10254373e-18 1.685047379e-06 0.01347184005 +0.02867672157 0.03157264943 + +H atom_index 2 n_descriptor 18 +1.303353049 0.03346686077 0.1340592591 0.1763495816 0.3349484635 0.02653638465 0.03130782483 0.03719299746 +2.433144873e-17 6.111884864e-05 0.1087590333 0.1288997838 0.1511863727 -1.243322584e-18 2.546503422e-07 0.01406352107 +0.0297910984 0.03292783384 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..1d814434365ee356b2ad1c3fe530b99a76559d19 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:34 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0873883 SEC) : SETUP UNITCELL + DONE(0.0877869 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105959 SEC) : INIT PLANEWAVE + DONE(0.155404 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.43791 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650647e+02 0.000000e+00 2.172e-01 5.601e-01 + GE2 -4.663127e+02 -1.247963e+00 9.703e-02 5.075e-01 + GE3 -4.663169e+02 -4.196494e-03 6.196e-02 5.727e-01 + GE4 -4.663175e+02 -5.638058e-04 2.065e-03 4.372e-01 + GE5 -4.663164e+02 1.049714e-03 9.498e-04 4.354e-01 + GE6 -4.663171e+02 -7.109474e-04 1.627e-04 4.296e-01 + GE7 -4.663169e+02 2.580855e-04 4.515e-05 4.301e-01 + GE8 -4.663169e+02 -6.249890e-05 2.393e-05 4.143e-01 + GE9 -4.663169e+02 2.329558e-05 2.063e-06 4.159e-01 + GE10 -4.663169e+02 -4.210197e-06 5.246e-07 4.152e-01 + GE11 -4.663169e+02 -3.311979e-07 1.635e-07 4.149e-01 + GE12 -4.663169e+02 -5.907428e-08 1.089e-08 3.483e-01 +E_delta_band = -7.30255594e-02 Ry = -9.93563708e-01 eV +E_delta_NN= -1.96023711e-01 Ry = -2.66703941e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6699 11 0.7 1e+02 % + Run_lcao lcao_line 7.6598 1 7.7 1e+02 % + Potential init_pot 0.28467 2 0.14 3.7 % + PW_Basis recip2real 0.30832 17 0.018 4 % + PW_Basis gathers_scatterp 0.13054 17 0.0077 1.7 % + Potential v_of_rho 1.0817 14 0.077 14 % + XC_Functional v_xc 0.31293 15 0.021 4.1 % + H_Hartree_pw v_hartree 0.72456 14 0.052 9.4 % + PW_Basis real2recip 0.69667 41 0.017 9.1 % + PW_Basis gatherp_scatters 0.26373 41 0.0064 3.4 % + ORB_control set_orb_tables 1.1014 1 1.1 14 % + ORB_gen_tables gen_tables 1.1014 1 1.1 14 % + ORB_table_phi init_Table 0.47742 1 0.48 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.47222 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18663 1 0.19 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18508 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.24925 1 0.25 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.24728 66 0.0037 3.2 % + LOOP_ions opt_ions 6.0426 1 6 79 % + ESolver_KS_LCAO Run 5.4438 1 5.4 71 % + HSolverLCAO solve 2.9608 12 0.25 39 % + HamiltLCAO updateHk 1.5186 12 0.13 20 % + LCAO_Hamilt cal_Hgamma 1.4818 12 0.12 19 % + Gint_interface cal_gint 2.8065 25 0.11 37 % + Gint_Gamma distri_vl 2.8372 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.8708 14 0.42 77 % + LCAO_gen_fixedH add_v_delta 2.6923 6 0.45 35 % + LCAO_DESCRIPTOR add_v_delta 2.6924 6 0.45 35 % + ElecStateLCAO psiToRho 1.4245 12 0.12 19 % + Charge mix_rho 0.84792 11 0.077 11 % + LOOP_ions force_stress 0.5986 1 0.6 7.8 % + Force_Stress_LCAO getForceStress 0.59856 1 0.6 7.8 % + Force_LCAO_gamma ftable_gamma 0.37859 1 0.38 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.37077 1 0.37 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:34 2022 + FINISH Time : Wed Sep 28 11:12:42 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/30/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..8cd33264a3cebe2ce1da42e801d1180cdb65b16c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.403015 0.683995 0.0657432 +H 0.428492 0.73829 0.0390765 +H 0.339257 0.69785 0.0790078 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d9c20cc3d91845915335c7ba07b01fd90e102113 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1419 2 + 2 -13.0603 2 + 3 -8.99029 2 + 4 -6.71046 2 + 5 1.22026 0 + 6 4.28594 0 + 7 11.1044 0 + 8 11.3455 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d653f8cfd651a68cb8d2d1b809e7bc90c3dab1dc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:30 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.2844114453 19.1518634135 1.84081078907 0 0 0 0 + tauc_H1 11.9977820924 20.6721137091 1.09414095002 0 0 0 0 + tauc_H2 9.49918991054 19.5397890488 2.21221977808 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0866333009469 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0969872306301 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115123015374 (SEC) + + DONE : INIT CHARGE Time : 0.165646270325 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447257 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000548 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00176 + + Density error is 0.214194968545 + + Energy Rydberg eV + E_KohnSham -34.1916489584 -465.20124985 + E_Harris -34.381355899 -467.782345192 + E_Fermi -0.39831349848 -5.41933316964 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000812921223666 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00141555801857 + + Density error is 0.0984067065141 + + Energy Rydberg eV + E_KohnSham -34.2807626922 -466.4137044 + E_Harris -34.2875818197 -466.50648339 + E_Fermi -0.207623233354 -2.8248590108 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000784251882278 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130260936442 + + Density error is 0.0632187281827 + + Energy Rydberg eV + E_KohnSham -34.2810833776 -466.418067548 + E_Harris -34.2854819716 -466.47791349 + E_Fermi -0.197870813943 -2.69217053752 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000755677353398 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109368800062 + + Density error is 0.0020238332902 + + Energy Rydberg eV + E_KohnSham -34.2810468947 -466.417571173 + E_Harris -34.281049112 -466.417601341 + E_Fermi -0.162563664898 -2.21179213038 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756687239766 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010910431714 + + Density error is 0.000893900821046 + + Energy Rydberg eV + E_KohnSham -34.2809986674 -466.416915007 + E_Harris -34.2809992076 -466.416922357 + E_Fermi -0.162046088545 -2.20475014283 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756237439901 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108841991005 + + Density error is 0.000180913435379 + + Energy Rydberg eV + E_KohnSham -34.2810253587 -466.417278161 + E_Harris -34.281025385 -466.417278518 + E_Fermi -0.161874021485 -2.20240905037 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756452004247 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108822933897 + + Density error is 3.45769843669e-05 + + Energy Rydberg eV + E_KohnSham -34.281015951 -466.417150163 + E_Harris -34.2810159567 -466.41715024 + E_Fermi -0.161770085652 -2.20099493081 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0007563954256 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108821441527 + + Density error is 1.62637166958e-05 + + Energy Rydberg eV + E_KohnSham -34.2810199065 -466.417203979 + E_Harris -34.2810199077 -466.417203996 + E_Fermi -0.161803356378 -2.20144760227 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756404051744 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108818531382 + + Density error is 1.97095484762e-06 + + Energy Rydberg eV + E_KohnSham -34.281018569 -466.417185782 + E_Harris -34.281018569 -466.417185782 + E_Fermi -0.161786911363 -2.20122385635 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756403807873 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108817904509 + + Density error is 3.90870098204e-07 + + Energy Rydberg eV + E_KohnSham -34.2810188247 -466.417189261 + E_Harris -34.2810188247 -466.417189261 + E_Fermi -0.161785119088 -2.20119947121 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756404506321 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108817929733 + + Density error is 1.3016890757e-07 + + Energy Rydberg eV + E_KohnSham -34.2810188434 -466.417189515 + E_Harris -34.2810188434 -466.417189515 + E_Fermi -0.161784959224 -2.20119729615 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756404698843 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108817906519 + + Density error is 1.05340118242e-08 + + Energy Rydberg eV + E_KohnSham -34.281018847 -466.417189565 + E_Harris -34.281018847 -466.417189565 + E_band -7.92359015483 -107.805974722 + E_one_elec -69.0678478599 -939.716279492 + E_Hartree +35.9390692956 +488.976123237 + E_xc -8.1932258551 -111.47455663 + E_Ewald +7.16579763397 +97.495678537 + E_demet -2.46718051245e-71 -3.35677129639e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194345282951 -2.64420322756 + E_Fermi -0.161784837172 -2.20119563554 + + charge density convergence is achieved + final etot is -466.417189565 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1419 2.00000 + 2 -13.0603 2.00000 + 3 -8.99029 2.00000 + 4 -6.71046 2.00000 + 5 1.22026 0.00000 + 6 4.28594 0.00000 + 7 11.1044 0.00000 + 8 11.3455 0.00000 + + EFERMI = -2.201195635537609 eV + OUT.ABACUS/ final etot is -466.4171895645533 eV + correction force for each atom along direction 1 is -4.02220e-05 + correction force for each atom along direction 2 is 0.000150861 + correction force for each atom along direction 3 is -9.46829e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.46419806 -0.20191353 +0.20213101 + H1 -0.11372532 +0.16579733 -0.025582710 + H2 +0.57792338 +0.036116196 -0.17654830 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4171895645533 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6051 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5955 1 7.6 1.e+02% + Potential init_pot 0.28766 2 0.14 3.8% + PW_Basis recip2real 0.30117 17 0.018 4.0% + PW_Basis gathers_scatterp 0.12995 17 0.0076 1.7% + Potential v_of_rho 1.0561 14 0.075 14.% + XC_Functional v_xc 0.30124 15 0.020 4.0% + H_Hartree_pw v_hartree 0.70914 14 0.051 9.3% + PW_Basis real2recip 0.70563 41 0.017 9.3% + PW_Basis gatherp_scatters 0.26694 41 0.0065 3.5% + ORB_control set_orb_tables 1.1025 1 1.1 14.% + ORB_gen_tables gen_tables 1.1025 1 1.1 14.% + ORB_table_phi init_Table 0.48106 1 0.48 6.3% + ORB_table_phi cal_ST_Phi12_R 0.47577 126 0.0038 6.3% + ORB_table_beta init_Table_Beta 0.18849 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18696 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24837 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24641 66 0.0037 3.2% + LOOP_ions opt_ions 5.9682 1 6.0 78.% + ESolver_KS_LCAO Run 5.3706 1 5.4 71.% + HSolverLCAO solve 2.9179 12 0.24 38.% + HamiltLCAO updateHk 1.4954 12 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.4657 12 0.12 19.% + Gint_interface cal_gint 2.7680 25 0.11 36.% + Gint_Gamma distri_vl 2.7930 6 0.47 37.% + LCAO_Deepks cal_projected_DM 5.7963 14 0.41 76.% + LCAO_gen_fixedH add_v_delta 2.6478 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6478 6 0.44 35.% + ElecStateLCAO psiToRho 1.4055 12 0.12 18.% + Charge mix_rho 0.85009 11 0.077 11.% + LOOP_ions force_stress 0.59745 1 0.60 7.9% + Force_Stress_LCAO getForceStress 0.59742 1 0.60 7.9% + Force_LCAO_gamma ftable_gamma 0.37925 1 0.38 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.37138 1 0.37 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:30 2022 + Finish Time : Wed Sep 28 11:07:38 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ed29c18211f0d34052fcec85a244607be82ba120 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123903 ima = 3.65184e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012345094614 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112321776689 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112919374481 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113138520022 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113103782852 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113124491719 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113117728912 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113120390446 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113119654391 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113119594567 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113119578642 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113119572399 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5027458df038d4865318179dc417e2a904084c98 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.715588554771 19.151863413544 1.840810789086 0 0 0 +H +0.0 +2 +-16.002217907642 20.672113709095 1.094140950048 0 0 0 +-18.500810089458 19.539789048783 2.212219778068 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/conv new file mode 100644 index 0000000000000000000000000000000000000000..281c64199c87334032e1561e600b16b7a8a18685 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/conv @@ -0,0 +1 @@ +31 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..eccd6068913899206d1700b88ad7d12b5163e014 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747424852 0.01257355954 1.265475265 1.357759014 1.468661343 0.008110670791 0.01899976619 0.03897702898 +2.502057571e-18 0.001038128057 0.002440743055 0.01199025218 0.04301422635 1.369914527e-19 1.683527127e-06 5.159303099e-06 +0.001686049777 0.005827996123 + +H atom_index 1 n_descriptor 18 +1.240308559 0.03437364628 0.1045235164 0.1461209383 0.3189832266 0.02149845721 0.02782887714 0.03755757222 +-1.719281978e-17 4.034452616e-05 0.09823738328 0.1147091191 0.1253434056 2.054373837e-18 4.605895708e-06 0.01314148142 +0.02557514689 0.03035747603 + +H atom_index 2 n_descriptor 18 +1.219300022 0.03509961409 0.09769585734 0.1368680308 0.3118583919 0.02054517475 0.02660441363 0.03832967115 +-2.422644407e-17 3.855386545e-05 0.09269041419 0.1141316376 0.1172842442 4.963130488e-19 5.518273783e-06 0.01349919318 +0.02475446805 0.02934151156 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..8f0836b0512f012cd3de95e3205e7c11553d0f37 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:30 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0866597 SEC) : SETUP UNITCELL + DONE(0.0970042 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115143 SEC) : INIT PLANEWAVE + DONE(0.165777 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447321 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652012e+02 0.000000e+00 2.142e-01 5.504e-01 + GE2 -4.664137e+02 -1.212455e+00 9.841e-02 5.006e-01 + GE3 -4.664181e+02 -4.363148e-03 6.322e-02 5.673e-01 + GE4 -4.664176e+02 4.963755e-04 2.024e-03 4.278e-01 + GE5 -4.664169e+02 6.561653e-04 8.939e-04 4.302e-01 + GE6 -4.664173e+02 -3.631537e-04 1.809e-04 4.257e-01 + GE7 -4.664172e+02 1.279979e-04 3.458e-05 4.194e-01 + GE8 -4.664172e+02 -5.381622e-05 1.626e-05 4.146e-01 + GE9 -4.664172e+02 1.819726e-05 1.971e-06 4.109e-01 + GE10 -4.664172e+02 -3.478473e-06 3.909e-07 4.071e-01 + GE11 -4.664172e+02 -2.544636e-07 1.302e-07 4.100e-01 + GE12 -4.664172e+02 -4.950024e-08 1.053e-08 3.445e-01 +E_delta_band = -6.95332214e-02 Ry = -9.46048011e-01 eV +E_delta_NN= -1.94345283e-01 Ry = -2.64420323e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6051 11 0.69 1e+02 % + Run_lcao lcao_line 7.5955 1 7.6 1e+02 % + Potential init_pot 0.28766 2 0.14 3.8 % + PW_Basis recip2real 0.30117 17 0.018 4 % + PW_Basis gathers_scatterp 0.12995 17 0.0076 1.7 % + Potential v_of_rho 1.0561 14 0.075 14 % + XC_Functional v_xc 0.30124 15 0.02 4 % + H_Hartree_pw v_hartree 0.70914 14 0.051 9.3 % + PW_Basis real2recip 0.70563 41 0.017 9.3 % + PW_Basis gatherp_scatters 0.26694 41 0.0065 3.5 % + ORB_control set_orb_tables 1.1025 1 1.1 14 % + ORB_gen_tables gen_tables 1.1025 1 1.1 14 % + ORB_table_phi init_Table 0.48106 1 0.48 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.47577 126 0.0038 6.3 % + ORB_table_beta init_Table_Beta 0.18849 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18696 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24837 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24641 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9682 1 6 78 % + ESolver_KS_LCAO Run 5.3706 1 5.4 71 % + HSolverLCAO solve 2.9179 12 0.24 38 % + HamiltLCAO updateHk 1.4954 12 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.4657 12 0.12 19 % + Gint_interface cal_gint 2.768 25 0.11 36 % + Gint_Gamma distri_vl 2.793 6 0.47 37 % + LCAO_Deepks cal_projected_DM 5.7963 14 0.41 76 % + LCAO_gen_fixedH add_v_delta 2.6478 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6478 6 0.44 35 % + ElecStateLCAO psiToRho 1.4055 12 0.12 18 % + Charge mix_rho 0.85009 11 0.077 11 % + LOOP_ions force_stress 0.59745 1 0.6 7.9 % + Force_Stress_LCAO getForceStress 0.59742 1 0.6 7.9 % + Force_LCAO_gamma ftable_gamma 0.37925 1 0.38 5 % + Force_LCAO_gamma cal_fvl_dphi 0.37138 1 0.37 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:30 2022 + FINISH Time : Wed Sep 28 11:07:38 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/31/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ff012a9a9b2a6c2cbf1bc2c0355fcf10c97643cf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.41579 0.686464 0.061916 +H 0.438359 0.724931 0.112489 +H 0.356564 0.671594 0.0816137 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c52aa6429f9aa86c04b37249eca3f8cfcb257d7a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2886 2 + 2 -12.9071 2 + 3 -9.20946 2 + 4 -6.74404 2 + 5 1.22196 0 + 6 4.3593 0 + 7 11.0814 0 + 8 11.3367 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..11395df5a5c4ed718008fd2aeadbf2f0ed5c79b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:21 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.6421276686 19.2209970171 1.73364807168 0 0 0 0 + tauc_H1 12.2740464305 20.298081151 3.14968235784 0 0 0 0 + tauc_H2 9.98380343793 18.8046381302 2.28518274644 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0949070454363 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.106753103339 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.125005513072 (SEC) + + DONE : INIT CHARGE Time : 0.168333618253 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451059 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000845 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00182 + + Density error is 0.214404071344 + + Energy Rydberg eV + E_KohnSham -34.1886897754 -465.1609881 + E_Harris -34.3798975112 -467.762502808 + E_Fermi -0.403720620697 -5.49290084157 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00121516715609 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00149689502449 + + Density error is 0.0981724911522 + + Energy Rydberg eV + E_KohnSham -34.2788794031 -466.388080937 + E_Harris -34.2857545795 -466.48162251 + E_Fermi -0.212519082385 -2.89147045416 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116085688922 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00137568357694 + + Density error is 0.0631306757282 + + Energy Rydberg eV + E_KohnSham -34.2792590604 -466.39324644 + E_Harris -34.2837003593 -466.453673411 + E_Fermi -0.202634380123 -2.75698218036 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108931381905 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115605975513 + + Density error is 0.0019668566549 + + Energy Rydberg eV + E_KohnSham -34.2792235691 -466.392763556 + E_Harris -34.279224787 -466.392780126 + E_Fermi -0.166945305868 -2.27140741416 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109242753108 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115530774273 + + Density error is 0.000940937990316 + + Energy Rydberg eV + E_KohnSham -34.2791660921 -466.391981541 + E_Harris -34.2791670783 -466.391994959 + E_Fermi -0.166461891082 -2.26483021857 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109106030218 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115238966709 + + Density error is 0.000146669052563 + + Energy Rydberg eV + E_KohnSham -34.2791988159 -466.392426772 + E_Harris -34.2791988443 -466.392427158 + E_Fermi -0.166315650951 -2.26284051952 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109115830074 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115224951764 + + Density error is 3.64890120809e-05 + + Energy Rydberg eV + E_KohnSham -34.2791874795 -466.392272531 + E_Harris -34.2791874855 -466.392272613 + E_Fermi -0.166221386729 -2.26155798898 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109109046549 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115223245231 + + Density error is 1.81167071432e-05 + + Energy Rydberg eV + E_KohnSham -34.2791910986 -466.392321772 + E_Harris -34.2791911001 -466.392321792 + E_Fermi -0.166256442389 -2.2620349457 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109109826668 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001152206179 + + Density error is 3.17922398539e-06 + + Energy Rydberg eV + E_KohnSham -34.2791896664 -466.392302286 + E_Harris -34.2791896664 -466.392302286 + E_Fermi -0.166239704835 -2.26180721959 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109109591276 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011521959532 + + Density error is 3.46020598542e-07 + + Energy Rydberg eV + E_KohnSham -34.2791899101 -466.392305601 + E_Harris -34.2791899101 -466.392305601 + E_Fermi -0.166236284003 -2.26176067679 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109109684431 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115219632837 + + Density error is 1.37538322926e-07 + + Energy Rydberg eV + E_KohnSham -34.2791899607 -466.39230629 + E_Harris -34.2791899607 -466.39230629 + E_Fermi -0.166236187494 -2.26175936372 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109109707131 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115219610418 + + Density error is 1.07548768765e-08 + + Energy Rydberg eV + E_KohnSham -34.2791899627 -466.392306318 + E_Harris -34.2791899627 -466.392306318 + E_band -7.95978541381 -108.298436485 + E_one_elec -69.2043976745 -941.574135031 + E_Hartree +35.9954944646 +489.743827047 + E_xc -8.20270122153 -111.603475604 + E_Ewald +7.25691142379 +98.7353452449 + E_demet -7.42876835442e-74 -1.01073578742e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194707355279 -2.64912947431 + E_Fermi -0.166236068855 -2.26175774955 + + charge density convergence is achieved + final etot is -466.392306318 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2886 2.00000 + 2 -12.9071 2.00000 + 3 -9.20946 2.00000 + 4 -6.74404 2.00000 + 5 1.22196 0.00000 + 6 4.35930 0.00000 + 7 11.0814 0.00000 + 8 11.3367 0.00000 + + EFERMI = -2.261757749546143 eV + OUT.ABACUS/ final etot is -466.3923063175707 eV + correction force for each atom along direction 1 is -0.000121550 + correction force for each atom along direction 2 is 0.000109610 + correction force for each atom along direction 3 is 0.000100043 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.5416632 +0.99069502 +0.54676504 + H1 -0.21433500 -0.57644121 -0.84945073 + H2 -1.3273282 -0.41425381 +0.30268569 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3923063175707 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5783 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5685 1 7.6 1.e+02% + Potential init_pot 0.28477 2 0.14 3.8% + PW_Basis recip2real 0.28842 17 0.017 3.8% + PW_Basis gathers_scatterp 0.13064 17 0.0077 1.7% + Potential v_of_rho 1.0532 14 0.075 14.% + XC_Functional v_xc 0.31743 15 0.021 4.2% + H_Hartree_pw v_hartree 0.68948 14 0.049 9.1% + PW_Basis real2recip 0.73609 41 0.018 9.7% + PW_Basis gatherp_scatters 0.28000 41 0.0068 3.7% + ORB_control set_orb_tables 1.0932 1 1.1 14.% + ORB_gen_tables gen_tables 1.0932 1 1.1 14.% + ORB_table_phi init_Table 0.47549 1 0.48 6.3% + ORB_table_phi cal_ST_Phi12_R 0.47015 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18392 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18233 56 0.0033 2.4% + ORB_table_alpha init_Table_Alpha 0.24680 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24475 66 0.0037 3.2% + LOOP_ions opt_ions 5.9482 1 5.9 78.% + ESolver_KS_LCAO Run 5.3564 1 5.4 71.% + HSolverLCAO solve 2.7230 12 0.23 36.% + HamiltLCAO updateHk 1.4124 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.3827 12 0.12 18.% + Gint_interface cal_gint 2.5584 25 0.10 34.% + Gint_Gamma distri_vl 2.7850 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.7828 14 0.41 76.% + LCAO_gen_fixedH add_v_delta 2.6370 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6370 6 0.44 35.% + ElecStateLCAO psiToRho 1.2932 12 0.11 17.% + Charge mix_rho 0.98265 11 0.089 13.% + LOOP_ions force_stress 0.59161 1 0.59 7.8% + Force_Stress_LCAO getForceStress 0.59159 1 0.59 7.8% + Force_LCAO_gamma ftable_gamma 0.37870 1 0.38 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.37050 1 0.37 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:21 2022 + Finish Time : Wed Sep 28 11:11:28 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ad772a4a4ac4162940f1c2352f17d98deb533e11 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123473 ima = 3.66726e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012315607014 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011190303578 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011252883912 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112778169072 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112732985008 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112759216408 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753191078 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756001421 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755217263 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755084143 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755072162 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112755065844 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/STRU new file mode 100644 index 0000000000000000000000000000000000000000..172d554ec4b93d46a3722af11111616fec9c92b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.357872331370 19.220997017080 1.733648071702 0 0 0 +H +0.0 +2 +-15.725953569565 20.298081150974 3.149682357829 0 0 0 +-18.016196562065 18.804638130202 2.285182746433 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/conv new file mode 100644 index 0000000000000000000000000000000000000000..1c629c6613399db2138ae12aecd14ad67905fdc5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/conv @@ -0,0 +1 @@ +32 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..49011034df9d32f455854d052a4848d597cb59d1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750990643 0.01265994056 1.26486329 1.359335715 1.469321868 0.008805312154 0.01793779169 0.03909424524 +-1.324759589e-18 0.0009880897417 0.00264907219 0.0124126063 0.04527740339 3.162998042e-19 2.150638868e-06 6.182677674e-06 +0.001609866131 0.005988892642 + +H atom_index 1 n_descriptor 18 +1.203967895 0.03597408 0.0936615591 0.1296759118 0.3046319721 0.02024942116 0.02558959311 0.03930267881 +-3.46861526e-17 4.221563791e-05 0.08952334012 0.1109878549 0.1134400562 -5.403949046e-18 6.096057858e-06 0.01410095099 +0.02452218983 0.02847938638 + +H atom_index 2 n_descriptor 18 +1.27614473 0.0335593627 0.1181422128 0.1624307533 0.3288555927 0.02365523348 0.02980224841 0.03693296923 +4.402474885e-17 4.888389645e-05 0.1063746749 0.1176761639 0.1393615913 -1.381396583e-18 2.445949737e-06 0.01325145703 +0.0272645648 0.03186953182 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d10b11dc175675405aa7b08a31e31f2b830ca9ca Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:21 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0949353 SEC) : SETUP UNITCELL + DONE(0.106771 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.125028 SEC) : INIT PLANEWAVE + DONE(0.168473 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451122 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651610e+02 0.000000e+00 2.144e-01 5.462e-01 + GE2 -4.663881e+02 -1.227093e+00 9.817e-02 5.011e-01 + GE3 -4.663932e+02 -5.165503e-03 6.313e-02 5.702e-01 + GE4 -4.663928e+02 4.828835e-04 1.967e-03 4.306e-01 + GE5 -4.663920e+02 7.820148e-04 9.409e-04 4.290e-01 + GE6 -4.663924e+02 -4.452302e-04 1.467e-04 4.250e-01 + GE7 -4.663923e+02 1.542407e-04 3.649e-05 4.155e-01 + GE8 -4.663923e+02 -4.924164e-05 1.812e-05 4.115e-01 + GE9 -4.663923e+02 1.948690e-05 3.179e-06 4.092e-01 + GE10 -4.663923e+02 -3.315532e-06 3.460e-07 4.090e-01 + GE11 -4.663923e+02 -6.889353e-07 1.375e-07 4.085e-01 + GE12 -4.663923e+02 -2.756890e-08 1.075e-08 3.381e-01 +E_delta_band = -7.02104001e-02 Ry = -9.55261500e-01 eV +E_delta_NN= -1.94707355e-01 Ry = -2.64912947e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5783 11 0.69 1e+02 % + Run_lcao lcao_line 7.5685 1 7.6 1e+02 % + Potential init_pot 0.28477 2 0.14 3.8 % + PW_Basis recip2real 0.28842 17 0.017 3.8 % + PW_Basis gathers_scatterp 0.13064 17 0.0077 1.7 % + Potential v_of_rho 1.0532 14 0.075 14 % + XC_Functional v_xc 0.31743 15 0.021 4.2 % + H_Hartree_pw v_hartree 0.68948 14 0.049 9.1 % + PW_Basis real2recip 0.73609 41 0.018 9.7 % + PW_Basis gatherp_scatters 0.28 41 0.0068 3.7 % + ORB_control set_orb_tables 1.0932 1 1.1 14 % + ORB_gen_tables gen_tables 1.0932 1 1.1 14 % + ORB_table_phi init_Table 0.47549 1 0.48 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.47015 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18392 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18233 56 0.0033 2.4 % + ORB_table_alpha init_Table_Alpha 0.2468 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24475 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9482 1 5.9 78 % + ESolver_KS_LCAO Run 5.3564 1 5.4 71 % + HSolverLCAO solve 2.723 12 0.23 36 % + HamiltLCAO updateHk 1.4124 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.3827 12 0.12 18 % + Gint_interface cal_gint 2.5584 25 0.1 34 % + Gint_Gamma distri_vl 2.785 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.7828 14 0.41 76 % + LCAO_gen_fixedH add_v_delta 2.637 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.637 6 0.44 35 % + ElecStateLCAO psiToRho 1.2932 12 0.11 17 % + Charge mix_rho 0.98265 11 0.089 13 % + LOOP_ions force_stress 0.59161 1 0.59 7.8 % + Force_Stress_LCAO getForceStress 0.59159 1 0.59 7.8 % + Force_LCAO_gamma ftable_gamma 0.3787 1 0.38 5 % + Force_LCAO_gamma cal_fvl_dphi 0.3705 1 0.37 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:21 2022 + FINISH Time : Wed Sep 28 11:11:28 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/32/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..ac90fa9b4c50fdb4a2bc968eb3fdefc318196353 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.426914 0.689053 0.0555484 +H 0.473009 0.664963 0.0919853 +H 0.37034 0.665449 0.0730744 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0495e1de72f1814a1607085b0507b7c03aaf5530 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4864 2 + 2 -13.6171 2 + 3 -8.86118 2 + 4 -6.78824 2 + 5 1.58738 0 + 6 4.89998 0 + 7 11.0065 0 + 8 11.2205 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ab83a2279eb4889a12f9d446cfc4e52657cad54a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:03 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 11.9535904565 19.2934868738 1.55535644359 0 0 0 0 + tauc_H1 13.2442517847 18.6189726063 2.57558872809 0 0 0 0 + tauc_H2 10.3695134681 18.6325766958 2.046082433 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0883498705368 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.099407108851 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.117714689314 (SEC) + + DONE : INIT CHARGE Time : 0.167168216534 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.453323 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000869 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00169 + + Density error is 0.220327701804 + + Energy Rydberg eV + E_KohnSham -34.1828742148 -465.081863339 + E_Harris -34.3860110657 -467.845681984 + E_Fermi -0.424099067401 -5.77016383314 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00117864345839 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00141422730992 + + Density error is 0.0975218526011 + + Energy Rydberg eV + E_KohnSham -34.2760365482 -466.349401912 + E_Harris -34.2825474573 -466.437987374 + E_Fermi -0.22873263175 -3.11206711033 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00112937165746 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129579188316 + + Density error is 0.0622112548248 + + Energy Rydberg eV + E_KohnSham -34.2763734132 -466.353985195 + E_Harris -34.2805016404 -466.410152608 + E_Fermi -0.213774293314 -2.90854847499 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00105939393687 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109169298762 + + Density error is 0.00215409243647 + + Energy Rydberg eV + E_KohnSham -34.2764329763 -466.354795593 + E_Harris -34.2764367542 -466.354846994 + E_Fermi -0.178217313753 -2.4247709493 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106149807232 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108717181796 + + Density error is 0.000929181111833 + + Energy Rydberg eV + E_KohnSham -34.2763512266 -466.35368333 + E_Harris -34.2763535478 -466.353714912 + E_Fermi -0.176847286917 -2.40613077791 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106030137781 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108566840608 + + Density error is 0.000198634883386 + + Energy Rydberg eV + E_KohnSham -34.2764039936 -466.354401263 + E_Harris -34.2764041236 -466.354403031 + E_Fermi -0.177208075843 -2.41103956309 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106055166059 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108528371329 + + Density error is 4.93567966987e-05 + + Energy Rydberg eV + E_KohnSham -34.2763839489 -466.354128541 + E_Harris -34.2763839623 -466.354128723 + E_Fermi -0.176982583868 -2.40797158737 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0010604812293 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108532047351 + + Density error is 1.91922672592e-05 + + Energy Rydberg eV + E_KohnSham -34.2763897401 -466.354207335 + E_Harris -34.2763897417 -466.354207355 + E_Fermi -0.177044693599 -2.40881663361 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106047600416 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108527301726 + + Density error is 1.41763553913e-06 + + Energy Rydberg eV + E_KohnSham -34.276388115 -466.354185224 + E_Harris -34.276388115 -466.354185224 + E_Fermi -0.177023419825 -2.40852718907 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106047629027 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108527004425 + + Density error is 1.65541284583e-07 + + Energy Rydberg eV + E_KohnSham -34.2763883825 -466.354188864 + E_Harris -34.2763883825 -466.354188864 + E_Fermi -0.177021987265 -2.40850769809 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00106047671696 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108527066645 + + Density error is 3.76706099526e-08 + + Energy Rydberg eV + E_KohnSham -34.276388408 -466.35418921 + E_Harris -34.276388408 -466.35418921 + E_band -8.04851848514 -109.505711856 + E_one_elec -69.9180776178 -951.284248809 + E_Hartree +36.344995526 +494.499032938 + E_xc -8.25881169841 -112.366897807 + E_Ewald +7.67858782664 +104.472547036 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195864118681 -2.66486804781 + E_Fermi -0.177022104641 -2.40850929508 + + charge density convergence is achieved + final etot is -466.35418921 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4864 2.00000 + 2 -13.6171 2.00000 + 3 -8.86118 2.00000 + 4 -6.78824 2.00000 + 5 1.58738 0.00000 + 6 4.89998 0.00000 + 7 11.0065 0.00000 + 8 11.2205 0.00000 + + EFERMI = -2.408509295076553 eV + OUT.ABACUS/ final etot is -466.3541892102609 eV + correction force for each atom along direction 1 is 2.20141e-05 + correction force for each atom along direction 2 is -0.000179647 + correction force for each atom along direction 3 is -1.74780e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.15762692 +1.6038495 -1.8611583 + H1 +1.0300251 -0.85314370 +1.1887000 + H2 -1.1876520 -0.75070584 +0.67245828 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3541892102609 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9736 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9641 1 7.0 1.e+02% + Potential init_pot 0.28872 2 0.14 4.1% + PW_Basis recip2real 0.28468 16 0.018 4.1% + PW_Basis gathers_scatterp 0.12821 16 0.0080 1.8% + Potential v_of_rho 0.98466 13 0.076 14.% + XC_Functional v_xc 0.29158 14 0.021 4.2% + H_Hartree_pw v_hartree 0.65067 13 0.050 9.3% + PW_Basis real2recip 0.66027 38 0.017 9.5% + PW_Basis gatherp_scatters 0.25568 38 0.0067 3.7% + ORB_control set_orb_tables 1.1157 1 1.1 16.% + ORB_gen_tables gen_tables 1.1157 1 1.1 16.% + ORB_table_phi init_Table 0.48093 1 0.48 6.9% + ORB_table_phi cal_ST_Phi12_R 0.47566 126 0.0038 6.8% + ORB_table_beta init_Table_Beta 0.18984 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18825 56 0.0034 2.7% + ORB_table_alpha init_Table_Alpha 0.25570 1 0.26 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25366 66 0.0038 3.6% + LOOP_ions opt_ions 5.3122 1 5.3 76.% + ESolver_KS_LCAO Run 4.7192 1 4.7 68.% + HSolverLCAO solve 2.4370 11 0.22 35.% + HamiltLCAO updateHk 1.2774 11 0.12 18.% + LCAO_Hamilt cal_Hgamma 1.2498 11 0.11 18.% + Gint_interface cal_gint 2.2929 23 0.10 33.% + Gint_Gamma distri_vl 2.2795 6 0.38 33.% + LCAO_Deepks cal_projected_DM 5.1482 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1301 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1301 6 0.36 31.% + ElecStateLCAO psiToRho 1.1435 11 0.10 16.% + Charge mix_rho 0.79141 10 0.079 11.% + LOOP_ions force_stress 0.59286 1 0.59 8.5% + Force_Stress_LCAO getForceStress 0.59283 1 0.59 8.5% + Force_LCAO_gamma ftable_gamma 0.37496 1 0.37 5.4% + Force_LCAO_gamma cal_fvl_dphi 0.36715 1 0.37 5.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:03 2022 + Finish Time : Wed Sep 28 11:11:10 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6c109e919ff7184ea3ab1638ea472429e7f54430 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123938 ima = 3.6473e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123487364458 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112713492924 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113077720648 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113367039861 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113295288752 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113337464389 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113326870265 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113330177163 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113329440817 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113329384534 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113329384046 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b279d141113420adeb2eff0bdf77a17478489f5c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-16.046409543482 19.293486873802 1.555356443580 0 0 0 +H +0.0 +2 +-14.755748215281 18.618972606304 2.575588728076 0 0 0 +-17.630486531875 18.632576695731 2.046082432986 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/conv new file mode 100644 index 0000000000000000000000000000000000000000..c2980d84b78aafd4018db0947a4d2c3efc0d4d01 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/conv @@ -0,0 +1 @@ +33 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ae11a23b8b4e4c4486b9e8d8a864c0097e1b8348 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.743949436 0.012768384 1.304219207 1.390110473 1.470517089 0.007916243936 0.02101456734 0.03888589418 +1.203632164e-17 0.001300155245 0.00251868858 0.01319554726 0.04545245617 1.390220752e-18 1.756989165e-06 5.382509987e-06 +0.001793735835 0.005614888551 + +H atom_index 1 n_descriptor 18 +1.283599329 0.03239135958 0.1214818304 0.1674681168 0.3323045214 0.02348860702 0.03037625369 0.03596618088 +3.0086506e-17 4.585835309e-05 0.1082909374 0.1200907746 0.1439781191 -3.043288102e-18 2.565516485e-06 0.01311480652 +0.02779129884 0.03225871853 + +H atom_index 2 n_descriptor 18 +1.277949738 0.03257667405 0.1193394352 0.1646120733 0.3307594149 0.02325157108 0.03005725827 0.03603880447 +-3.719381115e-17 4.537121525e-05 0.1080970928 0.1186806358 0.1415563939 -3.74602645e-18 2.858273496e-06 0.01302475846 +0.02760937301 0.03204846325 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a48d69b275fc2bed5046f24f0339f630d551afb1 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..bf138721489e0b37d3ce0a6d8f4cc81120505175 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..eb6addf2c92d9a79d65607272ec28903dd554ccf Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..9181f1a0c3e61c36db57ab28cb10c213776124af --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:03 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0883716 SEC) : SETUP UNITCELL + DONE(0.0994263 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.117737 SEC) : INIT PLANEWAVE + DONE(0.167294 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.453387 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650819e+02 0.000000e+00 2.203e-01 5.355e-01 + GE2 -4.663494e+02 -1.267539e+00 9.752e-02 4.791e-01 + GE3 -4.663540e+02 -4.583283e-03 6.221e-02 5.490e-01 + GE4 -4.663548e+02 -8.103979e-04 2.154e-03 4.137e-01 + GE5 -4.663537e+02 1.112262e-03 9.292e-04 4.128e-01 + GE6 -4.663544e+02 -7.179328e-04 1.986e-04 4.015e-01 + GE7 -4.663541e+02 2.727220e-04 4.936e-05 3.953e-01 + GE8 -4.663542e+02 -7.879330e-05 1.919e-05 3.854e-01 + GE9 -4.663542e+02 2.211108e-05 1.418e-06 3.831e-01 + GE10 -4.663542e+02 -3.640151e-06 1.655e-07 3.836e-01 + GE11 -4.663542e+02 -3.465832e-07 3.767e-08 3.177e-01 +E_delta_band = -7.27816743e-02 Ry = -9.90245480e-01 eV +E_delta_NN= -1.95864119e-01 Ry = -2.66486805e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9736 11 0.63 1e+02 % + Run_lcao lcao_line 6.9641 1 7 1e+02 % + Potential init_pot 0.28872 2 0.14 4.1 % + PW_Basis recip2real 0.28468 16 0.018 4.1 % + PW_Basis gathers_scatterp 0.12821 16 0.008 1.8 % + Potential v_of_rho 0.98466 13 0.076 14 % + XC_Functional v_xc 0.29158 14 0.021 4.2 % + H_Hartree_pw v_hartree 0.65067 13 0.05 9.3 % + PW_Basis real2recip 0.66027 38 0.017 9.5 % + PW_Basis gatherp_scatters 0.25568 38 0.0067 3.7 % + ORB_control set_orb_tables 1.1157 1 1.1 16 % + ORB_gen_tables gen_tables 1.1157 1 1.1 16 % + ORB_table_phi init_Table 0.48093 1 0.48 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.47566 126 0.0038 6.8 % + ORB_table_beta init_Table_Beta 0.18984 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18825 56 0.0034 2.7 % + ORB_table_alpha init_Table_Alpha 0.2557 1 0.26 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25366 66 0.0038 3.6 % + LOOP_ions opt_ions 5.3122 1 5.3 76 % + ESolver_KS_LCAO Run 4.7192 1 4.7 68 % + HSolverLCAO solve 2.437 11 0.22 35 % + HamiltLCAO updateHk 1.2774 11 0.12 18 % + LCAO_Hamilt cal_Hgamma 1.2498 11 0.11 18 % + Gint_interface cal_gint 2.2929 23 0.1 33 % + Gint_Gamma distri_vl 2.2795 6 0.38 33 % + LCAO_Deepks cal_projected_DM 5.1482 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.1301 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1301 6 0.36 31 % + ElecStateLCAO psiToRho 1.1435 11 0.1 16 % + Charge mix_rho 0.79141 10 0.079 11 % + LOOP_ions force_stress 0.59286 1 0.59 8.5 % + Force_Stress_LCAO getForceStress 0.59283 1 0.59 8.5 % + Force_LCAO_gamma ftable_gamma 0.37496 1 0.37 5.4 % + Force_LCAO_gamma cal_fvl_dphi 0.36715 1 0.37 5.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:03 2022 + FINISH Time : Wed Sep 28 11:11:10 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/33/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..156f2792752491f0ef8b50f147253a8f14f491a9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.440102 0.678074 0.0384362 +H 0.492363 0.635925 0.0287256 +H 0.397008 0.653647 0.993823 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1fdab0f389e47d183243e9b68b7125d18e483a3d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0788 2 + 2 -12.6043 2 + 3 -9.28478 2 + 4 -6.70205 2 + 5 1.03311 0 + 6 3.9645 0 + 7 11.1362 0 + 8 11.4049 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..52dc55f502bdccfdc31c0d7f44208675ff3743c6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:51 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.3228499019 18.9860642034 1.07621346071 0 0 0 0 + tauc_H1 13.7861721516 17.8058930318 0.80431594127 0 0 0 0 + tauc_H2 11.1162221426 18.3021102766 27.827039581 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0730733665222 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0733948505105 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0897321325314 (SEC) + + DONE : INIT CHARGE Time : 0.131193163423 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.37724 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 337 ; sender_size of each process is: +144 49 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000768 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119 + + Density error is 0.211153451312 + + Energy Rydberg eV + E_KohnSham -34.1907667686 -465.189247042 + E_Harris -34.3749167474 -467.694736041 + E_Fermi -0.388358590111 -5.28388969276 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.001031546004 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117142609472 + + Density error is 0.0985894492447 + + Energy Rydberg eV + E_KohnSham -34.2789810822 -466.389464352 + E_Harris -34.2861567226 -466.487093948 + E_Fermi -0.199733996608 -2.71752043819 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000985411932283 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109861691755 + + Density error is 0.0636473190666 + + Energy Rydberg eV + E_KohnSham -34.279451695 -466.395867368 + E_Harris -34.2840488932 -466.458415458 + E_Fermi -0.193150289594 -2.62794450883 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000931097419412 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000971237540849 + + Density error is 0.00191165663193 + + Energy Rydberg eV + E_KohnSham -34.2793529987 -466.394524536 + E_Harris -34.2793538931 -466.394536705 + E_Fermi -0.157783475338 -2.14675431483 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000932444461174 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000970689374813 + + Density error is 0.000964342083787 + + Energy Rydberg eV + E_KohnSham -34.2793149271 -466.394006545 + E_Harris -34.2793154291 -466.394013375 + E_Fermi -0.157778132887 -2.14668162707 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000931651658094 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968760394385 + + Density error is 0.000161284933752 + + Energy Rydberg eV + E_KohnSham -34.2793318366 -466.394236611 + E_Harris -34.2793318461 -466.394236739 + E_Fermi -0.157344979996 -2.14078827964 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000931835994745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00096886731786 + + Density error is 2.9483434907e-05 + + Energy Rydberg eV + E_KohnSham -34.279326704 -466.394166779 + E_Harris -34.2793267068 -466.394166816 + E_Fermi -0.157316319541 -2.14039833415 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000931783079424 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968806253681 + + Density error is 1.21757427869e-05 + + Energy Rydberg eV + E_KohnSham -34.2793292224 -466.394201043 + E_Harris -34.279329223 -466.394201051 + E_Fermi -0.157332829822 -2.14062296804 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000931786057278 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968795765727 + + Density error is 2.28825773293e-06 + + Energy Rydberg eV + E_KohnSham -34.27932823 -466.394187541 + E_Harris -34.2793282301 -466.394187541 + E_Fermi -0.157321373239 -2.14046709323 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000931784448004 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968792768099 + + Density error is 3.97841786564e-07 + + Energy Rydberg eV + E_KohnSham -34.2793283886 -466.394189698 + E_Harris -34.2793283886 -466.394189698 + E_Fermi -0.157319203499 -2.14043757241 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000931785118638 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968793303168 + + Density error is 1.30932276565e-07 + + Energy Rydberg eV + E_KohnSham -34.2793284152 -466.39419006 + E_Harris -34.2793284152 -466.39419006 + E_Fermi -0.157319033199 -2.14043525536 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000931785297996 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000968793338523 + + Density error is 1.10862029839e-08 + + Energy Rydberg eV + E_KohnSham -34.2793284189 -466.39419011 + E_Harris -34.2793284189 -466.39419011 + E_band -7.88933429594 -107.339899852 + E_one_elec -68.7126754193 -934.883910527 + E_Hartree +35.7597598848 +486.536493545 + E_xc -8.16465979949 -111.085895505 + E_Ewald +6.96372559778 +94.7463474382 + E_demet -9.59235262871e-62 -1.30510652976e-60 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193828493931 -2.63717195221 + E_Fermi -0.15731891528 -2.14043365099 + + charge density convergence is achieved + final etot is -466.39419011 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0788 2.00000 + 2 -12.6043 2.00000 + 3 -9.28478 2.00000 + 4 -6.70205 2.00000 + 5 1.03311 0.00000 + 6 3.96450 0.00000 + 7 11.1362 0.00000 + 8 11.4049 0.00000 + + EFERMI = -2.140433650987600 eV + OUT.ABACUS/ final etot is -466.3941901104092 eV + correction force for each atom along direction 1 is -3.67282e-05 + correction force for each atom along direction 2 is 8.61655e-06 + correction force for each atom along direction 3 is -1.70029e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.67447144 -1.2043922 -0.71219051 + H1 -0.79899536 +0.86611980 +0.34556228 + H2 +0.12452392 +0.33827240 +0.36662823 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3941901104092 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1078 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1002 1 6.1 1.e+02% + Potential init_pot 0.24464 2 0.12 4.0% + PW_Basis recip2real 0.26457 17 0.016 4.3% + PW_Basis gathers_scatterp 0.11170 17 0.0066 1.8% + Potential v_of_rho 0.96504 14 0.069 16.% + XC_Functional v_xc 0.27800 15 0.019 4.6% + H_Hartree_pw v_hartree 0.64475 14 0.046 11.% + PW_Basis real2recip 0.65010 41 0.016 11.% + PW_Basis gatherp_scatters 0.24367 41 0.0059 4.0% + ORB_control set_orb_tables 0.90415 1 0.90 15.% + ORB_gen_tables gen_tables 0.90415 1 0.90 15.% + ORB_table_phi init_Table 0.38001 1 0.38 6.2% + ORB_table_phi cal_ST_Phi12_R 0.37576 126 0.0030 6.2% + ORB_table_beta init_Table_Beta 0.15673 1 0.16 2.6% + ORB_table_beta VNL_PhiBeta_R 0.15545 56 0.0028 2.5% + ORB_table_alpha init_Table_Alpha 0.20873 1 0.21 3.4% + ORB_table_alpha S_PhiAlpha_R 0.20704 66 0.0031 3.4% + LOOP_ions opt_ions 4.7494 1 4.7 78.% + ESolver_KS_LCAO Run 4.2793 1 4.3 70.% + HSolverLCAO solve 1.9493 12 0.16 32.% + HamiltLCAO updateHk 1.0413 12 0.087 17.% + LCAO_Hamilt cal_Hgamma 1.0135 12 0.084 17.% + Gint_interface cal_gint 1.7607 25 0.070 29.% + Gint_Gamma distri_vl 2.2315 6 0.37 37.% + LCAO_Deepks cal_projected_DM 4.6188 14 0.33 76.% + LCAO_gen_fixedH add_v_delta 2.1038 6 0.35 34.% + LCAO_DESCRIPTOR add_v_delta 2.1038 6 0.35 34.% + ElecStateLCAO psiToRho 0.89077 12 0.074 15.% + Charge mix_rho 0.83015 11 0.075 14.% + LOOP_ions force_stress 0.47003 1 0.47 7.7% + Force_Stress_LCAO getForceStress 0.47000 1 0.47 7.7% + Force_LCAO_gamma ftable_gamma 0.27982 1 0.28 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.27229 1 0.27 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:51 2022 + Finish Time : Wed Sep 28 11:05:57 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b35a4baa2455f96e97bf9e716a766485570b73d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123496 ima = 3.68652e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123258536684 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111774049154 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112561693768 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112774707764 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753865099 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112766738846 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112762607794 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112764619567 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112764108875 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112764029037 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112764012922 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001127640065 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8c4c3ab777ebc681c5be7d05f015042b3d742a6c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.677150098125 18.986064203394 1.076213460723 0 0 0 +H +0.0 +2 +-14.213827848375 17.805893031785 0.804315941270 0 0 0 +-16.883777857453 18.302110276559 -0.172960418951 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/conv new file mode 100644 index 0000000000000000000000000000000000000000..501bb87cf148d861e35308a1051db302d48d2488 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/conv @@ -0,0 +1 @@ +34 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d6bd39541b0b56d6f11e66113355668b391c77c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752951064 0.01253152611 1.247992662 1.334840301 1.468429364 0.008995916907 0.01687607966 0.03917722847 +-3.412996787e-18 0.0008397985272 0.002558787598 0.01203172981 0.04306032435 -8.646088809e-19 2.039051376e-06 5.922568912e-06 +0.001575511946 0.006007555573 + +H atom_index 1 n_descriptor 18 +1.196877413 0.03639769418 0.09176832767 0.1266770431 0.3016903047 0.0199831544 0.02514698234 0.03985278702 +2.73525033e-17 3.91018205e-05 0.08615153393 0.1081589343 0.113415513 -1.145182087e-18 5.830785619e-06 0.01438191037 +0.02392349809 0.02805186267 + +H atom_index 2 n_descriptor 18 +1.2226679 0.035580093 0.09981835959 0.1374794873 0.3112749286 0.02121573811 0.02666502149 0.03882353113 +2.433948177e-19 4.135074796e-05 0.09279708321 0.1145072 0.117642132 -2.139672058e-18 4.795228924e-06 0.01370647967 +0.02498323816 0.02940009456 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..faa315ecd81909026e976a810d65e71314ee993f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:51 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0730895 SEC) : SETUP UNITCELL + DONE(0.0734047 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0897693 SEC) : INIT PLANEWAVE + DONE(0.131301 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.377284 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651892e+02 0.000000e+00 2.112e-01 4.416e-01 + GE2 -4.663895e+02 -1.200217e+00 9.859e-02 4.098e-01 + GE3 -4.663959e+02 -6.403016e-03 6.365e-02 4.661e-01 + GE4 -4.663945e+02 1.342833e-03 1.912e-03 3.405e-01 + GE5 -4.663940e+02 5.179909e-04 9.643e-04 3.419e-01 + GE6 -4.663942e+02 -2.300662e-04 1.613e-04 3.396e-01 + GE7 -4.663942e+02 6.983246e-05 2.948e-05 3.278e-01 + GE8 -4.663942e+02 -3.426408e-05 1.218e-05 3.198e-01 + GE9 -4.663942e+02 1.350180e-05 2.288e-06 3.300e-01 + GE10 -4.663942e+02 -2.157179e-06 3.978e-07 3.234e-01 + GE11 -4.663942e+02 -3.622473e-07 1.309e-07 3.262e-01 + GE12 -4.663942e+02 -5.020113e-08 1.109e-08 2.585e-01 +E_delta_band = -6.83498113e-02 Ry = -9.29946890e-01 eV +E_delta_NN= -1.93828494e-01 Ry = -2.63717195e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1078 11 0.56 1e+02 % + Run_lcao lcao_line 6.1002 1 6.1 1e+02 % + Potential init_pot 0.24464 2 0.12 4 % + PW_Basis recip2real 0.26457 17 0.016 4.3 % + PW_Basis gathers_scatterp 0.1117 17 0.0066 1.8 % + Potential v_of_rho 0.96504 14 0.069 16 % + XC_Functional v_xc 0.278 15 0.019 4.6 % + H_Hartree_pw v_hartree 0.64475 14 0.046 11 % + PW_Basis real2recip 0.6501 41 0.016 11 % + PW_Basis gatherp_scatters 0.24367 41 0.0059 4 % + ORB_control set_orb_tables 0.90415 1 0.9 15 % + ORB_gen_tables gen_tables 0.90415 1 0.9 15 % + ORB_table_phi init_Table 0.38001 1 0.38 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.37576 126 0.003 6.2 % + ORB_table_beta init_Table_Beta 0.15673 1 0.16 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.15545 56 0.0028 2.5 % + ORB_table_alpha init_Table_Alpha 0.20873 1 0.21 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.20704 66 0.0031 3.4 % + LOOP_ions opt_ions 4.7494 1 4.7 78 % + ESolver_KS_LCAO Run 4.2793 1 4.3 70 % + HSolverLCAO solve 1.9493 12 0.16 32 % + HamiltLCAO updateHk 1.0413 12 0.087 17 % + LCAO_Hamilt cal_Hgamma 1.0135 12 0.084 17 % + Gint_interface cal_gint 1.7607 25 0.07 29 % + Gint_Gamma distri_vl 2.2315 6 0.37 37 % + LCAO_Deepks cal_projected_DM 4.6188 14 0.33 76 % + LCAO_gen_fixedH add_v_delta 2.1038 6 0.35 34 % + LCAO_DESCRIPTOR add_v_delta 2.1038 6 0.35 34 % + ElecStateLCAO psiToRho 0.89077 12 0.074 15 % + Charge mix_rho 0.83015 11 0.075 14 % + LOOP_ions force_stress 0.47003 1 0.47 7.7 % + Force_Stress_LCAO getForceStress 0.47 1 0.47 7.7 % + Force_LCAO_gamma ftable_gamma 0.27982 1 0.28 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.27229 1 0.27 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:51 2022 + FINISH Time : Wed Sep 28 11:05:57 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/34/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9590683c50733aae6905a68d1662a565e9339325 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.464083 0.647716 0.0181093 +H 0.510089 0.689582 0.00103872 +H 0.429711 0.635517 0.965365 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8658b0e64033434671113c80203bfab18ad64914 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4375 2 + 2 -13.3458 2 + 3 -9.01619 2 + 4 -6.77735 2 + 5 1.48193 0 + 6 4.72154 0 + 7 11.0302 0 + 8 11.2661 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a33dc6857a7c4c47a08148641eeea48f94a16c5a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:25 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.9943361346 18.1360441594 0.507060707962 0 0 0 0 + tauc_H1 14.2825007156 19.3082936225 0.0290842912 0 0 0 0 + tauc_H2 12.0318947443 17.794463416 27.0302298848 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0888037971702 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0926391226405 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.111139468201 (SEC) + + DONE : INIT CHARGE Time : 0.162214511284 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445275 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 0 9 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00076 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114 + + Density error is 0.217853745765 + + Energy Rydberg eV + E_KohnSham -34.1878001089 -465.148883566 + E_Harris -34.3856445329 -467.84069505 + E_Fermi -0.41711968985 -5.67520452995 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0011298338316 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122176013437 + + Density error is 0.0976618181657 + + Energy Rydberg eV + E_KohnSham -34.2791869934 -466.392265918 + E_Harris -34.2857837863 -466.48201989 + E_Fermi -0.223851828692 -3.04566037794 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0010853075263 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115169591871 + + Density error is 0.0624223194476 + + Energy Rydberg eV + E_KohnSham -34.2794747561 -466.39618113 + E_Harris -34.2837015407 -466.453689485 + E_Fermi -0.210229344656 -2.86031697413 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102431501703 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103965827822 + + Density error is 0.00206756375874 + + Energy Rydberg eV + E_KohnSham -34.2795093485 -466.396651784 + E_Harris -34.2795116602 -466.396683236 + E_Fermi -0.174619506536 -2.37582027084 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102661931484 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103969067379 + + Density error is 0.000921030420186 + + Energy Rydberg eV + E_KohnSham -34.2794340449 -466.395627226 + E_Harris -34.2794361861 -466.395656358 + E_Fermi -0.17346627226 -2.36012971356 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102536730639 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103828687184 + + Density error is 0.000161368443556 + + Energy Rydberg eV + E_KohnSham -34.2794841497 -466.396308937 + E_Harris -34.2794842182 -466.396309868 + E_Fermi -0.173719922516 -2.36358080233 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102554451253 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103828954493 + + Density error is 4.49100026128e-05 + + Energy Rydberg eV + E_KohnSham -34.2794658232 -466.396059592 + E_Harris -34.2794658343 -466.396059742 + E_Fermi -0.173545112789 -2.36120239398 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102547174238 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103825116829 + + Density error is 1.6354860925e-05 + + Energy Rydberg eV + E_KohnSham -34.2794705075 -466.396123324 + E_Harris -34.2794705085 -466.396123339 + E_Fermi -0.173599284608 -2.3619394394 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102547002122 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103823513478 + + Density error is 1.75841700253e-06 + + Energy Rydberg eV + E_KohnSham -34.2794690268 -466.396103179 + E_Harris -34.2794690268 -466.396103179 + E_Fermi -0.173581694076 -2.36170010792 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00102547039917 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103823429511 + + Density error is 1.78498789832e-07 + + Energy Rydberg eV + E_KohnSham -34.2794692383 -466.396106056 + E_Harris -34.2794692383 -466.396106056 + E_Fermi -0.173579956754 -2.36167647045 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0010254710621 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103823491668 + + Density error is 7.59931005151e-08 + + Energy Rydberg eV + E_KohnSham -34.2794692677 -466.396106457 + E_Harris -34.2794692677 -466.396106457 + E_band -8.02265107495 -109.153767685 + E_one_elec -69.6904635664 -948.187400764 + E_Hartree +36.2321215836 +492.963304166 + E_xc -8.24063039557 -112.119528492 + E_Ewald +7.54302227959 +102.628083143 + E_demet -1.34674813284e-88 -1.83234483775e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195502588024 -2.65994917088 + E_Fermi -0.173579984826 -2.36167685239 + + charge density convergence is achieved + final etot is -466.396106457 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4375 2.00000 + 2 -13.3458 2.00000 + 3 -9.01619 2.00000 + 4 -6.77735 2.00000 + 5 1.48193 0.00000 + 6 4.72154 0.00000 + 7 11.0302 0.00000 + 8 11.2661 0.00000 + + EFERMI = -2.361676852386191 eV + OUT.ABACUS/ final etot is -466.3961064566964 eV + correction force for each atom along direction 1 is -2.54564e-05 + correction force for each atom along direction 2 is 8.32560e-05 + correction force for each atom along direction 3 is -0.000186407 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.027730163 -0.45695042 +1.5010932 + H1 +0.64450033 +0.62406275 -0.37278090 + H2 -0.61677017 -0.16711234 -1.1283123 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3961064566964 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.0150 11 0.55 1.0e+02% + Run_lcao lcao_line 6.0038 1 6.0 1.e+02% + Potential init_pot 0.28462 2 0.14 4.7% + PW_Basis recip2real 0.28844 16 0.018 4.8% + PW_Basis gathers_scatterp 0.12387 16 0.0077 2.1% + Potential v_of_rho 1.0072 13 0.077 17.% + XC_Functional v_xc 0.28614 14 0.020 4.8% + H_Hartree_pw v_hartree 0.67551 13 0.052 11.% + PW_Basis real2recip 0.65326 38 0.017 11.% + PW_Basis gatherp_scatters 0.24780 38 0.0065 4.1% + ORB_control set_orb_tables 1.0973 1 1.1 18.% + ORB_gen_tables gen_tables 1.0973 1 1.1 18.% + ORB_table_phi init_Table 0.47503 1 0.48 7.9% + ORB_table_phi cal_ST_Phi12_R 0.46986 126 0.0037 7.8% + ORB_table_beta init_Table_Beta 0.18523 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18362 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.25140 1 0.25 4.2% + ORB_table_alpha S_PhiAlpha_R 0.24942 66 0.0038 4.1% + LOOP_ions opt_ions 4.3846 1 4.4 73.% + ESolver_KS_LCAO Run 3.9148 1 3.9 65.% + HSolverLCAO solve 1.6085 11 0.15 27.% + HamiltLCAO updateHk 0.90837 11 0.083 15.% + LCAO_Hamilt cal_Hgamma 0.87684 11 0.080 15.% + Gint_interface cal_gint 1.3018 23 0.057 22.% + Gint_Gamma distri_vl 1.9196 6 0.32 32.% + LCAO_Deepks cal_projected_DM 4.2488 13 0.33 71.% + LCAO_gen_fixedH add_v_delta 1.7705 6 0.30 29.% + LCAO_DESCRIPTOR add_v_delta 1.7705 6 0.30 29.% + ElecStateLCAO psiToRho 0.68415 11 0.062 11.% + Charge mix_rho 0.78780 10 0.079 13.% + LOOP_ions force_stress 0.46962 1 0.47 7.8% + Force_Stress_LCAO getForceStress 0.46959 1 0.47 7.8% + Force_LCAO_gamma ftable_gamma 0.24849 1 0.25 4.1% + Force_LCAO_gamma cal_fvl_dphi 0.24024 1 0.24 4.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:25 2022 + Finish Time : Wed Sep 28 11:09:31 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1e9cd0fdf008994ae1ac8fde5d34fd482d4f29d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.01239 ima = 3.67377e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123165326216 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112270007417 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112700345185 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112973748973 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112905327653 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112945662931 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011293731622 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112940406907 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112939790809 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112939718457 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011293971358 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1190fe79dddff097924e6e3fefe2d0374816a063 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.005663865409 18.136044159413 0.507060707950 0 0 0 +H +0.0 +2 +-13.717499284370 19.308293622540 0.029084291202 0 0 0 +-15.968105255722 17.794463416006 -0.969770115209 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/conv new file mode 100644 index 0000000000000000000000000000000000000000..eaa88ab9307df4916db53fbc7b92b093665c242b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/conv @@ -0,0 +1 @@ +35 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..65cf262e4d7742432a88fad985c6b5f108b712c9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746970401 0.01276690004 1.291726684 1.378435885 1.470101685 0.008272813413 0.01971256602 0.03895900151 +-2.813638654e-18 0.001195402745 0.002607962666 0.01286390654 0.04605969481 2.03711401e-19 1.993548698e-06 5.847336725e-06 +0.00170852452 0.005838547134 + +H atom_index 1 n_descriptor 18 +1.264769466 0.0334285533 0.1138018895 0.1573531059 0.3260970918 0.02283740856 0.02921654416 0.03666650725 +3.188466933e-17 4.726453952e-05 0.1061581454 0.1160061478 0.135263582 -5.8338128e-18 3.505115924e-06 0.01304538991 +0.02708220787 0.03146236968 + +H atom_index 2 n_descriptor 18 +1.273154524 0.0331446318 0.1168681197 0.1614523288 0.3285670948 0.02321141927 0.02969714667 0.03648613874 +-1.0526713e-17 4.803660865e-05 0.1072998862 0.1172575495 0.1387658844 2.051894942e-18 3.039053356e-06 0.01309443397 +0.02736952606 0.03180381624 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..705f2dc7699c4a3993e0c34f964fec54e29a2dc5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:25 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0888319 SEC) : SETUP UNITCELL + DONE(0.0926564 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.111162 SEC) : INIT PLANEWAVE + DONE(0.162361 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445335 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651489e+02 0.000000e+00 2.179e-01 4.702e-01 + GE2 -4.663923e+02 -1.243382e+00 9.766e-02 4.087e-01 + GE3 -4.663962e+02 -3.915212e-03 6.242e-02 4.803e-01 + GE4 -4.663967e+02 -4.706546e-04 2.068e-03 3.355e-01 + GE5 -4.663956e+02 1.024558e-03 9.210e-04 3.339e-01 + GE6 -4.663963e+02 -6.817110e-04 1.614e-04 3.233e-01 + GE7 -4.663961e+02 2.493445e-04 4.491e-05 3.220e-01 + GE8 -4.663961e+02 -6.373199e-05 1.635e-05 3.069e-01 + GE9 -4.663961e+02 2.014558e-05 1.758e-06 3.155e-01 + GE10 -4.663961e+02 -2.877503e-06 1.785e-07 3.104e-01 + GE11 -4.663961e+02 -4.004808e-07 7.599e-08 2.448e-01 +E_delta_band = -7.19834190e-02 Ry = -9.79384661e-01 eV +E_delta_NN= -1.95502588e-01 Ry = -2.65994917e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.015 11 0.55 1e+02 % + Run_lcao lcao_line 6.0038 1 6 1e+02 % + Potential init_pot 0.28462 2 0.14 4.7 % + PW_Basis recip2real 0.28844 16 0.018 4.8 % + PW_Basis gathers_scatterp 0.12387 16 0.0077 2.1 % + Potential v_of_rho 1.0072 13 0.077 17 % + XC_Functional v_xc 0.28614 14 0.02 4.8 % + H_Hartree_pw v_hartree 0.67551 13 0.052 11 % + PW_Basis real2recip 0.65326 38 0.017 11 % + PW_Basis gatherp_scatters 0.2478 38 0.0065 4.1 % + ORB_control set_orb_tables 1.0973 1 1.1 18 % + ORB_gen_tables gen_tables 1.0973 1 1.1 18 % + ORB_table_phi init_Table 0.47503 1 0.48 7.9 % + ORB_table_phi cal_ST_Phi12_R 0.46986 126 0.0037 7.8 % + ORB_table_beta init_Table_Beta 0.18523 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18362 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.2514 1 0.25 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.24942 66 0.0038 4.1 % + LOOP_ions opt_ions 4.3846 1 4.4 73 % + ESolver_KS_LCAO Run 3.9148 1 3.9 65 % + HSolverLCAO solve 1.6085 11 0.15 27 % + HamiltLCAO updateHk 0.90837 11 0.083 15 % + LCAO_Hamilt cal_Hgamma 0.87684 11 0.08 15 % + Gint_interface cal_gint 1.3018 23 0.057 22 % + Gint_Gamma distri_vl 1.9196 6 0.32 32 % + LCAO_Deepks cal_projected_DM 4.2488 13 0.33 71 % + LCAO_gen_fixedH add_v_delta 1.7705 6 0.3 29 % + LCAO_DESCRIPTOR add_v_delta 1.7705 6 0.3 29 % + ElecStateLCAO psiToRho 0.68415 11 0.062 11 % + Charge mix_rho 0.7878 10 0.079 13 % + LOOP_ions force_stress 0.46962 1 0.47 7.8 % + Force_Stress_LCAO getForceStress 0.46959 1 0.47 7.8 % + Force_LCAO_gamma ftable_gamma 0.24849 1 0.25 4.1 % + Force_LCAO_gamma cal_fvl_dphi 0.24024 1 0.24 4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:25 2022 + FINISH Time : Wed Sep 28 11:09:31 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/35/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..00295cf41d3a0f92e972bf0b7750199f91297a24 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.493727 0.625983 0.00772688 +H 0.472738 0.683368 0.0355059 +H 0.4847 0.640545 0.944057 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c547e015784ff1a4dbc094033718319e01930567 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2061 2 + 2 -12.6818 2 + 3 -9.32211 2 + 4 -6.72947 2 + 5 1.13298 0 + 6 4.14229 0 + 7 11.1082 0 + 8 11.381 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..58f2b619461deda75ec5c9ea9a0030f4a55a743a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:54 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.8243639643 17.5275315603 0.216352660565 0 0 0 0 + tauc_H1 13.2366646776 19.1342921442 0.994164119773 0 0 0 0 + tauc_H2 13.5716083493 17.935261621 26.4335865485 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0863768392709 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100259347543 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118482864648 (SEC) + + DONE : INIT CHARGE Time : 0.167917587297 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451075 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 4 9 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000607 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000895 + + Density error is 0.211648225349 + + Energy Rydberg eV + E_KohnSham -34.1924406051 -465.212020756 + E_Harris -34.3775523537 -467.730595303 + E_Fermi -0.395119504888 -5.37587665742 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000886911312431 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012267003995 + + Density error is 0.0980149046091 + + Energy Rydberg eV + E_KohnSham -34.2799053419 -466.40203955 + E_Harris -34.286856213 -466.496611003 + E_Fermi -0.206880052719 -2.81474751952 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000851547969269 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117783242101 + + Density error is 0.0630704572582 + + Energy Rydberg eV + E_KohnSham -34.2802155151 -466.406259673 + E_Harris -34.2847080064 -466.467383154 + E_Fermi -0.197995410744 -2.69386576397 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000815596696614 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112465003017 + + Density error is 0.00191057524771 + + Energy Rydberg eV + E_KohnSham -34.2801542873 -466.405426626 + E_Harris -34.2801545233 -466.405429837 + E_Fermi -0.162500336004 -2.21093049658 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000817590491396 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112745586198 + + Density error is 0.000845040681963 + + Energy Rydberg eV + E_KohnSham -34.2801143695 -466.404883516 + E_Harris -34.2801151424 -466.404894032 + E_Fermi -0.162246955078 -2.20748307222 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00081693584927 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112640931189 + + Density error is 0.000129727262415 + + Energy Rydberg eV + E_KohnSham -34.2801376995 -466.405200937 + E_Harris -34.2801375453 -466.40519884 + E_Fermi -0.161976899389 -2.20380877607 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000817028743256 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011264907871 + + Density error is 2.74176849644e-05 + + Energy Rydberg eV + E_KohnSham -34.2801304666 -466.40510253 + E_Harris -34.2801304692 -466.405102565 + E_Fermi -0.161919415549 -2.2030266683 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000816990894825 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112642679883 + + Density error is 1.2858285824e-05 + + Energy Rydberg eV + E_KohnSham -34.2801327699 -466.405133867 + E_Harris -34.2801327707 -466.405133878 + E_Fermi -0.161940489446 -2.20331339338 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0008170004675 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112643718456 + + Density error is 2.2009478108e-06 + + Energy Rydberg eV + E_KohnSham -34.2801317441 -466.405119911 + E_Harris -34.2801317441 -466.405119911 + E_Fermi -0.161928224812 -2.20314652447 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000816999198286 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112643444225 + + Density error is 3.45585952992e-07 + + Energy Rydberg eV + E_KohnSham -34.2801319523 -466.405122743 + E_Harris -34.2801319523 -466.405122743 + E_Fermi -0.161926199192 -2.20311896449 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00081699986343 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112643539334 + + Density error is 9.65400120691e-08 + + Energy Rydberg eV + E_KohnSham -34.2801319702 -466.405122987 + E_Harris -34.2801319702 -466.405122987 + E_band -7.92895365493 -107.878948885 + E_one_elec -68.9590346259 -938.235799492 + E_Hartree +35.8753219105 +488.108795568 + E_xc -8.18314417917 -111.337388392 + E_Ewald +7.11170857649 +96.7597591557 + E_demet -5.96338929862e-68 -8.11360738534e-67 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194256701738 -2.64299801832 + E_Fermi -0.161926039762 -2.20311679534 + + charge density convergence is achieved + final etot is -466.405122987 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2061 2.00000 + 2 -12.6818 2.00000 + 3 -9.32211 2.00000 + 4 -6.72947 2.00000 + 5 1.13298 0.00000 + 6 4.14229 0.00000 + 7 11.1082 0.00000 + 8 11.3810 0.00000 + + EFERMI = -2.203116795335572 eV + OUT.ABACUS/ final etot is -466.4051229868911 eV + correction force for each atom along direction 1 is -0.000181312 + correction force for each atom along direction 2 is 1.95949e-05 + correction force for each atom along direction 3 is -3.16731e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.40398595 +1.0336784 +0.17150508 + H1 +0.29994598 -0.75915229 -0.025350951 + H2 +0.10403997 -0.27452611 -0.14615413 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4051229868911 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8396 11 0.53 1.0e+02% + Run_lcao lcao_line 5.8299 1 5.8 1.e+02% + Potential init_pot 0.28489 2 0.14 4.9% + PW_Basis recip2real 0.28475 16 0.018 4.9% + PW_Basis gathers_scatterp 0.12294 16 0.0077 2.1% + Potential v_of_rho 0.99323 13 0.076 17.% + XC_Functional v_xc 0.28559 14 0.020 4.9% + H_Hartree_pw v_hartree 0.66246 13 0.051 11.% + PW_Basis real2recip 0.65060 38 0.017 11.% + PW_Basis gatherp_scatters 0.25244 38 0.0066 4.3% + ORB_control set_orb_tables 1.1021 1 1.1 19.% + ORB_gen_tables gen_tables 1.1021 1 1.1 19.% + ORB_table_phi init_Table 0.47520 1 0.48 8.1% + ORB_table_phi cal_ST_Phi12_R 0.46995 126 0.0037 8.0% + ORB_table_beta init_Table_Beta 0.18804 1 0.19 3.2% + ORB_table_beta VNL_PhiBeta_R 0.18647 56 0.0033 3.2% + ORB_table_alpha init_Table_Alpha 0.25163 1 0.25 4.3% + ORB_table_alpha S_PhiAlpha_R 0.24966 66 0.0038 4.3% + LOOP_ions opt_ions 4.1910 1 4.2 72.% + ESolver_KS_LCAO Run 3.7442 1 3.7 64.% + HSolverLCAO solve 1.4606 11 0.13 25.% + HamiltLCAO updateHk 0.84001 11 0.076 14.% + LCAO_Hamilt cal_Hgamma 0.80816 11 0.073 14.% + Gint_interface cal_gint 1.1688 23 0.051 20.% + Gint_Gamma distri_vl 1.8259 6 0.30 31.% + LCAO_Deepks cal_projected_DM 4.0585 13 0.31 69.% + LCAO_gen_fixedH add_v_delta 1.6801 6 0.28 29.% + LCAO_DESCRIPTOR add_v_delta 1.6802 6 0.28 29.% + ElecStateLCAO psiToRho 0.60433 11 0.055 10.% + Charge mix_rho 0.77866 10 0.078 13.% + LOOP_ions force_stress 0.44661 1 0.45 7.6% + Force_Stress_LCAO getForceStress 0.44658 1 0.45 7.6% + Force_LCAO_gamma ftable_gamma 0.22661 1 0.23 3.9% + Force_LCAO_gamma cal_fvl_dphi 0.21863 1 0.22 3.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:54 2022 + Finish Time : Wed Sep 28 11:14:00 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..7f5a494295698dc984ffadd2246619be622f04a8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/OUT.ABACUS/warning.log @@ -0,0 +1,73 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123434 ima = 3.66173e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122895541265 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111713880811 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112382451011 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112598244792 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011256900981 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112586323629 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112582644503 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112584631655 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112584023298 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112583968263 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112583952259 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b78fed6c2156d8dde427673631c8cd5c28cf740d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.175636035721 17.527531560315 0.216352660578 0 0 0 +H +0.0 +2 +-14.763335322430 19.134292144207 0.994164119776 0 0 0 +-14.428391650740 17.935261620960 -1.566413451477 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/conv new file mode 100644 index 0000000000000000000000000000000000000000..e628df175b5094d5e4629f6e48e91885dbca12df --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/conv @@ -0,0 +1 @@ +36 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..27698bf20f30f2301bd52b7051b72ab6d3016b02 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75302343 0.01264261274 1.25761788 1.343047566 1.468919204 0.009103921132 0.01695245439 0.03915903398 +-8.101983384e-19 0.0008801334089 0.002657680072 0.01245564038 0.04452586726 -2.554731891e-19 2.278627649e-06 6.414110271e-06 +0.001585417056 0.006067318783 + +H atom_index 1 n_descriptor 18 +1.212727254 0.03593826171 0.09713280404 0.1331345854 0.3072865063 0.02090951656 0.02606577285 0.03921603979 +1.464181153e-17 4.271009196e-05 0.09142712129 0.113902666 0.1139234984 2.258995695e-19 5.28246048e-06 0.01396912883 +0.02489690806 0.02889675495 + +H atom_index 2 n_descriptor 18 +1.238814082 0.03507605884 0.1056879872 0.1445294708 0.316566455 0.02217074906 0.02760110966 0.03823248856 +-9.109612632e-18 4.508265029e-05 0.09814323369 0.114943231 0.1238437346 1.002244726e-18 4.023037051e-06 0.01344481805 +0.02593394443 0.03020067835 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..75e7eef246982efe8e8bee1c734dcfc154f61fab Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:54 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0864 SEC) : SETUP UNITCELL + DONE(0.100279 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118504 SEC) : INIT PLANEWAVE + DONE(0.168051 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451141 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652120e+02 0.000000e+00 2.116e-01 4.562e-01 + GE2 -4.664020e+02 -1.190019e+00 9.801e-02 3.905e-01 + GE3 -4.664063e+02 -4.220123e-03 6.307e-02 4.549e-01 + GE4 -4.664054e+02 8.330473e-04 1.911e-03 3.190e-01 + GE5 -4.664049e+02 5.431096e-04 8.450e-04 3.188e-01 + GE6 -4.664052e+02 -3.174210e-04 1.297e-04 3.146e-01 + GE7 -4.664051e+02 9.840750e-05 2.742e-05 2.981e-01 + GE8 -4.664051e+02 -3.133767e-05 1.286e-05 2.979e-01 + GE9 -4.664051e+02 1.395690e-05 2.201e-06 2.990e-01 + GE10 -4.664051e+02 -2.832944e-06 3.456e-07 2.995e-01 + GE11 -4.664051e+02 -2.434233e-07 9.654e-08 2.313e-01 +E_delta_band = -6.92730496e-02 Ry = -9.42508192e-01 eV +E_delta_NN= -1.94256702e-01 Ry = -2.64299802e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8396 11 0.53 1e+02 % + Run_lcao lcao_line 5.8299 1 5.8 1e+02 % + Potential init_pot 0.28489 2 0.14 4.9 % + PW_Basis recip2real 0.28475 16 0.018 4.9 % + PW_Basis gathers_scatterp 0.12294 16 0.0077 2.1 % + Potential v_of_rho 0.99323 13 0.076 17 % + XC_Functional v_xc 0.28559 14 0.02 4.9 % + H_Hartree_pw v_hartree 0.66246 13 0.051 11 % + PW_Basis real2recip 0.6506 38 0.017 11 % + PW_Basis gatherp_scatters 0.25244 38 0.0066 4.3 % + ORB_control set_orb_tables 1.1021 1 1.1 19 % + ORB_gen_tables gen_tables 1.1021 1 1.1 19 % + ORB_table_phi init_Table 0.4752 1 0.48 8.1 % + ORB_table_phi cal_ST_Phi12_R 0.46995 126 0.0037 8 % + ORB_table_beta init_Table_Beta 0.18804 1 0.19 3.2 % + ORB_table_beta VNL_PhiBeta_R 0.18647 56 0.0033 3.2 % + ORB_table_alpha init_Table_Alpha 0.25163 1 0.25 4.3 % + ORB_table_alpha S_PhiAlpha_R 0.24966 66 0.0038 4.3 % + LOOP_ions opt_ions 4.191 1 4.2 72 % + ESolver_KS_LCAO Run 3.7442 1 3.7 64 % + HSolverLCAO solve 1.4606 11 0.13 25 % + HamiltLCAO updateHk 0.84001 11 0.076 14 % + LCAO_Hamilt cal_Hgamma 0.80816 11 0.073 14 % + Gint_interface cal_gint 1.1688 23 0.051 20 % + Gint_Gamma distri_vl 1.8259 6 0.3 31 % + LCAO_Deepks cal_projected_DM 4.0585 13 0.31 69 % + LCAO_gen_fixedH add_v_delta 1.6801 6 0.28 29 % + LCAO_DESCRIPTOR add_v_delta 1.6802 6 0.28 29 % + ElecStateLCAO psiToRho 0.60433 11 0.055 10 % + Charge mix_rho 0.77866 10 0.078 13 % + LOOP_ions force_stress 0.44661 1 0.45 7.6 % + Force_Stress_LCAO getForceStress 0.44658 1 0.45 7.6 % + Force_LCAO_gamma ftable_gamma 0.22661 1 0.23 3.9 % + Force_LCAO_gamma cal_fvl_dphi 0.21863 1 0.22 3.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:54 2022 + FINISH Time : Wed Sep 28 11:14:00 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/36/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a7a9997d3696bcfee989bae64a4903507990b7fc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.517206 0.631067 0.994315 +H 0.494392 0.633857 0.0539788 +H 0.464837 0.63903 0.954677 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8f73c09c7f4bb750ee8b56a886ec273dcff012ac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3364 2 + 2 -13.1885 2 + 3 -9.04619 2 + 4 -6.75387 2 + 5 1.36008 0 + 6 4.54797 0 + 7 11.0588 0 + 8 11.2989 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ea8230e30ad3bef141829c94f42e514bb2d23956 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:42 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.481759142 17.6698646054 27.8408197005 0 0 0 0 + tauc_H1 13.8429867297 17.7480009218 1.51140553484 0 0 0 0 + tauc_H2 13.0154363891 17.8928319931 26.7309691008 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0866084745367 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0953732509025 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.113484313109 (SEC) + + DONE : INIT CHARGE Time : 0.160973808223 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.44185 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 4 9 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000797 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133 + + Density error is 0.216848938299 + + Energy Rydberg eV + E_KohnSham -34.187737176 -465.148027319 + E_Harris -34.3836343369 -467.813344931 + E_Fermi -0.411006784635 -5.5920341877 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00124483125704 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116205033486 + + Density error is 0.0981115624541 + + Energy Rydberg eV + E_KohnSham -34.2795472399 -466.397167323 + E_Harris -34.2862779838 -466.488743791 + E_Fermi -0.217153272173 -2.9545218409 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00120061600575 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108037391624 + + Density error is 0.0629701493336 + + Energy Rydberg eV + E_KohnSham -34.2799255741 -466.402314824 + E_Harris -34.2842674586 -466.461389193 + E_Fermi -0.205814618238 -2.80025153973 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00114821152366 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000945774958886 + + Density error is 0.00203106723337 + + Energy Rydberg eV + E_KohnSham -34.2799214088 -466.402258152 + E_Harris -34.2799235159 -466.40228682 + E_Fermi -0.170170048733 -2.31528229171 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00115025685138 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000945362072088 + + Density error is 0.000968879872904 + + Energy Rydberg eV + E_KohnSham -34.2798518608 -466.401311903 + E_Harris -34.2798532057 -466.4013302 + E_Fermi -0.169391771761 -2.30469329027 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00114913915592 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943710799691 + + Density error is 0.000159994911679 + + Energy Rydberg eV + E_KohnSham -34.2798922861 -466.401861917 + E_Harris -34.2798923353 -466.401862586 + E_Fermi -0.169399898348 -2.30480385815 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00114946685446 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943737658452 + + Density error is 4.32625460556e-05 + + Energy Rydberg eV + E_KohnSham -34.2798779012 -466.401666201 + E_Harris -34.2798779118 -466.401666344 + E_Fermi -0.169258805966 -2.30288419781 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00114933811872 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943713196914 + + Density error is 1.84773812473e-05 + + Energy Rydberg eV + E_KohnSham -34.2798824294 -466.40172781 + E_Harris -34.2798824308 -466.401727829 + E_Fermi -0.169308755369 -2.3035637943 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00114934069183 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943693475697 + + Density error is 2.03814335393e-06 + + Energy Rydberg eV + E_KohnSham -34.2798808315 -466.40170607 + E_Harris -34.2798808316 -466.40170607 + E_Fermi -0.169289266537 -2.30329863514 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0011493440762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943692096863 + + Density error is 3.63976260454e-07 + + Energy Rydberg eV + E_KohnSham -34.2798810871 -466.401709547 + E_Harris -34.2798810871 -466.401709547 + E_Fermi -0.169287443683 -2.30327383394 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00114934484667 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943692156977 + + Density error is 1.28741869887e-07 + + Energy Rydberg eV + E_KohnSham -34.2798811168 -466.401709951 + E_Harris -34.2798811168 -466.401709951 + E_Fermi -0.169287333197 -2.30327233071 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00114934498208 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000943691975328 + + Density error is 1.01901267766e-08 + + Energy Rydberg eV + E_KohnSham -34.2798811193 -466.401709985 + E_Harris -34.2798811193 -466.401709985 + E_band -7.98562119221 -108.649950284 + E_one_elec -69.4410743037 -944.794285771 + E_Hartree +36.1133262991 +491.347011401 + E_xc -8.22150967674 -111.859377766 + E_Ewald +7.39341383033 +100.592555764 + E_demet -2.19215682711e-81 -2.98258237583e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195064169911 -2.65398418643 + E_Fermi -0.169287215432 -2.30327072843 + + charge density convergence is achieved + final etot is -466.401709985 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3364 2.00000 + 2 -13.1885 2.00000 + 3 -9.04619 2.00000 + 4 -6.75387 2.00000 + 5 1.36008 0.00000 + 6 4.54797 0.00000 + 7 11.0588 0.00000 + 8 11.2989 0.00000 + + EFERMI = -2.303270728433648 eV + OUT.ABACUS/ final etot is -466.4017099852989 eV + correction force for each atom along direction 1 is -0.000166191 + correction force for each atom along direction 2 is 0.000179105 + correction force for each atom along direction 3 is -1.87796e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.43365295 -0.040997329 -1.6219018 + H1 -0.61772048 +0.073781950 +1.3755116 + H2 +0.18406753 -0.032784621 +0.24639025 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4017099852989 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6091 11 0.51 1.0e+02% + Run_lcao lcao_line 5.5991 1 5.6 1.e+02% + Potential init_pot 0.28599 2 0.14 5.1% + PW_Basis recip2real 0.28916 17 0.017 5.2% + PW_Basis gathers_scatterp 0.12773 17 0.0075 2.3% + Potential v_of_rho 0.93906 14 0.067 17.% + XC_Functional v_xc 0.25226 15 0.017 4.5% + H_Hartree_pw v_hartree 0.64330 14 0.046 11.% + PW_Basis real2recip 0.61046 41 0.015 11.% + PW_Basis gatherp_scatters 0.24316 41 0.0059 4.3% + ORB_control set_orb_tables 1.1087 1 1.1 20.% + ORB_gen_tables gen_tables 1.1087 1 1.1 20.% + ORB_table_phi init_Table 0.48699 1 0.49 8.7% + ORB_table_phi cal_ST_Phi12_R 0.48197 126 0.0038 8.6% + ORB_table_beta init_Table_Beta 0.19148 1 0.19 3.4% + ORB_table_beta VNL_PhiBeta_R 0.19000 56 0.0034 3.4% + ORB_table_alpha init_Table_Alpha 0.25282 1 0.25 4.5% + ORB_table_alpha S_PhiAlpha_R 0.25099 66 0.0038 4.5% + LOOP_ions opt_ions 3.9714 1 4.0 71.% + ESolver_KS_LCAO Run 3.5450 1 3.5 63.% + HSolverLCAO solve 1.3960 12 0.12 25.% + HamiltLCAO updateHk 0.79407 12 0.066 14.% + LCAO_Hamilt cal_Hgamma 0.75783 12 0.063 14.% + Gint_interface cal_gint 1.1376 25 0.046 20.% + Gint_Gamma distri_vl 1.8685 6 0.31 33.% + LCAO_Deepks cal_projected_DM 3.8461 14 0.27 69.% + LCAO_gen_fixedH add_v_delta 1.7352 6 0.29 31.% + LCAO_DESCRIPTOR add_v_delta 1.7352 6 0.29 31.% + ElecStateLCAO psiToRho 0.58652 12 0.049 10.% + Charge mix_rho 0.72233 11 0.066 13.% + LOOP_ions force_stress 0.42620 1 0.43 7.6% + Force_Stress_LCAO getForceStress 0.42617 1 0.43 7.6% + Force_LCAO_gamma ftable_gamma 0.21366 1 0.21 3.8% + Force_LCAO_gamma cal_fvl_dphi 0.20693 1 0.21 3.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:42 2022 + Finish Time : Wed Sep 28 11:11:47 2022 + Total Time : 0 h 0 mins 5 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..05481c44fb7d41674f423e2bc1b8abfc1c1fa26e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/OUT.ABACUS/warning.log @@ -0,0 +1,77 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123698 ima = 3.66292e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123356509337 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112203262838 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112746634851 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113013587352 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112957198448 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112989348772 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112981590193 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112984846864 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112984101952 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112984020109 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112984007398 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112984001467 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e5c0353c5a7801dfa4260408ae7cfc32b0cb43bf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.518240858035 17.669864605363 -0.159180299457 0 0 0 +H +0.0 +2 +-14.157013270234 17.748000921793 1.511405534848 0 0 0 +-14.984563610958 17.892831993159 -1.269030899181 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/conv new file mode 100644 index 0000000000000000000000000000000000000000..4a0c146ec920005e155c743bf8b2bf4e1dc95251 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/conv @@ -0,0 +1 @@ +37 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d9497736b9949323a4e5c2058bba58ca45a919d9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747855385 0.01269658285 1.27890787 1.370685356 1.469589169 0.00832794943 0.01919214128 0.03899009807 +-4.468222368e-18 0.001116391543 0.002577423284 0.01250978767 0.04522597521 -2.608365169e-19 1.93912606e-06 5.740010989e-06 +0.001680459242 0.005871111975 + +H atom_index 1 n_descriptor 18 +1.27832884 0.03309797565 0.1184892328 0.1639638389 0.3300914108 0.02341743545 0.02998467187 0.03653610852 +-9.542089353e-18 4.749579555e-05 0.1071793172 0.1179272314 0.1407960258 3.150063493e-18 2.6910241e-06 0.01316372048 +0.02732775594 0.03198911145 + +H atom_index 2 n_descriptor 18 +1.228951817 0.03479198953 0.1012123575 0.1407708784 0.3145742712 0.02117518677 0.02712803387 0.0379341034 +8.189746844e-18 4.299835061e-05 0.09673143895 0.1141485066 0.1208268155 -2.469910144e-18 5.292909341e-06 0.01335722115 +0.02553310761 0.02981590283 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..53d5cbc3b98244bfe0d7933ba165bb5f85abefa5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:41 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0866349 SEC) : SETUP UNITCELL + DONE(0.0953911 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.113504 SEC) : INIT PLANEWAVE + DONE(0.161107 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44192 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651480e+02 0.000000e+00 2.168e-01 4.143e-01 + GE2 -4.663972e+02 -1.249140e+00 9.811e-02 3.354e-01 + GE3 -4.664023e+02 -5.147501e-03 6.297e-02 3.948e-01 + GE4 -4.664023e+02 5.667199e-05 2.031e-03 2.819e-01 + GE5 -4.664013e+02 9.462487e-04 9.689e-04 2.903e-01 + GE6 -4.664019e+02 -5.500142e-04 1.600e-04 2.739e-01 + GE7 -4.664017e+02 1.957168e-04 4.326e-05 2.647e-01 + GE8 -4.664017e+02 -6.160948e-05 1.848e-05 2.583e-01 + GE9 -4.664017e+02 2.174022e-05 2.038e-06 2.545e-01 + GE10 -4.664017e+02 -3.477183e-06 3.640e-07 2.594e-01 + GE11 -4.664017e+02 -4.037159e-07 1.287e-07 2.553e-01 + GE12 -4.664017e+02 -3.457276e-08 1.019e-08 1.975e-01 +E_delta_band = -7.10269016e-02 Ry = -9.66370573e-01 eV +E_delta_NN= -1.95064170e-01 Ry = -2.65398419e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6091 11 0.51 1e+02 % + Run_lcao lcao_line 5.5991 1 5.6 1e+02 % + Potential init_pot 0.28599 2 0.14 5.1 % + PW_Basis recip2real 0.28916 17 0.017 5.2 % + PW_Basis gathers_scatterp 0.12773 17 0.0075 2.3 % + Potential v_of_rho 0.93906 14 0.067 17 % + XC_Functional v_xc 0.25226 15 0.017 4.5 % + H_Hartree_pw v_hartree 0.6433 14 0.046 11 % + PW_Basis real2recip 0.61046 41 0.015 11 % + PW_Basis gatherp_scatters 0.24316 41 0.0059 4.3 % + ORB_control set_orb_tables 1.1087 1 1.1 20 % + ORB_gen_tables gen_tables 1.1087 1 1.1 20 % + ORB_table_phi init_Table 0.48699 1 0.49 8.7 % + ORB_table_phi cal_ST_Phi12_R 0.48197 126 0.0038 8.6 % + ORB_table_beta init_Table_Beta 0.19148 1 0.19 3.4 % + ORB_table_beta VNL_PhiBeta_R 0.19 56 0.0034 3.4 % + ORB_table_alpha init_Table_Alpha 0.25282 1 0.25 4.5 % + ORB_table_alpha S_PhiAlpha_R 0.25099 66 0.0038 4.5 % + LOOP_ions opt_ions 3.9714 1 4 71 % + ESolver_KS_LCAO Run 3.545 1 3.5 63 % + HSolverLCAO solve 1.396 12 0.12 25 % + HamiltLCAO updateHk 0.79407 12 0.066 14 % + LCAO_Hamilt cal_Hgamma 0.75783 12 0.063 14 % + Gint_interface cal_gint 1.1376 25 0.046 20 % + Gint_Gamma distri_vl 1.8685 6 0.31 33 % + LCAO_Deepks cal_projected_DM 3.8461 14 0.27 69 % + LCAO_gen_fixedH add_v_delta 1.7352 6 0.29 31 % + LCAO_DESCRIPTOR add_v_delta 1.7352 6 0.29 31 % + ElecStateLCAO psiToRho 0.58652 12 0.049 10 % + Charge mix_rho 0.72233 11 0.066 13 % + LOOP_ions force_stress 0.4262 1 0.43 7.6 % + Force_Stress_LCAO getForceStress 0.42617 1 0.43 7.6 % + Force_LCAO_gamma ftable_gamma 0.21366 1 0.21 3.8 % + Force_LCAO_gamma cal_fvl_dphi 0.20693 1 0.21 3.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:42 2022 + FINISH Time : Wed Sep 28 11:11:47 2022 + TOTAL Time : 5 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/37/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..1d63db12cbad906d89ab63bb91db844b6495e94f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.520007 0.645601 0.991433 +H 0.52446 0.638838 0.0564396 +H 0.473096 0.605631 0.973581 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b8bc9def069d30f52e47633eeb5742c562a1c518 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3817 2 + 2 -13.1913 2 + 3 -9.08214 2 + 4 -6.76469 2 + 5 1.39763 0 + 6 4.59038 0 + 7 11.0495 0 + 8 11.2942 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..df91122d89a15d627abda0eeeffec0db8e521c16 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:15 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.5601888008 18.0768416308 27.7601104937 0 0 0 0 + tauc_H1 14.6848794334 17.8874608274 1.58030899769 0 0 0 0 + tauc_H2 13.2466917906 16.9576647331 27.2602669383 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0878940395739 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0920325955537 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.110289458753 (SEC) + + DONE : INIT CHARGE Time : 0.160379396989 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441482 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 4 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00145 + + Density error is 0.216509524914 + + Energy Rydberg eV + E_KohnSham -34.1892828707 -465.169057575 + E_Harris -34.384366397 -467.823305119 + E_Fermi -0.412149389401 -5.60758012308 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00134396451898 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00141132822177 + + Density error is 0.0977187769211 + + Energy Rydberg eV + E_KohnSham -34.2800171603 -466.403560918 + E_Harris -34.2866880616 -466.494323186 + E_Fermi -0.219667472193 -2.98872928709 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00126685331708 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131850550421 + + Density error is 0.0625742263773 + + Energy Rydberg eV + E_KohnSham -34.2803202566 -466.407684754 + E_Harris -34.2846171414 -466.466146871 + E_Fermi -0.207302092021 -2.82048965881 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114512376689 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116781157659 + + Density error is 0.00202541064492 + + Energy Rydberg eV + E_KohnSham -34.2803317387 -466.407840977 + E_Harris -34.2803333041 -466.407862274 + E_Fermi -0.171680259601 -2.3358297647 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114618359791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116784336876 + + Density error is 0.000914456175658 + + Energy Rydberg eV + E_KohnSham -34.2802628237 -466.406903341 + E_Harris -34.2802646259 -466.406927859 + E_Fermi -0.170754562354 -2.32323500751 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114453851551 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116602242475 + + Density error is 0.000151413503833 + + Energy Rydberg eV + E_KohnSham -34.2803070309 -466.40750481 + E_Harris -34.2803070801 -466.407505479 + E_Fermi -0.170870563302 -2.32481328137 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011445751512 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116597670899 + + Density error is 4.17104426825e-05 + + Energy Rydberg eV + E_KohnSham -34.2802911443 -466.407288662 + E_Harris -34.2802911538 -466.40728879 + E_Fermi -0.170723063918 -2.3228064493 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114453837046 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116595581741 + + Density error is 1.55564699927e-05 + + Energy Rydberg eV + E_KohnSham -34.2802953884 -466.407346405 + E_Harris -34.2802953893 -466.407346418 + E_Fermi -0.170771212302 -2.32346154167 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114452327264 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116593324252 + + Density error is 1.69518879709e-06 + + Energy Rydberg eV + E_KohnSham -34.280293986 -466.407327325 + E_Harris -34.2802939861 -466.407327325 + E_Fermi -0.17075439504 -2.32323273109 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114452097239 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011659302723 + + Density error is 1.71833731689e-07 + + Energy Rydberg eV + E_KohnSham -34.2802941807 -466.407329973 + E_Harris -34.2802941807 -466.407329973 + E_Fermi -0.170752814141 -2.32321122185 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114452154661 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116593083374 + + Density error is 8.07981819932e-08 + + Energy Rydberg eV + E_KohnSham -34.2802942114 -466.407330392 + E_Harris -34.2802942114 -466.407330392 + E_band -7.99957074048 -108.839743625 + E_one_elec -69.515681609 -945.809370236 + E_Hartree +36.1472253419 +491.80823154 + E_xc -8.22692344628 -111.933035879 + E_Ewald +7.43895850145 +101.212222805 + E_demet -7.08952196972e-84 -9.64578948843e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195204871619 -2.65589853137 + E_Fermi -0.170752871988 -2.32321200889 + + charge density convergence is achieved + final etot is -466.407330392 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3817 2.00000 + 2 -13.1913 2.00000 + 3 -9.08214 2.00000 + 4 -6.76469 2.00000 + 5 1.39763 0.00000 + 6 4.59038 0.00000 + 7 11.0495 0.00000 + 8 11.2942 0.00000 + + EFERMI = -2.323212008894798 eV + OUT.ABACUS/ final etot is -466.4073303916705 eV + correction force for each atom along direction 1 is -5.07089e-05 + correction force for each atom along direction 2 is -1.06260e-05 + correction force for each atom along direction 3 is 8.08157e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.97535520 +0.87267727 +0.13661777 + H1 -0.0092071725 -0.043007036 +0.19954138 + H2 -0.96614803 -0.82967023 -0.33615915 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4073303916705 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8839 11 0.53 1.0e+02% + Run_lcao lcao_line 5.8736 1 5.9 1.e+02% + Potential init_pot 0.28325 2 0.14 4.8% + PW_Basis recip2real 0.29182 16 0.018 5.0% + PW_Basis gathers_scatterp 0.12577 16 0.0079 2.1% + Potential v_of_rho 1.0123 13 0.078 17.% + XC_Functional v_xc 0.29107 14 0.021 4.9% + H_Hartree_pw v_hartree 0.67748 13 0.052 12.% + PW_Basis real2recip 0.65392 38 0.017 11.% + PW_Basis gatherp_scatters 0.25072 38 0.0066 4.3% + ORB_control set_orb_tables 1.0946 1 1.1 19.% + ORB_gen_tables gen_tables 1.0946 1 1.1 19.% + ORB_table_phi init_Table 0.47257 1 0.47 8.0% + ORB_table_phi cal_ST_Phi12_R 0.46745 126 0.0037 7.9% + ORB_table_beta init_Table_Beta 0.18365 1 0.18 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18212 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.24850 1 0.25 4.2% + ORB_table_alpha S_PhiAlpha_R 0.24654 66 0.0037 4.2% + LOOP_ions opt_ions 4.2599 1 4.3 72.% + ESolver_KS_LCAO Run 3.8066 1 3.8 65.% + HSolverLCAO solve 1.5017 11 0.14 26.% + HamiltLCAO updateHk 0.85522 11 0.078 15.% + LCAO_Hamilt cal_Hgamma 0.82324 11 0.075 14.% + Gint_interface cal_gint 1.2183 23 0.053 21.% + Gint_Gamma distri_vl 1.8583 6 0.31 32.% + LCAO_Deepks cal_projected_DM 4.1267 13 0.32 70.% + LCAO_gen_fixedH add_v_delta 1.7130 6 0.29 29.% + LCAO_DESCRIPTOR add_v_delta 1.7130 6 0.29 29.% + ElecStateLCAO psiToRho 0.63052 11 0.057 11.% + Charge mix_rho 0.78306 10 0.078 13.% + LOOP_ions force_stress 0.45315 1 0.45 7.7% + Force_Stress_LCAO getForceStress 0.45312 1 0.45 7.7% + Force_LCAO_gamma ftable_gamma 0.23350 1 0.23 4.0% + Force_LCAO_gamma cal_fvl_dphi 0.22555 1 0.23 3.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:15 2022 + Finish Time : Wed Sep 28 11:03:21 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2920e882bc33fb69672608ee94d4ba748a382b1f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123994 ima = 3.66314e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123123480792 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001121082265 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112599990181 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112861048263 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112800450952 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112835978284 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112828484236 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112831433629 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112830853203 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112830779298 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112830776588 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/STRU new file mode 100644 index 0000000000000000000000000000000000000000..80d7261eb8ef800c8c8381c2c7cba111ee7ef416 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.439811199230 18.076841630745 -0.239889506351 0 0 0 +H +0.0 +2 +-13.315120566606 17.887460827430 1.580308997710 0 0 0 +-14.753308209412 16.957664733141 -0.739733061670 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/conv new file mode 100644 index 0000000000000000000000000000000000000000..8105b199da0a3f58fca60cff6600e74539ce22e6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/conv @@ -0,0 +1 @@ +38 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..325b3b5cbacec5d31a674409678f54cdd24efdf3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748334713 0.01273765856 1.28273447 1.371142565 1.469765956 0.008430571929 0.01906924064 0.03899569592 +1.154360663e-18 0.001123728771 0.002623053494 0.0126723417 0.0458339006 -2.70340879e-19 2.059532264e-06 5.970670423e-06 +0.001672922463 0.005914002853 + +H atom_index 1 n_descriptor 18 +1.243865936 0.03433165119 0.1063469229 0.1473045065 0.3192517087 0.0219527451 0.02797699127 0.03745309686 +9.164678578e-17 4.572672171e-05 0.1009980661 0.1145978549 0.1265257752 1.336920741e-17 4.549695639e-06 0.01318432943 +0.02623374755 0.03051466839 + +H atom_index 2 n_descriptor 18 +1.273769379 0.03330845887 0.1169790222 0.1615348481 0.3285109049 0.02331982183 0.02970536245 0.03665518435 +-2.323940248e-17 4.850922896e-05 0.1069312364 0.1172623465 0.1387515803 4.274503838e-18 2.897983144e-06 0.01314739436 +0.02730299302 0.03180513161 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..8be69d5bd51848f89517856b74183e955998cb34 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:15 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0879204 SEC) : SETUP UNITCELL + DONE(0.0920526 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.110312 SEC) : INIT PLANEWAVE + DONE(0.160509 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.441549 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651691e+02 0.000000e+00 2.165e-01 4.645e-01 + GE2 -4.664036e+02 -1.234503e+00 9.772e-02 3.923e-01 + GE3 -4.664077e+02 -4.123836e-03 6.257e-02 4.607e-01 + GE4 -4.664078e+02 -1.562229e-04 2.025e-03 3.254e-01 + GE5 -4.664069e+02 9.376364e-04 9.145e-04 3.215e-01 + GE6 -4.664075e+02 -6.014695e-04 1.514e-04 3.155e-01 + GE7 -4.664073e+02 2.161480e-04 4.171e-05 3.120e-01 + GE8 -4.664073e+02 -5.774292e-05 1.556e-05 3.021e-01 + GE9 -4.664073e+02 1.907959e-05 1.695e-06 3.043e-01 + GE10 -4.664073e+02 -2.647802e-06 1.718e-07 3.080e-01 + GE11 -4.664073e+02 -4.185386e-07 8.080e-08 2.376e-01 +E_delta_band = -7.13318721e-02 Ry = -9.70519909e-01 eV +E_delta_NN= -1.95204872e-01 Ry = -2.65589853e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8839 11 0.53 1e+02 % + Run_lcao lcao_line 5.8736 1 5.9 1e+02 % + Potential init_pot 0.28325 2 0.14 4.8 % + PW_Basis recip2real 0.29182 16 0.018 5 % + PW_Basis gathers_scatterp 0.12577 16 0.0079 2.1 % + Potential v_of_rho 1.0123 13 0.078 17 % + XC_Functional v_xc 0.29107 14 0.021 4.9 % + H_Hartree_pw v_hartree 0.67748 13 0.052 12 % + PW_Basis real2recip 0.65392 38 0.017 11 % + PW_Basis gatherp_scatters 0.25072 38 0.0066 4.3 % + ORB_control set_orb_tables 1.0946 1 1.1 19 % + ORB_gen_tables gen_tables 1.0946 1 1.1 19 % + ORB_table_phi init_Table 0.47257 1 0.47 8 % + ORB_table_phi cal_ST_Phi12_R 0.46745 126 0.0037 7.9 % + ORB_table_beta init_Table_Beta 0.18365 1 0.18 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18212 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.2485 1 0.25 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.24654 66 0.0037 4.2 % + LOOP_ions opt_ions 4.2599 1 4.3 72 % + ESolver_KS_LCAO Run 3.8066 1 3.8 65 % + HSolverLCAO solve 1.5017 11 0.14 26 % + HamiltLCAO updateHk 0.85522 11 0.078 15 % + LCAO_Hamilt cal_Hgamma 0.82324 11 0.075 14 % + Gint_interface cal_gint 1.2183 23 0.053 21 % + Gint_Gamma distri_vl 1.8583 6 0.31 32 % + LCAO_Deepks cal_projected_DM 4.1267 13 0.32 70 % + LCAO_gen_fixedH add_v_delta 1.713 6 0.29 29 % + LCAO_DESCRIPTOR add_v_delta 1.713 6 0.29 29 % + ElecStateLCAO psiToRho 0.63052 11 0.057 11 % + Charge mix_rho 0.78306 10 0.078 13 % + LOOP_ions force_stress 0.45315 1 0.45 7.7 % + Force_Stress_LCAO getForceStress 0.45312 1 0.45 7.7 % + Force_LCAO_gamma ftable_gamma 0.2335 1 0.23 4 % + Force_LCAO_gamma cal_fvl_dphi 0.22555 1 0.23 3.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:15 2022 + FINISH Time : Wed Sep 28 11:03:21 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/38/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..e2af823300c45f97c99c2f9a78f63ff66b749c1c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.506949 0.671892 0.99483 +H 0.54056 0.645754 0.042301 +H 0.50267 0.627155 0.945834 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..20f8543548c566ba201137f1176d3e02022788e4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2831 2 + 2 -13.2764 2 + 3 -8.93647 2 + 4 -6.74042 2 + 5 1.34607 0 + 6 4.54618 0 + 7 11.0654 0 + 8 11.2943 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a12fa379a8da052c81483e08141604ccb37424c1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:33 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.1945719374 18.8129653767 27.855243251 0 0 0 0 + tauc_H1 15.135688287 18.0811199026 1.18442713491 0 0 0 0 + tauc_H2 14.0747516943 17.5603306698 26.4833627355 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.075546974738 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0758209601673 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0914986336708 (SEC) + + DONE : INIT CHARGE Time : 0.132704344404 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.38037 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 4 9 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00102 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000773 + + Density error is 0.216198581498 + + Energy Rydberg eV + E_KohnSham -34.1888056188 -465.16256423 + E_Harris -34.3831263263 -467.806433092 + E_Fermi -0.408520993446 -5.55821326349 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00108257879157 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108667757083 + + Density error is 0.0979695562292 + + Energy Rydberg eV + E_KohnSham -34.2787725058 -466.386626524 + E_Harris -34.2854249834 -466.477138125 + E_Fermi -0.216651190029 -2.94769066288 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00101868516688 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105310193704 + + Density error is 0.062713733793 + + Energy Rydberg eV + E_KohnSham -34.279025553 -466.390069409 + E_Harris -34.2832998696 -466.448224469 + E_Fermi -0.204394261532 -2.78092659534 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000919441865799 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101353053655 + + Density error is 0.00206899622039 + + Energy Rydberg eV + E_KohnSham -34.2790332139 -466.390173641 + E_Harris -34.2790360106 -466.390211692 + E_Fermi -0.168999911807 -2.29936176207 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000918656193522 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101370606558 + + Density error is 0.000859842071477 + + Energy Rydberg eV + E_KohnSham -34.2789747782 -466.389378581 + E_Harris -34.2789758337 -466.389392943 + E_Fermi -0.168109999619 -2.2872538856 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000917567343171 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101298315339 + + Density error is 0.000201212883943 + + Energy Rydberg eV + E_KohnSham -34.2790121809 -466.389887472 + E_Harris -34.2790122948 -466.389889021 + E_Fermi -0.168174991995 -2.28813815223 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000917755161661 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101338902684 + + Density error is 4.09576861035e-05 + + Energy Rydberg eV + E_KohnSham -34.2789970133 -466.389681106 + E_Harris -34.278997022 -466.389681224 + E_Fermi -0.168009674379 -2.28588889067 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00091770027034 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101327432244 + + Density error is 1.80774707707e-05 + + Energy Rydberg eV + E_KohnSham -34.2790025711 -466.389756723 + E_Harris -34.2790025723 -466.38975674 + E_Fermi -0.168054875092 -2.28650387792 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000917689226286 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101327646084 + + Density error is 2.97411121405e-06 + + Energy Rydberg eV + E_KohnSham -34.2790011079 -466.389736816 + E_Harris -34.279001108 -466.389736817 + E_Fermi -0.168037094907 -2.28626196611 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000917688162704 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101327908671 + + Density error is 4.26457684699e-07 + + Energy Rydberg eV + E_KohnSham -34.2790013229 -466.389739742 + E_Harris -34.2790013229 -466.389739742 + E_Fermi -0.168033980505 -2.28621959249 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000917688105872 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101327966227 + + Density error is 1.78825435208e-07 + + Energy Rydberg eV + E_KohnSham -34.279001363 -466.389740287 + E_Harris -34.279001363 -466.389740287 + E_Fermi -0.168033851982 -2.28621784384 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000917688054613 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101327993264 + + Density error is 1.0003322975e-08 + + Energy Rydberg eV + E_KohnSham -34.2790013638 -466.389740297 + E_Harris -34.2790013638 -466.389740297 + E_band -7.97261297583 -108.47296442 + E_one_elec -69.4052970466 -944.307511216 + E_Hartree +36.1005479766 +491.173153404 + E_xc -8.219391668 -111.830560779 + E_Ewald +7.36927068055 +100.26407136 + E_demet -4.67749512742e-80 -6.36405861001e-79 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194955784895 -2.65250953263 + E_Fermi -0.168033678563 -2.28621548436 + + charge density convergence is achieved + final etot is -466.389740297 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2831 2.00000 + 2 -13.2764 2.00000 + 3 -8.93647 2.00000 + 4 -6.74042 2.00000 + 5 1.34607 0.00000 + 6 4.54618 0.00000 + 7 11.0654 0.00000 + 8 11.2943 0.00000 + + EFERMI = -2.286215484355019 eV + OUT.ABACUS/ final etot is -466.3897402969354 eV + correction force for each atom along direction 1 is 0.000109592 + correction force for each atom along direction 2 is -6.53471e-05 + correction force for each atom along direction 3 is -5.41383e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0381648 +0.63941118 -1.6277078 + H1 +0.87300118 -0.87330667 +1.0648495 + H2 +0.16516358 +0.23389548 +0.56285829 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3897402969354 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6380 11 0.51 1.0e+02% + Run_lcao lcao_line 5.6287 1 5.6 1.e+02% + Potential init_pot 0.24532 2 0.12 4.4% + PW_Basis recip2real 0.28187 17 0.017 5.0% + PW_Basis gathers_scatterp 0.11445 17 0.0067 2.0% + Potential v_of_rho 0.99714 14 0.071 18.% + XC_Functional v_xc 0.29062 15 0.019 5.2% + H_Hartree_pw v_hartree 0.66366 14 0.047 12.% + PW_Basis real2recip 0.64792 41 0.016 11.% + PW_Basis gatherp_scatters 0.24390 41 0.0059 4.3% + ORB_control set_orb_tables 0.90214 1 0.90 16.% + ORB_gen_tables gen_tables 0.90214 1 0.90 16.% + ORB_table_phi init_Table 0.37798 1 0.38 6.7% + ORB_table_phi cal_ST_Phi12_R 0.37369 126 0.0030 6.6% + ORB_table_beta init_Table_Beta 0.15603 1 0.16 2.8% + ORB_table_beta VNL_PhiBeta_R 0.15470 56 0.0028 2.7% + ORB_table_alpha init_Table_Alpha 0.21085 1 0.21 3.7% + ORB_table_alpha S_PhiAlpha_R 0.20921 66 0.0032 3.7% + LOOP_ions opt_ions 4.2784 1 4.3 76.% + ESolver_KS_LCAO Run 3.8606 1 3.9 68.% + HSolverLCAO solve 1.4939 12 0.12 26.% + HamiltLCAO updateHk 0.83261 12 0.069 15.% + LCAO_Hamilt cal_Hgamma 0.79725 12 0.066 14.% + Gint_interface cal_gint 1.2342 25 0.049 22.% + Gint_Gamma distri_vl 2.0291 6 0.34 36.% + LCAO_Deepks cal_projected_DM 4.1632 14 0.30 74.% + LCAO_gen_fixedH add_v_delta 1.9024 6 0.32 34.% + LCAO_DESCRIPTOR add_v_delta 1.9024 6 0.32 34.% + ElecStateLCAO psiToRho 0.64006 12 0.053 11.% + Charge mix_rho 0.83023 11 0.075 15.% + LOOP_ions force_stress 0.41764 1 0.42 7.4% + Force_Stress_LCAO getForceStress 0.41762 1 0.42 7.4% + Force_LCAO_gamma ftable_gamma 0.21869 1 0.22 3.9% + Force_LCAO_gamma cal_fvl_dphi 0.21136 1 0.21 3.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:33 2022 + Finish Time : Wed Sep 28 11:06:39 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..7e330b05aa76044130d16445557782c774e42162 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/OUT.ABACUS/warning.log @@ -0,0 +1,77 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123559 ima = 3.66999e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123402342803 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112546788998 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113022885407 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113263290102 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113214413716 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113245330579 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113234890064 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113237881341 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113237203807 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113237096498 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113237085452 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113237076601 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/STRU new file mode 100644 index 0000000000000000000000000000000000000000..02b762d48cb3c7061be493ace4e6abc2d25c51ce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.805428062556 18.812965376744 -0.144756749004 0 0 0 +H +0.0 +2 +-12.864311713017 18.081119902661 1.184427134930 0 0 0 +-13.925248305740 17.560330669842 -1.516637264490 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/conv new file mode 100644 index 0000000000000000000000000000000000000000..12986671dd3dc511c796707f4abf65c84de23a76 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/conv @@ -0,0 +1 @@ +39 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..03d6ee40887be0c9ecb6b12299cbb1f9da628317 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746012196 0.01264481963 1.278183078 1.373410566 1.4693837 0.008027969507 0.01980777233 0.03893925848 +-1.487384081e-18 0.001141383507 0.00248089938 0.01237704328 0.0441434293 2.751306362e-19 1.705971516e-06 5.26227122e-06 +0.001724272453 0.005746941936 + +H atom_index 1 n_descriptor 18 +1.280248906 0.03281188839 0.1191304646 0.1654383474 0.3312975348 0.02327999155 0.03015423848 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:33 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0755623 SEC) : SETUP UNITCELL + DONE(0.0758296 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0915115 SEC) : INIT PLANEWAVE + DONE(0.132807 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.380413 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651626e+02 0.000000e+00 2.162e-01 4.115e-01 + GE2 -4.663866e+02 -1.224062e+00 9.797e-02 3.705e-01 + GE3 -4.663901e+02 -3.442885e-03 6.271e-02 4.362e-01 + GE4 -4.663902e+02 -1.042317e-04 2.069e-03 3.089e-01 + GE5 -4.663894e+02 7.950593e-04 8.598e-04 3.072e-01 + GE6 -4.663899e+02 -5.088905e-04 2.012e-04 3.031e-01 + GE7 -4.663897e+02 2.063659e-04 4.096e-05 2.948e-01 + GE8 -4.663898e+02 -7.561734e-05 1.808e-05 2.922e-01 + GE9 -4.663897e+02 1.990720e-05 2.974e-06 2.911e-01 + GE10 -4.663897e+02 -2.925543e-06 4.265e-07 2.856e-01 + GE11 -4.663897e+02 -5.452344e-07 1.788e-07 2.844e-01 + GE12 -4.663897e+02 -1.006350e-08 1.000e-08 2.201e-01 +E_delta_band = -7.08244786e-02 Ry = -9.63616467e-01 eV +E_delta_NN= -1.94955785e-01 Ry = -2.65250953e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.638 11 0.51 1e+02 % + Run_lcao lcao_line 5.6287 1 5.6 1e+02 % + Potential init_pot 0.24532 2 0.12 4.4 % + PW_Basis recip2real 0.28187 17 0.017 5 % + PW_Basis gathers_scatterp 0.11445 17 0.0067 2 % + Potential v_of_rho 0.99714 14 0.071 18 % + XC_Functional v_xc 0.29062 15 0.019 5.2 % + H_Hartree_pw v_hartree 0.66366 14 0.047 12 % + PW_Basis real2recip 0.64792 41 0.016 11 % + PW_Basis gatherp_scatters 0.2439 41 0.0059 4.3 % + ORB_control set_orb_tables 0.90214 1 0.9 16 % + ORB_gen_tables gen_tables 0.90214 1 0.9 16 % + ORB_table_phi init_Table 0.37798 1 0.38 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.37369 126 0.003 6.6 % + ORB_table_beta init_Table_Beta 0.15603 1 0.16 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.1547 56 0.0028 2.7 % + ORB_table_alpha init_Table_Alpha 0.21085 1 0.21 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.20921 66 0.0032 3.7 % + LOOP_ions opt_ions 4.2784 1 4.3 76 % + ESolver_KS_LCAO Run 3.8606 1 3.9 68 % + HSolverLCAO solve 1.4939 12 0.12 26 % + HamiltLCAO updateHk 0.83261 12 0.069 15 % + LCAO_Hamilt cal_Hgamma 0.79725 12 0.066 14 % + Gint_interface cal_gint 1.2342 25 0.049 22 % + Gint_Gamma distri_vl 2.0291 6 0.34 36 % + LCAO_Deepks cal_projected_DM 4.1632 14 0.3 74 % + LCAO_gen_fixedH add_v_delta 1.9024 6 0.32 34 % + LCAO_DESCRIPTOR add_v_delta 1.9024 6 0.32 34 % + ElecStateLCAO psiToRho 0.64006 12 0.053 11 % + Charge mix_rho 0.83023 11 0.075 15 % + LOOP_ions force_stress 0.41764 1 0.42 7.4 % + Force_Stress_LCAO getForceStress 0.41762 1 0.42 7.4 % + Force_LCAO_gamma ftable_gamma 0.21869 1 0.22 3.9 % + Force_LCAO_gamma cal_fvl_dphi 0.21136 1 0.21 3.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:33 2022 + FINISH Time : Wed Sep 28 11:06:39 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/39/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..563333acae0a252c6f0ff22a58f2051b21aebbbb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.518436 0.715159 0.312348 +H 0.578676 0.702498 0.285064 +H 0.49553 0.75353 0.261486 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..efb34f75998cbc8d761e8f0d50207795815677ae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1169 2 + 2 -12.366 2 + 3 -9.49183 2 + 4 -6.71363 2 + 5 0.970768 0 + 6 3.8727 0 + 7 11.1393 0 + 8 11.4271 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c741991cda351bf810ccf78406b701d8107cea78 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:51 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.5161942519 20.0244413048 8.74574203423 0 0 0 0 + tauc_H1 16.2029234933 19.6699397554 7.98178994474 0 0 0 0 + tauc_H2 13.8748297163 21.0988400294 7.32160927842 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.074775741203 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0750812967846 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0908531174778 (SEC) + + DONE : INIT CHARGE Time : 0.132517571372 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.378002 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00165 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000789 + + Density error is 0.210048614064 + + Energy Rydberg eV + E_KohnSham -34.1884056556 -465.157122452 + E_Harris -34.3709224024 -467.640390188 + E_Fermi -0.38670211493 -5.2613521917 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00139366434365 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098212122963 + + Density error is 0.098444993027 + + Energy Rydberg eV + E_KohnSham -34.2765516131 -466.356409729 + E_Harris -34.2838880562 -466.456227158 + E_Fermi -0.198649470816 -2.70276470778 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00129025443338 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000936188618226 + + Density error is 0.0636369586676 + + Energy Rydberg eV + E_KohnSham -34.277097695 -466.363839555 + E_Harris -34.2817720022 -466.427436767 + E_Fermi -0.193115883088 -2.6274763843 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00109208222826 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000879396267988 + + Density error is 0.00186295263503 + + Energy Rydberg eV + E_KohnSham -34.2769773138 -466.362201684 + E_Harris -34.2769770627 -466.362198268 + E_Fermi -0.157671259561 -2.14522754086 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00109282012768 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000879767273056 + + Density error is 0.00105059756223 + + Energy Rydberg eV + E_KohnSham -34.2769395942 -466.361688482 + E_Harris -34.2769403449 -466.361698697 + E_Fermi -0.157896287788 -2.14828920696 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108952371872 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000878922711612 + + Density error is 0.000114387286552 + + Energy Rydberg eV + E_KohnSham -34.2769553942 -466.361903452 + E_Harris -34.2769553926 -466.361903431 + E_Fermi -0.157391754288 -2.14142467654 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108940636484 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00087900494344 + + Density error is 2.59301718764e-05 + + Energy Rydberg eV + E_KohnSham -34.2769515974 -466.361851795 + E_Harris -34.2769515995 -466.361851823 + E_Fermi -0.157342670919 -2.14075686304 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108936351261 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000878940438937 + + Density error is 1.08367736331e-05 + + Energy Rydberg eV + E_KohnSham -34.2769530874 -466.361872068 + E_Harris -34.276953088 -466.361872075 + E_Fermi -0.157358060301 -2.14096624632 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108935121948 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000878943616409 + + Density error is 2.32921672908e-06 + + Energy Rydberg eV + E_KohnSham -34.2769521889 -466.361859842 + E_Harris -34.2769521889 -466.361859842 + E_Fermi -0.157348504265 -2.14083622979 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108934454498 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000878944765454 + + Density error is 3.05030401773e-07 + + Energy Rydberg eV + E_KohnSham -34.2769523387 -466.361861881 + E_Harris -34.2769523387 -466.361861881 + E_Fermi -0.15734621094 -2.14080502749 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108934485285 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00087894528623 + + Density error is 9.39470467926e-08 + + Energy Rydberg eV + E_KohnSham -34.2769523702 -466.361862309 + E_Harris -34.2769523702 -466.361862309 + E_band -7.8920402326 -107.376716009 + E_one_elec -68.6442352696 -933.952734519 + E_Hartree +35.7198675117 +485.993729964 + E_xc -8.15811980415 -110.996914303 + E_Ewald +6.93112280484 +94.3027636836 + E_demet -1.84651352535e-59 -2.51231053788e-58 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.1937254101 -2.63576942475 + E_Fermi -0.157346075268 -2.14080318159 + + charge density convergence is achieved + final etot is -466.361862309 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1169 2.00000 + 2 -12.3660 2.00000 + 3 -9.49183 2.00000 + 4 -6.71363 2.00000 + 5 0.970768 0.00000 + 6 3.87270 0.00000 + 7 11.1393 0.00000 + 8 11.4271 0.00000 + + EFERMI = -2.140803181587849 eV + OUT.ABACUS/ final etot is -466.3618623092256 eV + correction force for each atom along direction 1 is 1.51513e-05 + correction force for each atom along direction 2 is 7.93359e-05 + correction force for each atom along direction 3 is -6.46786e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.69558710 +0.66393981 -1.7892408 + H1 -0.54994036 -0.16733246 +0.76292334 + H2 -0.14564674 -0.49660736 +1.0263175 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3618623092256 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.7342 11 0.52 1.0e+02% + Run_lcao lcao_line 5.7257 1 5.7 1.e+02% + Potential init_pot 0.24225 2 0.12 4.2% + PW_Basis recip2real 0.22667 16 0.014 4.0% + PW_Basis gathers_scatterp 0.10551 16 0.0066 1.8% + Potential v_of_rho 0.87671 13 0.067 15.% + XC_Functional v_xc 0.27943 14 0.020 4.9% + H_Hartree_pw v_hartree 0.56204 13 0.043 9.8% + PW_Basis real2recip 0.60278 38 0.016 11.% + PW_Basis gatherp_scatters 0.24727 38 0.0065 4.3% + ORB_control set_orb_tables 0.89836 1 0.90 16.% + ORB_gen_tables gen_tables 0.89836 1 0.90 16.% + ORB_table_phi init_Table 0.37714 1 0.38 6.6% + ORB_table_phi cal_ST_Phi12_R 0.37292 126 0.0030 6.5% + ORB_table_beta init_Table_Beta 0.15391 1 0.15 2.7% + ORB_table_beta VNL_PhiBeta_R 0.15261 56 0.0027 2.7% + ORB_table_alpha init_Table_Alpha 0.20940 1 0.21 3.7% + ORB_table_alpha S_PhiAlpha_R 0.20773 66 0.0031 3.6% + LOOP_ions opt_ions 4.3812 1 4.4 76.% + ESolver_KS_LCAO Run 3.9208 1 3.9 68.% + HSolverLCAO solve 1.7456 11 0.16 30.% + HamiltLCAO updateHk 0.94980 11 0.086 17.% + LCAO_Hamilt cal_Hgamma 0.92648 11 0.084 16.% + Gint_interface cal_gint 0.91659 23 0.040 16.% + Gint_Gamma distri_vl_value 0.22605 11 0.021 3.9% + Gint_Gamma distri_vl 1.8954 6 0.32 33.% + LCAO_Deepks cal_projected_DM 4.1695 13 0.32 73.% + LCAO_gen_fixedH add_v_delta 1.7640 6 0.29 31.% + LCAO_DESCRIPTOR add_v_delta 1.7640 6 0.29 31.% + ElecStateLCAO psiToRho 0.77916 11 0.071 14.% + Charge mix_rho 0.76084 10 0.076 13.% + LOOP_ions force_stress 0.46021 1 0.46 8.0% + Force_Stress_LCAO getForceStress 0.46019 1 0.46 8.0% + Force_LCAO_gamma ftable_gamma 0.26354 1 0.26 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.17141 1 0.17 3.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:51 2022 + Finish Time : Wed Sep 28 11:11:57 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..27e36d958fe5eb896d930eeb5e276930252b6574 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012374 ima = 3.65199e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123008077122 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111319007682 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112190130405 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011241403755 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112393277335 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112404877713 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112402777138 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112404586667 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112404089205 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240400004 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240398546 + charge after normalized = 7.99999999999997 + charge before normalized = 7.99999999999997 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b37dc8e48e36fb2e6e655014500aeb27e7dbe8dc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.483805748163 20.024441304790 8.745742034231 0 0 0 +H +0.0 +2 +-11.797076506652 19.669939755349 7.981789944727 0 0 0 +-14.125170283703 21.098840029390 7.321609278419 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/conv new file mode 100644 index 0000000000000000000000000000000000000000..ec04b1df1677af42c7a274704c11bb2eb7f60c8e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/conv @@ -0,0 +1 @@ +4 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..132f51acb2532db4023feec89476e4c5e9ada50c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.756118202 0.01258085514 1.245119794 1.324019629 1.46858085 0.009675034617 0.01565364636 0.03928085086 +-5.048533622e-18 0.0007337362572 0.002676770741 0.01266032861 0.04338805007 -2.409577124e-19 2.39529838e-06 6.760352705e-06 +0.001564361758 0.006071289194 + +H atom_index 1 n_descriptor 18 +1.210367409 0.03635376949 0.0983190869 0.1320873955 0.3057871321 0.02130362495 0.02589623481 0.03966918639 +-5.879220314e-18 4.077547832e-05 0.09063397931 0.1127913022 0.1140403851 -9.842616788e-19 4.3941445e-06 0.01414710734 +0.02492198306 0.02874300212 + +H atom_index 2 n_descriptor 18 +1.202232032 0.03660245125 0.09574531712 0.1287019911 0.3026888201 0.02090013531 0.02541539502 0.03999410965 +-3.887137196e-18 4.008361714e-05 0.08857416676 0.1098178557 0.1136273754 6.452057314e-19 4.731565992e-06 0.01437365089 +0.02458373639 0.02831047938 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..6a83a8f0f7984c50996fef8bf8307943e7f09778 Binary files /dev/null and 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0000000000000000000000000000000000000000..43a8dda5a795ad416a927fd5d85c0a4d0e804c0b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:51 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0747913 SEC) : SETUP UNITCELL + DONE(0.0750904 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0908682 SEC) : INIT PLANEWAVE + DONE(0.132619 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.378045 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651571e+02 0.000000e+00 2.100e-01 4.465e-01 + GE2 -4.663564e+02 -1.199287e+00 9.844e-02 4.030e-01 + GE3 -4.663638e+02 -7.429825e-03 6.364e-02 4.619e-01 + GE4 -4.663622e+02 1.637871e-03 1.863e-03 3.427e-01 + GE5 -4.663617e+02 5.132015e-04 1.051e-03 3.421e-01 + GE6 -4.663619e+02 -2.149699e-04 1.144e-04 3.379e-01 + GE7 -4.663619e+02 5.165717e-05 2.593e-05 3.182e-01 + GE8 -4.663619e+02 -2.027280e-05 1.084e-05 3.204e-01 + GE9 -4.663619e+02 1.222582e-05 2.329e-06 3.223e-01 + GE10 -4.663619e+02 -2.039014e-06 3.050e-07 3.188e-01 + GE11 -4.663619e+02 -4.280176e-07 9.395e-08 2.541e-01 +E_delta_band = -6.81377971e-02 Ry = -9.27062290e-01 eV +E_delta_NN= -1.93725410e-01 Ry = -2.63576942e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.7342 11 0.52 1e+02 % + Run_lcao lcao_line 5.7257 1 5.7 1e+02 % + Potential init_pot 0.24225 2 0.12 4.2 % + PW_Basis recip2real 0.22667 16 0.014 4 % + PW_Basis gathers_scatterp 0.10551 16 0.0066 1.8 % + Potential v_of_rho 0.87671 13 0.067 15 % + XC_Functional v_xc 0.27943 14 0.02 4.9 % + H_Hartree_pw v_hartree 0.56204 13 0.043 9.8 % + PW_Basis real2recip 0.60278 38 0.016 11 % + PW_Basis gatherp_scatters 0.24727 38 0.0065 4.3 % + ORB_control set_orb_tables 0.89836 1 0.9 16 % + ORB_gen_tables gen_tables 0.89836 1 0.9 16 % + ORB_table_phi init_Table 0.37714 1 0.38 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.37292 126 0.003 6.5 % + ORB_table_beta init_Table_Beta 0.15391 1 0.15 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.15261 56 0.0027 2.7 % + ORB_table_alpha init_Table_Alpha 0.2094 1 0.21 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.20773 66 0.0031 3.6 % + LOOP_ions opt_ions 4.3812 1 4.4 76 % + ESolver_KS_LCAO Run 3.9208 1 3.9 68 % + HSolverLCAO solve 1.7456 11 0.16 30 % + HamiltLCAO updateHk 0.9498 11 0.086 17 % + LCAO_Hamilt cal_Hgamma 0.92648 11 0.084 16 % + Gint_interface cal_gint 0.91659 23 0.04 16 % + Gint_Gamma distri_vl_value 0.22605 11 0.021 3.9 % + Gint_Gamma distri_vl 1.8954 6 0.32 33 % + LCAO_Deepks cal_projected_DM 4.1695 13 0.32 73 % + LCAO_gen_fixedH add_v_delta 1.764 6 0.29 31 % + LCAO_DESCRIPTOR add_v_delta 1.764 6 0.29 31 % + ElecStateLCAO psiToRho 0.77916 11 0.071 14 % + Charge mix_rho 0.76084 10 0.076 13 % + LOOP_ions force_stress 0.46021 1 0.46 8 % + Force_Stress_LCAO getForceStress 0.46019 1 0.46 8 % + Force_LCAO_gamma ftable_gamma 0.26354 1 0.26 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.17141 1 0.17 3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:51 2022 + FINISH Time : Wed Sep 28 11:11:57 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/4/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..91479c35a5cb7f60c75726482df0939e2dbc04a7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.494386 0.691378 0.997285 +H 0.524483 0.725113 0.0467353 +H 0.546554 0.68309 0.95972 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..5336ef8d6b2bf095c4f768f198bfb03c67ab2f1e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3623 2 + 2 -12.6528 2 + 3 -9.45099 2 + 4 -6.76283 2 + 5 1.19107 0 + 6 4.29653 0 + 7 11.0795 0 + 8 11.3625 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..09488f2c3cc7fc421c5fa6e3c20c29254813fb3e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:13 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.8428027417 19.3585923167 27.9239909681 0 0 0 0 + tauc_H1 14.685536542 20.3031520392 1.30858912726 0 0 0 0 + tauc_H2 15.3035221779 19.1265169874 26.872164825 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0867653099369 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0971191211946 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115371346826 (SEC) + + DONE : INIT CHARGE Time : 0.16548645072 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445065 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 4 9 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000809 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00145 + + Density error is 0.213296251036 + + Energy Rydberg eV + E_KohnSham -34.1882071225 -465.15442127 + E_Harris -34.3774796427 -467.72960602 + E_Fermi -0.403586767835 -5.49107967996 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00123456388334 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124522381395 + + Density error is 0.0979822941154 + + Energy Rydberg eV + E_KohnSham -34.2780668596 -466.377025716 + E_Harris -34.2850439463 -466.471953851 + E_Fermi -0.212753654493 -2.89466197143 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00118146886805 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115327590803 + + Density error is 0.0629612449187 + + Energy Rydberg eV + E_KohnSham -34.2784841021 -466.382702591 + E_Harris -34.2829943896 -466.444068201 + E_Fermi -0.20351746405 -2.76899715358 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00111975484249 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00099722303716 + + Density error is 0.00191530873299 + + Energy Rydberg eV + E_KohnSham -34.2784348655 -466.382032693 + E_Harris -34.2784352628 -466.382038099 + E_Fermi -0.167666437074 -2.28121890756 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00112441306582 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998856864256 + + Density error is 0.00100463000664 + + Energy Rydberg eV + E_KohnSham -34.2783750206 -466.381218462 + E_Harris -34.2783764253 -466.381237573 + E_Fermi -0.167334605541 -2.27670410793 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00112276234848 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000996530253603 + + Density error is 9.93328296868e-05 + + Energy Rydberg eV + E_KohnSham -34.2784109429 -466.381707209 + E_Harris -34.2784109471 -466.381707267 + E_Fermi -0.16715300371 -2.27423328827 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00112252290109 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000996275329637 + + Density error is 3.34738289953e-05 + + Energy Rydberg eV + E_KohnSham -34.2784004418 -466.381564334 + E_Harris -34.2784004474 -466.381564411 + E_Fermi -0.167061040409 -2.27298206337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00112246856891 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000996286372555 + + Density error is 1.63774318474e-05 + + Energy Rydberg eV + E_KohnSham -34.2784021684 -466.381587826 + E_Harris -34.2784021696 -466.381587842 + E_Fermi -0.167098124545 -2.27348661892 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00112248316072 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000996275159108 + + Density error is 2.39455562904e-06 + + Energy Rydberg eV + E_KohnSham -34.2784008287 -466.381569598 + E_Harris -34.2784008287 -466.381569598 + E_Fermi -0.167082076641 -2.27326827599 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00112248608836 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000996271725191 + + Density error is 2.6744737225e-07 + + Energy Rydberg eV + E_KohnSham -34.2784010703 -466.381572886 + E_Harris -34.2784010703 -466.381572886 + E_Fermi -0.167080077578 -2.27324107734 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00112248660163 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00099627199072 + + Density error is 6.68052842387e-08 + + Energy Rydberg eV + E_KohnSham -34.2784011142 -466.381573482 + E_Harris -34.2784011142 -466.381573482 + E_band -7.97150974203 -108.457954154 + E_one_elec -69.1853702417 -941.315253526 + E_Hartree +35.9780584236 +489.506597537 + E_xc -8.19958879674 -111.561128893 + E_Ewald +7.25300324444 +98.6821717368 + E_demet -4.58998876275e-73 -6.24500009294e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19467903508 -2.64874415823 + E_Fermi -0.167079939032 -2.27323919233 + + charge density convergence is achieved + final etot is -466.381573482 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3623 2.00000 + 2 -12.6528 2.00000 + 3 -9.45099 2.00000 + 4 -6.76283 2.00000 + 5 1.19107 0.00000 + 6 4.29653 0.00000 + 7 11.0795 0.00000 + 8 11.3625 0.00000 + + EFERMI = -2.273239192334069 eV + OUT.ABACUS/ final etot is -466.3815734823394 eV + correction force for each atom along direction 1 is 6.03476e-05 + correction force for each atom along direction 2 is 5.24689e-05 + correction force for each atom along direction 3 is 6.10278e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.24007125 +0.67183679 +1.1378944 + H1 -0.73424927 -0.27721323 -0.19894367 + H2 +0.49417803 -0.39462355 -0.93895076 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3815734823394 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.4414 11 0.49 1.0e+02% + Run_lcao lcao_line 5.4310 1 5.4 1.e+02% + Potential init_pot 0.28432 2 0.14 5.2% + PW_Basis recip2real 0.26615 16 0.017 4.9% + PW_Basis gathers_scatterp 0.11343 16 0.0071 2.1% + Charge atomic_rho 0.10075 1 0.10 1.9% + Potential v_of_rho 0.87846 13 0.068 16.% + XC_Functional v_xc 0.24512 14 0.018 4.5% + H_Hartree_pw v_hartree 0.59496 13 0.046 11.% + PW_Basis real2recip 0.55739 38 0.015 10.% + PW_Basis gatherp_scatters 0.21595 38 0.0057 4.0% + ORB_control set_orb_tables 1.0968 1 1.1 20.% + ORB_gen_tables gen_tables 1.0968 1 1.1 20.% + ORB_table_phi init_Table 0.48135 1 0.48 8.8% + ORB_table_phi cal_ST_Phi12_R 0.47648 126 0.0038 8.8% + ORB_table_beta init_Table_Beta 0.18616 1 0.19 3.4% + ORB_table_beta VNL_PhiBeta_R 0.18469 56 0.0033 3.4% + ORB_table_alpha init_Table_Alpha 0.25073 1 0.25 4.6% + ORB_table_alpha S_PhiAlpha_R 0.24886 66 0.0038 4.6% + LOOP_ions opt_ions 3.8131 1 3.8 70.% + ESolver_KS_LCAO Run 3.3738 1 3.4 62.% + HSolverLCAO solve 1.3972 11 0.13 26.% + HamiltLCAO updateHk 0.79371 11 0.072 15.% + LCAO_Hamilt cal_Hgamma 0.75555 11 0.069 14.% + Gint_interface cal_gint 1.1618 23 0.051 21.% + Gint_Gamma distri_vl 1.6390 6 0.27 30.% + LCAO_Deepks cal_projected_DM 3.6861 13 0.28 68.% + LCAO_gen_fixedH add_v_delta 1.5094 6 0.25 28.% + LCAO_DESCRIPTOR add_v_delta 1.5094 6 0.25 28.% + ElecStateLCAO psiToRho 0.58882 11 0.054 11.% + Charge mix_rho 0.65492 10 0.065 12.% + LOOP_ions force_stress 0.43905 1 0.44 8.1% + Force_Stress_LCAO getForceStress 0.43902 1 0.44 8.1% + Force_LCAO_gamma ftable_gamma 0.22748 1 0.23 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.22075 1 0.22 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:13 2022 + Finish Time : Wed Sep 28 11:09:19 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..71153ac6c935825295128e163c5ede465623401f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/OUT.ABACUS/warning.log @@ -0,0 +1,73 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124021 ima = 3.67445e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012277616567 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111369214161 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112054881024 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112316806354 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112264692158 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112292806053 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112291073177 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112293693608 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011229293419 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112292818729 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112292806585 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1c827ee51eb0f03c812c2934501b66f301f8fc02 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.157197258316 19.358592316721 -0.076009031889 0 0 0 +H +0.0 +2 +-13.314463457999 20.303152039222 1.308589127253 0 0 0 +-12.696477822088 19.126516987388 -1.127835175030 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/conv new file mode 100644 index 0000000000000000000000000000000000000000..97cd915fbbd53f8b361350499ec4a59242a298e7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/conv @@ -0,0 +1 @@ +40 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f9985f2d7c1bd67782958dd1eb39ec13ee288401 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.7546145 0.01275496858 1.264246066 1.348777708 1.469521465 0.009538615084 0.01651801321 0.03919083387 +2.729722418e-18 0.0008692019566 0.002823210825 0.01316385518 0.04627411364 6.365940028e-20 2.723754414e-06 7.326405318e-06 +0.001582950988 0.006137771032 + +H atom_index 1 n_descriptor 18 +1.216483729 0.03604033384 0.09987016447 0.134599223 0.3078855798 0.0215658503 0.02625892274 0.03926075908 +-2.074203851e-17 4.576676443e-05 0.09424010229 0.1138635341 0.1151980721 -1.329473378e-17 4.718986971e-06 0.01397636338 +0.02559589637 0.02909229595 + +H atom_index 2 n_descriptor 18 +1.264405456 0.03445538896 0.1165172878 0.1564184126 0.3243331446 0.0239501583 0.02907735757 0.03764094152 +3.949960196e-17 5.019437057e-05 0.1053080335 0.1169343991 0.1340965123 -6.196437442e-18 2.181021153e-06 0.01335340584 +0.02742455646 0.03137601263 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..954cfdf98e1c0328cab924c4e7962319ab807092 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:13 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0867872 SEC) : SETUP UNITCELL + DONE(0.0971373 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11539 SEC) : INIT PLANEWAVE + DONE(0.165616 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445126 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651544e+02 0.000000e+00 2.133e-01 4.183e-01 + GE2 -4.663770e+02 -1.222604e+00 9.798e-02 3.461e-01 + GE3 -4.663827e+02 -5.676875e-03 6.296e-02 4.017e-01 + GE4 -4.663820e+02 6.698976e-04 1.915e-03 2.893e-01 + GE5 -4.663812e+02 8.142317e-04 1.005e-03 2.879e-01 + GE6 -4.663817e+02 -4.887471e-04 9.933e-05 2.857e-01 + GE7 -4.663816e+02 1.428749e-04 3.347e-05 2.764e-01 + GE8 -4.663816e+02 -2.349208e-05 1.638e-05 2.673e-01 + GE9 -4.663816e+02 1.822769e-05 2.395e-06 2.648e-01 + GE10 -4.663816e+02 -3.287721e-06 2.674e-07 2.688e-01 + GE11 -4.663816e+02 -5.964022e-07 6.681e-08 2.057e-01 +E_delta_band = -7.01752913e-02 Ry = -9.54783821e-01 eV +E_delta_NN= -1.94679035e-01 Ry = -2.64874416e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.4414 11 0.49 1e+02 % + Run_lcao lcao_line 5.431 1 5.4 1e+02 % + Potential init_pot 0.28432 2 0.14 5.2 % + PW_Basis recip2real 0.26615 16 0.017 4.9 % + PW_Basis gathers_scatterp 0.11343 16 0.0071 2.1 % + Charge atomic_rho 0.10075 1 0.1 1.9 % + Potential v_of_rho 0.87846 13 0.068 16 % + XC_Functional v_xc 0.24512 14 0.018 4.5 % + H_Hartree_pw v_hartree 0.59496 13 0.046 11 % + PW_Basis real2recip 0.55739 38 0.015 10 % + PW_Basis gatherp_scatters 0.21595 38 0.0057 4 % + ORB_control set_orb_tables 1.0968 1 1.1 20 % + ORB_gen_tables gen_tables 1.0968 1 1.1 20 % + ORB_table_phi init_Table 0.48135 1 0.48 8.8 % + ORB_table_phi cal_ST_Phi12_R 0.47648 126 0.0038 8.8 % + ORB_table_beta init_Table_Beta 0.18616 1 0.19 3.4 % + ORB_table_beta VNL_PhiBeta_R 0.18469 56 0.0033 3.4 % + ORB_table_alpha init_Table_Alpha 0.25073 1 0.25 4.6 % + ORB_table_alpha S_PhiAlpha_R 0.24886 66 0.0038 4.6 % + LOOP_ions opt_ions 3.8131 1 3.8 70 % + ESolver_KS_LCAO Run 3.3738 1 3.4 62 % + HSolverLCAO solve 1.3972 11 0.13 26 % + HamiltLCAO updateHk 0.79371 11 0.072 15 % + LCAO_Hamilt cal_Hgamma 0.75555 11 0.069 14 % + Gint_interface cal_gint 1.1618 23 0.051 21 % + Gint_Gamma distri_vl 1.639 6 0.27 30 % + LCAO_Deepks cal_projected_DM 3.6861 13 0.28 68 % + LCAO_gen_fixedH add_v_delta 1.5094 6 0.25 28 % + LCAO_DESCRIPTOR add_v_delta 1.5094 6 0.25 28 % + ElecStateLCAO psiToRho 0.58882 11 0.054 11 % + Charge mix_rho 0.65492 10 0.065 12 % + LOOP_ions force_stress 0.43905 1 0.44 8.1 % + Force_Stress_LCAO getForceStress 0.43902 1 0.44 8.1 % + Force_LCAO_gamma ftable_gamma 0.22748 1 0.23 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.22075 1 0.22 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:13 2022 + FINISH Time : Wed Sep 28 11:09:19 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/40/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..538789f57cb5fb1bbece1be2a2a291f9608b6dbb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.481504 0.698238 0.00179355 +H 0.4307 0.716862 0.962311 +H 0.486202 0.74564 0.0470155 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..99927d7d4fe2756f4458c3009057c5f16ed1c0cc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1305 2 + 2 -12.9698 2 + 3 -9.04862 2 + 4 -6.70885 2 + 5 1.18294 0 + 6 4.2245 0 + 7 11.1104 0 + 8 11.3575 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..0397a46b566438889d605f50d53214279819f05b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:33 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.4821131516 19.5506576243 0.0502193056745 0 0 0 0 + tauc_H1 12.0595935191 20.0721404407 26.9447033775 0 0 0 0 + tauc_H2 13.6136581187 20.877920747 1.31643418351 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0739752678732 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0823110643418 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0994034803747 (SEC) + + DONE : INIT CHARGE Time : 0.140839985559 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.383575 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 9 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000731 + + Density error is 0.213556869311 + + Energy Rydberg eV + E_KohnSham -34.1918906874 -465.204538742 + E_Harris -34.3803124267 -467.768148024 + E_Fermi -0.396405495628 -5.39337345906 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00122589634023 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000981867214813 + + Density error is 0.0984175566883 + + Energy Rydberg eV + E_KohnSham -34.2806761417 -466.412526819 + E_Harris -34.2875515561 -466.506071631 + E_Fermi -0.206178098416 -2.80519694127 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00115027084094 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000947163120919 + + Density error is 0.0633224075793 + + Energy Rydberg eV + E_KohnSham -34.2810082042 -466.417044762 + E_Harris -34.2854425288 -466.477376843 + E_Fermi -0.196964329832 -2.67983718847 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0010254791882 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908326535665 + + Density error is 0.00199806028964 + + Energy Rydberg eV + E_KohnSham -34.2809600127 -466.416389083 + E_Harris -34.2809621037 -466.416417533 + E_Fermi -0.161639444857 -2.19921747162 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00102515236004 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908469327229 + + Density error is 0.000889495138826 + + Energy Rydberg eV + E_KohnSham -34.2809145503 -466.415770536 + E_Harris -34.2809150561 -466.415777417 + E_Fermi -0.161210475975 -2.19338105055 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00102355390682 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000907966740479 + + Density error is 0.000174563720061 + + Energy Rydberg eV + E_KohnSham -34.2809393546 -466.416108014 + E_Harris -34.2809393805 -466.416108368 + E_Fermi -0.160992367251 -2.19041352912 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00102367022741 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908236520995 + + Density error is 3.33249914163e-05 + + Energy Rydberg eV + E_KohnSham -34.2809306313 -466.415989329 + E_Harris -34.2809306363 -466.415989396 + E_Fermi -0.160906901066 -2.18925070202 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00102362309056 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908161645084 + + Density error is 1.48685652824e-05 + + Energy Rydberg eV + E_KohnSham -34.2809343444 -466.416039848 + E_Harris -34.2809343454 -466.416039861 + E_Fermi -0.160936324462 -2.18965102786 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00102361074074 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908163298765 + + Density error is 1.76866686931e-06 + + Energy Rydberg eV + E_KohnSham -34.2809331063 -466.416023002 + E_Harris -34.2809331063 -466.416023002 + E_Fermi -0.160920945518 -2.18944178659 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00102360860867 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000908164924081 + + Density error is 1.8984696811e-07 + + Energy Rydberg eV + E_KohnSham -34.2809333221 -466.416025939 + E_Harris -34.2809333221 -466.416025939 + E_Fermi -0.160919263227 -2.18941889785 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00102360889944 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00090816539271 + + Density error is 4.95163735094e-08 + + Energy Rydberg eV + E_KohnSham -34.2809333486 -466.416026299 + E_Harris -34.2809333486 -466.416026299 + E_band -7.91694186912 -107.715520155 + E_one_elec -68.9980219215 -938.766248861 + E_Hartree +35.9037928419 +488.496162461 + E_xc -8.18763925167 -111.398546991 + E_Ewald +7.12587999741 +96.952571229 + E_demet -2.23142528035e-69 -3.03600984739e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194251198218 -2.64292313909 + E_Fermi -0.160919223925 -2.18941836311 + + charge density convergence is achieved + final etot is -466.416026299 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1305 2.00000 + 2 -12.9698 2.00000 + 3 -9.04862 2.00000 + 4 -6.70885 2.00000 + 5 1.18294 0.00000 + 6 4.22450 0.00000 + 7 11.1104 0.00000 + 8 11.3575 0.00000 + + EFERMI = -2.189418363113187 eV + OUT.ABACUS/ final etot is -466.4160262994899 eV + correction force for each atom along direction 1 is -2.50193e-05 + correction force for each atom along direction 2 is 6.05222e-05 + correction force for each atom along direction 3 is -5.08673e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.54393239 +0.030202215 -0.56965975 + H1 +0.60683752 -0.15303188 +0.53261057 + H2 -0.062905132 +0.12282966 +0.037049186 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4160262994899 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.4654 11 0.50 1.0e+02% + Run_lcao lcao_line 5.4575 1 5.5 1.e+02% + Potential init_pot 0.24116 2 0.12 4.4% + PW_Basis recip2real 0.26258 16 0.016 4.8% + PW_Basis gathers_scatterp 0.10549 16 0.0066 1.9% + Potential v_of_rho 0.93493 13 0.072 17.% + XC_Functional v_xc 0.28381 14 0.020 5.2% + H_Hartree_pw v_hartree 0.61102 13 0.047 11.% + PW_Basis real2recip 0.59666 38 0.016 11.% + PW_Basis gatherp_scatters 0.22135 38 0.0058 4.1% + ORB_control set_orb_tables 0.89690 1 0.90 16.% + ORB_gen_tables gen_tables 0.89690 1 0.90 16.% + ORB_table_phi init_Table 0.37468 1 0.37 6.9% + ORB_table_phi cal_ST_Phi12_R 0.37041 126 0.0029 6.8% + ORB_table_beta init_Table_Beta 0.15333 1 0.15 2.8% + ORB_table_beta VNL_PhiBeta_R 0.15196 56 0.0027 2.8% + ORB_table_alpha init_Table_Alpha 0.21113 1 0.21 3.9% + ORB_table_alpha S_PhiAlpha_R 0.20949 66 0.0032 3.8% + LOOP_ions opt_ions 4.1085 1 4.1 75.% + ESolver_KS_LCAO Run 3.6862 1 3.7 67.% + HSolverLCAO solve 1.5012 11 0.14 27.% + HamiltLCAO updateHk 0.84283 11 0.077 15.% + LCAO_Hamilt cal_Hgamma 0.81130 11 0.074 15.% + Gint_interface cal_gint 1.2609 23 0.055 23.% + Gint_Gamma distri_vl 1.7857 6 0.30 33.% + LCAO_Deepks cal_projected_DM 3.9893 13 0.31 73.% + LCAO_gen_fixedH add_v_delta 1.6575 6 0.28 30.% + LCAO_DESCRIPTOR add_v_delta 1.6576 6 0.28 30.% + ElecStateLCAO psiToRho 0.64194 11 0.058 12.% + Charge mix_rho 0.76018 10 0.076 14.% + LOOP_ions force_stress 0.42214 1 0.42 7.7% + Force_Stress_LCAO getForceStress 0.42211 1 0.42 7.7% + Force_LCAO_gamma ftable_gamma 0.22446 1 0.22 4.1% + Force_LCAO_gamma cal_fvl_dphi 0.21705 1 0.22 4.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:33 2022 + Finish Time : Wed Sep 28 11:12:39 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..404bba411e6d37d27ad5ee3603942cbbfb7edf7f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/OUT.ABACUS/warning.log @@ -0,0 +1,73 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123745 ima = 3.66895e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123395879855 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112231330363 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112859303231 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113073970167 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011304233362 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113061649052 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113055218566 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113057713293 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113057068205 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113056997168 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113056988089 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/STRU new file mode 100644 index 0000000000000000000000000000000000000000..f05fca4ccaeffe7aa676cac54c6da9e9a253c1d2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.517886848422 19.550657624340 0.050219305653 0 0 0 +H +0.0 +2 +-15.940406480912 20.072140440692 -1.055296622523 0 0 0 +-14.386341881323 20.877920746988 1.316434183530 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/conv new file mode 100644 index 0000000000000000000000000000000000000000..4802d59808b67163ca2aede83512d9a1eb2cdaa9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/conv @@ -0,0 +1 @@ +41 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..6322cb624bf006033062e740feab3f9891e20be0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748575483 0.01256437531 1.261564267 1.353641302 1.468612281 0.00827885555 0.01856790871 0.03901713158 +-8.02338783e-19 0.001000886325 0.002468033581 0.01194386998 0.04313285771 -2.488499921e-19 1.753553456e-06 5.308699324e-06 +0.00165708423 0.005876906725 + +H atom_index 1 n_descriptor 18 +1.211560605 0.03547905868 0.09526000757 0.1333497704 0.3086793992 0.02025239275 0.02611657318 0.03876711175 +3.494585626e-17 3.867546571e-05 0.09038570612 0.1139277645 0.1141747763 -5.480909596e-18 5.790986679e-06 0.0137443597 +0.02443281322 0.02891903122 + +H atom_index 2 n_descriptor 18 +1.240452763 0.03449530961 0.104567412 0.145955439 0.3186746788 0.02157855687 0.02780474336 0.0376818588 +-3.826244731e-17 4.11711542e-05 0.09799290147 0.1147916075 0.1251712159 2.515970548e-18 4.548051736e-06 0.01319648821 +0.02557356658 0.03033987045 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..423ea4b11e4b670550ed4fec712a640a254a14b8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:33 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0739908 SEC) : SETUP UNITCELL + DONE(0.0823244 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0994171 SEC) : INIT PLANEWAVE + DONE(0.140943 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.383618 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652045e+02 0.000000e+00 2.136e-01 4.210e-01 + GE2 -4.664125e+02 -1.207988e+00 9.842e-02 3.876e-01 + GE3 -4.664170e+02 -4.517942e-03 6.332e-02 4.438e-01 + GE4 -4.664164e+02 6.556789e-04 1.998e-03 3.216e-01 + GE5 -4.664158e+02 6.185469e-04 8.895e-04 3.176e-01 + GE6 -4.664161e+02 -3.374787e-04 1.746e-04 3.157e-01 + GE7 -4.664160e+02 1.186853e-04 3.332e-05 3.008e-01 + GE8 -4.664160e+02 -5.051891e-05 1.487e-05 3.013e-01 + GE9 -4.664160e+02 1.684569e-05 1.769e-06 2.975e-01 + GE10 -4.664160e+02 -2.936549e-06 1.898e-07 2.973e-01 + GE11 -4.664160e+02 -3.606282e-07 4.952e-08 2.281e-01 +E_delta_band = -6.93061835e-02 Ry = -9.42959002e-01 eV +E_delta_NN= -1.94251198e-01 Ry = -2.64292314e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.4654 11 0.5 1e+02 % + Run_lcao lcao_line 5.4575 1 5.5 1e+02 % + Potential init_pot 0.24116 2 0.12 4.4 % + PW_Basis recip2real 0.26258 16 0.016 4.8 % + PW_Basis gathers_scatterp 0.10549 16 0.0066 1.9 % + Potential v_of_rho 0.93493 13 0.072 17 % + XC_Functional v_xc 0.28381 14 0.02 5.2 % + H_Hartree_pw v_hartree 0.61102 13 0.047 11 % + PW_Basis real2recip 0.59666 38 0.016 11 % + PW_Basis gatherp_scatters 0.22135 38 0.0058 4.1 % + ORB_control set_orb_tables 0.8969 1 0.9 16 % + ORB_gen_tables gen_tables 0.8969 1 0.9 16 % + ORB_table_phi init_Table 0.37468 1 0.37 6.9 % + ORB_table_phi cal_ST_Phi12_R 0.37041 126 0.0029 6.8 % + ORB_table_beta init_Table_Beta 0.15333 1 0.15 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.15196 56 0.0027 2.8 % + ORB_table_alpha init_Table_Alpha 0.21113 1 0.21 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.20949 66 0.0032 3.8 % + LOOP_ions opt_ions 4.1085 1 4.1 75 % + ESolver_KS_LCAO Run 3.6862 1 3.7 67 % + HSolverLCAO solve 1.5012 11 0.14 27 % + HamiltLCAO updateHk 0.84283 11 0.077 15 % + LCAO_Hamilt cal_Hgamma 0.8113 11 0.074 15 % + Gint_interface cal_gint 1.2609 23 0.055 23 % + Gint_Gamma distri_vl 1.7857 6 0.3 33 % + LCAO_Deepks cal_projected_DM 3.9893 13 0.31 73 % + LCAO_gen_fixedH add_v_delta 1.6575 6 0.28 30 % + LCAO_DESCRIPTOR add_v_delta 1.6576 6 0.28 30 % + ElecStateLCAO psiToRho 0.64194 11 0.058 12 % + Charge mix_rho 0.76018 10 0.076 14 % + LOOP_ions force_stress 0.42214 1 0.42 7.7 % + Force_Stress_LCAO getForceStress 0.42211 1 0.42 7.7 % + Force_LCAO_gamma ftable_gamma 0.22446 1 0.22 4.1 % + Force_LCAO_gamma cal_fvl_dphi 0.21705 1 0.22 4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:33 2022 + FINISH Time : Wed Sep 28 11:12:39 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/41/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..8de418d40ec2d98e5e12afc9cfb284e3c434db88 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.46334 0.693549 0.00645873 +H 0.522787 0.668307 0.0221648 +H 0.425811 0.650978 0.967887 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f5443aa1488e99ae1784229a32193e95ac5ace53 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.7975 2 + 2 -13.1319 2 + 3 -8.62655 2 + 4 -6.62179 2 + 5 0.975626 0 + 6 4.01119 0 + 7 11.1737 0 + 8 11.3837 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9f66e4f6a02c30a3ebbb8576f9521a315b7bfad7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:45 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.9735323841 19.4193847716 0.180844449686 0 0 0 0 + tauc_H1 14.6380398175 18.7126061884 0.620614703417 0 0 0 0 + tauc_H2 11.9227114278 18.2273926542 27.1008475198 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0995762492909 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.099934393714 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118017053737 (SEC) + + DONE : INIT CHARGE Time : 0.161008872275 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.442049 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 0 9 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000901 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000936 + + Density error is 0.213613007263 + + Energy Rydberg eV + E_KohnSham -34.1853901006 -465.116093721 + E_Harris -34.3734315422 -467.674528787 + E_Fermi -0.383547826659 -5.21843589807 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000996163211617 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00096220372374 + + Density error is 0.0994566191674 + + Energy Rydberg eV + E_KohnSham -34.2741545248 -466.32379567 + E_Harris -34.2812391184 -466.42018651 + E_Fermi -0.192750509607 -2.62250522306 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000947575620716 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000914207553198 + + Density error is 0.0641342991877 + + Energy Rydberg eV + E_KohnSham -34.2745352978 -466.328976353 + E_Harris -34.2790211888 -466.390010031 + E_Fermi -0.185983880888 -2.53044051623 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000874851781478 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000827561849066 + + Density error is 0.00223972823908 + + Energy Rydberg eV + E_KohnSham -34.274449791 -466.327812973 + E_Harris -34.2744581836 -466.327927159 + E_Fermi -0.151316075528 -2.05876082617 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000873343815992 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00082328056244 + + Density error is 0.000892903565328 + + Energy Rydberg eV + E_KohnSham -34.2744252125 -466.327478565 + E_Harris -34.2744252977 -466.327479723 + E_Fermi -0.150971650367 -2.05407468146 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000872429923788 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000822020995951 + + Density error is 0.000210746217485 + + Energy Rydberg eV + E_KohnSham -34.2744374488 -466.327645048 + E_Harris -34.2744376009 -466.327647118 + E_Fermi -0.15057789705 -2.04871739274 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000872541567817 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000822023223726 + + Density error is 2.5406730283e-05 + + Energy Rydberg eV + E_KohnSham -34.274434122 -466.327599785 + E_Harris -34.2744341238 -466.32759981 + E_Fermi -0.150537203651 -2.04816373064 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000872483117672 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821976195422 + + Density error is 1.16851121609e-05 + + Energy Rydberg eV + E_KohnSham -34.2744366742 -466.32763451 + E_Harris -34.2744366748 -466.327634518 + E_Fermi -0.150552669512 -2.04837415448 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000872484130599 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821970262235 + + Density error is 2.20396363151e-06 + + Energy Rydberg eV + E_KohnSham -34.2744358041 -466.32762267 + E_Harris -34.2744358041 -466.32762267 + E_Fermi -0.150541316954 -2.048219695 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000872482821225 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821967536298 + + Density error is 5.4069188764e-07 + + Energy Rydberg eV + E_KohnSham -34.2744360145 -466.327625534 + E_Harris -34.2744360145 -466.327625534 + E_Fermi -0.150539921605 -2.0482007103 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000872482893001 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821967866819 + + Density error is 1.96945567597e-07 + + Energy Rydberg eV + E_KohnSham -34.2744360034 -466.327625383 + E_Harris -34.2744360034 -466.327625383 + E_Fermi -0.150539664889 -2.0481972175 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000872482870269 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000821967867879 + + Density error is 1.00139076896e-08 + + Energy Rydberg eV + E_KohnSham -34.2744360064 -466.327625424 + E_Harris -34.2744360064 -466.327625424 + E_band -7.81698562014 -106.355545618 + E_one_elec -68.5596526302 -932.801928671 + E_Hartree +35.7140729386 +485.914890753 + E_xc -8.15652484879 -110.975213822 + E_Ewald +6.85355287938 +93.2473707039 + E_demet -2.65506257009e-56 -3.61239794997e-55 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19324164217 -2.62918742439 + E_Fermi -0.150539474482 -2.04819462688 + + charge density convergence is achieved + final etot is -466.327625424 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.7975 2.00000 + 2 -13.1319 2.00000 + 3 -8.62655 2.00000 + 4 -6.62179 2.00000 + 5 0.975626 0.00000 + 6 4.01119 0.00000 + 7 11.1737 0.00000 + 8 11.3837 0.00000 + + EFERMI = -2.048194626883414 eV + OUT.ABACUS/ final etot is -466.3276254237630 eV + correction force for each atom along direction 1 is -1.13151e-05 + correction force for each atom along direction 2 is -1.22041e-05 + correction force for each atom along direction 3 is 6.84193e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.86791497 -0.46432005 -0.63325386 + H1 -0.68761096 -0.32383559 -0.48520358 + H2 +1.5555259 +0.78815565 +1.1184574 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3276254237630 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3489 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3393 1 7.3 1.e+02% + Potential init_pot 0.28263 2 0.14 3.8% + PW_Basis recip2real 0.30002 17 0.018 4.1% + PW_Basis gathers_scatterp 0.12769 17 0.0075 1.7% + Potential v_of_rho 1.0783 14 0.077 15.% + XC_Functional v_xc 0.30294 15 0.020 4.1% + H_Hartree_pw v_hartree 0.72822 14 0.052 9.9% + PW_Basis real2recip 0.76292 41 0.019 10.% + PW_Basis gatherp_scatters 0.30135 41 0.0073 4.1% + ORB_control set_orb_tables 1.0995 1 1.1 15.% + ORB_gen_tables gen_tables 1.0995 1 1.1 15.% + ORB_table_phi init_Table 0.47510 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.46993 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18621 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18465 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24919 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24722 66 0.0037 3.4% + LOOP_ions opt_ions 5.7211 1 5.7 78.% + ESolver_KS_LCAO Run 5.1718 1 5.2 70.% + HSolverLCAO solve 2.4922 12 0.21 34.% + HamiltLCAO updateHk 1.3027 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2729 12 0.11 17.% + Gint_interface cal_gint 2.2785 25 0.091 31.% + Gint_Gamma distri_vl 2.6970 6 0.45 37.% + LCAO_Deepks cal_projected_DM 5.5680 14 0.40 76.% + LCAO_gen_fixedH add_v_delta 2.5497 6 0.42 35.% + LCAO_DESCRIPTOR add_v_delta 2.5497 6 0.42 35.% + ElecStateLCAO psiToRho 1.1710 12 0.098 16.% + Charge mix_rho 0.99016 11 0.090 13.% + LOOP_ions force_stress 0.54904 1 0.55 7.5% + Force_Stress_LCAO getForceStress 0.54901 1 0.55 7.5% + Force_LCAO_gamma ftable_gamma 0.33035 1 0.33 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.32210 1 0.32 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:45 2022 + Finish Time : Wed Sep 28 11:05:53 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8b15a8fc03756127a447e8958b8e82127307bf8e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012331 ima = 3.65212e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012450142601 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001132809528 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113984280962 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114145514072 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114135205622 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114143528536 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114139677175 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114141341681 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114140793041 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114140804044 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00114140785757 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011414077565 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7e502c99154e783f5716a7a1c3a3f7036a4e40cc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.026467615972 19.419384771567 0.180844449695 0 0 0 +H +0.0 +2 +-13.361960182501 18.712606188359 0.620614703398 0 0 0 +-16.077288572214 18.227392654213 -0.899152480268 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/conv new file mode 100644 index 0000000000000000000000000000000000000000..54a289566abdd15ca324d79e8ab5de9756de5018 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/conv @@ -0,0 +1 @@ +42 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..653a37e7f1e13f158fb38ff7d1ae709313f2159b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.741851408 0.01223813413 1.246957432 1.352836273 1.467075611 0.007163176847 0.02054385996 0.0388207364 +2.575966356e-18 0.0009858686385 0.002064314965 0.01130797266 0.03753683629 -3.149957539e-19 1.002060493e-06 3.475949417e-06 +0.001822575248 0.005339071489 + +H atom_index 1 n_descriptor 18 +1.214974713 0.03473111406 0.09708202926 0.1373018243 0.3138301127 0.02000817994 0.02667285455 0.0380551761 +1.689509443e-17 2.759145695e-05 0.090903462 0.1143163103 0.1174524714 -1.951954997e-19 4.716140714e-06 0.01320979286 +0.02409246818 0.02933653453 + +H atom_index 2 n_descriptor 18 +1.166825443 0.03627793176 0.08306871501 0.1180506993 0.2963357192 0.01792988645 0.02389520885 0.04007761935 +2.962151307e-17 2.456030569e-05 0.07840330848 0.1004756447 0.1125516238 4.469679292e-18 5.584693762e-06 0.01460626554 +0.02210388319 0.02681409898 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..37f8b47e5737a2043d2c50b2225e0a3343a4fc63 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:45 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0995986 SEC) : SETUP UNITCELL + DONE(0.0999487 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118037 SEC) : INIT PLANEWAVE + DONE(0.161142 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.442114 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651161e+02 0.000000e+00 2.136e-01 5.283e-01 + GE2 -4.663238e+02 -1.207702e+00 9.946e-02 4.909e-01 + GE3 -4.663290e+02 -5.180682e-03 6.413e-02 5.583e-01 + GE4 -4.663278e+02 1.163380e-03 2.240e-03 4.173e-01 + GE5 -4.663275e+02 3.344083e-04 8.929e-04 4.182e-01 + GE6 -4.663276e+02 -1.664834e-04 2.107e-04 4.103e-01 + GE7 -4.663276e+02 4.526298e-05 2.541e-05 3.962e-01 + GE8 -4.663276e+02 -3.472462e-05 1.169e-05 3.931e-01 + GE9 -4.663276e+02 1.183929e-05 2.204e-06 3.934e-01 + GE10 -4.663276e+02 -2.863891e-06 5.407e-07 3.918e-01 + GE11 -4.663276e+02 1.516441e-07 1.969e-07 3.941e-01 + GE12 -4.663276e+02 -4.115473e-08 1.001e-08 3.175e-01 +E_delta_band = -6.73572967e-02 Ry = -9.16443037e-01 eV +E_delta_NN= -1.93241642e-01 Ry = -2.62918742e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3489 11 0.67 1e+02 % + Run_lcao lcao_line 7.3393 1 7.3 1e+02 % + Potential init_pot 0.28263 2 0.14 3.8 % + PW_Basis recip2real 0.30002 17 0.018 4.1 % + PW_Basis gathers_scatterp 0.12769 17 0.0075 1.7 % + Potential v_of_rho 1.0783 14 0.077 15 % + XC_Functional v_xc 0.30294 15 0.02 4.1 % + H_Hartree_pw v_hartree 0.72822 14 0.052 9.9 % + PW_Basis real2recip 0.76292 41 0.019 10 % + PW_Basis gatherp_scatters 0.30135 41 0.0073 4.1 % + ORB_control set_orb_tables 1.0995 1 1.1 15 % + ORB_gen_tables gen_tables 1.0995 1 1.1 15 % + ORB_table_phi init_Table 0.4751 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.46993 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18621 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18465 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24919 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24722 66 0.0037 3.4 % + LOOP_ions opt_ions 5.7211 1 5.7 78 % + ESolver_KS_LCAO Run 5.1718 1 5.2 70 % + HSolverLCAO solve 2.4922 12 0.21 34 % + HamiltLCAO updateHk 1.3027 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.2729 12 0.11 17 % + Gint_interface cal_gint 2.2785 25 0.091 31 % + Gint_Gamma distri_vl 2.697 6 0.45 37 % + LCAO_Deepks cal_projected_DM 5.568 14 0.4 76 % + LCAO_gen_fixedH add_v_delta 2.5497 6 0.42 35 % + LCAO_DESCRIPTOR add_v_delta 2.5497 6 0.42 35 % + ElecStateLCAO psiToRho 1.171 12 0.098 16 % + Charge mix_rho 0.99016 11 0.09 13 % + LOOP_ions force_stress 0.54904 1 0.55 7.5 % + Force_Stress_LCAO getForceStress 0.54901 1 0.55 7.5 % + Force_LCAO_gamma ftable_gamma 0.33035 1 0.33 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.3221 1 0.32 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:45 2022 + FINISH Time : Wed Sep 28 11:05:53 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/42/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..2175c5b0766ae43e8a5532997a0104c5f3c9f2a0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.451644 0.691316 0.997519 +H 0.442551 0.757904 0.00633156 +H 0.516003 0.695722 0.00345681 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..14f27d41c720e50bc20fb34e1d17d0c25ddcb9c5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4008 2 + 2 -12.3692 2 + 3 -9.67375 2 + 4 -6.77159 2 + 5 1.08046 0 + 6 4.20196 0 + 7 11.0864 0 + 8 11.3882 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d5763fbbbe0ed25fadc4c4ca33c984d14d42f1bf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:45 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.6460403853 19.3568415582 27.9305437866 0 0 0 0 + tauc_H1 12.3914158561 21.2213179358 0.177283747995 0 0 0 0 + tauc_H2 14.4480701765 19.4802280051 0.0967907123413 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0745859706831 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0765554593806 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0927768484556 (SEC) + + DONE : INIT CHARGE Time : 0.134128794011 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.376449 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0006 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00196 + + Density error is 0.211055079637 + + Energy Rydberg eV + E_KohnSham -34.1855767914 -465.11863378 + E_Harris -34.3710891406 -467.642658778 + E_Fermi -0.40013353366 -5.44409601865 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000931656579829 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00152927665365 + + Density error is 0.097531378134 + + Energy Rydberg eV + E_KohnSham -34.2735233698 -466.315208365 + E_Harris -34.2805867722 -466.411310886 + E_Fermi -0.21228005085 -2.8882182633 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000890967357045 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00139579838891 + + Density error is 0.0627597241914 + + Energy Rydberg eV + E_KohnSham -34.2738730503 -466.319966013 + E_Harris -34.2784408689 -466.382114374 + E_Fermi -0.203361214681 -2.76687127187 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000852545969098 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114732424492 + + Density error is 0.00189845061092 + + Energy Rydberg eV + E_KohnSham -34.2738077445 -466.319077481 + E_Harris -34.2738079317 -466.319080028 + E_Fermi -0.167400113847 -2.27759539417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000856970626777 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114811200996 + + Density error is 0.000888493803202 + + Energy Rydberg eV + E_KohnSham -34.2737679731 -466.318536364 + E_Harris -34.2737688574 -466.318548396 + E_Fermi -0.167349868483 -2.27691177092 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000856043494224 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114476328403 + + Density error is 0.000120382417242 + + Energy Rydberg eV + E_KohnSham -34.2737904508 -466.318842189 + E_Harris -34.2737904675 -466.318842416 + E_Fermi -0.167036054107 -2.27264210729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000855789316172 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114430255619 + + Density error is 3.18247023807e-05 + + Energy Rydberg eV + E_KohnSham -34.2737849585 -466.318767463 + E_Harris -34.2737849605 -466.31876749 + E_Fermi -0.166960079 -2.27160841293 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000855726428658 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114423603323 + + Density error is 1.54643558474e-05 + + Energy Rydberg eV + E_KohnSham -34.2737862071 -466.31878445 + E_Harris -34.2737862083 -466.318784466 + E_Fermi -0.166973668045 -2.27179330137 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000855741170987 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114421797888 + + Density error is 1.99875344121e-06 + + Energy Rydberg eV + E_KohnSham -34.2737850268 -466.318768391 + E_Harris -34.2737850268 -466.318768391 + E_Fermi -0.166959731731 -2.27160368809 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000855744722031 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114421621419 + + Density error is 7.86517926598e-07 + + Energy Rydberg eV + E_KohnSham -34.2737853163 -466.31877233 + E_Harris -34.2737853163 -466.31877233 + E_Fermi -0.166959240878 -2.2715970097 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000855746059794 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114421520711 + + Density error is 1.71948749996e-07 + + Energy Rydberg eV + E_KohnSham -34.2737853214 -466.318772399 + E_Harris -34.2737853214 -466.318772399 + E_Fermi -0.166958656502 -2.27158905885 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000855746166968 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114421469459 + + Density error is 1.2433902281e-08 + + Energy Rydberg eV + E_KohnSham -34.2737853329 -466.318772556 + E_Harris -34.2737853329 -466.318772556 + E_band -7.96949728108 -108.430573218 + E_one_elec -69.0866582577 -939.972208084 + E_Hartree +35.9238128865 +488.768549142 + E_xc -8.19065911455 -111.439634334 + E_Ewald +7.20439431337 +98.0208133007 + E_demet -1.41259085194e-68 -1.9219284529e-67 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194498056155 -2.64628181363 + E_Fermi -0.166958468559 -2.27158650176 + + charge density convergence is achieved + final etot is -466.318772556 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4008 2.00000 + 2 -12.3692 2.00000 + 3 -9.67375 2.00000 + 4 -6.77159 2.00000 + 5 1.08046 0.00000 + 6 4.20196 0.00000 + 7 11.0864 0.00000 + 8 11.3882 0.00000 + + EFERMI = -2.271586501757546 eV + OUT.ABACUS/ final etot is -466.3187725556857 eV + correction force for each atom along direction 1 is 0.000114143 + correction force for each atom along direction 2 is 0.000114047 + correction force for each atom along direction 3 is 0.000173135 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.48587909 +1.8732039 +0.23629323 + H1 -0.73749504 -1.0466285 -0.21477576 + H2 +1.2233741 -0.82657544 -0.021517468 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3187725556857 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.7205 11 0.52 1.0e+02% + Run_lcao lcao_line 5.7116 1 5.7 1.e+02% + Potential init_pot 0.23920 2 0.12 4.2% + PW_Basis recip2real 0.26414 17 0.016 4.6% + PW_Basis gathers_scatterp 0.11033 17 0.0065 1.9% + Potential v_of_rho 0.96601 14 0.069 17.% + XC_Functional v_xc 0.28097 15 0.019 4.9% + H_Hartree_pw v_hartree 0.64174 14 0.046 11.% + PW_Basis real2recip 0.64632 41 0.016 11.% + PW_Basis gatherp_scatters 0.24042 41 0.0059 4.2% + ORB_control set_orb_tables 0.89718 1 0.90 16.% + ORB_gen_tables gen_tables 0.89718 1 0.90 16.% + ORB_table_phi init_Table 0.37376 1 0.37 6.5% + ORB_table_phi cal_ST_Phi12_R 0.36960 126 0.0029 6.5% + ORB_table_beta init_Table_Beta 0.15664 1 0.16 2.7% + ORB_table_beta VNL_PhiBeta_R 0.15531 56 0.0028 2.7% + ORB_table_alpha init_Table_Alpha 0.20870 1 0.21 3.6% + ORB_table_alpha S_PhiAlpha_R 0.20706 66 0.0031 3.6% + LOOP_ions opt_ions 4.3677 1 4.4 76.% + ESolver_KS_LCAO Run 3.9445 1 3.9 69.% + HSolverLCAO solve 1.6130 12 0.13 28.% + HamiltLCAO updateHk 0.89824 12 0.075 16.% + LCAO_Hamilt cal_Hgamma 0.86325 12 0.072 15.% + Gint_interface cal_gint 1.3650 25 0.055 24.% + Gint_Gamma distri_vl 2.0646 6 0.34 36.% + LCAO_Deepks cal_projected_DM 4.2471 14 0.30 74.% + LCAO_gen_fixedH add_v_delta 1.9349 6 0.32 34.% + LCAO_DESCRIPTOR add_v_delta 1.9349 6 0.32 34.% + ElecStateLCAO psiToRho 0.69748 12 0.058 12.% + Charge mix_rho 0.82288 11 0.075 14.% + LOOP_ions force_stress 0.42301 1 0.42 7.4% + Force_Stress_LCAO getForceStress 0.42297 1 0.42 7.4% + Force_LCAO_gamma ftable_gamma 0.22840 1 0.23 4.0% + Force_LCAO_gamma cal_fvl_dphi 0.22097 1 0.22 3.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:45 2022 + Finish Time : Wed Sep 28 11:13:51 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..61793277627ab6c7e7aefd62f5f7fb4b23c6cb1b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124007 ima = 3.65874e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012240521045 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111056037505 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111776295436 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112022724911 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111988187847 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112004816244 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112004213798 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112006362709 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112005546352 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112005497801 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112005460218 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112005451012 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/STRU new file mode 100644 index 0000000000000000000000000000000000000000..401bceefbd01dfd51028d0e1039004358ec08294 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.353959614728 19.356841558222 -0.069456213423 0 0 0 +H +0.0 +2 +-15.608584143939 21.221317935775 0.177283747985 0 0 0 +-13.551929823532 19.480228005054 0.096790712342 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/conv new file mode 100644 index 0000000000000000000000000000000000000000..468f29ad8b25a18a4eb168f215ce0aa7fbb9e1fb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/conv @@ -0,0 +1 @@ +43 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b10008c078dc8de3fc151e0d67ef4188a766f579 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.757912463 0.01279545626 1.257421593 1.3391177 1.46961896 0.01031731125 0.01519044966 0.03929704869 +-5.790376799e-19 0.0007319383202 0.002957344268 0.01405427367 0.0462688732 1.73293853e-19 3.135202298e-06 8.393144809e-06 +0.001603263644 0.006149804428 + +H atom_index 1 n_descriptor 18 +1.201515864 0.03695891081 0.09859681952 0.1285017641 0.3015039525 0.02171175743 0.02536815016 0.04031066994 +-7.314986442e-18 4.265927668e-05 0.09213195966 0.1096491099 0.1131052082 2.464372463e-18 3.921314246e-06 0.01451080205 +0.02558664102 0.02830983828 + +H atom_index 2 n_descriptor 18 +1.266955609 0.0348684107 0.1216793818 0.1579605101 0.3246985425 0.02511407003 0.02923590318 0.03803619234 +-2.472214269e-18 4.802252353e-05 0.1062046519 0.1186059902 0.1351912785 1.024696378e-18 9.191004496e-07 0.01347020786 +0.02811994056 0.03151182781 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..df22d02dde62e5f726421c6c2bba6b4b8e309770 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:45 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0746019 SEC) : SETUP UNITCELL + DONE(0.076565 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0927906 SEC) : INIT PLANEWAVE + DONE(0.134231 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.376497 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651186e+02 0.000000e+00 2.111e-01 4.214e-01 + GE2 -4.663152e+02 -1.196575e+00 9.753e-02 3.783e-01 + GE3 -4.663200e+02 -4.757648e-03 6.276e-02 4.392e-01 + GE4 -4.663191e+02 8.885316e-04 1.898e-03 3.147e-01 + GE5 -4.663185e+02 5.411177e-04 8.885e-04 3.162e-01 + GE6 -4.663188e+02 -3.058253e-04 1.204e-04 3.113e-01 + GE7 -4.663188e+02 7.472649e-05 3.182e-05 2.935e-01 + GE8 -4.663188e+02 -1.698756e-05 1.546e-05 3.004e-01 + GE9 -4.663188e+02 1.605884e-05 1.999e-06 2.938e-01 + GE10 -4.663188e+02 -3.938953e-06 7.865e-07 2.978e-01 + GE11 -4.663188e+02 -6.923746e-08 1.719e-07 2.964e-01 + GE12 -4.663188e+02 -1.562502e-07 1.243e-08 2.273e-01 +E_delta_band = -6.98228957e-02 Ry = -9.49989232e-01 eV +E_delta_NN= -1.94498056e-01 Ry = -2.64628181e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.7205 11 0.52 1e+02 % + Run_lcao lcao_line 5.7116 1 5.7 1e+02 % + Potential init_pot 0.2392 2 0.12 4.2 % + PW_Basis recip2real 0.26414 17 0.016 4.6 % + PW_Basis gathers_scatterp 0.11033 17 0.0065 1.9 % + Potential v_of_rho 0.96601 14 0.069 17 % + XC_Functional v_xc 0.28097 15 0.019 4.9 % + H_Hartree_pw v_hartree 0.64174 14 0.046 11 % + PW_Basis real2recip 0.64632 41 0.016 11 % + PW_Basis gatherp_scatters 0.24042 41 0.0059 4.2 % + ORB_control set_orb_tables 0.89718 1 0.9 16 % + ORB_gen_tables gen_tables 0.89718 1 0.9 16 % + ORB_table_phi init_Table 0.37376 1 0.37 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.3696 126 0.0029 6.5 % + ORB_table_beta init_Table_Beta 0.15664 1 0.16 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.15531 56 0.0028 2.7 % + ORB_table_alpha init_Table_Alpha 0.2087 1 0.21 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.20706 66 0.0031 3.6 % + LOOP_ions opt_ions 4.3677 1 4.4 76 % + ESolver_KS_LCAO Run 3.9445 1 3.9 69 % + HSolverLCAO solve 1.613 12 0.13 28 % + HamiltLCAO updateHk 0.89824 12 0.075 16 % + LCAO_Hamilt cal_Hgamma 0.86325 12 0.072 15 % + Gint_interface cal_gint 1.365 25 0.055 24 % + Gint_Gamma distri_vl 2.0646 6 0.34 36 % + LCAO_Deepks cal_projected_DM 4.2471 14 0.3 74 % + LCAO_gen_fixedH add_v_delta 1.9349 6 0.32 34 % + LCAO_DESCRIPTOR add_v_delta 1.9349 6 0.32 34 % + ElecStateLCAO psiToRho 0.69748 12 0.058 12 % + Charge mix_rho 0.82288 11 0.075 14 % + LOOP_ions force_stress 0.42301 1 0.42 7.4 % + Force_Stress_LCAO getForceStress 0.42297 1 0.42 7.4 % + Force_LCAO_gamma ftable_gamma 0.2284 1 0.23 4 % + Force_LCAO_gamma cal_fvl_dphi 0.22097 1 0.22 3.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:45 2022 + FINISH Time : Wed Sep 28 11:13:51 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/43/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..03f96ad32775de1e1022219b8bd45ccf1ff54623 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.445961 0.697141 0.00871077 +H 0.394768 0.69053 0.97247 +H 0.435902 0.73368 0.0617053 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3fa7de392324c321c2beb906f01dc58269e2f984 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3398 2 + 2 -13.6931 2 + 3 -8.67874 2 + 4 -6.75198 2 + 5 1.50443 0 + 6 4.81153 0 + 7 11.0335 0 + 8 11.2304 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f98fd8c14c40c6f332a98828432f5c139548936e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:04 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.4869003098 19.5199507901 0.243901655143 0 0 0 0 + tauc_H1 11.0534975102 19.3348262249 27.2291511054 0 0 0 0 + tauc_H2 12.2052430817 20.5430507179 1.72774972434 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0734421166528 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0737249738424 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0896119958536 (SEC) + + DONE : INIT CHARGE Time : 0.131266794378 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.380358 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 9 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00109 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000589 + + Density error is 0.219878759459 + + Energy Rydberg eV + E_KohnSham -34.1819655394 -465.069500175 + E_Harris -34.3839707799 -467.817922472 + E_Fermi -0.418751030955 -5.69740006436 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00131716600552 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000794829781254 + + Density error is 0.0978739994014 + + Energy Rydberg eV + E_KohnSham -34.2744997121 -466.328492183 + E_Harris -34.2809967574 -466.41688902 + E_Fermi -0.223199572046 -3.03678597098 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00125314280069 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00077331527227 + + Density error is 0.0625036764526 + + Energy Rydberg eV + E_KohnSham -34.2747906607 -466.332450743 + E_Harris -34.2789071581 -466.388458564 + E_Fermi -0.20898497652 -2.84338647707 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00115198229673 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000748950784166 + + Density error is 0.00221021580212 + + Energy Rydberg eV + E_KohnSham -34.2748369456 -466.333080482 + E_Harris -34.2748418489 -466.333147193 + E_Fermi -0.173738823588 -2.36383796462 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00115094247478 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000749246435935 + + Density error is 0.000895390486903 + + Energy Rydberg eV + E_KohnSham -34.2747660249 -466.332115556 + E_Harris -34.2747675739 -466.33213663 + E_Fermi -0.17247611179 -2.34665788922 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00114976094633 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00074868590901 + + Density error is 0.000242271038617 + + Energy Rydberg eV + E_KohnSham -34.274811524 -466.332734603 + E_Harris -34.274811718 -466.332737242 + E_Fermi -0.172738352396 -2.35022585572 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00114999141378 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000749053165933 + + Density error is 4.65211923622e-05 + + Energy Rydberg eV + E_KohnSham -34.2747928517 -466.332480552 + E_Harris -34.2747928633 -466.332480711 + E_Fermi -0.172493604478 -2.34689588946 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00114991766764 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000748974388024 + + Density error is 1.98019844252e-05 + + Energy Rydberg eV + E_KohnSham -34.2747995437 -466.332571602 + E_Harris -34.2747995451 -466.332571621 + E_Fermi -0.17255108098 -2.34767789739 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0011498970095 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000748975101832 + + Density error is 2.95666910827e-06 + + Energy Rydberg eV + E_KohnSham -34.2747980079 -466.332550707 + E_Harris -34.274798008 -466.332550707 + E_Fermi -0.172531031315 -2.34740510769 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00114989683793 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000748977832832 + + Density error is 3.47078604863e-07 + + Energy Rydberg eV + E_KohnSham -34.2747982161 -466.332553539 + E_Harris -34.2747982161 -466.332553539 + E_Fermi -0.172527812802 -2.34736131758 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00114989700646 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000748978077262 + + Density error is 1.81974726713e-07 + + Energy Rydberg eV + E_KohnSham -34.2747982617 -466.33255416 + E_Harris -34.2747982617 -466.33255416 + E_Fermi -0.172527781492 -2.34736089158 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00114989703702 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000748978277899 + + Density error is 9.04596131464e-09 + + Energy Rydberg eV + E_KohnSham -34.2747982599 -466.332554135 + E_Harris -34.2747982599 -466.332554135 + E_band -8.00599607053 -108.927164725 + E_one_elec -69.7337256343 -948.776011395 + E_Hartree +36.2653195624 +493.414985839 + E_xc -8.24552482811 -112.186120663 + E_Ewald +7.56263811589 +102.894970288 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195392782543 -2.65845519066 + E_Fermi -0.172527605657 -2.34735849923 + + charge density convergence is achieved + final etot is -466.332554135 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3398 2.00000 + 2 -13.6931 2.00000 + 3 -8.67874 2.00000 + 4 -6.75198 2.00000 + 5 1.50443 0.00000 + 6 4.81153 0.00000 + 7 11.0335 0.00000 + 8 11.2304 0.00000 + + EFERMI = -2.347358499231219 eV + OUT.ABACUS/ final etot is -466.3325541349736 eV + correction force for each atom along direction 1 is -0.000106082 + correction force for each atom along direction 2 is -8.47152e-05 + correction force for each atom along direction 3 is -2.44834e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +2.6370270 -0.34671260 +0.78335617 + H1 -2.0325627 +0.13058785 -0.81822507 + H2 -0.60446433 +0.21612475 +0.034868901 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3325541349736 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2579 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2502 1 6.3 1.e+02% + Potential init_pot 0.24874 2 0.12 4.0% + PW_Basis recip2real 0.28906 17 0.017 4.6% + PW_Basis gathers_scatterp 0.12043 17 0.0071 1.9% + Potential v_of_rho 1.0086 14 0.072 16.% + XC_Functional v_xc 0.29417 15 0.020 4.7% + H_Hartree_pw v_hartree 0.67116 14 0.048 11.% + PW_Basis real2recip 0.66206 41 0.016 11.% + PW_Basis gatherp_scatters 0.24828 41 0.0061 4.0% + ORB_control set_orb_tables 0.89850 1 0.90 14.% + ORB_gen_tables gen_tables 0.89849 1 0.90 14.% + ORB_table_phi init_Table 0.37561 1 0.38 6.0% + ORB_table_phi cal_ST_Phi12_R 0.37130 126 0.0029 5.9% + ORB_table_beta init_Table_Beta 0.15425 1 0.15 2.5% + ORB_table_beta VNL_PhiBeta_R 0.15293 56 0.0027 2.4% + ORB_table_alpha init_Table_Alpha 0.21049 1 0.21 3.4% + ORB_table_alpha S_PhiAlpha_R 0.20883 66 0.0032 3.3% + LOOP_ions opt_ions 4.9016 1 4.9 78.% + ESolver_KS_LCAO Run 4.4129 1 4.4 71.% + HSolverLCAO solve 2.0278 12 0.17 32.% + HamiltLCAO updateHk 1.0781 12 0.090 17.% + LCAO_Hamilt cal_Hgamma 1.0448 12 0.087 17.% + Gint_interface cal_gint 1.8357 25 0.073 29.% + Gint_Gamma distri_vl 2.3079 6 0.38 37.% + LCAO_Deepks cal_projected_DM 4.7705 14 0.34 76.% + LCAO_gen_fixedH add_v_delta 2.1796 6 0.36 35.% + LCAO_DESCRIPTOR add_v_delta 2.1796 6 0.36 35.% + ElecStateLCAO psiToRho 0.93239 12 0.078 15.% + Charge mix_rho 0.83795 11 0.076 13.% + LOOP_ions force_stress 0.48855 1 0.49 7.8% + Force_Stress_LCAO getForceStress 0.48852 1 0.49 7.8% + Force_LCAO_gamma ftable_gamma 0.28551 1 0.29 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.27809 1 0.28 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:04 2022 + Finish Time : Wed Sep 28 11:12:10 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d6b8446726301600740bea295ea712a406b0d0ff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123637 ima = 3.6649e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123903465955 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113201060765 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113572664605 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113833534523 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113773228648 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113810141086 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113797422711 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113800583953 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113799929252 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113799815756 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113799811565 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113799803181 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/STRU new file mode 100644 index 0000000000000000000000000000000000000000..10466bcb40f3f7a2f599e798beeb731a3eaddf94 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.513099690230 19.519950790099 0.243901655129 0 0 0 +H +0.0 +2 +-16.946502489798 19.334826224871 -0.770848894628 0 0 0 +-15.794756918328 20.543050717926 1.727749724351 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/conv new file mode 100644 index 0000000000000000000000000000000000000000..719879f30289eee388c8f7290dcc3a8f114ad2a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/conv @@ -0,0 +1 @@ +44 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..89e68a0ef566eb35b5d7a3e4f9e37647d9bb5e3c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.740626231 0.01266271248 1.298243569 1.390457421 1.46983004 0.007415639002 0.02188597008 0.03878668248 +-1.542887678e-18 0.001273699964 0.002321720032 0.01308978268 0.04263505279 -2.025991458e-19 1.40096051e-06 4.566402355e-06 +0.001889826858 0.005369274156 + +H atom_index 1 n_descriptor 18 +1.289649512 0.03184282321 0.1248319505 0.1719227018 0.3352646251 0.02349421055 0.03086107042 0.03570528839 +-4.1487879e-17 3.935808891e-05 0.1080629367 0.1219010905 0.1476221631 4.656922611e-19 2.191580859e-06 0.01309542975 +0.02776676671 0.03252922254 + +H atom_index 2 n_descriptor 18 +1.242815571 0.03346424017 0.107780013 0.1491368026 0.3221074003 0.02159971758 0.02821329503 0.03660934276 +2.629704258e-17 3.581531633e-05 0.1022292197 0.1144377184 0.1281720252 6.027173333e-18 4.294758575e-06 0.0127530513 +0.02617020856 0.03067770113 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..1a2234915b057d31be9fdba067047480e89c5e6a Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:04 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0734571 SEC) : SETUP UNITCELL + DONE(0.0737341 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0896261 SEC) : INIT PLANEWAVE + DONE(0.131371 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.380401 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650695e+02 0.000000e+00 2.199e-01 4.538e-01 + GE2 -4.663285e+02 -1.258992e+00 9.787e-02 4.202e-01 + GE3 -4.663325e+02 -3.958560e-03 6.250e-02 4.799e-01 + GE4 -4.663331e+02 -6.297386e-04 2.210e-03 3.566e-01 + GE5 -4.663321e+02 9.649256e-04 8.954e-04 3.555e-01 + GE6 -4.663327e+02 -6.190470e-04 2.423e-04 3.491e-01 + GE7 -4.663325e+02 2.540506e-04 4.652e-05 3.422e-01 + GE8 -4.663326e+02 -9.104942e-05 1.980e-05 3.313e-01 + GE9 -4.663326e+02 2.089500e-05 2.957e-06 3.337e-01 + GE10 -4.663326e+02 -2.831944e-06 3.471e-07 3.352e-01 + GE11 -4.663326e+02 -6.214230e-07 1.820e-07 3.362e-01 + GE12 -4.663326e+02 2.524060e-08 9.046e-09 2.658e-01 +E_delta_band = -7.18873067e-02 Ry = -9.78076985e-01 eV +E_delta_NN= -1.95392783e-01 Ry = -2.65845519e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2579 11 0.57 1e+02 % + Run_lcao lcao_line 6.2502 1 6.3 1e+02 % + Potential init_pot 0.24874 2 0.12 4 % + PW_Basis recip2real 0.28906 17 0.017 4.6 % + PW_Basis gathers_scatterp 0.12043 17 0.0071 1.9 % + Potential v_of_rho 1.0086 14 0.072 16 % + XC_Functional v_xc 0.29417 15 0.02 4.7 % + H_Hartree_pw v_hartree 0.67116 14 0.048 11 % + PW_Basis real2recip 0.66206 41 0.016 11 % + PW_Basis gatherp_scatters 0.24828 41 0.0061 4 % + ORB_control set_orb_tables 0.8985 1 0.9 14 % + ORB_gen_tables gen_tables 0.89849 1 0.9 14 % + ORB_table_phi init_Table 0.37561 1 0.38 6 % + ORB_table_phi cal_ST_Phi12_R 0.3713 126 0.0029 5.9 % + ORB_table_beta init_Table_Beta 0.15425 1 0.15 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.15293 56 0.0027 2.4 % + ORB_table_alpha init_Table_Alpha 0.21049 1 0.21 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.20883 66 0.0032 3.3 % + LOOP_ions opt_ions 4.9016 1 4.9 78 % + ESolver_KS_LCAO Run 4.4129 1 4.4 71 % + HSolverLCAO solve 2.0278 12 0.17 32 % + HamiltLCAO updateHk 1.0781 12 0.09 17 % + LCAO_Hamilt cal_Hgamma 1.0448 12 0.087 17 % + Gint_interface cal_gint 1.8357 25 0.073 29 % + Gint_Gamma distri_vl 2.3079 6 0.38 37 % + LCAO_Deepks cal_projected_DM 4.7705 14 0.34 76 % + LCAO_gen_fixedH add_v_delta 2.1796 6 0.36 35 % + LCAO_DESCRIPTOR add_v_delta 2.1796 6 0.36 35 % + ElecStateLCAO psiToRho 0.93239 12 0.078 15 % + Charge mix_rho 0.83795 11 0.076 13 % + LOOP_ions force_stress 0.48855 1 0.49 7.8 % + Force_Stress_LCAO getForceStress 0.48852 1 0.49 7.8 % + Force_LCAO_gamma ftable_gamma 0.28551 1 0.29 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.27809 1 0.28 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:04 2022 + FINISH Time : Wed Sep 28 11:12:10 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/44/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5af5917c9b173027bb5d14332abdc27301bfee78 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.437876 0.701596 0.0064947 +H 0.429742 0.648467 0.964374 +H 0.421054 0.668817 0.0615378 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..77a6c8e9f7978037c7b86bd5d1844c44d307a838 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.173 2 + 2 -12.3765 2 + 3 -9.52016 2 + 4 -6.72529 2 + 5 0.989158 0 + 6 3.9469 0 + 7 11.1281 0 + 8 11.417 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..675a55e087cee24821e3ea6e006546abcbc1a10e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:28 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.2605394295 19.6446805142 0.181851546906 0 0 0 0 + tauc_H1 12.0327640931 18.1570666486 27.0024843174 0 0 0 0 + tauc_H2 11.78951189 18.7268843059 1.72305869959 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0859741556038 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0962772783022 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.11438415712 (SEC) + + DONE : INIT CHARGE Time : 0.163755519763 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.444784 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 9 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000826 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000978 + + Density error is 0.20963998681 + + Energy Rydberg eV + E_KohnSham -34.1895289593 -465.172405783 + E_Harris -34.3710672869 -467.642361443 + E_Fermi -0.388719408161 -5.28879887418 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000982220251189 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129432065443 + + Density error is 0.0980335673408 + + Energy Rydberg eV + E_KohnSham -34.2761228274 -466.3505758 + E_Harris -34.2832921506 -466.448119446 + E_Fermi -0.20229393833 -2.75235023215 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000929487875222 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123719491016 + + Density error is 0.0631997481616 + + Energy Rydberg eV + E_KohnSham -34.2765078842 -466.355814767 + E_Harris -34.281117989 -466.418538461 + E_Fermi -0.195255133563 -2.65658238021 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000859367062536 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117347858702 + + Density error is 0.00185687887092 + + Energy Rydberg eV + E_KohnSham -34.276406265 -466.354432166 + E_Harris -34.2764054703 -466.354421354 + E_Fermi -0.159721618842 -2.17312411004 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00086134692615 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117631183331 + + Density error is 0.000890435720067 + + Energy Rydberg eV + E_KohnSham -34.2763793519 -466.354065996 + E_Harris -34.2763802796 -466.354078617 + E_Fermi -0.159884132689 -2.17533522435 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000860251995204 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117514328989 + + Density error is 0.000110874505463 + + Energy Rydberg eV + E_KohnSham -34.2763917802 -466.35423509 + E_Harris -34.2763917788 -466.354235072 + E_Fermi -0.159388305264 -2.16858914615 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000860261566161 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117511161041 + + Density error is 2.42322481345e-05 + + Energy Rydberg eV + E_KohnSham -34.2763891506 -466.354199313 + E_Harris -34.2763891517 -466.354199329 + E_Fermi -0.159363797291 -2.16825569807 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000860241739791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117506004212 + + Density error is 8.68729907684e-06 + + Energy Rydberg eV + E_KohnSham -34.2763902931 -466.354214858 + E_Harris -34.2763902934 -466.354214862 + E_Fermi -0.159370761196 -2.16835044686 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000860245961596 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117506738911 + + Density error is 2.6688913987e-06 + + Energy Rydberg eV + E_KohnSham -34.2763895861 -466.354205239 + E_Harris -34.2763895861 -466.354205239 + E_Fermi -0.159364203284 -2.16826122189 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000860243695786 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117506548643 + + Density error is 2.24140450408e-07 + + Energy Rydberg eV + E_KohnSham -34.2763896839 -466.35420657 + E_Harris -34.2763896839 -466.35420657 + E_Fermi -0.159361429659 -2.16822348479 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000860244064629 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117506618051 + + Density error is 7.42075160042e-08 + + Energy Rydberg eV + E_KohnSham -34.2763897237 -466.354207112 + E_Harris -34.2763897237 -466.354207112 + E_band -7.90771971856 -107.590046359 + E_one_elec -68.7362139095 -935.204168117 + E_Hartree +35.7625683249 +486.574704333 + E_xc -8.16501861081 -111.090777383 + E_Ewald +6.98766967806 +95.0721233635 + E_demet -3.81942316255e-61 -5.19659180839e-60 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193894590998 -2.63807124895 + E_Fermi -0.159361338408 -2.16822224325 + + charge density convergence is achieved + final etot is -466.354207112 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1730 2.00000 + 2 -12.3765 2.00000 + 3 -9.52016 2.00000 + 4 -6.72529 2.00000 + 5 0.989158 0.00000 + 6 3.94690 0.00000 + 7 11.1281 0.00000 + 8 11.4170 0.00000 + + EFERMI = -2.168222243250430 eV + OUT.ABACUS/ final etot is -466.3542071115209 eV + correction force for each atom along direction 1 is -5.90836e-05 + correction force for each atom along direction 2 is -3.45196e-05 + correction force for each atom along direction 3 is 6.34387e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.41877277 -1.9128062 -0.66709546 + H1 +0.32142816 +1.3837027 +0.35259501 + H2 +0.097344612 +0.52910341 +0.31450045 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3542071115209 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4352 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4255 1 6.4 1.e+02% + Potential init_pot 0.28408 2 0.14 4.4% + PW_Basis recip2real 0.28706 16 0.018 4.5% + PW_Basis gathers_scatterp 0.12433 16 0.0078 1.9% + Potential v_of_rho 1.0007 13 0.077 16.% + XC_Functional v_xc 0.28677 14 0.020 4.5% + H_Hartree_pw v_hartree 0.66884 13 0.051 10.% + PW_Basis real2recip 0.67277 38 0.018 10.% + PW_Basis gatherp_scatters 0.27257 38 0.0072 4.2% + ORB_control set_orb_tables 1.0974 1 1.1 17.% + ORB_gen_tables gen_tables 1.0974 1 1.1 17.% + ORB_table_phi init_Table 0.47654 1 0.48 7.4% + ORB_table_phi cal_ST_Phi12_R 0.47136 126 0.0037 7.3% + ORB_table_beta init_Table_Beta 0.18548 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18393 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.24942 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.24747 66 0.0037 3.8% + LOOP_ions opt_ions 4.8052 1 4.8 75.% + ESolver_KS_LCAO Run 4.2807 1 4.3 67.% + HSolverLCAO solve 1.9716 11 0.18 31.% + HamiltLCAO updateHk 1.0711 11 0.097 17.% + LCAO_Hamilt cal_Hgamma 1.0383 11 0.094 16.% + Gint_interface cal_gint 1.7446 23 0.076 27.% + Gint_Gamma distri_vl 2.0827 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.6606 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9380 6 0.32 30.% + LCAO_DESCRIPTOR add_v_delta 1.9380 6 0.32 30.% + ElecStateLCAO psiToRho 0.88208 11 0.080 14.% + Charge mix_rho 0.77985 10 0.078 12.% + LOOP_ions force_stress 0.52437 1 0.52 8.1% + Force_Stress_LCAO getForceStress 0.52434 1 0.52 8.1% + Force_LCAO_gamma ftable_gamma 0.30464 1 0.30 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.29674 1 0.30 4.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:28 2022 + Finish Time : Wed Sep 28 11:11:34 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..40907747e9f0a895e6f80fa5d2ee11695679576d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/OUT.ABACUS/warning.log @@ -0,0 +1,73 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012343 ima = 3.67065e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122775173691 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111422277732 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112207544258 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112416427764 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112402942103 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112410577971 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112409031965 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112410442571 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112410065234 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011240996121 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112409950677 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3b6333763bc79db97d20638a10ef9080f9d8d0cc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.739460570533 19.644680514164 0.181851546919 0 0 0 +H +0.0 +2 +-15.967235906872 18.157066648610 -0.997515682662 0 0 0 +-16.210488109997 18.726884305867 1.723058699589 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/conv new file mode 100644 index 0000000000000000000000000000000000000000..3353160702e6e877e366fc90b0a77868e99f7027 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/conv @@ -0,0 +1 @@ +45 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..aebef4e870adaa24d28ed9bce38a3fe010b6e6e1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.756380874 0.01262007992 1.246753132 1.328406148 1.468821447 0.009780685988 0.01560815215 0.03928897582 +-1.467623549e-18 0.0007382840874 0.002728527355 0.01287495664 0.04400020506 6.35541097e-20 2.513781955e-06 7.036012267e-06 +0.001568241526 0.006085381869 + +H atom_index 1 n_descriptor 18 +1.189746691 0.03701124084 0.09231194074 0.1236330684 0.297630117 0.02040487766 0.02467435088 0.04053103059 +-2.210682721e-17 3.968561361e-05 0.08602241995 0.1053637351 0.1128364899 3.400132577e-19 5.126005989e-06 0.01477793317 +0.02421694818 0.02763588018 + +H atom_index 2 n_descriptor 18 +1.234487111 0.03562477986 0.106769268 0.1425579644 0.3144183565 0.02264153406 0.02731939857 0.03878397112 +3.305969862e-18 4.349535384e-05 0.09726948982 0.1151287977 0.121945258 -5.301455364e-18 3.168945861e-06 0.01363616755 +0.02605301183 0.02997681065 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..43663a8d86cae8909d61d023b7b2585c875e8374 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:28 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0859961 SEC) : SETUP UNITCELL + DONE(0.096295 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.114404 SEC) : INIT PLANEWAVE + DONE(0.163883 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444853 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651724e+02 0.000000e+00 2.096e-01 4.990e-01 + GE2 -4.663506e+02 -1.178170e+00 9.803e-02 4.435e-01 + GE3 -4.663558e+02 -5.238967e-03 6.320e-02 5.059e-01 + GE4 -4.663544e+02 1.382601e-03 1.857e-03 3.788e-01 + GE5 -4.663541e+02 3.661705e-04 8.904e-04 3.668e-01 + GE6 -4.663542e+02 -1.690945e-04 1.109e-04 3.636e-01 + GE7 -4.663542e+02 3.577704e-05 2.423e-05 3.558e-01 + GE8 -4.663542e+02 -1.554463e-05 8.687e-06 3.417e-01 + GE9 -4.663542e+02 9.619168e-06 2.669e-06 3.448e-01 + GE10 -4.663542e+02 -1.330939e-06 2.241e-07 3.420e-01 + GE11 -4.663542e+02 -5.417420e-07 7.421e-08 2.765e-01 +E_delta_band = -6.84993847e-02 Ry = -9.31981941e-01 eV +E_delta_NN= -1.93894591e-01 Ry = -2.63807125e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4352 11 0.59 1e+02 % + Run_lcao lcao_line 6.4255 1 6.4 1e+02 % + Potential init_pot 0.28408 2 0.14 4.4 % + PW_Basis recip2real 0.28706 16 0.018 4.5 % + PW_Basis gathers_scatterp 0.12433 16 0.0078 1.9 % + Potential v_of_rho 1.0007 13 0.077 16 % + XC_Functional v_xc 0.28677 14 0.02 4.5 % + H_Hartree_pw v_hartree 0.66884 13 0.051 10 % + PW_Basis real2recip 0.67277 38 0.018 10 % + PW_Basis gatherp_scatters 0.27257 38 0.0072 4.2 % + ORB_control set_orb_tables 1.0974 1 1.1 17 % + ORB_gen_tables gen_tables 1.0974 1 1.1 17 % + ORB_table_phi init_Table 0.47654 1 0.48 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.47136 126 0.0037 7.3 % + ORB_table_beta init_Table_Beta 0.18548 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18393 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.24942 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.24747 66 0.0037 3.8 % + LOOP_ions opt_ions 4.8052 1 4.8 75 % + ESolver_KS_LCAO Run 4.2807 1 4.3 67 % + HSolverLCAO solve 1.9716 11 0.18 31 % + HamiltLCAO updateHk 1.0711 11 0.097 17 % + LCAO_Hamilt cal_Hgamma 1.0383 11 0.094 16 % + Gint_interface cal_gint 1.7446 23 0.076 27 % + Gint_Gamma distri_vl 2.0827 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.6606 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.938 6 0.32 30 % + LCAO_DESCRIPTOR add_v_delta 1.938 6 0.32 30 % + ElecStateLCAO psiToRho 0.88208 11 0.08 14 % + Charge mix_rho 0.77985 10 0.078 12 % + LOOP_ions force_stress 0.52437 1 0.52 8.1 % + Force_Stress_LCAO getForceStress 0.52434 1 0.52 8.1 % + Force_LCAO_gamma ftable_gamma 0.30464 1 0.3 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.29674 1 0.3 4.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:28 2022 + FINISH Time : Wed Sep 28 11:11:34 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/45/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..65fca56cbb9d729d25d3a04036d5d1270306c237 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.441529 0.702838 0.00112915 +H 0.442167 0.665657 0.948381 +H 0.451655 0.667258 0.0569926 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d04990a7eaba272541c2a6bfb1aa18051543bc19 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0948 2 + 2 -13.3631 2 + 3 -8.71268 2 + 4 -6.69342 2 + 5 1.25039 0 + 6 4.41922 0 + 7 11.1015 0 + 8 11.3124 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9b9ab25b8b2b05b26be753a3472d9ec68248d1f4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:36 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.3628160336 19.6794686441 0.031616213535 0 0 0 0 + tauc_H1 12.3806836192 18.6384005266 26.554674152 0 0 0 0 + tauc_H2 12.6463483328 18.683219692 1.59579408686 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.106183980155 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.106535677118 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124569740455 (SEC) + + DONE : INIT CHARGE Time : 0.167810818232 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450737 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 9 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000769 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000866 + + Density error is 0.215800394086 + + Energy Rydberg eV + E_KohnSham -34.1878737395 -465.149885362 + E_Harris -34.3808816329 -467.775892471 + E_Fermi -0.400577318938 -5.45013402713 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00089753651478 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120033360416 + + Density error is 0.098412261007 + + Energy Rydberg eV + E_KohnSham -34.2772624802 -466.366081572 + E_Harris -34.2839464935 -466.457022238 + E_Fermi -0.209096710756 -2.84490669933 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00085584240163 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116305705977 + + Density error is 0.0630687326539 + + Energy Rydberg eV + E_KohnSham -34.2775063639 -466.36939978 + E_Harris -34.28178708 -466.427641911 + E_Fermi -0.198007020945 -2.69402372885 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000798483242168 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011189903601 + + Density error is 0.00216161252562 + + Energy Rydberg eV + E_KohnSham -34.2774940846 -466.369232712 + E_Harris -34.2774991938 -466.369302226 + E_Fermi -0.162994562604 -2.21765479443 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000798089303432 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111848836724 + + Density error is 0.0008345089733 + + Energy Rydberg eV + E_KohnSham -34.2774481732 -466.368608055 + E_Harris -34.2774487051 -466.368615293 + E_Fermi -0.162193070591 -2.20674993615 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000797397667394 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111783457313 + + Density error is 0.000213322825238 + + Energy Rydberg eV + E_KohnSham -34.2774775137 -466.369007253 + E_Harris -34.2774776128 -466.369008602 + E_Fermi -0.162135081415 -2.20596095294 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00079762391308 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111823953705 + + Density error is 3.86237686764e-05 + + Energy Rydberg eV + E_KohnSham -34.2774654214 -466.36884273 + E_Harris -34.2774654291 -466.368842834 + E_Fermi -0.161990613454 -2.20399536548 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00079756155809 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111811883353 + + Density error is 1.68269682425e-05 + + Energy Rydberg eV + E_KohnSham -34.2774708378 -466.368916422 + E_Harris -34.2774708389 -466.368916438 + E_Fermi -0.16203018172 -2.20453371937 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000797559776909 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111811964324 + + Density error is 2.25531403282e-06 + + Energy Rydberg eV + E_KohnSham -34.2774694406 -466.368897414 + E_Harris -34.2774694407 -466.368897414 + E_Fermi -0.162013082429 -2.20430107158 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000797560693772 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111812219014 + + Density error is 5.10483932139e-07 + + Energy Rydberg eV + E_KohnSham -34.2774696689 -466.368900519 + E_Harris -34.2774696689 -466.368900519 + E_Fermi -0.162011055754 -2.20427349725 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000797560836194 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111812291191 + + Density error is 1.76104053266e-07 + + Energy Rydberg eV + E_KohnSham -34.27746969 -466.368900807 + E_Harris -34.27746969 -466.368900807 + E_Fermi -0.162010821672 -2.2042703124 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000797560873434 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111812313666 + + Density error is 9.91277408237e-09 + + Energy Rydberg eV + E_KohnSham -34.277469693 -466.368900847 + E_Harris -34.277469693 -466.368900847 + E_band -7.9178663671 -107.728098595 + E_one_elec -69.1621802575 -940.999737605 + E_Hartree +35.9947649331 +489.733901261 + E_xc -8.20180568349 -111.591291184 + E_Ewald +7.21641918804 +98.1844201139 + E_demet -1.13049069787e-72 -1.5381115027e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194360401788 -2.64440892988 + E_Fermi -0.162010648456 -2.20426795568 + + charge density convergence is achieved + final etot is -466.368900847 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0948 2.00000 + 2 -13.3631 2.00000 + 3 -8.71268 2.00000 + 4 -6.69342 2.00000 + 5 1.25039 0.00000 + 6 4.41922 0.00000 + 7 11.1015 0.00000 + 8 11.3124 0.00000 + + EFERMI = -2.204267955682298 eV + OUT.ABACUS/ final etot is -466.3689008471528 eV + correction force for each atom along direction 1 is 4.36048e-05 + correction force for each atom along direction 2 is -5.93397e-05 + correction force for each atom along direction 3 is -3.05729e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.014060232 +0.85654324 +1.5167367 + H1 +0.10172614 -0.94347198 -0.37155722 + H2 -0.11578637 +0.086928739 -1.1451794 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3689008471528 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3032 11 0.66 1.0e+02% + Run_lcao lcao_line 7.2927 1 7.3 1.e+02% + Potential init_pot 0.28363 2 0.14 3.9% + PW_Basis recip2real 0.29346 17 0.017 4.0% + PW_Basis gathers_scatterp 0.13029 17 0.0077 1.8% + Potential v_of_rho 1.0707 14 0.076 15.% + XC_Functional v_xc 0.30634 15 0.020 4.2% + H_Hartree_pw v_hartree 0.71586 14 0.051 9.8% + PW_Basis real2recip 0.75645 41 0.018 10.% + PW_Basis gatherp_scatters 0.29576 41 0.0072 4.0% + ORB_control set_orb_tables 1.1016 1 1.1 15.% + ORB_gen_tables gen_tables 1.1016 1 1.1 15.% + ORB_table_phi init_Table 0.47798 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47275 126 0.0038 6.5% + ORB_table_beta init_Table_Beta 0.18549 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18393 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24899 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24701 66 0.0037 3.4% + LOOP_ions opt_ions 5.6623 1 5.7 78.% + ESolver_KS_LCAO Run 5.1153 1 5.1 70.% + HSolverLCAO solve 2.4337 12 0.20 33.% + HamiltLCAO updateHk 1.2744 12 0.11 17.% + LCAO_Hamilt cal_Hgamma 1.2444 12 0.10 17.% + Gint_interface cal_gint 2.2207 25 0.089 30.% + Gint_Gamma distri_vl 2.6672 6 0.44 37.% + LCAO_Deepks cal_projected_DM 5.5102 14 0.39 75.% + LCAO_gen_fixedH add_v_delta 2.5198 6 0.42 35.% + LCAO_DESCRIPTOR add_v_delta 2.5198 6 0.42 35.% + ElecStateLCAO psiToRho 1.1410 12 0.095 16.% + Charge mix_rho 1.0005 11 0.091 14.% + LOOP_ions force_stress 0.54674 1 0.55 7.5% + Force_Stress_LCAO getForceStress 0.54671 1 0.55 7.5% + Force_LCAO_gamma ftable_gamma 0.32976 1 0.33 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.32161 1 0.32 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:36 2022 + Finish Time : Wed Sep 28 11:13:44 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a1d4c578d0ef464922136c61188959af963dde41 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/OUT.ABACUS/warning.log @@ -0,0 +1,77 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123522 ima = 3.6868e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123897508529 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113059802516 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113561131306 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113765486903 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113729733259 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011375355666 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113743452443 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113746310141 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113745639374 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113745571693 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113745555064 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113745546141 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/STRU new file mode 100644 index 0000000000000000000000000000000000000000..2a70d2ebc9e5dcf5c3e7e89428b3d8e077ac8c2d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.637183966433 19.679468644152 0.031616213538 0 0 0 +H +0.0 +2 +-15.619316380859 18.638400526645 -1.445325847971 0 0 0 +-15.353651667226 18.683219691966 1.595794086884 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/conv new file mode 100644 index 0000000000000000000000000000000000000000..c85b9c5996ca2bc1615612098c5d563bfb50773c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/conv @@ -0,0 +1 @@ +46 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..50955997246a012d8407484f6ffaca15a9f91ee2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.742181623 0.01250363706 1.271818695 1.371266811 1.46847024 0.0073987849 0.02082425435 0.03881521489 +3.677655116e-19 0.001123989767 0.002247789501 0.0121274558 0.04088364223 1.583411015e-19 1.284329303e-06 4.263330031e-06 +0.001829830474 0.005476352897 + +H atom_index 1 n_descriptor 18 +1.258903794 0.03314574488 0.1120091539 0.1564128707 0.3268622928 0.0220772637 0.02911110449 0.03647800911 +1.0566092e-17 3.531284011e-05 0.1038097329 0.115352341 0.1342209964 4.034775482e-18 3.553116667e-06 0.01275822846 +0.02623279621 0.03131742247 + +H atom_index 2 n_descriptor 18 +1.203556495 0.03510256649 0.09391383879 0.1318848219 0.3089259906 0.0197050675 0.02592177076 0.0384100265 +4.321713083e-18 3.126025671e-05 0.0894863576 0.1129112722 0.1136987379 -6.791867318e-18 5.557087796e-06 0.01353034178 +0.02410500743 0.02872945131 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..141bee86f1529fc5809cafb195d58fe2ebc2044d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:36 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.106207 SEC) : SETUP UNITCELL + DONE(0.106554 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.12459 SEC) : INIT PLANEWAVE + DONE(0.16795 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.4508 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651499e+02 0.000000e+00 2.158e-01 5.236e-01 + GE2 -4.663661e+02 -1.216196e+00 9.841e-02 4.858e-01 + GE3 -4.663694e+02 -3.318208e-03 6.307e-02 5.513e-01 + GE4 -4.663692e+02 1.670677e-04 2.162e-03 4.142e-01 + GE5 -4.663686e+02 6.246569e-04 8.345e-04 4.127e-01 + GE6 -4.663690e+02 -3.991973e-04 2.133e-04 4.048e-01 + GE7 -4.663688e+02 1.645232e-04 3.862e-05 3.956e-01 + GE8 -4.663689e+02 -7.369277e-05 1.683e-05 3.877e-01 + GE9 -4.663689e+02 1.900878e-05 2.255e-06 3.877e-01 + GE10 -4.663689e+02 -3.105222e-06 5.105e-07 3.897e-01 + GE11 -4.663689e+02 -2.881362e-07 1.761e-07 3.866e-01 + GE12 -4.663689e+02 -4.023787e-08 9.913e-09 3.130e-01 +E_delta_band = -6.96925286e-02 Ry = -9.48215497e-01 eV +E_delta_NN= -1.94360402e-01 Ry = -2.64440893e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3032 11 0.66 1e+02 % + Run_lcao lcao_line 7.2927 1 7.3 1e+02 % + Potential init_pot 0.28363 2 0.14 3.9 % + PW_Basis recip2real 0.29346 17 0.017 4 % + PW_Basis gathers_scatterp 0.13029 17 0.0077 1.8 % + Potential v_of_rho 1.0707 14 0.076 15 % + XC_Functional v_xc 0.30634 15 0.02 4.2 % + H_Hartree_pw v_hartree 0.71586 14 0.051 9.8 % + PW_Basis real2recip 0.75645 41 0.018 10 % + PW_Basis gatherp_scatters 0.29576 41 0.0072 4 % + ORB_control set_orb_tables 1.1016 1 1.1 15 % + ORB_gen_tables gen_tables 1.1016 1 1.1 15 % + ORB_table_phi init_Table 0.47798 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.47275 126 0.0038 6.5 % + ORB_table_beta init_Table_Beta 0.18549 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18393 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24899 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24701 66 0.0037 3.4 % + LOOP_ions opt_ions 5.6623 1 5.7 78 % + ESolver_KS_LCAO Run 5.1153 1 5.1 70 % + HSolverLCAO solve 2.4337 12 0.2 33 % + HamiltLCAO updateHk 1.2744 12 0.11 17 % + LCAO_Hamilt cal_Hgamma 1.2444 12 0.1 17 % + Gint_interface cal_gint 2.2207 25 0.089 30 % + Gint_Gamma distri_vl 2.6672 6 0.44 37 % + LCAO_Deepks cal_projected_DM 5.5102 14 0.39 75 % + LCAO_gen_fixedH add_v_delta 2.5198 6 0.42 35 % + LCAO_DESCRIPTOR add_v_delta 2.5198 6 0.42 35 % + ElecStateLCAO psiToRho 1.141 12 0.095 16 % + Charge mix_rho 1.0005 11 0.091 14 % + LOOP_ions force_stress 0.54674 1 0.55 7.5 % + Force_Stress_LCAO getForceStress 0.54671 1 0.55 7.5 % + Force_LCAO_gamma ftable_gamma 0.32976 1 0.33 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.32161 1 0.32 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:36 2022 + FINISH Time : Wed Sep 28 11:13:44 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/46/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c47df25a3936c60b95b5276e4b3d5feecd4439b3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.452189 0.709296 0.99999 +H 0.433595 0.648944 0.982637 +H 0.485757 0.694667 0.0528948 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9c9646c34901f5fde6d7e1973ae705d281a8a64f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4994 2 + 2 -12.867 2 + 3 -9.39769 2 + 4 -6.79179 2 + 5 1.35 0 + 6 4.54453 0 + 7 11.0421 0 + 8 11.3205 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b2ab5e644953af913611a8636fcb421704c5a072 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:22 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.6612842012 19.860282084 27.9997112833 0 0 0 0 + tauc_H1 12.1406559254 18.1704195199 27.5138441137 0 0 0 0 + tauc_H2 13.6011933204 19.4506698569 1.48105525563 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0893786294569 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0982686162299 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116686012578 (SEC) + + DONE : INIT CHARGE Time : 0.166281939385 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446758 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 9 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000584 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123 + + Density error is 0.214506008124 + + Energy Rydberg eV + E_KohnSham -34.1898127694 -465.176267218 + E_Harris -34.3812961097 -467.781531717 + E_Fermi -0.412000672489 -5.60555672569 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000860597798792 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138427647682 + + Density error is 0.0973343006809 + + Energy Rydberg eV + E_KohnSham -34.2787625593 -466.386491196 + E_Harris -34.2855057048 -466.478236396 + E_Fermi -0.221977227879 -3.0201551254 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000825184545907 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00130733220701 + + Density error is 0.0622811113315 + + Energy Rydberg eV + E_KohnSham -34.2789888928 -466.38957062 + E_Harris -34.2833469284 -466.448864737 + E_Fermi -0.209440265141 -2.84958099655 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000786587531806 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119205873181 + + Density error is 0.00196216482734 + + Energy Rydberg eV + E_KohnSham -34.2789977568 -466.389691221 + E_Harris -34.2789988262 -466.389705771 + E_Fermi -0.173600036915 -2.36194967505 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000790394639984 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119554186055 + + Density error is 0.000866825419384 + + Energy Rydberg eV + E_KohnSham -34.2789330717 -466.388811136 + E_Harris -34.2789350876 -466.388838564 + E_Fermi -0.17273533057 -2.35018474166 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000789131911748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119345605427 + + Density error is 9.82749224517e-05 + + Energy Rydberg eV + E_KohnSham -34.2789800095 -466.389449757 + E_Harris -34.2789800188 -466.389449884 + E_Fermi -0.172865216908 -2.35195193596 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000789002954785 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119312056305 + + Density error is 3.96201191526e-05 + + Energy Rydberg eV + E_KohnSham -34.278965234 -466.389248726 + E_Harris -34.2789652424 -466.389248841 + E_Fermi -0.172760482558 -2.35052695202 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000788961797281 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119308016553 + + Density error is 1.77777027515e-05 + + Energy Rydberg eV + E_KohnSham -34.278967384 -466.389277979 + E_Harris -34.2789673855 -466.389277998 + E_Fermi -0.17280756021 -2.35116747633 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000788980562596 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119308605121 + + Density error is 2.58766882306e-06 + + Energy Rydberg eV + E_KohnSham -34.278965865 -466.389257312 + E_Harris -34.278965865 -466.389257312 + E_Fermi -0.17279000594 -2.35092863824 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000788983263502 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119308721298 + + Density error is 4.31737079762e-07 + + Energy Rydberg eV + E_KohnSham -34.2789661299 -466.389260915 + E_Harris -34.2789661299 -466.389260915 + E_Fermi -0.172787929778 -2.3509003906 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000788983961518 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119308781806 + + Density error is 1.11835474905e-07 + + Energy Rydberg eV + E_KohnSham -34.2789661692 -466.389261451 + E_Harris -34.2789661692 -466.389261451 + E_Fermi -0.172787637786 -2.35089641785 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000788983999038 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119308772703 + + Density error is 1.04848301456e-08 + + Energy Rydberg eV + E_KohnSham -34.2789661749 -466.389261528 + E_Harris -34.2789661749 -466.389261528 + E_band -8.01956535507 -109.111784312 + E_one_elec -69.5202196231 -945.871113086 + E_Hartree +36.1385365494 +491.690014453 + E_xc -8.22547919862 -111.913385882 + E_Ewald +7.45201430198 +101.389856084 + E_demet -5.23818794418e-83 -7.12692032357e-82 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195274044945 -2.65683968276 + E_Fermi -0.172787514137 -2.35089473551 + + charge density convergence is achieved + final etot is -466.389261528 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4994 2.00000 + 2 -12.8670 2.00000 + 3 -9.39769 2.00000 + 4 -6.79179 2.00000 + 5 1.35000 0.00000 + 6 4.54453 0.00000 + 7 11.0421 0.00000 + 8 11.3205 0.00000 + + EFERMI = -2.350894735514158 eV + OUT.ABACUS/ final etot is -466.3892615282888 eV + correction force for each atom along direction 1 is 9.47130e-05 + correction force for each atom along direction 2 is -2.79396e-05 + correction force for each atom along direction 3 is 2.79507e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.45251526 +0.042707598 -0.69219672 + H1 -0.34004360 -0.19548801 -0.47289172 + H2 +0.79255886 +0.15278042 +1.1650884 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3892615282888 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4444 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4335 1 6.4 1.e+02% + Potential init_pot 0.28134 2 0.14 4.4% + PW_Basis recip2real 0.30512 17 0.018 4.7% + PW_Basis gathers_scatterp 0.12784 17 0.0075 2.0% + Potential v_of_rho 1.0630 14 0.076 16.% + XC_Functional v_xc 0.29694 15 0.020 4.6% + H_Hartree_pw v_hartree 0.71858 14 0.051 11.% + PW_Basis real2recip 0.69144 41 0.017 11.% + PW_Basis gatherp_scatters 0.25814 41 0.0063 4.0% + ORB_control set_orb_tables 1.0895 1 1.1 17.% + ORB_gen_tables gen_tables 1.0895 1 1.1 17.% + ORB_table_phi init_Table 0.47755 1 0.48 7.4% + ORB_table_phi cal_ST_Phi12_R 0.47233 126 0.0037 7.3% + ORB_table_beta init_Table_Beta 0.18140 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.17989 56 0.0032 2.8% + ORB_table_alpha init_Table_Alpha 0.24425 1 0.24 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24231 66 0.0037 3.8% + LOOP_ions opt_ions 4.8191 1 4.8 75.% + ESolver_KS_LCAO Run 4.3327 1 4.3 67.% + HSolverLCAO solve 1.8668 12 0.16 29.% + HamiltLCAO updateHk 1.0245 12 0.085 16.% + LCAO_Hamilt cal_Hgamma 0.98769 12 0.082 15.% + Gint_interface cal_gint 1.6046 25 0.064 25.% + Gint_Gamma distri_vl 2.2761 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.6795 14 0.33 73.% + LCAO_gen_fixedH add_v_delta 2.1323 6 0.36 33.% + LCAO_DESCRIPTOR add_v_delta 2.1323 6 0.36 33.% + ElecStateLCAO psiToRho 0.82496 12 0.069 13.% + Charge mix_rho 0.84582 11 0.077 13.% + LOOP_ions force_stress 0.48626 1 0.49 7.5% + Force_Stress_LCAO getForceStress 0.48623 1 0.49 7.5% + Force_LCAO_gamma ftable_gamma 0.26679 1 0.27 4.1% + Force_LCAO_gamma cal_fvl_dphi 0.25890 1 0.26 4.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:22 2022 + Finish Time : Wed Sep 28 11:03:29 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..edb0f231255ada79186d1525271e8dff5991571d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123702 ima = 3.66845e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122495424076 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001115705587 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112079204346 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112347322215 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112281206558 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318141634 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112315858857 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318846902 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112318035585 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112317922644 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112317903455 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011231789804 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1e445c463209e731ab02948931ea1c44ffe520bf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.338715798793 19.860282084008 -0.000288716704 0 0 0 +H +0.0 +2 +-15.859344074567 18.170419519925 -0.486155886329 0 0 0 +-14.398806679625 19.450669856900 1.481055255644 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/conv new file mode 100644 index 0000000000000000000000000000000000000000..75ddfecc81453fa379e09d13b8d82854156d2045 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/conv @@ -0,0 +1 @@ +47 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4bb5716a824efd58f2e5e48711a75fdd198cfb02 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753329513 0.01284267088 1.279398317 1.361701529 1.470137328 0.009386693713 0.01723766728 0.03913767031 +-5.270789643e-18 0.0009778646228 0.002881801179 0.01341143288 0.04781435022 8.772602164e-19 2.847482672e-06 7.470971521e-06 +0.001597142951 0.006144905227 + +H atom_index 1 n_descriptor 18 +1.24859991 0.03483455895 0.1102457208 0.1488460452 0.3191142926 0.02304761961 0.02815278282 0.03792716261 +4.846049049e-17 5.149172542e-05 0.1034596729 0.1151095536 0.1277520072 -5.794493212e-19 3.41810281e-06 0.0134021544 +0.02706749572 0.03068645879 + +H atom_index 2 n_descriptor 18 +1.273922163 0.03399419669 0.1195384473 0.1610221571 0.327170212 0.02429540908 0.02962899357 0.03724970121 +-2.292032912e-17 5.393487452e-05 0.1075929187 0.1183301399 0.1381970231 -4.55096929e-18 1.986470662e-06 0.01337558488 +0.02796614825 0.03178951299 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d96cb4ea2911d1474b33cf98f795d3671ac9a4dc Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:22 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0894009 SEC) : SETUP UNITCELL + DONE(0.0982885 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116708 SEC) : INIT PLANEWAVE + DONE(0.16641 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446829 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651763e+02 0.000000e+00 2.145e-01 4.762e-01 + GE2 -4.663865e+02 -1.210224e+00 9.733e-02 4.135e-01 + GE3 -4.663896e+02 -3.079424e-03 6.228e-02 4.798e-01 + GE4 -4.663897e+02 -1.206012e-04 1.962e-03 3.448e-01 + GE5 -4.663888e+02 8.800853e-04 8.668e-04 3.434e-01 + GE6 -4.663894e+02 -6.386214e-04 9.827e-05 3.358e-01 + GE7 -4.663892e+02 2.010313e-04 3.962e-05 3.310e-01 + GE8 -4.663893e+02 -2.925249e-05 1.778e-05 3.201e-01 + GE9 -4.663893e+02 2.066688e-05 2.588e-06 3.227e-01 + GE10 -4.663893e+02 -3.603358e-06 4.317e-07 3.224e-01 + GE11 -4.663893e+02 -5.355207e-07 1.118e-07 3.227e-01 + GE12 -4.663893e+02 -7.763816e-08 1.048e-08 2.570e-01 +E_delta_band = -7.14558404e-02 Ry = -9.72206584e-01 eV +E_delta_NN= -1.95274045e-01 Ry = -2.65683968e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4444 11 0.59 1e+02 % + Run_lcao lcao_line 6.4335 1 6.4 1e+02 % + Potential init_pot 0.28134 2 0.14 4.4 % + PW_Basis recip2real 0.30512 17 0.018 4.7 % + PW_Basis gathers_scatterp 0.12784 17 0.0075 2 % + Potential v_of_rho 1.063 14 0.076 16 % + XC_Functional v_xc 0.29694 15 0.02 4.6 % + H_Hartree_pw v_hartree 0.71858 14 0.051 11 % + PW_Basis real2recip 0.69144 41 0.017 11 % + PW_Basis gatherp_scatters 0.25814 41 0.0063 4 % + ORB_control set_orb_tables 1.0895 1 1.1 17 % + ORB_gen_tables gen_tables 1.0895 1 1.1 17 % + ORB_table_phi init_Table 0.47755 1 0.48 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.47233 126 0.0037 7.3 % + ORB_table_beta init_Table_Beta 0.1814 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.17989 56 0.0032 2.8 % + ORB_table_alpha init_Table_Alpha 0.24425 1 0.24 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24231 66 0.0037 3.8 % + LOOP_ions opt_ions 4.8191 1 4.8 75 % + ESolver_KS_LCAO Run 4.3327 1 4.3 67 % + HSolverLCAO solve 1.8668 12 0.16 29 % + HamiltLCAO updateHk 1.0245 12 0.085 16 % + LCAO_Hamilt cal_Hgamma 0.98769 12 0.082 15 % + Gint_interface cal_gint 1.6046 25 0.064 25 % + Gint_Gamma distri_vl 2.2761 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.6795 14 0.33 73 % + LCAO_gen_fixedH add_v_delta 2.1323 6 0.36 33 % + LCAO_DESCRIPTOR add_v_delta 2.1323 6 0.36 33 % + ElecStateLCAO psiToRho 0.82496 12 0.069 13 % + Charge mix_rho 0.84582 11 0.077 13 % + LOOP_ions force_stress 0.48626 1 0.49 7.5 % + Force_Stress_LCAO getForceStress 0.48623 1 0.49 7.5 % + Force_LCAO_gamma ftable_gamma 0.26679 1 0.27 4.1 % + Force_LCAO_gamma cal_fvl_dphi 0.2589 1 0.26 4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:22 2022 + FINISH Time : Wed Sep 28 11:03:29 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/47/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..09cd3914dda6758af2b55717dac796c1894eecbc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.456731 0.708594 0.994318 +H 0.421807 0.656318 0.00976956 +H 0.498294 0.723626 0.0421833 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..616fac0cd3149bb2cdd0847584655c5d7505f35b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2476 2 + 2 -13.4382 2 + 3 -8.79408 2 + 4 -6.73212 2 + 5 1.39525 0 + 6 4.59348 0 + 7 11.0652 0 + 8 11.2827 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..256b66d43e0fdcfa0977ab18bf4b992a3f4d94a1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:39 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.7884735041 19.840623146 27.8409130674 0 0 0 0 + tauc_H1 11.8105834338 18.3768981827 0.273547691249 0 0 0 0 + tauc_H2 13.9522413848 20.261535358 1.18113339276 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871611522151 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0967940072519 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115013255364 (SEC) + + DONE : INIT CHARGE Time : 0.16372396797 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445983 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 9 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000685 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129 + + Density error is 0.217110543243 + + Energy Rydberg eV + E_KohnSham -34.1884656109 -465.157938185 + E_Harris -34.3843141587 -467.82259438 + E_Fermi -0.40910815098 -5.56620195157 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000984148073682 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131065785695 + + Density error is 0.0980421641096 + + Energy Rydberg eV + E_KohnSham -34.2788673201 -466.387916539 + E_Harris -34.2854549977 -466.477546491 + E_Fermi -0.216532021021 -2.94606928534 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000946539730018 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123326831862 + + Density error is 0.0627481789173 + + Energy Rydberg eV + E_KohnSham -34.2791141239 -466.391274477 + E_Harris -34.283332859 -466.448673313 + E_Fermi -0.203865176211 -2.77372802024 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000893181174373 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011054116462 + + Density error is 0.00212469139714 + + Energy Rydberg eV + E_KohnSham -34.279130849 -466.391502034 + E_Harris -34.2791348555 -466.391556545 + E_Fermi -0.168635373659 -2.29440196612 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000893223871343 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110385248572 + + Density error is 0.000871415364039 + + Energy Rydberg eV + E_KohnSham -34.2790698319 -466.390671854 + E_Harris -34.2790709906 -466.390687619 + E_Fermi -0.167626438882 -2.28067470425 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00089240442562 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001102397797 + + Density error is 0.000217678731923 + + Energy Rydberg eV + E_KohnSham -34.2791094785 -466.391211273 + E_Harris -34.2791096077 -466.391213031 + E_Fermi -0.167746534183 -2.28230868463 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000892656768685 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110244248368 + + Density error is 4.25137243767e-05 + + Energy Rydberg eV + E_KohnSham -34.2790933405 -466.390991705 + E_Harris -34.2790933502 -466.390991837 + E_Fermi -0.167554263327 -2.27969270544 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000892591550689 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110240280591 + + Density error is 1.76803498958e-05 + + Energy Rydberg eV + E_KohnSham -34.2790992628 -466.391072282 + E_Harris -34.2790992641 -466.391072299 + E_Fermi -0.167603312594 -2.28036005495 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000892586649225 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110237955811 + + Density error is 1.70910590825e-06 + + Energy Rydberg eV + E_KohnSham -34.2790977788 -466.391052091 + E_Harris -34.2790977788 -466.391052091 + E_Fermi -0.167584283302 -2.28010114815 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000892586945774 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110237743847 + + Density error is 2.64514576036e-07 + + Energy Rydberg eV + E_KohnSham -34.279098018 -466.391055345 + E_Harris -34.279098018 -466.391055345 + E_Fermi -0.167582710707 -2.2800797519 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000892587605938 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110237806376 + + Density error is 8.9142730798e-08 + + Energy Rydberg eV + E_KohnSham -34.279098039 -466.391055631 + E_Harris -34.279098039 -466.391055631 + E_band -7.96900422813 -108.423864889 + E_one_elec -69.4485516686 -944.89602054 + E_Hartree +36.1264525076 +491.52560263 + E_xc -8.22313821542 -111.881535171 + E_Ewald +7.39019932533 +100.54882018 + E_demet -6.68620399966e-82 -9.09704723858e-81 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194921390713 -2.65204157578 + E_Fermi -0.167582628817 -2.28007863773 + + charge density convergence is achieved + final etot is -466.391055631 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2476 2.00000 + 2 -13.4382 2.00000 + 3 -8.79408 2.00000 + 4 -6.73212 2.00000 + 5 1.39525 0.00000 + 6 4.59348 0.00000 + 7 11.0652 0.00000 + 8 11.2827 0.00000 + + EFERMI = -2.280078637731349 eV + OUT.ABACUS/ final etot is -466.3910556305532 eV + correction force for each atom along direction 1 is -3.75925e-06 + correction force for each atom along direction 2 is 2.91865e-06 + correction force for each atom along direction 3 is 2.54008e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.082696198 +0.84369000 -1.0456981 + H1 -0.15146989 -0.57552673 +0.55587121 + H2 +0.068773692 -0.26816327 +0.48982691 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3910556305532 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6982 11 0.52 1.0e+02% + Run_lcao lcao_line 5.6881 1 5.7 1.e+02% + Potential init_pot 0.28754 2 0.14 5.0% + PW_Basis recip2real 0.27333 16 0.017 4.8% + PW_Basis gathers_scatterp 0.11993 16 0.0075 2.1% + Charge atomic_rho 0.10025 1 0.10 1.8% + Potential v_of_rho 0.88557 13 0.068 16.% + XC_Functional v_xc 0.25071 14 0.018 4.4% + H_Hartree_pw v_hartree 0.59742 13 0.046 10.% + PW_Basis real2recip 0.55823 38 0.015 9.8% + PW_Basis gatherp_scatters 0.21601 38 0.0057 3.8% + ORB_control set_orb_tables 1.1103 1 1.1 19.% + ORB_gen_tables gen_tables 1.1103 1 1.1 19.% + ORB_table_phi init_Table 0.48950 1 0.49 8.6% + ORB_table_phi cal_ST_Phi12_R 0.48442 126 0.0038 8.5% + ORB_table_beta init_Table_Beta 0.18807 1 0.19 3.3% + ORB_table_beta VNL_PhiBeta_R 0.18660 56 0.0033 3.3% + ORB_table_alpha init_Table_Alpha 0.25165 1 0.25 4.4% + ORB_table_alpha S_PhiAlpha_R 0.24979 66 0.0038 4.4% + LOOP_ions opt_ions 4.0546 1 4.1 71.% + ESolver_KS_LCAO Run 3.5851 1 3.6 63.% + HSolverLCAO solve 1.6013 11 0.15 28.% + HamiltLCAO updateHk 0.88620 11 0.081 16.% + LCAO_Hamilt cal_Hgamma 0.84832 11 0.077 15.% + Gint_interface cal_gint 1.3929 23 0.061 24.% + Gint_Gamma distri_vl 1.7426 6 0.29 31.% + LCAO_Deepks cal_projected_DM 3.9172 13 0.30 69.% + LCAO_gen_fixedH add_v_delta 1.6104 6 0.27 28.% + LCAO_DESCRIPTOR add_v_delta 1.6103 6 0.27 28.% + ElecStateLCAO psiToRho 0.70156 11 0.064 12.% + Charge mix_rho 0.65870 10 0.066 12.% + LOOP_ions force_stress 0.46932 1 0.47 8.2% + Force_Stress_LCAO getForceStress 0.46929 1 0.47 8.2% + Force_LCAO_gamma ftable_gamma 0.25572 1 0.26 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.24893 1 0.25 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:39 2022 + Finish Time : Wed Sep 28 11:12:45 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c95d6f3fbd204b54994a7985cdf054bef092e1ee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123905 ima = 3.65294e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123615762956 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112809522902 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113251430757 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113488652987 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113437087829 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113469501645 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113458340138 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113461386948 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113460708066 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113460649875 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113460639675 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/STRU new file mode 100644 index 0000000000000000000000000000000000000000..239f8700aa07c1e92a1e0cafd3077c2f5c2b430c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.211526495832 19.840623145972 -0.159086932624 0 0 0 +H +0.0 +2 +-16.189416566155 18.376898182734 0.273547691232 0 0 0 +-14.047758615259 20.261535357994 1.181133392750 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/conv new file mode 100644 index 0000000000000000000000000000000000000000..535aedaebef530444094f41923dcc9cc590a181f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/conv @@ -0,0 +1 @@ +48 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..6c9e9e271b0be28dfd86cac510d23470a00428a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.743206851 0.01263761061 1.284983226 1.37662494 1.469229187 0.007621571114 0.02070903137 0.03884472035 +-2.183226905e-18 0.001186427587 0.00236710178 0.012542902 0.04284984117 1.863234552e-19 1.504013864e-06 4.781633034e-06 +0.001809616274 0.005591468311 + +H atom_index 1 n_descriptor 18 +1.25556537 0.03334362163 0.110814227 0.1542158669 0.3250707443 0.0220845189 0.02884411488 0.03658359929 +-4.584714139e-17 3.878361963e-05 0.103782568 0.1151231711 0.1324631854 -2.322812324e-18 3.876728833e-06 0.01283025263 +0.02638272832 0.03114759159 + +H atom_index 2 n_descriptor 18 +1.24636323 0.03367097649 0.1076301611 0.1499270401 0.3222554962 0.02168974781 0.02831542148 0.03684944416 +-2.593343367e-17 3.804468274e-05 0.1016199196 0.1146520665 0.1287671918 -3.182028068e-18 4.30239116e-06 0.01287037792 +0.02604714857 0.030746172 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..414501057f8a1c29271f324edb1035ed0f1b27ee Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:39 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0871832 SEC) : SETUP UNITCELL + DONE(0.0968106 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115034 SEC) : INIT PLANEWAVE + DONE(0.163853 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44604 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651579e+02 0.000000e+00 2.171e-01 4.358e-01 + GE2 -4.663879e+02 -1.229978e+00 9.804e-02 3.659e-01 + GE3 -4.663913e+02 -3.357938e-03 6.275e-02 4.220e-01 + GE4 -4.663915e+02 -2.275571e-04 2.125e-03 3.113e-01 + GE5 -4.663907e+02 8.301805e-04 8.714e-04 3.081e-01 + GE6 -4.663912e+02 -5.394194e-04 2.177e-04 2.995e-01 + GE7 -4.663910e+02 2.195684e-04 4.251e-05 2.948e-01 + GE8 -4.663911e+02 -8.057704e-05 1.768e-05 2.845e-01 + GE9 -4.663911e+02 2.019063e-05 1.709e-06 2.865e-01 + GE10 -4.663911e+02 -3.253594e-06 2.645e-07 2.873e-01 + GE11 -4.663911e+02 -2.857825e-07 8.914e-08 2.276e-01 +E_delta_band = -7.08614028e-02 Ry = -9.64118847e-01 eV +E_delta_NN= -1.94921391e-01 Ry = -2.65204158e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6982 11 0.52 1e+02 % + Run_lcao lcao_line 5.6881 1 5.7 1e+02 % + Potential init_pot 0.28754 2 0.14 5 % + PW_Basis recip2real 0.27333 16 0.017 4.8 % + PW_Basis gathers_scatterp 0.11993 16 0.0075 2.1 % + Charge atomic_rho 0.10025 1 0.1 1.8 % + Potential v_of_rho 0.88557 13 0.068 16 % + XC_Functional v_xc 0.25071 14 0.018 4.4 % + H_Hartree_pw v_hartree 0.59742 13 0.046 10 % + PW_Basis real2recip 0.55823 38 0.015 9.8 % + PW_Basis gatherp_scatters 0.21601 38 0.0057 3.8 % + ORB_control set_orb_tables 1.1103 1 1.1 19 % + ORB_gen_tables gen_tables 1.1103 1 1.1 19 % + ORB_table_phi init_Table 0.4895 1 0.49 8.6 % + ORB_table_phi cal_ST_Phi12_R 0.48442 126 0.0038 8.5 % + ORB_table_beta init_Table_Beta 0.18807 1 0.19 3.3 % + ORB_table_beta VNL_PhiBeta_R 0.1866 56 0.0033 3.3 % + ORB_table_alpha init_Table_Alpha 0.25165 1 0.25 4.4 % + ORB_table_alpha S_PhiAlpha_R 0.24979 66 0.0038 4.4 % + LOOP_ions opt_ions 4.0546 1 4.1 71 % + ESolver_KS_LCAO Run 3.5851 1 3.6 63 % + HSolverLCAO solve 1.6013 11 0.15 28 % + HamiltLCAO updateHk 0.8862 11 0.081 16 % + LCAO_Hamilt cal_Hgamma 0.84832 11 0.077 15 % + Gint_interface cal_gint 1.3929 23 0.061 24 % + Gint_Gamma distri_vl 1.7426 6 0.29 31 % + LCAO_Deepks cal_projected_DM 3.9172 13 0.3 69 % + LCAO_gen_fixedH add_v_delta 1.6104 6 0.27 28 % + LCAO_DESCRIPTOR add_v_delta 1.6103 6 0.27 28 % + ElecStateLCAO psiToRho 0.70156 11 0.064 12 % + Charge mix_rho 0.6587 10 0.066 12 % + LOOP_ions force_stress 0.46932 1 0.47 8.2 % + Force_Stress_LCAO getForceStress 0.46929 1 0.47 8.2 % + Force_LCAO_gamma ftable_gamma 0.25572 1 0.26 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.24893 1 0.25 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:39 2022 + FINISH Time : Wed Sep 28 11:12:45 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/48/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..975d7fb7f58aef7d6acffd4eb4b5dedc5cb14855 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.446972 0.708548 0.000224829 +H 0.496946 0.66331 0.0117646 +H 0.478198 0.76431 0.0140359 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b5c3d5372e0d186591c55099c905134ae73ec545 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1415 2 + 2 -12.6673 2 + 3 -9.27777 2 + 4 -6.71414 2 + 5 1.06208 0 + 6 4.07653 0 + 7 11.1213 0 + 8 11.385 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..866362143b12e34e5cd7247cf44dd4c9519e7ebe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:35 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.5152078665 19.8393539507 0.00629521913652 0 0 0 0 + tauc_H1 13.9144780161 18.5726897778 0.329409379905 0 0 0 0 + tauc_H2 13.3895384721 21.40066892 0.393005957958 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0878012144944 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0979230554593 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116194200074 (SEC) + + DONE : INIT CHARGE Time : 0.165901167091 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448861 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00144 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000893 + + Density error is 0.211168424131 + + Energy Rydberg eV + E_KohnSham -34.1912213361 -465.19543175 + E_Harris -34.3754824109 -467.702432287 + E_Fermi -0.392649810574 -5.34227474242 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00135160085213 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972404206629 + + Density error is 0.0982498769226 + + Energy Rydberg eV + E_KohnSham -34.2784092824 -466.381684617 + E_Harris -34.2854140307 -466.476989106 + E_Fermi -0.204238523498 -2.77880767069 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00124597474914 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000924451685916 + + Density error is 0.0632636917608 + + Energy Rydberg eV + E_KohnSham -34.2786981013 -466.3856142 + E_Harris -34.2832161514 -466.447085425 + E_Fermi -0.195946744036 -2.66599222343 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00104941886747 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000859777633053 + + Density error is 0.00191667792195 + + Energy Rydberg eV + E_KohnSham -34.2786225338 -466.384586051 + E_Harris -34.2786232097 -466.384595246 + E_Fermi -0.160491884069 -2.1836041061 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00104789107102 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000860779062618 + + Density error is 0.000830785393477 + + Energy Rydberg eV + E_KohnSham -34.2785900711 -466.384144374 + E_Harris -34.2785904213 -466.384149138 + E_Fermi -0.160355785937 -2.18175239602 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00104525771918 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000859970306272 + + Density error is 0.000135463177538 + + Energy Rydberg eV + E_KohnSham -34.2786064393 -466.384367074 + E_Harris -34.2786064523 -466.384367251 + E_Fermi -0.159982051236 -2.17666747454 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00104537680245 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000860123381408 + + Density error is 2.9921890432e-05 + + Energy Rydberg eV + E_KohnSham -34.2786018578 -466.384304739 + E_Harris -34.2786018604 -466.384304774 + E_Fermi -0.159959947979 -2.1763667443 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00104531097084 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000860084807606 + + Density error is 1.15101908305e-05 + + Energy Rydberg eV + E_KohnSham -34.2786040697 -466.384334835 + E_Harris -34.2786040703 -466.384334843 + E_Fermi -0.159974142852 -2.17655987546 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00104528635037 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000860085088343 + + Density error is 1.46026921088e-06 + + Energy Rydberg eV + E_KohnSham -34.2786030885 -466.384321485 + E_Harris -34.2786030886 -466.384321485 + E_Fermi -0.15996168919 -2.17639043469 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00104528686007 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00086008437518 + + Density error is 4.02764455843e-07 + + Energy Rydberg eV + E_KohnSham -34.2786032754 -466.384324027 + E_Harris -34.2786032754 -466.384324027 + E_Fermi -0.15996130955 -2.17638526942 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00104528710855 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000860084802567 + + Density error is 1.21927871263e-07 + + Energy Rydberg eV + E_KohnSham -34.27860329 -466.384324225 + E_Harris -34.27860329 -466.384324225 + E_Fermi -0.15996112859 -2.17638280733 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00104528697979 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000860084904666 + + Density error is 1.12041776471e-08 + + Energy Rydberg eV + E_KohnSham -34.2786032939 -466.384324279 + E_Harris -34.2786032939 -466.384324279 + E_band -7.90854830745 -107.60131989 + E_one_elec -68.8400910563 -936.617489204 + E_Hartree +35.8203788045 +487.36125626 + E_xc -8.17453830973 -111.220299532 + E_Ewald +7.0408625703 +95.795849791 + E_demet -3.47077308961e-64 -4.72222904838e-63 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194074281497 -2.64051606362 + E_Fermi -0.159961016345 -2.17638128017 + + charge density convergence is achieved + final etot is -466.384324279 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1415 2.00000 + 2 -12.6673 2.00000 + 3 -9.27777 2.00000 + 4 -6.71414 2.00000 + 5 1.06208 0.00000 + 6 4.07653 0.00000 + 7 11.1213 0.00000 + 8 11.3850 0.00000 + + EFERMI = -2.176381280169736 eV + OUT.ABACUS/ final etot is -466.3843242786891 eV + correction force for each atom along direction 1 is 3.04952e-05 + correction force for each atom along direction 2 is 6.83240e-05 + correction force for each atom along direction 3 is -1.39260e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.2549265 -1.3690853 +0.27018313 + H1 -1.2734863 +0.84136584 -0.31791911 + H2 +0.018559840 +0.52771949 +0.047735980 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3843242786891 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2793 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2694 1 6.3 1.e+02% + Potential init_pot 0.28463 2 0.14 4.5% + PW_Basis recip2real 0.30466 17 0.018 4.9% + PW_Basis gathers_scatterp 0.13368 17 0.0079 2.1% + Potential v_of_rho 1.0536 14 0.075 17.% + XC_Functional v_xc 0.29529 15 0.020 4.7% + H_Hartree_pw v_hartree 0.71292 14 0.051 11.% + PW_Basis real2recip 0.69756 41 0.017 11.% + PW_Basis gatherp_scatters 0.26318 41 0.0064 4.2% + ORB_control set_orb_tables 1.0930 1 1.1 17.% + ORB_gen_tables gen_tables 1.0930 1 1.1 17.% + ORB_table_phi init_Table 0.47508 1 0.48 7.6% + ORB_table_phi cal_ST_Phi12_R 0.46995 126 0.0037 7.5% + ORB_table_beta init_Table_Beta 0.18345 1 0.18 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18193 56 0.0032 2.9% + ORB_table_alpha init_Table_Alpha 0.24971 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.24774 66 0.0038 3.9% + LOOP_ions opt_ions 4.6490 1 4.6 74.% + ESolver_KS_LCAO Run 4.1797 1 4.2 67.% + HSolverLCAO solve 1.7303 12 0.14 28.% + HamiltLCAO updateHk 0.96096 12 0.080 15.% + LCAO_Hamilt cal_Hgamma 0.93112 12 0.078 15.% + Gint_interface cal_gint 1.4625 25 0.059 23.% + Gint_Gamma distri_vl 2.1889 6 0.36 35.% + LCAO_Deepks cal_projected_DM 4.5132 14 0.32 72.% + LCAO_gen_fixedH add_v_delta 2.0436 6 0.34 33.% + LCAO_DESCRIPTOR add_v_delta 2.0436 6 0.34 33.% + ElecStateLCAO psiToRho 0.75360 12 0.063 12.% + Charge mix_rho 0.85124 11 0.077 14.% + LOOP_ions force_stress 0.46914 1 0.47 7.5% + Force_Stress_LCAO getForceStress 0.46911 1 0.47 7.5% + Force_LCAO_gamma ftable_gamma 0.25553 1 0.26 4.1% + Force_LCAO_gamma cal_fvl_dphi 0.24763 1 0.25 3.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:35 2022 + Finish Time : Wed Sep 28 11:11:42 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..9e46d12b8c981ea302c9da8ea2ac2389cdba0cac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123528 ima = 3.68272e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123049726749 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111871767835 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112568831916 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112775672994 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756391508 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112768114703 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112764380271 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112766327762 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112765795957 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112765746562 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112765730387 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112765724307 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b5985caa4fa468a923702d7f8faaef2f3862b3d7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.484792133535 19.839353950726 0.006295219127 0 0 0 +H +0.0 +2 +-14.085521983914 18.572689777803 0.329409379888 0 0 0 +-14.610461527923 21.400668919985 0.393005957944 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/conv new file mode 100644 index 0000000000000000000000000000000000000000..3742b6e94575489fb31c4d33f1aa26d0e6881bf4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/conv @@ -0,0 +1 @@ +49 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..be577bc9da1d238eff1a520afc47c5ba3c225f31 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752692095 0.01255948489 1.250118057 1.342837053 1.468717076 0.009000052383 0.01708663655 0.03917042998 +-1.8214436e-19 0.0008703568206 0.002595721306 0.01212424272 0.04376350614 -1.147515367e-19 2.082503121e-06 6.052498997e-06 +0.001577651125 0.006001415864 + +H atom_index 1 n_descriptor 18 +1.184538758 0.0367287504 0.08809260707 0.1217653609 0.2968835416 0.01940132654 0.02442525331 0.04031286855 +-6.38645368e-18 3.880116727e-05 0.08341640342 0.1038632737 0.1126836629 7.268610914e-18 6.351722731e-06 0.01476559192 +0.02348431095 0.02738872622 + +H atom_index 2 n_descriptor 18 +1.250595888 0.03460816716 0.1091831475 0.1500289203 0.3208348748 0.02255515895 0.02830513223 0.03779823767 +-4.337681627e-17 4.46576136e-05 0.1002602814 0.1155181813 0.1285846557 -9.039992692e-19 3.505666944e-06 0.01328105314 +0.02614679363 0.03075231743 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5c1be130cf4d428ac3d5c554a26816ce495f5813 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:35 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0878264 SEC) : SETUP UNITCELL + DONE(0.0979411 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116215 SEC) : INIT PLANEWAVE + DONE(0.166044 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448926 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651954e+02 0.000000e+00 2.112e-01 4.615e-01 + GE2 -4.663817e+02 -1.186253e+00 9.825e-02 4.019e-01 + GE3 -4.663856e+02 -3.929583e-03 6.326e-02 4.696e-01 + GE4 -4.663846e+02 1.028149e-03 1.917e-03 3.341e-01 + GE5 -4.663841e+02 4.416771e-04 8.308e-04 3.302e-01 + GE6 -4.663844e+02 -2.226999e-04 1.355e-04 3.274e-01 + GE7 -4.663843e+02 6.233480e-05 2.992e-05 3.119e-01 + GE8 -4.663843e+02 -3.009565e-05 1.151e-05 3.115e-01 + GE9 -4.663843e+02 1.334988e-05 1.460e-06 3.098e-01 + GE10 -4.663843e+02 -2.542487e-06 4.028e-07 3.109e-01 + GE11 -4.663843e+02 -1.979000e-07 1.219e-07 3.080e-01 + GE12 -4.663843e+02 -5.364621e-08 1.120e-08 2.407e-01 +E_delta_band = -6.88589788e-02 Ry = -9.36874470e-01 eV +E_delta_NN= -1.94074281e-01 Ry = -2.64051606e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2793 11 0.57 1e+02 % + Run_lcao lcao_line 6.2694 1 6.3 1e+02 % + Potential init_pot 0.28463 2 0.14 4.5 % + PW_Basis recip2real 0.30466 17 0.018 4.9 % + PW_Basis gathers_scatterp 0.13368 17 0.0079 2.1 % + Potential v_of_rho 1.0536 14 0.075 17 % + XC_Functional v_xc 0.29529 15 0.02 4.7 % + H_Hartree_pw v_hartree 0.71292 14 0.051 11 % + PW_Basis real2recip 0.69756 41 0.017 11 % + PW_Basis gatherp_scatters 0.26318 41 0.0064 4.2 % + ORB_control set_orb_tables 1.093 1 1.1 17 % + ORB_gen_tables gen_tables 1.093 1 1.1 17 % + ORB_table_phi init_Table 0.47508 1 0.48 7.6 % + ORB_table_phi cal_ST_Phi12_R 0.46995 126 0.0037 7.5 % + ORB_table_beta init_Table_Beta 0.18345 1 0.18 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18193 56 0.0032 2.9 % + ORB_table_alpha init_Table_Alpha 0.24971 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.24774 66 0.0038 3.9 % + LOOP_ions opt_ions 4.649 1 4.6 74 % + ESolver_KS_LCAO Run 4.1797 1 4.2 67 % + HSolverLCAO solve 1.7303 12 0.14 28 % + HamiltLCAO updateHk 0.96096 12 0.08 15 % + LCAO_Hamilt cal_Hgamma 0.93112 12 0.078 15 % + Gint_interface cal_gint 1.4625 25 0.059 23 % + Gint_Gamma distri_vl 2.1889 6 0.36 35 % + LCAO_Deepks cal_projected_DM 4.5132 14 0.32 72 % + LCAO_gen_fixedH add_v_delta 2.0436 6 0.34 33 % + LCAO_DESCRIPTOR add_v_delta 2.0436 6 0.34 33 % + ElecStateLCAO psiToRho 0.7536 12 0.063 12 % + Charge mix_rho 0.85124 11 0.077 14 % + LOOP_ions force_stress 0.46914 1 0.47 7.5 % + Force_Stress_LCAO getForceStress 0.46911 1 0.47 7.5 % + Force_LCAO_gamma ftable_gamma 0.25553 1 0.26 4.1 % + Force_LCAO_gamma cal_fvl_dphi 0.24763 1 0.25 3.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:35 2022 + FINISH Time : Wed Sep 28 11:11:42 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/49/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..dae727fbb8c9a9401f0b16ea7fb72110cc45e5c5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.515395 0.717901 0.298015 +H 0.573992 0.725446 0.321181 +H 0.485996 0.773256 0.292857 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..fb2044969a0d60cfb6641a1f99105f30a4aa0f16 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.554 2 + 2 -13.7208 2 + 3 -8.84171 2 + 4 -6.80388 2 + 5 1.65296 0 + 6 5.0097 0 + 7 10.987 0 + 8 11.194 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..31abb5b1a1fdf99b1c68fdd3b5e28168af111a61 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:01 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.4310530752 20.1012168283 8.3444253894 0 0 0 0 + tauc_H1 16.0717773679 20.3124798787 8.9930718056 0 0 0 0 + tauc_H2 13.6078837183 21.6511694377 8.19998303774 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0871923641098 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101936731376 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.120331459569 (SEC) + + DONE : INIT CHARGE Time : 0.170207100518 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.464085 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 144 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00149 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00096 + + Density error is 0.220777694616 + + Energy Rydberg eV + E_KohnSham -34.1814098416 -465.061939519 + E_Harris -34.3856619916 -467.840932588 + E_Fermi -0.42863763086 -5.83191415692 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00137748822464 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106346812294 + + Density error is 0.0972599083964 + + Energy Rydberg eV + E_KohnSham -34.2739246154 -466.320667592 + E_Harris -34.2804015186 -466.408790381 + E_Fermi -0.23355563005 -3.17768736866 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00126796863524 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100401503354 + + Density error is 0.0618362034758 + + Energy Rydberg eV + E_KohnSham -34.2741728051 -466.324044386 + E_Harris -34.2782198667 -466.379107484 + E_Fermi -0.216869700244 -2.95066364687 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109333616382 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00090841133385 + + Density error is 0.00218949374314 + + Energy Rydberg eV + E_KohnSham -34.2742607501 -466.325240939 + E_Harris -34.2742649345 -466.32529787 + E_Fermi -0.181424848804 -2.46841170253 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00109047803856 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000907195893617 + + Density error is 0.000924239415307 + + Energy Rydberg eV + E_KohnSham -34.2741761762 -466.324090252 + E_Harris -34.2741793416 -466.32413332 + E_Fermi -0.179757938466 -2.44573222387 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108950080661 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906288577342 + + Density error is 0.000213164935223 + + Energy Rydberg eV + E_KohnSham -34.2742357833 -466.324901249 + E_Harris -34.2742359613 -466.32490367 + E_Fermi -0.180321866818 -2.45340486272 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108924670464 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906327742021 + + Density error is 5.19559397629e-05 + + Energy Rydberg eV + E_KohnSham -34.2742126165 -466.324586048 + E_Harris -34.2742126309 -466.324586244 + E_Fermi -0.180059980249 -2.44984171316 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108927508061 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906296491924 + + Density error is 1.81570438643e-05 + + Energy Rydberg eV + E_KohnSham -34.2742188455 -466.324670797 + E_Harris -34.2742188468 -466.324670815 + E_Fermi -0.180124684668 -2.45072206194 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108924007975 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906276964999 + + Density error is 1.80113636105e-06 + + Energy Rydberg eV + E_KohnSham -34.2742172461 -466.324649037 + E_Harris -34.2742172461 -466.324649037 + E_Fermi -0.180105125488 -2.45045594565 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108923601497 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906277039229 + + Density error is 1.98266645714e-07 + + Energy Rydberg eV + E_KohnSham -34.274217487 -466.324652314 + E_Harris -34.274217487 -466.324652314 + E_Fermi -0.180103293152 -2.45043101544 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108923612982 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906277446741 + + Density error is 1.00279339635e-07 + + Energy Rydberg eV + E_KohnSham -34.2742175127 -466.324652665 + E_Harris -34.2742175127 -466.324652665 + E_Fermi -0.18010330992 -2.45043124357 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00108923591243 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000906277488899 + + Density error is 9.16006044639e-09 + + Energy Rydberg eV + E_KohnSham -34.2742175127 -466.324652664 + E_Harris -34.2742175127 -466.324652664 + E_band -8.07314931603 -109.840831503 + E_one_elec -70.0797715961 -953.484208245 + E_Hartree +36.4217953406 +495.543948022 + E_xc -8.27133954938 -112.537347964 + E_Ewald +7.77786017166 +105.823216582 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196173623588 -2.6690790781 + E_Fermi -0.180103225559 -2.45043009579 + + charge density convergence is achieved + final etot is -466.324652664 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5540 2.00000 + 2 -13.7208 2.00000 + 3 -8.84171 2.00000 + 4 -6.80388 2.00000 + 5 1.65296 0.00000 + 6 5.00970 0.00000 + 7 10.9870 0.00000 + 8 11.1940 0.00000 + + EFERMI = -2.450430095787584 eV + OUT.ABACUS/ final etot is -466.3246526638027 eV + correction force for each atom along direction 1 is 4.60761e-05 + correction force for each atom along direction 2 is 0.000120591 + correction force for each atom along direction 3 is -0.000108783 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.79810513 -2.8119151 -0.61863207 + H1 +1.5711547 +0.58752793 +0.66685896 + H2 -0.77304959 +2.2243871 -0.048226886 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3246526638027 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6991 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6895 1 6.7 1.e+02% + Potential init_pot 0.29641 2 0.15 4.4% + PW_Basis recip2real 0.28815 17 0.017 4.3% + PW_Basis gathers_scatterp 0.13583 17 0.0080 2.0% + Potential v_of_rho 1.0600 14 0.076 16.% + XC_Functional v_xc 0.32242 15 0.021 4.8% + H_Hartree_pw v_hartree 0.69196 14 0.049 10.% + PW_Basis real2recip 0.70102 41 0.017 10.% + PW_Basis gatherp_scatters 0.29568 41 0.0072 4.4% + ORB_control set_orb_tables 1.1024 1 1.1 16.% + ORB_gen_tables gen_tables 1.1024 1 1.1 16.% + ORB_table_phi init_Table 0.48041 1 0.48 7.2% + ORB_table_phi cal_ST_Phi12_R 0.47511 126 0.0038 7.1% + ORB_table_beta init_Table_Beta 0.18491 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18335 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24954 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.24763 66 0.0038 3.7% + LOOP_ions opt_ions 5.0429 1 5.0 75.% + ESolver_KS_LCAO Run 4.5319 1 4.5 68.% + HSolverLCAO solve 2.0470 12 0.17 31.% + HamiltLCAO updateHk 1.0937 12 0.091 16.% + LCAO_Hamilt cal_Hgamma 1.0641 12 0.089 16.% + Gint_interface cal_gint 0.87325 25 0.035 13.% + Gint_Gamma distri_vl_value 0.33906 12 0.028 5.1% + Gint_Gamma distri_vl 2.3784 6 0.40 36.% + LCAO_Deepks cal_projected_DM 4.7870 14 0.34 71.% + LCAO_gen_fixedH add_v_delta 2.2326 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.2326 6 0.37 33.% + ElecStateLCAO psiToRho 0.92822 12 0.077 14.% + Charge mix_rho 0.84212 11 0.077 13.% + LOOP_ions force_stress 0.51085 1 0.51 7.6% + Force_Stress_LCAO getForceStress 0.51082 1 0.51 7.6% + Force_LCAO_gamma ftable_gamma 0.29324 1 0.29 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.17458 1 0.17 2.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:01 2022 + Finish Time : Wed Sep 28 11:03:08 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..a37b6e3ae9adfe265b038d87c9f545d1c0aefa93 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123786 ima = 3.66823e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 3 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123393401156 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112861599761 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113143534813 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011343609112 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113356198926 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113404320016 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011339265501 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113395950766 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113395283621 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113395221472 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113395217128 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113395213252 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/STRU new file mode 100644 index 0000000000000000000000000000000000000000..696c6cce067b694e28f75b6932763ae50bbc05ef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.568946924824 20.101216828304 8.344425389414 0 0 0 +H +0.0 +2 +-11.928222632124 20.312479878740 8.993071805618 0 0 0 +-14.392116281726 21.651169437703 8.199983037735 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/conv new file mode 100644 index 0000000000000000000000000000000000000000..610bd0e48c0d386007665636c587e7dfb006a570 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/conv @@ -0,0 +1 @@ +5 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ac9227e54c5ea6bfe66cf4a16b5d190d08ba6a8d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.743477102 0.01278811232 1.311528922 1.395836832 1.470937367 0.007926692294 0.02139768908 0.03888375222 +1.862860244e-18 0.001347838576 0.00253169662 0.01345072816 0.0458533388 2.021157234e-20 1.761940485e-06 5.406423739e-06 +0.001808469256 0.005551040017 + +H atom_index 1 n_descriptor 18 +1.28378798 0.03229085039 0.1219301449 0.1676659031 0.3323807451 0.02352532177 0.03039566675 0.03586671063 +2.614170447e-17 4.62313138e-05 0.1084525884 0.120618672 0.1442181969 3.995990326e-18 2.556777803e-06 0.01311027976 +0.02793727441 0.03228097178 + +H atom_index 2 n_descriptor 18 +1.29650709 0.03189448562 0.1268973696 0.1742665228 0.335692533 0.02404611846 0.03110636928 0.03579361524 +3.307336923e-17 4.732724428e-05 0.1082694862 0.1244082172 0.1497811771 6.190574544e-18 1.926164951e-06 0.01341370094 +0.0283258439 0.03272176937 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ae54345b1651a9da42d007d65e99d2c6f13baa25 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/e_base.npy 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/dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..9cc067c06e21dc2683b5553946b76abdff87fcd4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..5e387b15a455aeb19cd4687019bd7a552a8df97a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:01 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872135 SEC) : SETUP UNITCELL + DONE(0.101957 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.120355 SEC) : INIT PLANEWAVE + DONE(0.170341 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.464151 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650619e+02 0.000000e+00 2.208e-01 4.917e-01 + GE2 -4.663207e+02 -1.258728e+00 9.726e-02 4.312e-01 + GE3 -4.663240e+02 -3.376794e-03 6.184e-02 5.014e-01 + GE4 -4.663252e+02 -1.196553e-03 2.189e-03 3.608e-01 + GE5 -4.663241e+02 1.150688e-03 9.242e-04 3.621e-01 + GE6 -4.663249e+02 -8.109971e-04 2.132e-04 3.492e-01 + GE7 -4.663246e+02 3.152004e-04 5.196e-05 3.490e-01 + GE8 -4.663247e+02 -8.474903e-05 1.816e-05 3.364e-01 + GE9 -4.663246e+02 2.176031e-05 1.801e-06 3.398e-01 + GE10 -4.663247e+02 -3.277276e-06 1.983e-07 3.380e-01 + GE11 -4.663247e+02 -3.505361e-07 1.003e-07 3.380e-01 + GE12 -4.663247e+02 9.470214e-10 9.160e-09 2.725e-01 +E_delta_band = -7.34117441e-02 Ry = -9.98818020e-01 eV +E_delta_NN= -1.96173624e-01 Ry = -2.66907908e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6991 11 0.61 1e+02 % + Run_lcao lcao_line 6.6895 1 6.7 1e+02 % + Potential init_pot 0.29641 2 0.15 4.4 % + PW_Basis recip2real 0.28815 17 0.017 4.3 % + PW_Basis gathers_scatterp 0.13583 17 0.008 2 % + Potential v_of_rho 1.06 14 0.076 16 % + XC_Functional v_xc 0.32242 15 0.021 4.8 % + H_Hartree_pw v_hartree 0.69196 14 0.049 10 % + PW_Basis real2recip 0.70102 41 0.017 10 % + PW_Basis gatherp_scatters 0.29568 41 0.0072 4.4 % + ORB_control set_orb_tables 1.1024 1 1.1 16 % + ORB_gen_tables gen_tables 1.1024 1 1.1 16 % + ORB_table_phi init_Table 0.48041 1 0.48 7.2 % + ORB_table_phi cal_ST_Phi12_R 0.47511 126 0.0038 7.1 % + ORB_table_beta init_Table_Beta 0.18491 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18335 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24954 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.24763 66 0.0038 3.7 % + LOOP_ions opt_ions 5.0429 1 5 75 % + ESolver_KS_LCAO Run 4.5319 1 4.5 68 % + HSolverLCAO solve 2.047 12 0.17 31 % + HamiltLCAO updateHk 1.0937 12 0.091 16 % + LCAO_Hamilt cal_Hgamma 1.0641 12 0.089 16 % + Gint_interface cal_gint 0.87325 25 0.035 13 % + Gint_Gamma distri_vl_value 0.33906 12 0.028 5.1 % + Gint_Gamma distri_vl 2.3784 6 0.4 36 % + LCAO_Deepks cal_projected_DM 4.787 14 0.34 71 % + LCAO_gen_fixedH add_v_delta 2.2326 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.2326 6 0.37 33 % + ElecStateLCAO psiToRho 0.92822 12 0.077 14 % + Charge mix_rho 0.84212 11 0.077 13 % + LOOP_ions force_stress 0.51085 1 0.51 7.6 % + Force_Stress_LCAO getForceStress 0.51082 1 0.51 7.6 % + Force_LCAO_gamma ftable_gamma 0.29324 1 0.29 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.17458 1 0.17 2.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:01 2022 + FINISH Time : Wed Sep 28 11:03:08 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/5/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a0124cde43707a62da660df4fc377475587ad53b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.448039 0.717126 0.00667725 +H 0.482534 0.676326 0.972847 +H 0.393046 0.717779 0.971843 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bbf13bf1a50a11c9e63b31edd4e02a1dfea8f32e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6049 2 + 2 -13.0478 2 + 3 -9.34314 2 + 4 -6.81344 2 + 5 1.4559 0 + 6 4.7407 0 + 7 11.0122 0 + 8 11.2795 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..10c4e08338156220fdb2221360aec09be05e480c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:31 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.5450883522 20.0795404721 0.186962939173 0 0 0 0 + tauc_H1 13.5109407813 18.9371388397 27.2397205781 0 0 0 0 + tauc_H2 11.0052753648 20.0978093042 27.2115973438 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0739256389845 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.086641410772 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.102283612216 (SEC) + + DONE : INIT CHARGE Time : 0.143827688401 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.390552 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000672 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0016 + + Density error is 0.217248923691 + + Energy Rydberg eV + E_KohnSham -34.1853678541 -465.115791042 + E_Harris -34.3827573259 -467.801412583 + E_Fermi -0.420769415992 -5.72486160162 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00108918711609 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00140134981898 + + Density error is 0.0974087661639 + + Energy Rydberg eV + E_KohnSham -34.2769985396 -466.362490477 + E_Harris -34.2837061764 -466.453752556 + E_Fermi -0.228042459277 -3.1026768321 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00104928380139 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129177987004 + + Density error is 0.062259618527 + + Energy Rydberg eV + E_KohnSham -34.2773128029 -466.366766247 + E_Harris -34.281630189 -466.425507299 + E_Fermi -0.214555508104 -2.91917744749 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00100240247897 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011045849695 + + Density error is 0.00202622259206 + + Energy Rydberg eV + E_KohnSham -34.2773443539 -466.367195522 + E_Harris -34.2773465377 -466.367225233 + E_Fermi -0.17850449513 -2.42867825238 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00100680414973 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110347708865 + + Density error is 0.000958632658123 + + Energy Rydberg eV + E_KohnSham -34.2772651559 -466.366117977 + E_Harris -34.2772676363 -466.366151725 + E_Fermi -0.177461843827 -2.41449225363 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00100528711832 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110146921565 + + Density error is 0.000101099186703 + + Energy Rydberg eV + E_KohnSham -34.2773177893 -466.366834091 + E_Harris -34.2773178018 -466.366834261 + E_Fermi -0.177664082331 -2.41724384964 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0010051276817 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110104247088 + + Density error is 5.20116556514e-05 + + Energy Rydberg eV + E_KohnSham -34.2773017308 -466.366615604 + E_Harris -34.2773017458 -466.366615808 + E_Fermi -0.177533416496 -2.41546604975 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00100506079388 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110110148272 + + Density error is 1.60158172763e-05 + + Energy Rydberg eV + E_KohnSham -34.2773041258 -466.366648189 + E_Harris -34.2773041269 -466.366648204 + E_Fermi -0.177600131099 -2.41637374849 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00100507921904 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110108301559 + + Density error is 2.09763824032e-06 + + Energy Rydberg eV + E_KohnSham -34.277302525 -466.36662641 + E_Harris -34.2773025251 -466.366626411 + E_Fermi -0.177583676281 -2.41614986921 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00100508233035 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110107948582 + + Density error is 1.72659222801e-07 + + Energy Rydberg eV + E_KohnSham -34.2773027506 -466.366629479 + E_Harris -34.2773027506 -466.366629479 + E_Fermi -0.177581363142 -2.41611839734 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00100508269586 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110108008667 + + Density error is 3.51392922348e-08 + + Energy Rydberg eV + E_KohnSham -34.2773027945 -466.366630076 + E_Harris -34.2773027945 -466.366630076 + E_band -8.05681749561 -109.618625686 + E_one_elec -69.7791939292 -949.394639284 + E_Hartree +36.2627413811 +493.379907884 + E_xc -8.24569704934 -112.188463853 + E_Ewald +7.60814790309 +103.514162709 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195769546546 -2.6635813279 + E_Fermi -0.177581492337 -2.41612015512 + + charge density convergence is achieved + final etot is -466.366630076 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6049 2.00000 + 2 -13.0478 2.00000 + 3 -9.34314 2.00000 + 4 -6.81344 2.00000 + 5 1.45590 0.00000 + 6 4.74070 0.00000 + 7 11.0122 0.00000 + 8 11.2795 0.00000 + + EFERMI = -2.416120155124995 eV + OUT.ABACUS/ final etot is -466.3666300761708 eV + correction force for each atom along direction 1 is -7.91791e-05 + correction force for each atom along direction 2 is 5.06184e-05 + correction force for each atom along direction 3 is -6.18395e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.85054733 +1.1833724 +1.0773169 + H1 +1.5539285 -1.4397493 -0.97422370 + H2 -0.70338113 +0.25637689 -0.10309317 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3666300761708 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.7370 11 0.52 1.0e+02% + Run_lcao lcao_line 5.7293 1 5.7 1.e+02% + Potential init_pot 0.24413 2 0.12 4.3% + PW_Basis recip2real 0.25101 16 0.016 4.4% + PW_Basis gathers_scatterp 0.10694 16 0.0067 1.9% + Potential v_of_rho 0.89949 13 0.069 16.% + XC_Functional v_xc 0.26912 14 0.019 4.7% + H_Hartree_pw v_hartree 0.59388 13 0.046 10.% + PW_Basis real2recip 0.59875 38 0.016 10.% + PW_Basis gatherp_scatters 0.22209 38 0.0058 3.9% + ORB_control set_orb_tables 0.90334 1 0.90 16.% + ORB_gen_tables gen_tables 0.90333 1 0.90 16.% + ORB_table_phi init_Table 0.37782 1 0.38 6.6% + ORB_table_phi cal_ST_Phi12_R 0.37355 126 0.0030 6.5% + ORB_table_beta init_Table_Beta 0.15724 1 0.16 2.7% + ORB_table_beta VNL_PhiBeta_R 0.15588 56 0.0028 2.7% + ORB_table_alpha init_Table_Alpha 0.21065 1 0.21 3.7% + ORB_table_alpha S_PhiAlpha_R 0.20898 66 0.0032 3.6% + LOOP_ions opt_ions 4.3666 1 4.4 76.% + ESolver_KS_LCAO Run 3.9085 1 3.9 68.% + HSolverLCAO solve 1.7467 11 0.16 30.% + HamiltLCAO updateHk 0.95788 11 0.087 17.% + LCAO_Hamilt cal_Hgamma 0.93244 11 0.085 16.% + Gint_interface cal_gint 1.3633 23 0.059 24.% + Gint_Gamma distri_vl 1.9011 6 0.32 33.% + LCAO_Deepks cal_projected_DM 4.2205 13 0.32 74.% + LCAO_gen_fixedH add_v_delta 1.7695 6 0.29 31.% + LCAO_DESCRIPTOR add_v_delta 1.7695 6 0.29 31.% + ElecStateLCAO psiToRho 0.77389 11 0.070 13.% + Charge mix_rho 0.75761 10 0.076 13.% + LOOP_ions force_stress 0.45795 1 0.46 8.0% + Force_Stress_LCAO getForceStress 0.45793 1 0.46 8.0% + Force_LCAO_gamma ftable_gamma 0.26016 1 0.26 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.23369 1 0.23 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:31 2022 + Finish Time : Wed Sep 28 11:13:37 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..21666f8e4e575d7c710388e9403741fe0d6730c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124089 ima = 3.66662e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122668794387 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111635994131 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112114315797 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112416504935 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112339295038 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112380195288 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112377710721 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112381014924 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112380315172 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112380212314 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112380210699 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b4977d6d0d985a2e9b6db6393009c0e5add0d90e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.454911647804 20.079540472136 0.186962939179 0 0 0 +H +0.0 +2 +-14.489059218688 18.937138839705 -0.760279421898 0 0 0 +-16.994724635184 20.097809304203 -0.788402656219 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/conv new file mode 100644 index 0000000000000000000000000000000000000000..59c8f9607786e36f9ba997912e04dff4d66461ba --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/conv @@ -0,0 +1 @@ +50 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5664b22cce556cae12f34d24a7bfc971f4932e69 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752296044 0.01287136261 1.289329926 1.37366226 1.470681058 0.009274813144 0.01792679156 0.03910820899 +-6.175717252e-18 0.001072519435 0.00291273637 0.01353878096 0.0488817787 -1.155961745e-18 2.852872297e-06 7.448614533e-06 +0.001605101221 0.006096529263 + +H atom_index 1 n_descriptor 18 +1.297194841 0.03312463977 0.1281623055 0.1729596999 0.3338513488 0.02527762127 0.03096274576 0.03677721701 +-6.282777011e-17 5.798533548e-05 0.1086436346 0.1245553716 0.1484352015 7.813876543e-18 1.058642329e-06 0.01374711442 +0.02882562458 0.03268151147 + +H atom_index 2 n_descriptor 18 +1.256212905 0.03442517038 0.1124824208 0.1524024419 0.3216334844 0.02329349371 0.0286022274 0.03752598127 +-6.46584998e-18 5.395852664e-05 0.1058788134 0.1155151379 0.1309561481 -3.565078611e-18 3.283363999e-06 0.01332568794 +0.02747040038 0.03104793274 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..582e98c48c650650eb15cd86eea2641526ff0fca Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:31 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0739408 SEC) : SETUP UNITCELL + DONE(0.0866529 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.102296 SEC) : INIT PLANEWAVE + DONE(0.14393 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.390604 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651158e+02 0.000000e+00 2.172e-01 4.445e-01 + GE2 -4.663625e+02 -1.246699e+00 9.741e-02 3.998e-01 + GE3 -4.663668e+02 -4.275771e-03 6.226e-02 4.605e-01 + GE4 -4.663672e+02 -4.292741e-04 2.026e-03 3.411e-01 + GE5 -4.663661e+02 1.077544e-03 9.586e-04 3.440e-01 + GE6 -4.663668e+02 -7.161139e-04 1.011e-04 3.172e-01 + GE7 -4.663666e+02 2.184869e-04 5.201e-05 3.297e-01 + GE8 -4.663666e+02 -3.258501e-05 1.602e-05 3.220e-01 + GE9 -4.663666e+02 2.177876e-05 2.098e-06 3.187e-01 + GE10 -4.663666e+02 -3.068917e-06 1.727e-07 3.255e-01 + GE11 -4.663666e+02 -5.968144e-07 3.514e-08 2.521e-01 +E_delta_band = -7.24684464e-02 Ry = -9.85983796e-01 eV +E_delta_NN= -1.95769547e-01 Ry = -2.66358133e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.737 11 0.52 1e+02 % + Run_lcao lcao_line 5.7293 1 5.7 1e+02 % + Potential init_pot 0.24413 2 0.12 4.3 % + PW_Basis recip2real 0.25101 16 0.016 4.4 % + PW_Basis gathers_scatterp 0.10694 16 0.0067 1.9 % + Potential v_of_rho 0.89949 13 0.069 16 % + XC_Functional v_xc 0.26912 14 0.019 4.7 % + H_Hartree_pw v_hartree 0.59388 13 0.046 10 % + PW_Basis real2recip 0.59875 38 0.016 10 % + PW_Basis gatherp_scatters 0.22209 38 0.0058 3.9 % + ORB_control set_orb_tables 0.90334 1 0.9 16 % + ORB_gen_tables gen_tables 0.90333 1 0.9 16 % + ORB_table_phi init_Table 0.37782 1 0.38 6.6 % + ORB_table_phi cal_ST_Phi12_R 0.37355 126 0.003 6.5 % + ORB_table_beta init_Table_Beta 0.15724 1 0.16 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.15588 56 0.0028 2.7 % + ORB_table_alpha init_Table_Alpha 0.21065 1 0.21 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.20898 66 0.0032 3.6 % + LOOP_ions opt_ions 4.3666 1 4.4 76 % + ESolver_KS_LCAO Run 3.9085 1 3.9 68 % + HSolverLCAO solve 1.7467 11 0.16 30 % + HamiltLCAO updateHk 0.95788 11 0.087 17 % + LCAO_Hamilt cal_Hgamma 0.93244 11 0.085 16 % + Gint_interface cal_gint 1.3633 23 0.059 24 % + Gint_Gamma distri_vl 1.9011 6 0.32 33 % + LCAO_Deepks cal_projected_DM 4.2205 13 0.32 74 % + LCAO_gen_fixedH add_v_delta 1.7695 6 0.29 31 % + LCAO_DESCRIPTOR add_v_delta 1.7695 6 0.29 31 % + ElecStateLCAO psiToRho 0.77389 11 0.07 13 % + Charge mix_rho 0.75761 10 0.076 13 % + LOOP_ions force_stress 0.45795 1 0.46 8 % + Force_Stress_LCAO getForceStress 0.45793 1 0.46 8 % + Force_LCAO_gamma ftable_gamma 0.26016 1 0.26 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.23369 1 0.23 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:31 2022 + FINISH Time : Wed Sep 28 11:13:37 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/50/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..6f2448cd4cba1cf9ab66dacb88c0cd59a7dc1a25 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.450824 0.719051 0.00447173 +H 0.504283 0.721236 0.966374 +H 0.452431 0.665178 0.0405356 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6715dc104b01e1992b83244d46f573811f628aae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2237 2 + 2 -13.3208 2 + 3 -8.86177 2 + 4 -6.72725 2 + 5 1.34684 0 + 6 4.50866 0 + 7 11.0756 0 + 8 11.3013 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b17fd1de3191ea6b3dd55a4f8cb1661462b201e9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:30 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 12.6230809429 20.1334203846 0.12520843574 0 0 0 0 + tauc_H1 14.1199336598 20.1946173737 27.0584637507 0 0 0 0 + tauc_H2 12.668056459 18.6249975094 1.13499574834 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0872222662121 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0898019355892 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.108008389999 (SEC) + + DONE : INIT CHARGE Time : 0.158693053123 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438751 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 9 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00141 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000664 + + Density error is 0.216191991724 + + Energy Rydberg eV + E_KohnSham -34.189825838 -465.176445024 + E_Harris -34.3837955862 -467.81553884 + E_Fermi -0.406472004451 -5.53033533801 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00137779486011 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000890825113123 + + Density error is 0.0981253245852 + + Energy Rydberg eV + E_KohnSham -34.2798166508 -466.400832846 + E_Harris -34.2864642433 -466.491277982 + E_Fermi -0.214194619871 -2.9142673112 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00128183302795 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000862898140288 + + Density error is 0.0628718336951 + + Energy Rydberg eV + E_KohnSham -34.2800738968 -466.404332857 + E_Harris -34.2843456911 -466.4624536 + E_Fermi -0.202316404669 -2.75265590238 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00111806463181 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830787254537 + + Density error is 0.00209074644605 + + Energy Rydberg eV + E_KohnSham -34.2800763832 -466.404366687 + E_Harris -34.2800797087 -466.404411932 + E_Fermi -0.167040656695 -2.27270472871 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00111613316726 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830960169515 + + Density error is 0.000875869166657 + + Energy Rydberg eV + E_KohnSham -34.2800187863 -466.40358304 + E_Harris -34.2800197163 -466.403595695 + E_Fermi -0.166176711002 -2.26095014453 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00111439683294 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830455196285 + + Density error is 0.000198307319447 + + Energy Rydberg eV + E_KohnSham -34.2800545541 -466.404069686 + E_Harris -34.2800546275 -466.404070686 + E_Fermi -0.166205364756 -2.26133999885 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00111434077968 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830765027606 + + Density error is 4.02976512681e-05 + + Energy Rydberg eV + E_KohnSham -34.2800408389 -466.403883082 + E_Harris -34.2800408475 -466.403883198 + E_Fermi -0.166044494882 -2.25915125192 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00111431572303 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830692471165 + + Density error is 1.74089347357e-05 + + Energy Rydberg eV + E_KohnSham -34.2800459481 -466.403952596 + E_Harris -34.2800459494 -466.403952613 + E_Fermi -0.16608939518 -2.25976215182 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00111428781949 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830693294553 + + Density error is 1.8169225776e-06 + + Energy Rydberg eV + E_KohnSham -34.2800444843 -466.40393268 + E_Harris -34.2800444843 -466.40393268 + E_Fermi -0.166070955527 -2.25951126747 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00111428465673 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830694823014 + + Density error is 2.97944659132e-07 + + Energy Rydberg eV + E_KohnSham -34.2800447359 -466.403936103 + E_Harris -34.2800447359 -466.403936103 + E_Fermi -0.166069256103 -2.25948814562 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00111428475123 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830695172695 + + Density error is 1.2460742245e-07 + + Energy Rydberg eV + E_KohnSham -34.2800447571 -466.403936392 + E_Harris -34.2800447571 -466.403936392 + E_Fermi -0.166069193224 -2.25948729011 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00111428454793 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000830695270819 + + Density error is 9.9244518066e-09 + + Energy Rydberg eV + E_KohnSham -34.2800447582 -466.403936407 + E_Harris -34.2800447582 -466.403936407 + E_band -7.95747126002 -108.266950808 + E_one_elec -69.3443620443 -943.478447978 + E_Hartree +36.0747043136 +490.82153233 + E_xc -8.21492673406 -111.769812236 + E_Ewald +7.32880374157 +99.7134904091 + E_demet -5.91570390157e-79 -8.04872807422e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194774199186 -2.65003893232 + E_Fermi -0.166069076383 -2.2594857004 + + charge density convergence is achieved + final etot is -466.403936407 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2237 2.00000 + 2 -13.3208 2.00000 + 3 -8.86177 2.00000 + 4 -6.72725 2.00000 + 5 1.34684 0.00000 + 6 4.50866 0.00000 + 7 11.0756 0.00000 + 8 11.3013 0.00000 + + EFERMI = -2.259485700402001 eV + OUT.ABACUS/ final etot is -466.4039364065933 eV + correction force for each atom along direction 1 is 0.000166842 + correction force for each atom along direction 2 is -6.77313e-05 + correction force for each atom along direction 3 is 3.33949e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.40699876 +0.92288654 -0.35312291 + H1 +0.084331982 -0.30547917 +0.15042649 + H2 +0.32266677 -0.61740737 +0.20269642 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4039364065933 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4179 11 0.58 1.0e+02% + Run_lcao lcao_line 6.4078 1 6.4 1.e+02% + Potential init_pot 0.28411 2 0.14 4.4% + PW_Basis recip2real 0.30802 17 0.018 4.8% + PW_Basis gathers_scatterp 0.13195 17 0.0078 2.1% + Potential v_of_rho 1.0801 14 0.077 17.% + XC_Functional v_xc 0.30329 15 0.020 4.7% + H_Hartree_pw v_hartree 0.72911 14 0.052 11.% + PW_Basis real2recip 0.71165 41 0.017 11.% + PW_Basis gatherp_scatters 0.27675 41 0.0067 4.3% + ORB_control set_orb_tables 1.0961 1 1.1 17.% + ORB_gen_tables gen_tables 1.0961 1 1.1 17.% + ORB_table_phi init_Table 0.47812 1 0.48 7.4% + ORB_table_phi cal_ST_Phi12_R 0.47297 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18211 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18056 56 0.0032 2.8% + ORB_table_alpha init_Table_Alpha 0.24920 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.24718 66 0.0037 3.9% + LOOP_ions opt_ions 4.7931 1 4.8 75.% + ESolver_KS_LCAO Run 4.3088 1 4.3 67.% + HSolverLCAO solve 1.8116 12 0.15 28.% + HamiltLCAO updateHk 0.99375 12 0.083 15.% + LCAO_Hamilt cal_Hgamma 0.96068 12 0.080 15.% + Gint_interface cal_gint 1.5437 25 0.062 24.% + Gint_Gamma distri_vl 2.2631 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.6554 14 0.33 73.% + LCAO_gen_fixedH add_v_delta 2.1183 6 0.35 33.% + LCAO_DESCRIPTOR add_v_delta 2.1184 6 0.35 33.% + ElecStateLCAO psiToRho 0.79960 12 0.067 12.% + Charge mix_rho 0.84962 11 0.077 13.% + LOOP_ions force_stress 0.48418 1 0.48 7.5% + Force_Stress_LCAO getForceStress 0.48414 1 0.48 7.5% + Force_LCAO_gamma ftable_gamma 0.26387 1 0.26 4.1% + Force_LCAO_gamma cal_fvl_dphi 0.25591 1 0.26 4.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:30 2022 + Finish Time : Wed Sep 28 11:08:36 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d52b806bc2cd1962907069ccfc45391b48a1cc68 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/OUT.ABACUS/warning.log @@ -0,0 +1,77 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123638 ima = 3.67196e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123537852406 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112650163889 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011313394722 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113366787317 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113319713727 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113348174948 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113338956734 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113341926899 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113341214099 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113341156049 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113341147043 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113341141241 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/STRU new file mode 100644 index 0000000000000000000000000000000000000000..aac89078c3266720c34cf22b37c579b8dc3e1ba7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-15.376919057140 20.133420384595 0.125208435724 0 0 0 +H +0.0 +2 +-13.880066340216 20.194617373679 -0.941536249329 0 0 0 +-15.331943540982 18.624997509369 1.134995748316 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/conv new file mode 100644 index 0000000000000000000000000000000000000000..26962b961d9456ba0c89ae461027b644d4af4c96 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/conv @@ -0,0 +1 @@ +51 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..71aac70c38b034f42a6d71ed6460a2c6f8e75859 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.744637593 0.01262619517 1.27916364 1.371306133 1.469079429 0.007785492052 0.02014783102 0.03888683916 +-3.410661104e-19 0.001145404943 0.002402082294 0.01234979773 0.04311328976 1.325005234e-19 1.575067227e-06 4.94006425e-06 +0.001765603337 0.005684321247 + +H atom_index 1 n_descriptor 18 +1.236177506 0.0341995681 0.1037212019 0.1448890082 0.3184883735 0.0212556864 0.02767413175 0.03735616076 +3.499974624e-17 3.848451273e-05 0.09841239038 0.1143880485 0.1243725337 4.662595003e-18 4.819449056e-06 0.01305113802 +0.02558720904 0.03023860868 + +H atom_index 2 n_descriptor 18 +1.254801797 0.03354024926 0.1100585805 0.1534451589 0.3243724046 0.02207227099 0.0287500557 0.03677036807 +7.444042971e-18 4.002414886e-05 0.1030619793 0.1150967115 0.1317680421 9.441069865e-20 3.955060419e-06 0.01290091097 +0.0262804377 0.03107726382 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ce6c4888cb5f32203f958e44c9d7716989a36adb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:30 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872483 SEC) : SETUP UNITCELL + DONE(0.0898198 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.108026 SEC) : INIT PLANEWAVE + DONE(0.158808 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438815 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651764e+02 0.000000e+00 2.162e-01 4.704e-01 + GE2 -4.664008e+02 -1.224388e+00 9.813e-02 4.100e-01 + GE3 -4.664043e+02 -3.500012e-03 6.287e-02 4.771e-01 + GE4 -4.664044e+02 -3.383019e-05 2.091e-03 3.405e-01 + GE5 -4.664036e+02 7.836469e-04 8.759e-04 3.413e-01 + GE6 -4.664041e+02 -4.866458e-04 1.983e-04 3.325e-01 + GE7 -4.664039e+02 1.866047e-04 4.030e-05 3.292e-01 + GE8 -4.664040e+02 -6.951434e-05 1.741e-05 3.219e-01 + GE9 -4.664039e+02 1.991599e-05 1.817e-06 3.254e-01 + GE10 -4.664039e+02 -3.423369e-06 2.979e-07 3.206e-01 + GE11 -4.664039e+02 -2.883266e-07 1.246e-07 3.225e-01 + GE12 -4.664039e+02 -1.499293e-08 9.924e-09 2.537e-01 +E_delta_band = -7.05101642e-02 Ry = -9.59340000e-01 eV +E_delta_NN= -1.94774199e-01 Ry = -2.65003893e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4179 11 0.58 1e+02 % + Run_lcao lcao_line 6.4078 1 6.4 1e+02 % + Potential init_pot 0.28411 2 0.14 4.4 % + PW_Basis recip2real 0.30802 17 0.018 4.8 % + PW_Basis gathers_scatterp 0.13195 17 0.0078 2.1 % + Potential v_of_rho 1.0801 14 0.077 17 % + XC_Functional v_xc 0.30329 15 0.02 4.7 % + H_Hartree_pw v_hartree 0.72911 14 0.052 11 % + PW_Basis real2recip 0.71165 41 0.017 11 % + PW_Basis gatherp_scatters 0.27675 41 0.0067 4.3 % + ORB_control set_orb_tables 1.0961 1 1.1 17 % + ORB_gen_tables gen_tables 1.0961 1 1.1 17 % + ORB_table_phi init_Table 0.47812 1 0.48 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.47297 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18211 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18056 56 0.0032 2.8 % + ORB_table_alpha init_Table_Alpha 0.2492 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.24718 66 0.0037 3.9 % + LOOP_ions opt_ions 4.7931 1 4.8 75 % + ESolver_KS_LCAO Run 4.3088 1 4.3 67 % + HSolverLCAO solve 1.8116 12 0.15 28 % + HamiltLCAO updateHk 0.99375 12 0.083 15 % + LCAO_Hamilt cal_Hgamma 0.96068 12 0.08 15 % + Gint_interface cal_gint 1.5437 25 0.062 24 % + Gint_Gamma distri_vl 2.2631 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.6554 14 0.33 73 % + LCAO_gen_fixedH add_v_delta 2.1183 6 0.35 33 % + LCAO_DESCRIPTOR add_v_delta 2.1184 6 0.35 33 % + ElecStateLCAO psiToRho 0.7996 12 0.067 12 % + Charge mix_rho 0.84962 11 0.077 13 % + LOOP_ions force_stress 0.48418 1 0.48 7.5 % + Force_Stress_LCAO getForceStress 0.48414 1 0.48 7.5 % + Force_LCAO_gamma ftable_gamma 0.26387 1 0.26 4.1 % + Force_LCAO_gamma cal_fvl_dphi 0.25591 1 0.26 4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:30 2022 + FINISH Time : Wed Sep 28 11:08:36 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/51/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..13bf1713c746f1fe5a83674032a71c98a9f06fed --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.468857 0.712666 0.999986 +H 0.504344 0.728439 0.946233 +H 0.510213 0.670936 0.0283297 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..9cd485224c308f4426ee063c629959dcce363adf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3379 2 + 2 -12.7753 2 + 3 -9.34978 2 + 4 -6.75759 2 + 5 1.2376 0 + 6 4.33018 0 + 7 11.078 0 + 8 11.3536 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7e8f69469f74bd4c897c1cb294b174046d9fc746 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:13 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.1279841741 19.9546443694 27.9996197414 0 0 0 0 + tauc_H1 14.1216335624 20.3962843004 26.4945233391 0 0 0 0 + tauc_H2 14.2859509691 18.7861992715 0.793231895928 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0750764246741 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0826608270411 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0997472136121 (SEC) + + DONE : INIT CHARGE Time : 0.143200429443 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.387413 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 0 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00122 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113 + + Density error is 0.213546763033 + + Energy Rydberg eV + E_KohnSham -34.1905521726 -465.186327314 + E_Harris -34.3799564569 -467.763304805 + E_Fermi -0.403882379838 -5.49510168759 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00138356558647 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113248764674 + + Density error is 0.0979159091883 + + Energy Rydberg eV + E_KohnSham -34.2799566944 -466.402738237 + E_Harris -34.286840181 -466.496392878 + E_Fermi -0.213155316594 -2.90012686467 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00130071653008 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106387725889 + + Density error is 0.0629202865756 + + Energy Rydberg eV + E_KohnSham -34.2803070078 -466.407504496 + E_Harris -34.2847629613 -466.468130853 + E_Fermi -0.20320543005 -2.76475171322 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116699169819 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959353367703 + + Density error is 0.0019301371564 + + Energy Rydberg eV + E_KohnSham -34.2802708338 -466.407012323 + E_Harris -34.2802711219 -466.407016243 + E_Fermi -0.167477960102 -2.2786545468 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116835428691 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000960728503298 + + Density error is 0.00094526736102 + + Energy Rydberg eV + E_KohnSham -34.2802117014 -466.406207786 + E_Harris -34.280213035 -466.40622593 + E_Fermi -0.167002361268 -2.27218369269 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116635493472 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959199154333 + + Density error is 9.96724499473e-05 + + Energy Rydberg eV + E_KohnSham -34.2802484367 -466.406707595 + E_Harris -34.2802485988 -466.4067098 + E_Fermi -0.166888291444 -2.27063169312 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116622122207 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959156585973 + + Density error is 3.37916876334e-05 + + Energy Rydberg eV + E_KohnSham -34.2802373101 -466.406556209 + E_Harris -34.2802371563 -466.406554117 + E_Fermi -0.166789616584 -2.26928915278 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116618753621 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959133328591 + + Density error is 1.08769121455e-05 + + Energy Rydberg eV + E_KohnSham -34.2802391964 -466.406581874 + E_Harris -34.2802393572 -466.406584062 + E_Fermi -0.166828686911 -2.26982073185 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116617752555 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959128075396 + + Density error is 8.15291041404e-07 + + Energy Rydberg eV + E_KohnSham -34.2802380137 -466.406565783 + E_Harris -34.2802380137 -466.406565783 + E_Fermi -0.16681604904 -2.26964878479 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116617794352 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959127674818 + + Density error is 1.09162417758e-07 + + Energy Rydberg eV + E_KohnSham -34.2802383761 -466.406570713 + E_Harris -34.2802382158 -466.406568533 + E_Fermi -0.166815913868 -2.26964694568 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116617840748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959127966538 + + Density error is 4.52001460566e-08 + + Energy Rydberg eV + E_KohnSham -34.2802382235 -466.406568638 + E_Harris -34.2802383838 -466.406570818 + E_band -7.97027486702 -108.441152818 + E_one_elec -69.2186906669 -941.76860117 + E_Hartree +35.9974184122 +489.770003696 + E_xc -8.20274280325 -111.604041353 + E_Ewald +7.26822334082 +98.8892517718 + E_demet -8.05348967083e-75 -1.09573348307e-73 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194718791121 -2.64928506692 + E_Fermi -0.166815940734 -2.26964731122 + + charge density convergence is achieved + final etot is -466.406568638 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3379 2.00000 + 2 -12.7753 2.00000 + 3 -9.34978 2.00000 + 4 -6.75759 2.00000 + 5 1.23760 0.00000 + 6 4.33018 0.00000 + 7 11.0780 0.00000 + 8 11.3536 0.00000 + + EFERMI = -2.269647311218057 eV + OUT.ABACUS/ final etot is -466.4065686375719 eV + correction force for each atom along direction 1 is 5.66945e-05 + correction force for each atom along direction 2 is -0.000144583 + correction force for each atom along direction 3 is -2.41937e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.25008598 +0.25130111 -0.60065793 + H1 -0.38466451 +0.17907631 +0.057905092 + H2 +0.13457853 -0.43037742 +0.54275284 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4065686375719 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.1995 11 0.47 1.0e+02% + Run_lcao lcao_line 5.1910 1 5.2 1.e+02% + Potential init_pot 0.24315 2 0.12 4.7% + PW_Basis recip2real 0.25910 16 0.016 5.0% + PW_Basis gathers_scatterp 0.10334 16 0.0065 2.0% + Potential v_of_rho 0.90572 13 0.070 17.% + XC_Functional v_xc 0.26411 14 0.019 5.1% + H_Hartree_pw v_hartree 0.60519 13 0.047 12.% + PW_Basis real2recip 0.62266 38 0.016 12.% + PW_Basis gatherp_scatters 0.24041 38 0.0063 4.6% + ORB_control set_orb_tables 0.89180 1 0.89 17.% + ORB_gen_tables gen_tables 0.89180 1 0.89 17.% + ORB_table_phi init_Table 0.37265 1 0.37 7.2% + ORB_table_phi cal_ST_Phi12_R 0.36849 126 0.0029 7.1% + ORB_table_beta init_Table_Beta 0.15276 1 0.15 2.9% + ORB_table_beta VNL_PhiBeta_R 0.15149 56 0.0027 2.9% + ORB_table_alpha init_Table_Alpha 0.20890 1 0.21 4.0% + ORB_table_alpha S_PhiAlpha_R 0.20726 66 0.0031 4.0% + LOOP_ions opt_ions 3.8411 1 3.8 74.% + ESolver_KS_LCAO Run 3.4441 1 3.4 66.% + HSolverLCAO solve 1.2803 11 0.12 25.% + HamiltLCAO updateHk 0.74494 11 0.068 14.% + LCAO_Hamilt cal_Hgamma 0.71346 11 0.065 14.% + Gint_interface cal_gint 0.96316 23 0.042 19.% + Gint_Gamma distri_vl 1.6747 6 0.28 32.% + LCAO_Deepks cal_projected_DM 3.7180 13 0.29 72.% + LCAO_gen_fixedH add_v_delta 1.5472 6 0.26 30.% + LCAO_DESCRIPTOR add_v_delta 1.5473 6 0.26 30.% + ElecStateLCAO psiToRho 0.51911 11 0.047 10.% + Charge mix_rho 0.76100 10 0.076 15.% + LOOP_ions force_stress 0.39689 1 0.40 7.6% + Force_Stress_LCAO getForceStress 0.39687 1 0.40 7.6% + Force_LCAO_gamma ftable_gamma 0.19962 1 0.20 3.8% + Force_LCAO_gamma cal_fvl_dphi 0.18608 1 0.19 3.6% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:13 2022 + Finish Time : Wed Sep 28 11:06:18 2022 + Total Time : 0 h 0 mins 5 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..9df65a4f0c0809e43ca4d7b601687d9df3877641 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123448 ima = 3.65996e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122830475209 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111598574569 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112229533716 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112482365748 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112430725968 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112459358753 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112456546139 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112459003435 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112458474313 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112458452465 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112458445336 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3761c4463d5cdcd6ebf66d1c07e2836530830fdf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.872015825885 19.954644369401 -0.000380258628 0 0 0 +H +0.0 +2 +-13.878366437647 20.396284300368 -1.505476660862 0 0 0 +-13.714049030916 18.786199271538 0.793231895928 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/conv new file mode 100644 index 0000000000000000000000000000000000000000..64f8bd4eeac5a7c7d2363624f2a82fb9ac424186 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/conv @@ -0,0 +1 @@ +52 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4ac04713e08f9eb449fbe86b25d001beb3075e01 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753003325 0.01274216592 1.267883069 1.351907281 1.469446068 0.00919842527 0.01711644593 0.0391396465 +-1.472672693e-18 0.0009287081633 0.002754777701 0.01287374178 0.04601676799 -1.468643295e-19 2.51891825e-06 6.873135957e-06 +0.001594003415 0.006109836681 + +H atom_index 1 n_descriptor 18 +1.230404613 0.03538027767 0.1032948547 0.1406930729 0.3133314377 0.02191729064 0.02709679568 0.03852542535 +-5.608901591e-17 4.669827677e-05 0.09730864303 0.1144029817 0.1205871751 2.508946473e-18 4.491976182e-06 0.01360599013 +0.02593239134 0.02980251109 + +H atom_index 2 n_descriptor 18 +1.254269722 0.03457595598 0.1115303615 0.1515866591 0.3214038801 0.02308083618 0.0284972547 0.03772046885 +-1.175358859e-17 4.894343002e-05 0.1030813126 0.115627657 0.1300222258 -6.553943168e-18 3.190500561e-06 0.01331532035 +0.0268390849 0.03092919048 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..2bae425405953bf2ef0652e4c303dfd0722cf97a Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..f150c6df0afe9954e45865200e331eef3718ba9d Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..0eb4d9c6ba9e5139349874e4961bfd509b2c4991 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..68f429aff7b898e36416e5174f2037a0fb01c541 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:13 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0750923 SEC) : SETUP UNITCELL + DONE(0.0826734 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0997619 SEC) : INIT PLANEWAVE + DONE(0.143327 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.387455 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651863e+02 0.000000e+00 2.135e-01 4.035e-01 + GE2 -4.664027e+02 -1.216411e+00 9.792e-02 3.638e-01 + GE3 -4.664075e+02 -4.766258e-03 6.292e-02 4.205e-01 + GE4 -4.664070e+02 4.921727e-04 1.930e-03 2.980e-01 + GE5 -4.664062e+02 8.045373e-04 9.453e-04 2.961e-01 + GE6 -4.664067e+02 -4.998090e-04 9.967e-05 2.860e-01 + GE7 -4.664066e+02 1.513853e-04 3.379e-05 2.763e-01 + GE8 -4.664066e+02 -2.566488e-05 1.088e-05 2.756e-01 + GE9 -4.664066e+02 1.609118e-05 8.153e-07 2.809e-01 + GE10 -4.664066e+02 -4.930202e-06 1.092e-07 2.806e-01 + GE11 -4.664066e+02 2.075778e-06 4.520e-08 2.057e-01 +E_delta_band = -7.02722847e-02 Ry = -9.56103483e-01 eV +E_delta_NN= -1.94718791e-01 Ry = -2.64928507e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.1995 11 0.47 1e+02 % + Run_lcao lcao_line 5.191 1 5.2 1e+02 % + Potential init_pot 0.24315 2 0.12 4.7 % + PW_Basis recip2real 0.2591 16 0.016 5 % + PW_Basis gathers_scatterp 0.10334 16 0.0065 2 % + Potential v_of_rho 0.90572 13 0.07 17 % + XC_Functional v_xc 0.26411 14 0.019 5.1 % + H_Hartree_pw v_hartree 0.60519 13 0.047 12 % + PW_Basis real2recip 0.62266 38 0.016 12 % + PW_Basis gatherp_scatters 0.24041 38 0.0063 4.6 % + ORB_control set_orb_tables 0.8918 1 0.89 17 % + ORB_gen_tables gen_tables 0.8918 1 0.89 17 % + ORB_table_phi init_Table 0.37265 1 0.37 7.2 % + ORB_table_phi cal_ST_Phi12_R 0.36849 126 0.0029 7.1 % + ORB_table_beta init_Table_Beta 0.15276 1 0.15 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.15149 56 0.0027 2.9 % + ORB_table_alpha init_Table_Alpha 0.2089 1 0.21 4 % + ORB_table_alpha S_PhiAlpha_R 0.20726 66 0.0031 4 % + LOOP_ions opt_ions 3.8411 1 3.8 74 % + ESolver_KS_LCAO Run 3.4441 1 3.4 66 % + HSolverLCAO solve 1.2803 11 0.12 25 % + HamiltLCAO updateHk 0.74494 11 0.068 14 % + LCAO_Hamilt cal_Hgamma 0.71346 11 0.065 14 % + Gint_interface cal_gint 0.96316 23 0.042 19 % + Gint_Gamma distri_vl 1.6747 6 0.28 32 % + LCAO_Deepks cal_projected_DM 3.718 13 0.29 72 % + LCAO_gen_fixedH add_v_delta 1.5472 6 0.26 30 % + LCAO_DESCRIPTOR add_v_delta 1.5473 6 0.26 30 % + ElecStateLCAO psiToRho 0.51911 11 0.047 10 % + Charge mix_rho 0.761 10 0.076 15 % + LOOP_ions force_stress 0.39689 1 0.4 7.6 % + Force_Stress_LCAO getForceStress 0.39687 1 0.4 7.6 % + Force_LCAO_gamma ftable_gamma 0.19962 1 0.2 3.8 % + Force_LCAO_gamma cal_fvl_dphi 0.18608 1 0.19 3.6 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:13 2022 + FINISH Time : Wed Sep 28 11:06:18 2022 + TOTAL Time : 5 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/52/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..afd41738b55b44916c905597f65a5a51907dd526 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.485579 0.690367 0.986585 +H 0.520846 0.717903 0.940573 +H 0.531824 0.674527 0.0359223 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6625e47a2f47c12ad05708042a80f9fa070820d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1026 2 + 2 -12.8512 2 + 3 -9.09078 2 + 4 -6.69878 2 + 5 1.0292 0 + 6 4.16304 0 + 7 11.1214 0 + 8 11.3583 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..527fc4ca2a02c48214d195980e8d6cf826223af5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:22 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.596209208 19.3302864581 27.6243928639 0 0 0 0 + tauc_H1 14.5836794718 20.1012864556 26.336045442 0 0 0 0 + tauc_H2 14.8910640654 18.8867557974 1.00582357877 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.104473823293 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.104840444398 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124005683074 (SEC) + + DONE : INIT CHARGE Time : 0.16719731179 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449958 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 9 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000706 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000987 + + Density error is 0.213670804578 + + Energy Rydberg eV + E_KohnSham -34.1849474664 -465.110071374 + E_Harris -34.3746460888 -467.691053541 + E_Fermi -0.395052640904 -5.37496692624 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00108716302853 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00094308779131 + + Density error is 0.0989445034153 + + Energy Rydberg eV + E_KohnSham -34.2753169946 -466.339611883 + E_Harris -34.2824165694 -466.436206554 + E_Fermi -0.203671863429 -2.77109786492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00104740275618 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000887192126535 + + Density error is 0.0637463073123 + + Energy Rydberg eV + E_KohnSham -34.2757720611 -466.34580338 + E_Harris -34.2803155878 -466.407621233 + E_Fermi -0.196202939692 -2.66947794416 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100683595588 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000800715747682 + + Density error is 0.001988964407 + + Energy Rydberg eV + E_KohnSham -34.2756928949 -466.344726269 + E_Harris -34.2756950186 -466.344755164 + E_Fermi -0.160715818848 -2.18665089506 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100618289761 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000800277927316 + + Density error is 0.000971397795098 + + Energy Rydberg eV + E_KohnSham -34.2756475279 -466.344109019 + E_Harris -34.2756481165 -466.344117027 + E_Fermi -0.160520577305 -2.1839944976 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100558932919 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000799087389255 + + Density error is 0.000178207654744 + + Energy Rydberg eV + E_KohnSham -34.2756676014 -466.344382134 + E_Harris -34.2756674703 -466.344380349 + E_Fermi -0.160151083884 -2.17896728169 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100588226784 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000799314501791 + + Density error is 3.62937784566e-05 + + Energy Rydberg eV + E_KohnSham -34.2756609294 -466.344291356 + E_Harris -34.2756609338 -466.344291416 + E_Fermi -0.160111200719 -2.1784246434 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100576724326 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00079924801614 + + Density error is 1.42904527038e-05 + + Energy Rydberg eV + E_KohnSham -34.2756643385 -466.344337739 + E_Harris -34.2756643393 -466.34433775 + E_Fermi -0.160131862748 -2.17870576473 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.001005774411 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000799245288329 + + Density error is 2.6361039384e-06 + + Energy Rydberg eV + E_KohnSham -34.2756631604 -466.34432171 + E_Harris -34.2756631604 -466.34432171 + E_Fermi -0.160118243487 -2.17852046517 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100577603358 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000799245133652 + + Density error is 6.03535397488e-07 + + Energy Rydberg eV + E_KohnSham -34.2756633517 -466.344324312 + E_Harris -34.2756633517 -466.344324312 + E_Fermi -0.160115952559 -2.1784892955 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100577699474 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000799245236785 + + Density error is 1.98227312906e-07 + + Energy Rydberg eV + E_KohnSham -34.2756633724 -466.344324594 + E_Harris -34.2756633724 -466.344324594 + E_Fermi -0.160115649587 -2.17848517335 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00100577728788 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000799245190462 + + Density error is 1.17695296375e-08 + + Energy Rydberg eV + E_KohnSham -34.2756633772 -466.34432466 + E_Harris -34.2756633772 -466.34432466 + E_band -7.90013249777 -107.486816925 + E_one_elec -68.8608128612 -936.899423825 + E_Hartree +35.8369453738 +487.586655998 + E_xc -8.17755343233 -111.261322379 + E_Ewald +7.05094082743 +95.9329715139 + E_demet -5.05975582748e-63 -6.88415097424e-62 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194128217882 -2.64124990579 + E_Fermi -0.160115457605 -2.17848256131 + + charge density convergence is achieved + final etot is -466.34432466 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1026 2.00000 + 2 -12.8512 2.00000 + 3 -9.09078 2.00000 + 4 -6.69878 2.00000 + 5 1.02920 0.00000 + 6 4.16304 0.00000 + 7 11.1214 0.00000 + 8 11.3583 0.00000 + + EFERMI = -2.178482561310664 eV + OUT.ABACUS/ final etot is -466.3443246595552 eV + correction force for each atom along direction 1 is 4.44061e-05 + correction force for each atom along direction 2 is -6.72354e-05 + correction force for each atom along direction 3 is -5.04579e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.66797952 -1.1105345 +2.5635498 + H1 +0.78773183 +0.58787738 -0.96455919 + H2 -1.4557114 +0.52265716 -1.5989906 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3443246595552 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4425 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4324 1 7.4 1.e+02% + Potential init_pot 0.28282 2 0.14 3.8% + PW_Basis recip2real 0.28839 17 0.017 3.9% + PW_Basis gathers_scatterp 0.12894 17 0.0076 1.7% + Potential v_of_rho 1.0556 14 0.075 14.% + XC_Functional v_xc 0.30620 15 0.020 4.1% + H_Hartree_pw v_hartree 0.70063 14 0.050 9.4% + PW_Basis real2recip 0.74750 41 0.018 10.% + PW_Basis gatherp_scatters 0.29498 41 0.0072 4.0% + ORB_control set_orb_tables 1.1025 1 1.1 15.% + ORB_gen_tables gen_tables 1.1025 1 1.1 15.% + ORB_table_phi init_Table 0.47787 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.47258 126 0.0038 6.3% + ORB_table_beta init_Table_Beta 0.18576 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18421 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24909 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24714 66 0.0037 3.3% + LOOP_ions opt_ions 5.8040 1 5.8 78.% + ESolver_KS_LCAO Run 5.2656 1 5.3 71.% + HSolverLCAO solve 2.6146 12 0.22 35.% + HamiltLCAO updateHk 1.3616 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.3319 12 0.11 18.% + Gint_interface cal_gint 2.1631 25 0.087 29.% + Gint_Gamma distri_vl 2.7428 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.6370 14 0.40 76.% + LCAO_gen_fixedH add_v_delta 2.6008 6 0.43 35.% + LCAO_DESCRIPTOR add_v_delta 2.6007 6 0.43 35.% + ElecStateLCAO psiToRho 1.2340 12 0.10 17.% + Charge mix_rho 0.98944 11 0.090 13.% + LOOP_ions force_stress 0.53822 1 0.54 7.2% + Force_Stress_LCAO getForceStress 0.53819 1 0.54 7.2% + Force_LCAO_gamma ftable_gamma 0.32448 1 0.32 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.30574 1 0.31 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:22 2022 + Finish Time : Wed Sep 28 11:05:29 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..78cf8c9b39d3becf844520849bfda099dc7c6198 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/OUT.ABACUS/warning.log @@ -0,0 +1,77 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012376 ima = 3.67442e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123614300696 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112149069983 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112891619099 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113120662531 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113094657647 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113110576753 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113104691304 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113107075688 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113106493191 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113106421791 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113106398945 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011310638856 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/STRU new file mode 100644 index 0000000000000000000000000000000000000000..26cbdb7f1d6b564b61967fbad7badc180ee0a774 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.403790792027 19.330286458134 -0.375607136132 0 0 0 +H +0.0 +2 +-13.416320528159 20.101286455641 -1.663954558000 0 0 0 +-13.108935934599 18.886755797409 1.005823578787 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/conv new file mode 100644 index 0000000000000000000000000000000000000000..47c80f00c10a7dd4718fc005c3a6e3f5a5490d15 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/conv @@ -0,0 +1 @@ +53 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..7bb1f29ed2664b1bc71deb7ec704efd7f1f19726 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749937526 0.01245015094 1.246498159 1.355545713 1.468605655 0.008516344922 0.01824393545 0.03909677811 +9.85533139e-19 0.0009468527453 0.002479361143 0.01162256769 0.04298771842 1.010040432e-19 1.685341747e-06 5.299826741e-06 +0.00160643493 0.00581612853 + +H atom_index 1 n_descriptor 18 +1.274634907 0.03343726157 0.1164252112 0.1620983965 0.3292985053 0.02314035455 0.02976859072 0.03687694117 +-4.824933211e-17 4.388321216e-05 0.1048987378 0.1169671227 0.1389901246 -8.344125283e-18 2.713139395e-06 0.01314719272 +0.02666176343 0.03181520863 + +H atom_index 2 n_descriptor 18 +1.158251906 0.03712091858 0.07976193592 0.1123422078 0.287864441 0.01780245631 0.02299261394 0.04105737889 +-1.937390577e-17 3.402122814e-05 0.07622289382 0.09553364384 0.1112179716 4.977191421e-18 7.07766221e-06 0.01549288733 +0.02202925944 0.02599225893 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..8e2f28004f5d3a53e46e2203cc037d78e3143a2e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:22 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.104498 SEC) : SETUP UNITCELL + DONE(0.104855 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124028 SEC) : INIT PLANEWAVE + DONE(0.16733 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450018 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651101e+02 0.000000e+00 2.137e-01 5.319e-01 + GE2 -4.663396e+02 -1.229541e+00 9.894e-02 4.944e-01 + GE3 -4.663458e+02 -6.191497e-03 6.375e-02 5.669e-01 + GE4 -4.663447e+02 1.077111e-03 1.989e-03 4.303e-01 + GE5 -4.663441e+02 6.172495e-04 9.714e-04 4.231e-01 + GE6 -4.663444e+02 -2.731145e-04 1.782e-04 4.232e-01 + GE7 -4.663443e+02 9.077714e-05 3.629e-05 4.047e-01 + GE8 -4.663443e+02 -4.638281e-05 1.429e-05 3.988e-01 + GE9 -4.663443e+02 1.602913e-05 2.636e-06 4.002e-01 + GE10 -4.663443e+02 -2.602176e-06 6.035e-07 3.986e-01 + GE11 -4.663443e+02 -2.820420e-07 1.982e-07 3.983e-01 + GE12 -4.663443e+02 -6.521465e-08 1.177e-08 3.324e-01 +E_delta_band = -6.89449331e-02 Ry = -9.38043938e-01 eV +E_delta_NN= -1.94128218e-01 Ry = -2.64124991e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4425 11 0.68 1e+02 % + Run_lcao lcao_line 7.4324 1 7.4 1e+02 % + Potential init_pot 0.28282 2 0.14 3.8 % + PW_Basis recip2real 0.28839 17 0.017 3.9 % + PW_Basis gathers_scatterp 0.12894 17 0.0076 1.7 % + Potential v_of_rho 1.0556 14 0.075 14 % + XC_Functional v_xc 0.3062 15 0.02 4.1 % + H_Hartree_pw v_hartree 0.70063 14 0.05 9.4 % + PW_Basis real2recip 0.7475 41 0.018 10 % + PW_Basis gatherp_scatters 0.29498 41 0.0072 4 % + ORB_control set_orb_tables 1.1025 1 1.1 15 % + ORB_gen_tables gen_tables 1.1025 1 1.1 15 % + ORB_table_phi init_Table 0.47787 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.47258 126 0.0038 6.3 % + ORB_table_beta init_Table_Beta 0.18576 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18421 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24909 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24714 66 0.0037 3.3 % + LOOP_ions opt_ions 5.804 1 5.8 78 % + ESolver_KS_LCAO Run 5.2656 1 5.3 71 % + HSolverLCAO solve 2.6146 12 0.22 35 % + HamiltLCAO updateHk 1.3616 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.3319 12 0.11 18 % + Gint_interface cal_gint 2.1631 25 0.087 29 % + Gint_Gamma distri_vl 2.7428 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.637 14 0.4 76 % + LCAO_gen_fixedH add_v_delta 2.6008 6 0.43 35 % + LCAO_DESCRIPTOR add_v_delta 2.6007 6 0.43 35 % + ElecStateLCAO psiToRho 1.234 12 0.1 17 % + Charge mix_rho 0.98944 11 0.09 13 % + LOOP_ions force_stress 0.53822 1 0.54 7.2 % + Force_Stress_LCAO getForceStress 0.53819 1 0.54 7.2 % + Force_LCAO_gamma ftable_gamma 0.32448 1 0.32 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.30574 1 0.31 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:22 2022 + FINISH Time : Wed Sep 28 11:05:29 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/53/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..21d837bbe9f7c922aea3bfdca283c15bf7f4c5cd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.486082 0.683741 0.980901 +H 0.514229 0.735128 0.945348 +H 0.536226 0.663436 0.0164397 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..5a103b56fc614b34b0fa59b68386347ea5c619ab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1638 2 + 2 -12.7658 2 + 3 -9.21575 2 + 4 -6.71668 2 + 5 1.08842 0 + 6 4.16099 0 + 7 11.1126 0 + 8 11.3674 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c30871803f22660d59d8f2bc794a9e2773bd9aa4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:16 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.610282338 19.1447469788 27.4652233253 0 0 0 0 + tauc_H1 14.3984032423 20.5835963468 26.4697543069 0 0 0 0 + tauc_H2 15.014328353 18.576199558 0.460310263319 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0875806387612 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0971443831133 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115445071044 (SEC) + + DONE : INIT CHARGE Time : 0.164998252035 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445419 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 0 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000826 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00139 + + Density error is 0.212573413655 + + Energy Rydberg eV + E_KohnSham -34.1891976521 -465.167898117 + E_Harris -34.3763436562 -467.71415013 + E_Fermi -0.395886280822 -5.38630917921 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00111922852477 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00122122553702 + + Density error is 0.0984222924463 + + Energy Rydberg eV + E_KohnSham -34.2778788379 -466.37446755 + E_Harris -34.2848795255 -466.46971679 + E_Fermi -0.205890720616 -2.8012869657 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00106545322682 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00113714084205 + + Density error is 0.0633463752167 + + Energy Rydberg eV + E_KohnSham -34.2782384479 -466.379360294 + E_Harris -34.2827463621 -466.440693613 + E_Fermi -0.197490962503 -2.68700239354 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000991055644762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000995176603532 + + Density error is 0.00194519435152 + + Energy Rydberg eV + E_KohnSham -34.2781710123 -466.378442785 + E_Harris -34.2781716982 -466.378452118 + E_Fermi -0.161975716544 -2.20379268263 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000992629293122 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000996452499855 + + Density error is 0.000891951902356 + + Energy Rydberg eV + E_KohnSham -34.2781295756 -466.377879011 + E_Harris -34.2781302361 -466.377887997 + E_Fermi -0.161743290284 -2.20063036114 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000991521257077 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000994325963061 + + Density error is 0.000155636173418 + + Energy Rydberg eV + E_KohnSham -34.2781505276 -466.378164078 + E_Harris -34.2781505455 -466.37816432 + E_Fermi -0.161426699492 -2.19632292243 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000991654772198 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000994361176982 + + Density error is 3.0612732397e-05 + + Energy Rydberg eV + E_KohnSham -34.2781437326 -466.378071626 + E_Harris -34.2781437353 -466.378071663 + E_Fermi -0.161380354001 -2.19569235968 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000991603519592 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000994347594461 + + Density error is 1.45105054127e-05 + + Energy Rydberg eV + E_KohnSham -34.2781465769 -466.378110325 + E_Harris -34.2781465778 -466.378110337 + E_Fermi -0.161400405746 -2.19596517765 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000991607614128 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000994340617786 + + Density error is 2.96979864942e-06 + + Energy Rydberg eV + E_KohnSham -34.2781454727 -466.378095301 + E_Harris -34.2781454727 -466.378095302 + E_Fermi -0.161387722914 -2.19579261888 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000991603399624 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000994332663255 + + Density error is 4.68749403399e-07 + + Energy Rydberg eV + E_KohnSham -34.2781456827 -466.378098159 + E_Harris -34.2781456827 -466.378098159 + E_Fermi -0.161384744453 -2.19575209483 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000991604282046 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000994332834291 + + Density error is 1.74850400047e-07 + + Energy Rydberg eV + E_KohnSham -34.2781457158 -466.37809861 + E_Harris -34.2781457158 -466.37809861 + E_Fermi -0.161384557706 -2.195749554 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000991604479702 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000994332641889 + + Density error is 1.09463330735e-08 + + Energy Rydberg eV + E_KohnSham -34.2781457186 -466.378098647 + E_Harris -34.2781457186 -466.378098647 + E_band -7.91757372278 -107.724116965 + E_one_elec -68.9241274551 -937.760863068 + E_Hartree +35.8623905426 +487.932855281 + E_xc -8.18136568581 -111.313190749 + E_Ewald +7.09000813142 +96.4645094536 + E_demet -6.1942628403e-66 -8.42772695378e-65 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194227749558 -2.6426041037 + E_Fermi -0.161384393359 -2.19574731796 + + charge density convergence is achieved + final etot is -466.378098647 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1638 2.00000 + 2 -12.7658 2.00000 + 3 -9.21575 2.00000 + 4 -6.71668 2.00000 + 5 1.08842 0.00000 + 6 4.16099 0.00000 + 7 11.1126 0.00000 + 8 11.3674 0.00000 + + EFERMI = -2.195747317956816 eV + OUT.ABACUS/ final etot is -466.3780986473224 eV + correction force for each atom along direction 1 is 4.34268e-05 + correction force for each atom along direction 2 is 6.14680e-05 + correction force for each atom along direction 3 is 2.74560e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.16059158 +1.6383160 -1.3886315 + H1 -0.81390081 -1.2265343 +0.79708511 + H2 +0.65330923 -0.41178177 +0.59154638 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3780986473224 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2097 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1996 1 6.2 1.e+02% + Potential init_pot 0.28327 2 0.14 4.6% + PW_Basis recip2real 0.29683 17 0.017 4.8% + PW_Basis gathers_scatterp 0.12701 17 0.0075 2.0% + Potential v_of_rho 1.0523 14 0.075 17.% + XC_Functional v_xc 0.29007 15 0.019 4.7% + H_Hartree_pw v_hartree 0.71417 14 0.051 12.% + PW_Basis real2recip 0.70214 41 0.017 11.% + PW_Basis gatherp_scatters 0.27337 41 0.0067 4.4% + ORB_control set_orb_tables 1.1052 1 1.1 18.% + ORB_gen_tables gen_tables 1.1052 1 1.1 18.% + ORB_table_phi init_Table 0.47813 1 0.48 7.7% + ORB_table_phi cal_ST_Phi12_R 0.47287 126 0.0038 7.6% + ORB_table_beta init_Table_Beta 0.18470 1 0.18 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18310 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.24655 1 0.25 4.0% + ORB_table_alpha S_PhiAlpha_R 0.24453 66 0.0037 3.9% + LOOP_ions opt_ions 4.5708 1 4.6 74.% + ESolver_KS_LCAO Run 4.1203 1 4.1 66.% + HSolverLCAO solve 1.6623 12 0.14 27.% + HamiltLCAO updateHk 0.92989 12 0.077 15.% + LCAO_Hamilt cal_Hgamma 0.90014 12 0.075 14.% + Gint_interface cal_gint 1.1349 25 0.045 18.% + Gint_Gamma distri_vl 2.1646 6 0.36 35.% + LCAO_Deepks cal_projected_DM 4.4163 14 0.32 71.% + LCAO_gen_fixedH add_v_delta 2.0197 6 0.34 33.% + LCAO_DESCRIPTOR add_v_delta 2.0197 6 0.34 33.% + ElecStateLCAO psiToRho 0.71121 12 0.059 11.% + Charge mix_rho 0.84898 11 0.077 14.% + LOOP_ions force_stress 0.45028 1 0.45 7.3% + Force_Stress_LCAO getForceStress 0.45024 1 0.45 7.3% + Force_LCAO_gamma ftable_gamma 0.23521 1 0.24 3.8% + Force_LCAO_gamma cal_fvl_dphi 0.20641 1 0.21 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:16 2022 + Finish Time : Wed Sep 28 11:06:22 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e1558746dbc43b72e59ecfd9b2d6f4822a8c6dc6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123926 ima = 3.6847e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123193726884 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111887650925 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112584504378 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112806869359 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112779944734 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112796223736 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112791432855 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112793544493 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112792886454 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011279279181 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112792775523 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011279276663 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/STRU new file mode 100644 index 0000000000000000000000000000000000000000..c98bc8ae0e7e8cab861c6d664ddf4209a289aff2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.389717661994 19.144746978780 -0.534776674732 0 0 0 +H +0.0 +2 +-13.601596757703 20.583596346795 -1.530245693106 0 0 0 +-12.985671647033 18.576199558008 0.460310263317 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/conv new file mode 100644 index 0000000000000000000000000000000000000000..a172cd11a929677ef774a9d27f645358ed2ffa0c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/conv @@ -0,0 +1 @@ +54 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c86a2dfe0719fb80dbda39c96bb003dbdae285aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751645547 0.01255360315 1.252050375 1.34996127 1.468803673 0.008830104899 0.01755991782 0.03913196955 +-2.224976272e-18 0.0009155973831 0.002578605974 0.01203849866 0.0439300253 1.023917877e-19 1.991666876e-06 5.883274278e-06 +0.001589420594 0.005957559875 + +H atom_index 1 n_descriptor 18 +1.180302443 0.03673239472 0.08647770606 0.1202480042 0.2956352046 0.01907183968 0.02420387068 0.04036036424 +7.920428914e-18 3.821376351e-05 0.08234915568 0.1025609684 0.1124530972 1.169180891e-17 6.649450534e-06 0.01484760931 +0.0232526214 0.0271790632 + +H atom_index 2 n_descriptor 18 +1.264154136 0.03401684546 0.1135005282 0.15658456 0.3254269499 0.02302678472 0.02911388756 0.03728914133 +-3.998703522e-18 4.566524128e-05 0.10339425 0.116233856 0.1342681609 5.565754675e-18 3.003637493e-06 0.01318909966 +0.02658427946 0.03136282939 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5b3c40780c02b2d80fbd25da6e2d857cce11c452 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:16 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0876034 SEC) : SETUP UNITCELL + DONE(0.0971631 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115466 SEC) : INIT PLANEWAVE + DONE(0.165129 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445484 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651679e+02 0.000000e+00 2.126e-01 4.612e-01 + GE2 -4.663745e+02 -1.206569e+00 9.842e-02 3.985e-01 + GE3 -4.663794e+02 -4.892744e-03 6.335e-02 4.651e-01 + GE4 -4.663784e+02 9.175087e-04 1.945e-03 3.251e-01 + GE5 -4.663779e+02 5.637745e-04 8.920e-04 3.247e-01 + GE6 -4.663782e+02 -2.850669e-04 1.556e-04 3.195e-01 + GE7 -4.663781e+02 9.245127e-05 3.061e-05 3.064e-01 + GE8 -4.663781e+02 -3.869851e-05 1.451e-05 3.016e-01 + GE9 -4.663781e+02 1.502359e-05 2.970e-06 3.040e-01 + GE10 -4.663781e+02 -2.857855e-06 4.687e-07 3.051e-01 + GE11 -4.663781e+02 -4.504543e-07 1.749e-07 3.075e-01 + GE12 -4.663781e+02 -3.769921e-08 1.095e-08 2.383e-01 +E_delta_band = -6.91764978e-02 Ry = -9.41194538e-01 eV +E_delta_NN= -1.94227750e-01 Ry = -2.64260410e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2097 11 0.56 1e+02 % + Run_lcao lcao_line 6.1996 1 6.2 1e+02 % + Potential init_pot 0.28327 2 0.14 4.6 % + PW_Basis recip2real 0.29683 17 0.017 4.8 % + PW_Basis gathers_scatterp 0.12701 17 0.0075 2 % + Potential v_of_rho 1.0523 14 0.075 17 % + XC_Functional v_xc 0.29007 15 0.019 4.7 % + H_Hartree_pw v_hartree 0.71417 14 0.051 12 % + PW_Basis real2recip 0.70214 41 0.017 11 % + PW_Basis gatherp_scatters 0.27337 41 0.0067 4.4 % + ORB_control set_orb_tables 1.1052 1 1.1 18 % + ORB_gen_tables gen_tables 1.1052 1 1.1 18 % + ORB_table_phi init_Table 0.47813 1 0.48 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.47287 126 0.0038 7.6 % + ORB_table_beta init_Table_Beta 0.1847 1 0.18 3 % + ORB_table_beta VNL_PhiBeta_R 0.1831 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.24655 1 0.25 4 % + ORB_table_alpha S_PhiAlpha_R 0.24453 66 0.0037 3.9 % + LOOP_ions opt_ions 4.5708 1 4.6 74 % + ESolver_KS_LCAO Run 4.1203 1 4.1 66 % + HSolverLCAO solve 1.6623 12 0.14 27 % + HamiltLCAO updateHk 0.92989 12 0.077 15 % + LCAO_Hamilt cal_Hgamma 0.90014 12 0.075 14 % + Gint_interface cal_gint 1.1349 25 0.045 18 % + Gint_Gamma distri_vl 2.1646 6 0.36 35 % + LCAO_Deepks cal_projected_DM 4.4163 14 0.32 71 % + LCAO_gen_fixedH add_v_delta 2.0197 6 0.34 33 % + LCAO_DESCRIPTOR add_v_delta 2.0197 6 0.34 33 % + ElecStateLCAO psiToRho 0.71121 12 0.059 11 % + Charge mix_rho 0.84898 11 0.077 14 % + LOOP_ions force_stress 0.45028 1 0.45 7.3 % + Force_Stress_LCAO getForceStress 0.45024 1 0.45 7.3 % + Force_LCAO_gamma ftable_gamma 0.23521 1 0.24 3.8 % + Force_LCAO_gamma cal_fvl_dphi 0.20641 1 0.21 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:16 2022 + FINISH Time : Wed Sep 28 11:06:22 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/54/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..94a041ead6b3a7df073cae3d98d00768d879513b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.484534 0.690965 0.97796 +H 0.525776 0.714618 0.935455 +H 0.483271 0.626559 0.972726 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..193ad392fa76af435aae76bb4b5a5eab3fc28288 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4084 2 + 2 -13.4778 2 + 3 -8.89765 2 + 4 -6.7702 2 + 5 1.50195 0 + 6 4.76136 0 + 7 11.0296 0 + 8 11.252 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..c53948a90f3144b17334c22067613c372755778b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:58 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.56694187 19.3470276624 27.3828686407 0 0 0 0 + tauc_H1 14.7217178728 20.0092922359 26.1927416571 0 0 0 0 + tauc_H2 13.5315745508 17.5436595022 27.2363339687 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0731531467315 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0734466330274 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0894039942304 (SEC) + + DONE : INIT CHARGE Time : 0.131051289529 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375354 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 0 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0017 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000763 + + Density error is 0.217493965747 + + Energy Rydberg eV + E_KohnSham -34.1882797039 -465.155408791 + E_Harris -34.3855533825 -467.839454885 + E_Fermi -0.41734770398 -5.67830682134 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00150865650585 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104596051723 + + Density error is 0.0975962926208 + + Energy Rydberg eV + E_KohnSham -34.2782366352 -466.379335632 + E_Harris -34.2847641369 -466.468146848 + E_Fermi -0.224825987581 -3.05891448957 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0013757992652 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101419436848 + + Density error is 0.0622012376778 + + Energy Rydberg eV + E_KohnSham -34.278386987 -466.381381273 + E_Harris -34.2825306292 -466.437758417 + E_Fermi -0.209919676978 -2.85610372922 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011483847086 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972611556037 + + Density error is 0.0021073696589 + + Energy Rydberg eV + E_KohnSham -34.2784412238 -466.382119201 + E_Harris -34.2784445097 -466.382163909 + E_Fermi -0.174585467997 -2.37535715276 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114316843239 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973503228194 + + Density error is 0.000868728629946 + + Energy Rydberg eV + E_KohnSham -34.2783710529 -466.381164478 + E_Harris -34.2783733881 -466.381196249 + E_Fermi -0.17324733794 -2.35715095932 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114180057868 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972603812258 + + Density error is 0.000216153195651 + + Energy Rydberg eV + E_KohnSham -34.2784219832 -466.38185742 + E_Harris -34.2784221568 -466.381859782 + E_Fermi -0.173623328533 -2.36226657378 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011413996522 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973009232763 + + Density error is 4.51829709543e-05 + + Energy Rydberg eV + E_KohnSham -34.278401228 -466.381575031 + E_Harris -34.2784012389 -466.381575179 + E_Fermi -0.173390838178 -2.35910338022 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114144442299 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972917414384 + + Density error is 1.71829954696e-05 + + Energy Rydberg eV + E_KohnSham -34.2784074445 -466.38165961 + E_Harris -34.2784074455 -466.381659625 + E_Fermi -0.173445429491 -2.35984613313 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114139518081 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00097291106837 + + Density error is 2.52578547854e-06 + + Energy Rydberg eV + E_KohnSham -34.2784059766 -466.381639638 + E_Harris -34.2784059766 -466.381639639 + E_Fermi -0.173427831035 -2.35960669385 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114138792755 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972913230741 + + Density error is 3.84003862021e-07 + + Energy Rydberg eV + E_KohnSham -34.2784061713 -466.381642288 + E_Harris -34.2784061713 -466.381642288 + E_Fermi -0.173425232861 -2.35957134389 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00114138778989 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972913684374 + + Density error is 1.55728459993e-07 + + Energy Rydberg eV + E_KohnSham -34.2784062048 -466.381642744 + E_Harris -34.2784062048 -466.381642744 + E_Fermi -0.173425102429 -2.35956956926 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011413874324 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000972913892397 + + Density error is 9.54293972996e-09 + + Energy Rydberg eV + E_KohnSham -34.2784062063 -466.381642765 + E_Harris -34.2784062063 -466.381642765 + E_band -8.01928774014 -109.108007167 + E_one_elec -69.7193587107 -948.580539371 + E_Hartree +36.2501045437 +493.20797489 + E_xc -8.24343401271 -112.15767366 + E_Ewald +7.55776411105 +102.82865605 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195500946118 -2.6599268316 + E_Fermi -0.173424958339 -2.35956760883 + + charge density convergence is achieved + final etot is -466.381642765 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4084 2.00000 + 2 -13.4778 2.00000 + 3 -8.89765 2.00000 + 4 -6.77020 2.00000 + 5 1.50195 0.00000 + 6 4.76136 0.00000 + 7 11.0296 0.00000 + 8 11.2520 0.00000 + + EFERMI = -2.359567608827941 eV + OUT.ABACUS/ final etot is -466.3816427647915 eV + correction force for each atom along direction 1 is 1.56692e-05 + correction force for each atom along direction 2 is -0.000100832 + correction force for each atom along direction 3 is -0.000155617 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.2527084 +0.47791864 +1.4074204 + H1 +1.0633862 +0.29255396 -1.1253321 + H2 +0.18932226 -0.77047260 -0.28208835 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3816427647915 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6199 11 0.51 1.0e+02% + Run_lcao lcao_line 5.6125 1 5.6 1.e+02% + Potential init_pot 0.24085 2 0.12 4.3% + PW_Basis recip2real 0.26273 17 0.015 4.7% + PW_Basis gathers_scatterp 0.11531 17 0.0068 2.1% + Potential v_of_rho 0.96748 14 0.069 17.% + XC_Functional v_xc 0.28757 15 0.019 5.1% + H_Hartree_pw v_hartree 0.64019 14 0.046 11.% + PW_Basis real2recip 0.65578 41 0.016 12.% + PW_Basis gatherp_scatters 0.25259 41 0.0062 4.5% + ORB_control set_orb_tables 0.89834 1 0.90 16.% + ORB_gen_tables gen_tables 0.89833 1 0.90 16.% + ORB_table_phi init_Table 0.37462 1 0.37 6.7% + ORB_table_phi cal_ST_Phi12_R 0.37047 126 0.0029 6.6% + ORB_table_beta init_Table_Beta 0.15442 1 0.15 2.7% + ORB_table_beta VNL_PhiBeta_R 0.15310 56 0.0027 2.7% + ORB_table_alpha init_Table_Alpha 0.20861 1 0.21 3.7% + ORB_table_alpha S_PhiAlpha_R 0.20700 66 0.0031 3.7% + LOOP_ions opt_ions 4.2697 1 4.3 76.% + ESolver_KS_LCAO Run 3.8664 1 3.9 69.% + HSolverLCAO solve 1.4936 12 0.12 27.% + HamiltLCAO updateHk 0.84363 12 0.070 15.% + LCAO_Hamilt cal_Hgamma 0.81828 12 0.068 15.% + Gint_interface cal_gint 0.84582 25 0.034 15.% + Gint_Gamma distri_vl_value 0.15037 12 0.013 2.7% + Gint_Gamma distri_vl 2.0285 6 0.34 36.% + LCAO_Deepks cal_projected_DM 4.1058 14 0.29 73.% + LCAO_gen_fixedH add_v_delta 1.9009 6 0.32 34.% + LCAO_DESCRIPTOR add_v_delta 1.9008 6 0.32 34.% + ElecStateLCAO psiToRho 0.63281 12 0.053 11.% + Charge mix_rho 0.84186 11 0.077 15.% + LOOP_ions force_stress 0.40319 1 0.40 7.2% + Force_Stress_LCAO getForceStress 0.40317 1 0.40 7.2% + Force_LCAO_gamma ftable_gamma 0.21156 1 0.21 3.8% + Force_LCAO_gamma cal_fvl_dphi 0.15815 1 0.16 2.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:58 2022 + Finish Time : Wed Sep 28 11:03:03 2022 + Total Time : 0 h 0 mins 5 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..45156b0222f4d3e1d3fa8a6834354a62314dc5c5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123841 ima = 3.68446e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123213515525 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112646660494 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011299670401 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113256972766 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113189929995 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113232248559 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113220287674 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113223336713 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113222744892 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113222655248 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113222643805 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113222636675 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/STRU new file mode 100644 index 0000000000000000000000000000000000000000..89c852cc66e336f47daa75295d651d679b196c12 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.433058130038 19.347027662436 -0.617131359327 0 0 0 +H +0.0 +2 +-13.278282127237 20.009292235944 -1.807258342885 0 0 0 +-14.468425449178 17.543659502192 -0.763666031267 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/conv new file mode 100644 index 0000000000000000000000000000000000000000..0ee4fdb2fc7577a9c19234372fffb003ba4f1d27 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/conv @@ -0,0 +1 @@ +55 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9156359e53e61c562db2ee53c4fe800c36e8e9da --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.744817786 0.0127365236 1.294714847 1.382881349 1.470047122 0.007958418641 0.02048028928 0.03890210247 +-4.42861165e-19 0.001237552954 0.002511592429 0.01288150918 0.04504782542 5.674756787e-19 1.763765019e-06 5.382941377e-06 +0.001766191376 0.0056936223 + +H atom_index 1 n_descriptor 18 +1.278757899 0.03268981897 0.1191782868 0.1648374968 0.3308858418 0.02326844091 0.03008495269 0.03616925895 +-1.544488328e-17 4.533662056e-05 0.1078068705 0.1184235481 0.1416631775 -3.320723892e-18 2.802743687e-06 0.01306013684 +0.02747142977 0.03205704088 + +H atom_index 2 n_descriptor 18 +1.259619068 0.03334226301 0.1121751546 0.1554629963 0.3253401742 0.02244218491 0.02899210439 0.03655890192 +-2.567758177e-17 4.366083903e-05 0.1053405972 0.1154334377 0.1336584151 1.876028146e-18 3.811130426e-06 0.01292689947 +0.0268190958 0.03128800028 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f6e3ce91c0d949baac01d2ff31ae492b784ffef5 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:58 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0731735 SEC) : SETUP UNITCELL + DONE(0.073456 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0894182 SEC) : INIT PLANEWAVE + DONE(0.131156 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.3754 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651554e+02 0.000000e+00 2.175e-01 4.123e-01 + GE2 -4.663793e+02 -1.223927e+00 9.760e-02 3.732e-01 + GE3 -4.663814e+02 -2.045641e-03 6.220e-02 4.302e-01 + GE4 -4.663821e+02 -7.379285e-04 2.107e-03 3.068e-01 + GE5 -4.663812e+02 9.547238e-04 8.687e-04 3.089e-01 + GE6 -4.663819e+02 -6.929428e-04 2.162e-04 2.976e-01 + GE7 -4.663816e+02 2.823898e-04 4.518e-05 2.992e-01 + GE8 -4.663817e+02 -8.457958e-05 1.718e-05 2.881e-01 + GE9 -4.663816e+02 1.997185e-05 2.526e-06 2.915e-01 + GE10 -4.663816e+02 -2.649332e-06 3.840e-07 2.928e-01 + GE11 -4.663816e+02 -4.562840e-07 1.557e-07 2.887e-01 + GE12 -4.663816e+02 -2.082132e-08 9.543e-09 2.234e-01 +E_delta_band = -7.20188084e-02 Ry = -9.79866158e-01 eV +E_delta_NN= -1.95500946e-01 Ry = -2.65992683e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6199 11 0.51 1e+02 % + Run_lcao lcao_line 5.6125 1 5.6 1e+02 % + Potential init_pot 0.24085 2 0.12 4.3 % + PW_Basis recip2real 0.26273 17 0.015 4.7 % + PW_Basis gathers_scatterp 0.11531 17 0.0068 2.1 % + Potential v_of_rho 0.96748 14 0.069 17 % + XC_Functional v_xc 0.28757 15 0.019 5.1 % + H_Hartree_pw v_hartree 0.64019 14 0.046 11 % + PW_Basis real2recip 0.65578 41 0.016 12 % + PW_Basis gatherp_scatters 0.25259 41 0.0062 4.5 % + ORB_control set_orb_tables 0.89834 1 0.9 16 % + ORB_gen_tables gen_tables 0.89833 1 0.9 16 % + ORB_table_phi init_Table 0.37462 1 0.37 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.37047 126 0.0029 6.6 % + ORB_table_beta init_Table_Beta 0.15442 1 0.15 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.1531 56 0.0027 2.7 % + ORB_table_alpha init_Table_Alpha 0.20861 1 0.21 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.207 66 0.0031 3.7 % + LOOP_ions opt_ions 4.2697 1 4.3 76 % + ESolver_KS_LCAO Run 3.8664 1 3.9 69 % + HSolverLCAO solve 1.4936 12 0.12 27 % + HamiltLCAO updateHk 0.84363 12 0.07 15 % + LCAO_Hamilt cal_Hgamma 0.81828 12 0.068 15 % + Gint_interface cal_gint 0.84582 25 0.034 15 % + Gint_Gamma distri_vl_value 0.15037 12 0.013 2.7 % + Gint_Gamma distri_vl 2.0285 6 0.34 36 % + LCAO_Deepks cal_projected_DM 4.1058 14 0.29 73 % + LCAO_gen_fixedH add_v_delta 1.9009 6 0.32 34 % + LCAO_DESCRIPTOR add_v_delta 1.9008 6 0.32 34 % + ElecStateLCAO psiToRho 0.63281 12 0.053 11 % + Charge mix_rho 0.84186 11 0.077 15 % + LOOP_ions force_stress 0.40319 1 0.4 7.2 % + Force_Stress_LCAO getForceStress 0.40317 1 0.4 7.2 % + Force_LCAO_gamma ftable_gamma 0.21156 1 0.21 3.8 % + Force_LCAO_gamma cal_fvl_dphi 0.15815 1 0.16 2.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:58 2022 + FINISH Time : Wed Sep 28 11:03:03 2022 + TOTAL Time : 5 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/55/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9208a244a07900256da16595c84f9f2ab4c62a69 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.483076 0.689399 0.986949 +H 0.514123 0.678399 0.929741 +H 0.424926 0.655023 0.97279 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..36d238b02da3842444da07cd13e3b779e9837ed2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0902 2 + 2 -12.4574 2 + 3 -9.39721 2 + 4 -6.70548 2 + 5 0.956624 0 + 6 3.90705 0 + 7 11.1402 0 + 8 11.4133 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1d93968193b6229b852da068a4757b362967d2ec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:34 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.5261229876 19.3031830038 27.6345609234 0 0 0 0 + tauc_H1 14.3954438603 18.9951857145 26.0327376718 0 0 0 0 + tauc_H2 11.8979176095 18.3406307676 27.2381323871 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0873726874617 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0972653139997 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115596879706 (SEC) + + DONE : INIT CHARGE Time : 0.165350120088 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449637 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 0 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000926 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00146 + + Density error is 0.21077937737 + + Energy Rydberg eV + E_KohnSham -34.1873659662 -465.142976752 + E_Harris -34.3712902301 -467.645394741 + E_Fermi -0.387139368383 -5.26730133013 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00118838495917 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129211204613 + + Density error is 0.0986651227622 + + Energy Rydberg eV + E_KohnSham -34.2761466133 -466.350899425 + E_Harris -34.2834867064 -466.450766515 + E_Fermi -0.198630604337 -2.70250801616 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00112971857383 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120402892372 + + Density error is 0.063763149682 + + Energy Rydberg eV + E_KohnSham -34.2767105403 -466.358572045 + E_Harris -34.2813789358 -466.422088824 + E_Fermi -0.193079665145 -2.62698361391 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105201245717 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010368951346 + + Density error is 0.00188345208715 + + Energy Rydberg eV + E_KohnSham -34.2765922298 -466.356962348 + E_Harris -34.2765924785 -466.356965732 + E_Fermi -0.157615760998 -2.14447244417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105247007491 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103640766923 + + Density error is 0.00104559232507 + + Energy Rydberg eV + E_KohnSham -34.2765524889 -466.356421644 + E_Harris -34.2765531544 -466.3564307 + E_Fermi -0.157778392587 -2.14668516046 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105128230073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103358429177 + + Density error is 0.000145103736018 + + Energy Rydberg eV + E_KohnSham -34.2765685587 -466.356640286 + E_Harris -34.2765685653 -466.356640375 + E_Fermi -0.157272394035 -2.13980069698 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105149390069 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001033666556 + + Density error is 3.08952050487e-05 + + Energy Rydberg eV + E_KohnSham -34.2765640151 -466.356578468 + E_Harris -34.2765640178 -466.356578504 + E_Fermi -0.157249706942 -2.13949202324 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105140250067 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103360171829 + + Density error is 1.17018702825e-05 + + Energy Rydberg eV + E_KohnSham -34.2765661774 -466.356607886 + E_Harris -34.2765661779 -466.356607893 + E_Fermi -0.15726338751 -2.13967815692 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105140274342 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103358738485 + + Density error is 2.6525624962e-06 + + Energy Rydberg eV + E_KohnSham -34.2765652182 -466.356594836 + E_Harris -34.2765652182 -466.356594837 + E_Fermi -0.157252902642 -2.13953550297 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010514032865 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103358256348 + + Density error is 4.09014994547e-07 + + Energy Rydberg eV + E_KohnSham -34.2765653529 -466.356596669 + E_Harris -34.2765653529 -466.356596669 + E_Fermi -0.157250291271 -2.13949997344 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.001051403739 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103358277244 + + Density error is 1.48867197381e-07 + + Energy Rydberg eV + E_KohnSham -34.2765653878 -466.356597143 + E_Harris -34.2765653878 -466.356597143 + E_Fermi -0.157250129347 -2.13949777036 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105140380542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103358264561 + + Density error is 1.1694695084e-08 + + Energy Rydberg eV + E_KohnSham -34.2765653909 -466.356597185 + E_Harris -34.2765653909 -466.356597185 + E_band -7.88644311722 -107.300563347 + E_one_elec -68.642518656 -933.929378793 + E_Hartree +35.722267383 +486.026381888 + E_xc -8.15881017435 -111.006307272 + E_Ewald +6.92808601186 +94.2614459954 + E_demet -6.7440992108e-59 -9.17581771442e-58 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193755037925 -2.63617253199 + E_Fermi -0.157249999955 -2.13949600989 + + charge density convergence is achieved + final etot is -466.356597185 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0902 2.00000 + 2 -12.4574 2.00000 + 3 -9.39721 2.00000 + 4 -6.70548 2.00000 + 5 0.956624 0.00000 + 6 3.90705 0.00000 + 7 11.1402 0.00000 + 8 11.4133 0.00000 + + EFERMI = -2.139496009892296 eV + OUT.ABACUS/ final etot is -466.3565971853580 eV + correction force for each atom along direction 1 is 2.29426e-05 + correction force for each atom along direction 2 is -0.000182353 + correction force for each atom along direction 3 is -0.000175500 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.7430972 -1.2143285 -0.81743037 + H1 +0.36778812 +0.21463281 +0.076776246 + H2 +1.3753091 +0.99969566 +0.74065413 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3565971853580 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4265 11 0.58 1.0e+02% + Run_lcao lcao_line 6.4165 1 6.4 1.e+02% + Potential init_pot 0.28697 2 0.14 4.5% + PW_Basis recip2real 0.29507 17 0.017 4.6% + PW_Basis gathers_scatterp 0.13660 17 0.0080 2.1% + Potential v_of_rho 1.0386 14 0.074 16.% + XC_Functional v_xc 0.29563 15 0.020 4.6% + H_Hartree_pw v_hartree 0.69686 14 0.050 11.% + PW_Basis real2recip 0.71276 41 0.017 11.% + PW_Basis gatherp_scatters 0.28755 41 0.0070 4.5% + ORB_control set_orb_tables 1.1103 1 1.1 17.% + ORB_gen_tables gen_tables 1.1103 1 1.1 17.% + ORB_table_phi init_Table 0.48396 1 0.48 7.5% + ORB_table_phi cal_ST_Phi12_R 0.47866 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18793 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18629 56 0.0033 2.9% + ORB_table_alpha init_Table_Alpha 0.25269 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25067 66 0.0038 3.9% + LOOP_ions opt_ions 4.7782 1 4.8 74.% + ESolver_KS_LCAO Run 4.3014 1 4.3 67.% + HSolverLCAO solve 1.8330 12 0.15 29.% + HamiltLCAO updateHk 1.0067 12 0.084 16.% + LCAO_Hamilt cal_Hgamma 0.97736 12 0.081 15.% + Gint_interface cal_gint 1.1231 25 0.045 17.% + Gint_Gamma distri_vl_value 0.16562 12 0.014 2.6% + Gint_Gamma distri_vl 2.2520 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.5888 14 0.33 71.% + LCAO_gen_fixedH add_v_delta 2.1068 6 0.35 33.% + LCAO_DESCRIPTOR add_v_delta 2.1069 6 0.35 33.% + ElecStateLCAO psiToRho 0.80448 12 0.067 13.% + Charge mix_rho 0.85390 11 0.078 13.% + LOOP_ions force_stress 0.47664 1 0.48 7.4% + Force_Stress_LCAO getForceStress 0.47661 1 0.48 7.4% + Force_LCAO_gamma ftable_gamma 0.26274 1 0.26 4.1% + Force_LCAO_gamma cal_fvl_dphi 0.20467 1 0.20 3.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:34 2022 + Finish Time : Wed Sep 28 11:14:40 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8f6d0ef179e676f1c470f2e0fc5a21cea70565bb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123573 ima = 3.68012e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123189128409 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111503448669 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112370141131 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112597189268 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112576353228 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112588852079 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112585403014 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112587369883 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112586898899 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112586799493 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112586783994 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112586776706 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/STRU new file mode 100644 index 0000000000000000000000000000000000000000..2c4e91083b0232776de7e02dec23df7c513ec501 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.473877012360 19.303183003745 -0.365439076569 0 0 0 +H +0.0 +2 +-13.604556139679 18.995185714488 -1.967262328229 0 0 0 +-16.102082390483 18.340630767577 -0.761867612929 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/conv new file mode 100644 index 0000000000000000000000000000000000000000..7d4f3a3c61887f688ce4f14d06f271dd8c5379e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/conv @@ -0,0 +1 @@ +56 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..1203b7a885ddae49476fdbf3c4acd2540105583c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754893511 0.01252182184 1.241537571 1.331037333 1.468531583 0.009399019953 0.01619868401 0.03925541473 +2.931670408e-18 0.0007738445826 0.002618590189 0.01224022617 0.04318375025 2.283808366e-19 2.179629292e-06 6.307408354e-06 +0.001554039978 0.006016903673 + +H atom_index 1 n_descriptor 18 +1.238356728 0.03526975776 0.1061923579 0.1443223655 0.3163257249 0.02231538361 0.02756305722 0.03845257758 +2.555090746e-17 4.292094487e-05 0.09696704533 0.1152579526 0.1235258261 -1.388818089e-18 3.565549661e-06 0.01349862221 +0.02576186077 0.0301606432 + +H atom_index 2 n_descriptor 18 +1.172657169 0.03726537742 0.08567613614 0.1170390098 0.2914539382 0.01912209533 0.02369406475 0.04102334448 +-2.59437094e-17 3.7287373e-05 0.08041027071 0.09956362549 0.1119362978 6.336419592e-18 6.15387984e-06 0.01527077011 +0.02304468865 0.02668753999 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..545290ae97d09061f7e02c0e75fa5be5a34cc166 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:34 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0873966 SEC) : SETUP UNITCELL + DONE(0.097283 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115617 SEC) : INIT PLANEWAVE + DONE(0.1655 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449699 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651430e+02 0.000000e+00 2.108e-01 4.716e-01 + GE2 -4.663509e+02 -1.207923e+00 9.867e-02 4.130e-01 + GE3 -4.663586e+02 -7.672620e-03 6.376e-02 4.826e-01 + GE4 -4.663570e+02 1.609697e-03 1.883e-03 3.414e-01 + GE5 -4.663564e+02 5.407033e-04 1.046e-03 3.422e-01 + GE6 -4.663566e+02 -2.186413e-04 1.451e-04 3.403e-01 + GE7 -4.663566e+02 6.181815e-05 3.090e-05 3.226e-01 + GE8 -4.663566e+02 -2.941864e-05 1.170e-05 3.195e-01 + GE9 -4.663566e+02 1.304979e-05 2.653e-06 3.191e-01 + GE10 -4.663566e+02 -1.832182e-06 4.090e-07 3.181e-01 + GE11 -4.663566e+02 -4.748149e-07 1.489e-07 3.168e-01 + GE12 -4.663566e+02 -4.189004e-08 1.169e-08 2.519e-01 +E_delta_band = -6.81650825e-02 Ry = -9.27433527e-01 eV +E_delta_NN= -1.93755038e-01 Ry = -2.63617253e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4265 11 0.58 1e+02 % + Run_lcao lcao_line 6.4165 1 6.4 1e+02 % + Potential init_pot 0.28697 2 0.14 4.5 % + PW_Basis recip2real 0.29507 17 0.017 4.6 % + PW_Basis gathers_scatterp 0.1366 17 0.008 2.1 % + Potential v_of_rho 1.0386 14 0.074 16 % + XC_Functional v_xc 0.29563 15 0.02 4.6 % + H_Hartree_pw v_hartree 0.69686 14 0.05 11 % + PW_Basis real2recip 0.71276 41 0.017 11 % + PW_Basis gatherp_scatters 0.28755 41 0.007 4.5 % + ORB_control set_orb_tables 1.1103 1 1.1 17 % + ORB_gen_tables gen_tables 1.1103 1 1.1 17 % + ORB_table_phi init_Table 0.48396 1 0.48 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.47866 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18793 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18629 56 0.0033 2.9 % + ORB_table_alpha init_Table_Alpha 0.25269 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25067 66 0.0038 3.9 % + LOOP_ions opt_ions 4.7782 1 4.8 74 % + ESolver_KS_LCAO Run 4.3014 1 4.3 67 % + HSolverLCAO solve 1.833 12 0.15 29 % + HamiltLCAO updateHk 1.0067 12 0.084 16 % + LCAO_Hamilt cal_Hgamma 0.97736 12 0.081 15 % + Gint_interface cal_gint 1.1231 25 0.045 17 % + Gint_Gamma distri_vl_value 0.16562 12 0.014 2.6 % + Gint_Gamma distri_vl 2.252 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.5888 14 0.33 71 % + LCAO_gen_fixedH add_v_delta 2.1068 6 0.35 33 % + LCAO_DESCRIPTOR add_v_delta 2.1069 6 0.35 33 % + ElecStateLCAO psiToRho 0.80448 12 0.067 13 % + Charge mix_rho 0.8539 11 0.078 13 % + LOOP_ions force_stress 0.47664 1 0.48 7.4 % + Force_Stress_LCAO getForceStress 0.47661 1 0.48 7.4 % + Force_LCAO_gamma ftable_gamma 0.26274 1 0.26 4.1 % + Force_LCAO_gamma cal_fvl_dphi 0.20467 1 0.2 3.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:34 2022 + FINISH Time : Wed Sep 28 11:14:40 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/56/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4242aa41a460ba925334748427e38f7c36d46250 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.477524 0.679881 0.99948 +H 0.523378 0.683407 0.951629 +H 0.419251 0.688006 0.973263 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f58ae359181cb68029d4273bf11ec0699372c767 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2124 2 + 2 -13.2877 2 + 3 -8.87379 2 + 4 -6.72436 2 + 5 1.31856 0 + 6 4.48265 0 + 7 11.0796 0 + 8 11.3056 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b66832964375ad779e850b07ca20c2098400ad6c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:02 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.3706774905 19.0366682125 27.9854494654 0 0 0 0 + tauc_H1 14.6545827457 19.1354064845 26.6456173348 0 0 0 0 + tauc_H2 11.739038491 19.2641642023 27.2513773488 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105370524026 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105718920139 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123733896676 (SEC) + + DONE : INIT CHARGE Time : 0.16667863565 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450289 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 0 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000866 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00172 + + Density error is 0.21699095747 + + Energy Rydberg eV + E_KohnSham -34.1872843689 -465.141866563 + E_Harris -34.3831603922 -467.806896582 + E_Fermi -0.406027562645 -5.52428839703 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00129809515355 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00139929249064 + + Density error is 0.0983930174734 + + Energy Rydberg eV + E_KohnSham -34.2792336318 -466.392900466 + E_Harris -34.2859774647 -466.484655019 + E_Fermi -0.212426086841 -2.89020518488 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00124915444553 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128510417717 + + Density error is 0.0631916283061 + + Energy Rydberg eV + E_KohnSham -34.2796507207 -466.398575251 + E_Harris -34.2839876815 -466.45758263 + E_Fermi -0.201872161038 -2.74661165769 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011874403055 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010738342238 + + Density error is 0.00208310037607 + + Energy Rydberg eV + E_KohnSham -34.2796351645 -466.398363598 + E_Harris -34.2796386374 -466.39841085 + E_Fermi -0.166468244848 -2.264916666 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011896376289 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010706246912 + + Density error is 0.000969654710878 + + Energy Rydberg eV + E_KohnSham -34.2795710097 -466.397490728 + E_Harris -34.2795719542 -466.397503578 + E_Fermi -0.165745266098 -2.25508003546 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00118853456471 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010680215723 + + Density error is 0.000200239257795 + + Energy Rydberg eV + E_KohnSham -34.2796063491 -466.397971545 + E_Harris -34.2796064221 -466.397972537 + E_Fermi -0.165683801428 -2.25424376572 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00118888116561 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106780943386 + + Density error is 4.16692791512e-05 + + Energy Rydberg eV + E_KohnSham -34.2795929816 -466.39778967 + E_Harris -34.2795929908 -466.397789796 + E_Fermi -0.165538225751 -2.25226310702 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00118879027494 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106780869276 + + Density error is 1.95710334692e-05 + + Energy Rydberg eV + E_KohnSham -34.2795981964 -466.397860621 + E_Harris -34.2795981979 -466.397860643 + E_Fermi -0.165584242859 -2.25288920189 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00118879376634 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106776958447 + + Density error is 2.81237619633e-06 + + Energy Rydberg eV + E_KohnSham -34.2795966281 -466.397839284 + E_Harris -34.2795966281 -466.397839284 + E_Fermi -0.165564991473 -2.25262727335 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011887909039 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106776197577 + + Density error is 5.10216514551e-07 + + Energy Rydberg eV + E_KohnSham -34.2795968826 -466.397842746 + E_Harris -34.2795968826 -466.397842746 + E_Fermi -0.165562182015 -2.25258904872 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00118879206645 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106776212101 + + Density error is 1.72265453137e-07 + + Energy Rydberg eV + E_KohnSham -34.2795969181 -466.397843229 + E_Harris -34.2795969181 -466.397843229 + E_Fermi -0.165561952931 -2.25258593187 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011887923443 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106776183146 + + Density error is 9.96783648474e-09 + + Energy Rydberg eV + E_KohnSham -34.2795969218 -466.39784328 + E_Harris -34.2795969218 -466.39784328 + E_band -7.95229191601 -108.196482217 + E_one_elec -69.3051032345 -942.944304468 + E_Hartree +36.0557235838 +490.563286252 + E_xc -8.2119807327 -111.729729831 + E_Ewald +7.30610833227 +99.4047035242 + E_demet -1.79218680532e-77 -2.43839524328e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194721411567 -2.64932071992 + E_Fermi -0.165561785492 -2.25258365374 + + charge density convergence is achieved + final etot is -466.39784328 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2124 2.00000 + 2 -13.2877 2.00000 + 3 -8.87379 2.00000 + 4 -6.72436 2.00000 + 5 1.31856 0.00000 + 6 4.48265 0.00000 + 7 11.0796 0.00000 + 8 11.3056 0.00000 + + EFERMI = -2.252583653744561 eV + OUT.ABACUS/ final etot is -466.3978432800094 eV + correction force for each atom along direction 1 is -5.44789e-05 + correction force for each atom along direction 2 is -2.16835e-05 + correction force for each atom along direction 3 is -3.75543e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.3708114 -0.18635085 +0.57320567 + H1 -0.59738870 +0.023489407 +0.14921090 + H2 -0.77342271 +0.16286144 -0.72241658 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3978432800094 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3953 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3864 1 7.4 1.e+02% + Potential init_pot 0.28453 2 0.14 3.8% + PW_Basis recip2real 0.27892 17 0.016 3.8% + PW_Basis gathers_scatterp 0.12831 17 0.0075 1.7% + Potential v_of_rho 0.94940 14 0.068 13.% + XC_Functional v_xc 0.26770 15 0.018 3.6% + H_Hartree_pw v_hartree 0.63754 14 0.046 8.6% + PW_Basis real2recip 0.73184 41 0.018 9.9% + PW_Basis gatherp_scatters 0.29583 41 0.0072 4.0% + ORB_control set_orb_tables 1.0906 1 1.1 15.% + ORB_gen_tables gen_tables 1.0906 1 1.1 15.% + ORB_table_phi init_Table 0.47300 1 0.47 6.4% + ORB_table_phi cal_ST_Phi12_R 0.46779 126 0.0037 6.3% + ORB_table_beta init_Table_Beta 0.18190 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18039 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24882 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24686 66 0.0037 3.3% + LOOP_ions opt_ions 5.7603 1 5.8 78.% + ESolver_KS_LCAO Run 5.2224 1 5.2 71.% + HSolverLCAO solve 2.6754 12 0.22 36.% + HamiltLCAO updateHk 1.3916 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.3623 12 0.11 18.% + Gint_interface cal_gint 1.9237 25 0.077 26.% + Gint_Gamma distri_vl_value 0.22471 12 0.019 3.0% + Gint_Gamma distri_vl 2.7166 6 0.45 37.% + LCAO_Deepks cal_projected_DM 5.5711 14 0.40 75.% + LCAO_gen_fixedH add_v_delta 2.5707 6 0.43 35.% + LCAO_DESCRIPTOR add_v_delta 2.5707 6 0.43 35.% + ElecStateLCAO psiToRho 1.2652 12 0.11 17.% + Charge mix_rho 0.98199 11 0.089 13.% + LOOP_ions force_stress 0.53773 1 0.54 7.3% + Force_Stress_LCAO getForceStress 0.53770 1 0.54 7.3% + Force_LCAO_gamma ftable_gamma 0.33388 1 0.33 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.29528 1 0.30 4.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:02 2022 + Finish Time : Wed Sep 28 11:10:09 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..f9c466fc25f9d7ccde4cccda37b047a61c7c1cee --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012334 ima = 3.64979e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123779289224 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112605510661 + charge after normalized = 7.99999999999996 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113163659614 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113410155695 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011336214496 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113390372664 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113381115903 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113384289782 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113383513481 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113383408791 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113383390481 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113383382082 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/STRU new file mode 100644 index 0000000000000000000000000000000000000000..fe0b3003e37e46eeb3e726d97be18b386a79c205 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.629322509450 19.036668212500 -0.014550534568 0 0 0 +H +0.0 +2 +-13.345417254311 19.135406484522 -1.354382665221 0 0 0 +-16.260961508981 19.264164202342 -0.748622651212 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/conv new file mode 100644 index 0000000000000000000000000000000000000000..6d2c257b607dbd767fb587e7b7269b99452115f1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/conv @@ -0,0 +1 @@ +57 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b6d7cecad34017045af383acb192b52c6823c597 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.744966275 0.01260798293 1.276154452 1.370609318 1.469053677 0.007827142063 0.02002831352 0.03890650533 +-4.197564414e-18 0.001131720645 0.002405590675 0.01226347869 0.04309210903 -9.545002524e-19 1.572716488e-06 4.946588686e-06 +0.001753325242 0.005690263475 + +H atom_index 1 n_descriptor 18 +1.221177892 0.03476050411 0.09874247375 0.1382407181 0.3134008241 0.02058192143 0.02679476873 0.03794998533 +-2.191503381e-18 3.733941831e-05 0.094204513 0.1140403186 0.1185699789 8.853077294e-18 5.439491736e-06 0.01331732584 +0.02496271047 0.02951052617 + +H atom_index 2 n_descriptor 18 +1.264884429 0.03322467427 0.1135043448 0.1581897559 0.3273337083 0.02250361818 0.0293200327 0.03655393167 +-1.170923852e-17 4.095389939e-05 0.1049803335 0.1158538792 0.1358287385 6.486082423e-18 3.4563592e-06 0.01291654223 +0.02659987107 0.0314962975 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..95c81ca293458c92822a3cedff58fa21707a3513 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:02 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105392 SEC) : SETUP UNITCELL + DONE(0.105735 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123755 SEC) : INIT PLANEWAVE + DONE(0.166812 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450348 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651419e+02 0.000000e+00 2.170e-01 5.293e-01 + GE2 -4.663929e+02 -1.251034e+00 9.839e-02 4.885e-01 + GE3 -4.663986e+02 -5.674785e-03 6.319e-02 5.579e-01 + GE4 -4.663984e+02 2.116531e-04 2.083e-03 4.205e-01 + GE5 -4.663975e+02 8.728700e-04 9.697e-04 4.182e-01 + GE6 -4.663980e+02 -4.808175e-04 2.002e-04 4.148e-01 + GE7 -4.663978e+02 1.818750e-04 4.167e-05 4.074e-01 + GE8 -4.663979e+02 -7.095059e-05 1.957e-05 3.980e-01 + GE9 -4.663978e+02 2.133711e-05 2.812e-06 3.972e-01 + GE10 -4.663978e+02 -3.462369e-06 5.102e-07 3.995e-01 + GE11 -4.663978e+02 -4.825202e-07 1.723e-07 3.954e-01 + GE12 -4.663978e+02 -5.125662e-08 9.968e-09 3.332e-01 +E_delta_band = -7.03765410e-02 Ry = -9.57521963e-01 eV +E_delta_NN= -1.94721412e-01 Ry = -2.64932072e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3953 11 0.67 1e+02 % + Run_lcao lcao_line 7.3864 1 7.4 1e+02 % + Potential init_pot 0.28453 2 0.14 3.8 % + PW_Basis recip2real 0.27892 17 0.016 3.8 % + PW_Basis gathers_scatterp 0.12831 17 0.0075 1.7 % + Potential v_of_rho 0.9494 14 0.068 13 % + XC_Functional v_xc 0.2677 15 0.018 3.6 % + H_Hartree_pw v_hartree 0.63754 14 0.046 8.6 % + PW_Basis real2recip 0.73184 41 0.018 9.9 % + PW_Basis gatherp_scatters 0.29583 41 0.0072 4 % + ORB_control set_orb_tables 1.0906 1 1.1 15 % + ORB_gen_tables gen_tables 1.0906 1 1.1 15 % + ORB_table_phi init_Table 0.473 1 0.47 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.46779 126 0.0037 6.3 % + ORB_table_beta init_Table_Beta 0.1819 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18039 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24882 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24686 66 0.0037 3.3 % + LOOP_ions opt_ions 5.7603 1 5.8 78 % + ESolver_KS_LCAO Run 5.2224 1 5.2 71 % + HSolverLCAO solve 2.6754 12 0.22 36 % + HamiltLCAO updateHk 1.3916 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.3623 12 0.11 18 % + Gint_interface cal_gint 1.9237 25 0.077 26 % + Gint_Gamma distri_vl_value 0.22471 12 0.019 3 % + Gint_Gamma distri_vl 2.7166 6 0.45 37 % + LCAO_Deepks cal_projected_DM 5.5711 14 0.4 75 % + LCAO_gen_fixedH add_v_delta 2.5707 6 0.43 35 % + LCAO_DESCRIPTOR add_v_delta 2.5707 6 0.43 35 % + ElecStateLCAO psiToRho 1.2652 12 0.11 17 % + Charge mix_rho 0.98199 11 0.089 13 % + LOOP_ions force_stress 0.53773 1 0.54 7.3 % + Force_Stress_LCAO getForceStress 0.5377 1 0.54 7.3 % + Force_LCAO_gamma ftable_gamma 0.33388 1 0.33 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.29528 1 0.3 4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:02 2022 + FINISH Time : Wed Sep 28 11:10:09 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/57/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..1cd05c3e8d0f9a1e71d27032fe912152b08af714 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.467339 0.680816 0.0116071 +H 0.514326 0.699873 0.973467 +H 0.419781 0.674903 0.969515 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..015489c9c719526470971195fcb54b74ab4cb72f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6991 2 + 2 -13.1351 2 + 3 -9.35153 2 + 4 -6.8341 2 + 5 1.54052 0 + 6 4.87316 0 + 7 10.9892 0 + 8 11.2565 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..aeead9f49553373bf0eab98fd150ed84fc3a3e22 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:10 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.0854871857 19.0628417852 0.324999550714 0 0 0 0 + tauc_H1 14.4011173562 19.5964464468 27.2570769608 0 0 0 0 + tauc_H2 11.7538579567 18.897293566 27.1464280056 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0752199774223 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0853275245505 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.101442303965 (SEC) + + DONE : INIT CHARGE Time : 0.143147299712 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.398776 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000839 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00142 + + Density error is 0.218687194459 + + Energy Rydberg eV + E_KohnSham -34.1829101057 -465.08235166 + E_Harris -34.3835675284 -467.812435954 + E_Fermi -0.427038889736 -5.81016216801 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00131256901192 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131188021378 + + Density error is 0.097237697318 + + Energy Rydberg eV + E_KohnSham -34.2758013561 -466.346201959 + E_Harris -34.2824855957 -466.437145704 + E_Fermi -0.232794293174 -3.16732884904 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00126045580963 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012123294542 + + Density error is 0.0620828915261 + + Energy Rydberg eV + E_KohnSham -34.2761492919 -466.350935868 + E_Harris -34.2804337819 -466.409229345 + E_Fermi -0.218392140137 -2.97137750428 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00119274863906 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104753997503 + + Density error is 0.00206862856483 + + Energy Rydberg eV + E_KohnSham -34.2761993865 -466.35161744 + E_Harris -34.2762023813 -466.351658187 + E_Fermi -0.182231703925 -2.47938952964 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00119842420664 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104753779637 + + Density error is 0.00098388422006 + + Energy Rydberg eV + E_KohnSham -34.2761122977 -466.350432537 + E_Harris -34.2761154485 -466.350475406 + E_Fermi -0.181018809404 -2.46288725307 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0011963875884 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104561504309 + + Density error is 0.000113403189996 + + Energy Rydberg eV + E_KohnSham -34.2761708935 -466.351229773 + E_Harris -34.2761709213 -466.351230151 + E_Fermi -0.18133255576 -2.46715599124 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00119619656152 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104519266252 + + Density error is 4.96289667848e-05 + + Energy Rydberg eV + E_KohnSham -34.2761521347 -466.350974547 + E_Harris -34.2761521491 -466.350974742 + E_Fermi -0.181192358135 -2.4652485047 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00119611794624 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104523359836 + + Density error is 2.63600307006e-05 + + Energy Rydberg eV + E_KohnSham -34.2761551263 -466.351015249 + E_Harris -34.2761551293 -466.35101529 + E_Fermi -0.181264987783 -2.46623668175 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00119612877813 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104519907043 + + Density error is 1.90204363221e-06 + + Energy Rydberg eV + E_KohnSham -34.2761532048 -466.350989106 + E_Harris -34.2761532048 -466.350989106 + E_Fermi -0.181235806921 -2.46583965575 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0011961307461 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104519719725 + + Density error is 2.27824049857e-07 + + Energy Rydberg eV + E_KohnSham -34.2761535962 -466.350994432 + E_Harris -34.2761535962 -466.350994432 + E_Fermi -0.181233803205 -2.4658123938 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00119613161391 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104519799887 + + Density error is 3.89146475788e-08 + + Energy Rydberg eV + E_KohnSham -34.2761536323 -466.350994923 + E_Harris -34.2761536323 -466.350994923 + E_band -8.08775407504 -110.039539443 + E_one_elec -69.9744970548 -952.051874629 + E_Hartree +36.3547479171 +494.631721026 + E_xc -8.2605872656 -112.391055638 + E_Ewald +7.72708072468 +105.132326762 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196135460919 -2.66855984836 + E_Fermi -0.181233914506 -2.46581390812 + + charge density convergence is achieved + final etot is -466.350994923 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6991 2.00000 + 2 -13.1351 2.00000 + 3 -9.35153 2.00000 + 4 -6.83410 2.00000 + 5 1.54052 0.00000 + 6 4.87316 0.00000 + 7 10.9892 0.00000 + 8 11.2565 0.00000 + + EFERMI = -2.465813908122959 eV + OUT.ABACUS/ final etot is -466.3509949227247 eV + correction force for each atom along direction 1 is 4.87864e-05 + correction force for each atom along direction 2 is -0.000105200 + correction force for each atom along direction 3 is -0.000160375 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.22485722 -0.36411802 +1.7854464 + H1 +1.7979991 +0.64417853 -0.92410353 + H2 -1.5731419 -0.28006051 -0.86134286 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3509949227247 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5149 11 0.50 1.0e+02% + Run_lcao lcao_line 5.5063 1 5.5 1.e+02% + Potential init_pot 0.25369 2 0.13 4.6% + PW_Basis recip2real 0.26176 16 0.016 4.7% + PW_Basis gathers_scatterp 0.11857 16 0.0074 2.1% + Charge atomic_rho 0.10436 1 0.10 1.9% + Potential v_of_rho 0.91659 13 0.071 17.% + XC_Functional v_xc 0.28023 14 0.020 5.1% + H_Hartree_pw v_hartree 0.59747 13 0.046 11.% + PW_Basis real2recip 0.59632 38 0.016 11.% + PW_Basis gatherp_scatters 0.22124 38 0.0058 4.0% + ORB_control set_orb_tables 0.89690 1 0.90 16.% + ORB_gen_tables gen_tables 0.89690 1 0.90 16.% + ORB_table_phi init_Table 0.37458 1 0.37 6.8% + ORB_table_phi cal_ST_Phi12_R 0.37027 126 0.0029 6.7% + ORB_table_beta init_Table_Beta 0.15431 1 0.15 2.8% + ORB_table_beta VNL_PhiBeta_R 0.15296 56 0.0027 2.8% + ORB_table_alpha init_Table_Alpha 0.21016 1 0.21 3.8% + ORB_table_alpha S_PhiAlpha_R 0.20849 66 0.0032 3.8% + LOOP_ions opt_ions 4.1430 1 4.1 75.% + ESolver_KS_LCAO Run 3.7136 1 3.7 67.% + HSolverLCAO solve 1.5346 11 0.14 28.% + HamiltLCAO updateHk 0.85984 11 0.078 16.% + LCAO_Hamilt cal_Hgamma 0.83182 11 0.076 15.% + Gint_interface cal_gint 1.1798 23 0.051 21.% + Gint_Gamma distri_vl 1.8097 6 0.30 33.% + LCAO_Deepks cal_projected_DM 4.0088 13 0.31 73.% + LCAO_gen_fixedH add_v_delta 1.6806 6 0.28 30.% + LCAO_DESCRIPTOR add_v_delta 1.6806 6 0.28 30.% + ElecStateLCAO psiToRho 0.66048 11 0.060 12.% + Charge mix_rho 0.75446 10 0.075 14.% + LOOP_ions force_stress 0.42924 1 0.43 7.8% + Force_Stress_LCAO getForceStress 0.42922 1 0.43 7.8% + Force_LCAO_gamma ftable_gamma 0.23274 1 0.23 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.21151 1 0.21 3.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:10 2022 + Finish Time : Wed Sep 28 11:13:15 2022 + Total Time : 0 h 0 mins 5 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4fee56499f857f381fd7b214f5474f156ccb6a85 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012421 ima = 3.65202e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122630145029 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111571976314 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112017378529 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112338453836 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112252741097 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011229926374 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112295854551 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001122994923 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298386395 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298300954 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112298295583 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/STRU new file mode 100644 index 0000000000000000000000000000000000000000..4c186a7c61cb5efbb27d892e3d01b02302159795 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.914512814296 19.062841785197 0.324999550720 0 0 0 +H +0.0 +2 +-13.598882643848 19.596446446874 -0.742923039177 0 0 0 +-16.246142043331 18.897293566014 -0.853571994370 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/conv new file mode 100644 index 0000000000000000000000000000000000000000..24e6839043171c70b1b37e9a8de1402c143d04c9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/conv @@ -0,0 +1 @@ +58 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..442d846a25ede0928c274437c9158125bc35901f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752233392 0.01291993479 1.298563704 1.378967833 1.471143938 0.009341671692 0.01814658336 0.03910632204 +-8.760091843e-19 0.001120940278 0.00297312478 0.01382948184 0.04988429078 -7.45854551e-19 3.00745364e-06 7.691796185e-06 +0.001607764979 0.006095168801 + +H atom_index 1 n_descriptor 18 +1.292404665 0.03325822745 0.1264851544 0.1703723551 0.3323059979 0.02513689154 0.03068422999 0.03678511495 +-3.135953051e-18 5.953392154e-05 0.1090129217 0.123764738 0.1463475485 7.289784165e-18 1.260417496e-06 0.0136552721 +0.02892058097 0.03252274153 + +H atom_index 2 n_descriptor 18 +1.285010402 0.03348161744 0.1235484751 0.1665389385 0.3302068556 0.02477968653 0.03026218669 0.03686868643 +-1.814894545e-17 5.880838589e-05 0.1090811081 0.1215745502 0.1431108914 -3.232695699e-18 1.63134647e-06 0.01351205173 +0.02869120714 0.03224924894 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3cded8f6e605a7eef3cb1db11c39ea0735bc62ae Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:10 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0752363 SEC) : SETUP UNITCELL + DONE(0.0853399 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.101457 SEC) : INIT PLANEWAVE + DONE(0.143248 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.398832 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650824e+02 0.000000e+00 2.187e-01 4.237e-01 + GE2 -4.663462e+02 -1.263850e+00 9.724e-02 3.849e-01 + GE3 -4.663509e+02 -4.733909e-03 6.208e-02 4.478e-01 + GE4 -4.663516e+02 -6.815726e-04 2.069e-03 3.208e-01 + GE5 -4.663504e+02 1.184904e-03 9.839e-04 3.217e-01 + GE6 -4.663512e+02 -7.972368e-04 1.134e-04 3.075e-01 + GE7 -4.663510e+02 2.552263e-04 4.963e-05 3.152e-01 + GE8 -4.663510e+02 -4.070194e-05 2.636e-05 2.980e-01 + GE9 -4.663510e+02 2.614297e-05 1.902e-06 3.022e-01 + GE10 -4.663510e+02 -5.325870e-06 2.278e-07 3.033e-01 + GE11 -4.663510e+02 -4.907842e-07 3.891e-08 2.352e-01 +E_delta_band = -7.32375072e-02 Ry = -9.96447405e-01 eV +E_delta_NN= -1.96135461e-01 Ry = -2.66855985e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5149 11 0.5 1e+02 % + Run_lcao lcao_line 5.5063 1 5.5 1e+02 % + Potential init_pot 0.25369 2 0.13 4.6 % + PW_Basis recip2real 0.26176 16 0.016 4.7 % + PW_Basis gathers_scatterp 0.11857 16 0.0074 2.1 % + Charge atomic_rho 0.10436 1 0.1 1.9 % + Potential v_of_rho 0.91659 13 0.071 17 % + XC_Functional v_xc 0.28023 14 0.02 5.1 % + H_Hartree_pw v_hartree 0.59747 13 0.046 11 % + PW_Basis real2recip 0.59632 38 0.016 11 % + PW_Basis gatherp_scatters 0.22124 38 0.0058 4 % + ORB_control set_orb_tables 0.8969 1 0.9 16 % + ORB_gen_tables gen_tables 0.8969 1 0.9 16 % + ORB_table_phi init_Table 0.37458 1 0.37 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.37027 126 0.0029 6.7 % + ORB_table_beta init_Table_Beta 0.15431 1 0.15 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.15296 56 0.0027 2.8 % + ORB_table_alpha init_Table_Alpha 0.21016 1 0.21 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.20849 66 0.0032 3.8 % + LOOP_ions opt_ions 4.143 1 4.1 75 % + ESolver_KS_LCAO Run 3.7136 1 3.7 67 % + HSolverLCAO solve 1.5346 11 0.14 28 % + HamiltLCAO updateHk 0.85984 11 0.078 16 % + LCAO_Hamilt cal_Hgamma 0.83182 11 0.076 15 % + Gint_interface cal_gint 1.1798 23 0.051 21 % + Gint_Gamma distri_vl 1.8097 6 0.3 33 % + LCAO_Deepks cal_projected_DM 4.0088 13 0.31 73 % + LCAO_gen_fixedH add_v_delta 1.6806 6 0.28 30 % + LCAO_DESCRIPTOR add_v_delta 1.6806 6 0.28 30 % + ElecStateLCAO psiToRho 0.66048 11 0.06 12 % + Charge mix_rho 0.75446 10 0.075 14 % + LOOP_ions force_stress 0.42924 1 0.43 7.8 % + Force_Stress_LCAO getForceStress 0.42922 1 0.43 7.8 % + Force_LCAO_gamma ftable_gamma 0.23274 1 0.23 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.21151 1 0.21 3.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:10 2022 + FINISH Time : Wed Sep 28 11:13:15 2022 + TOTAL Time : 5 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/58/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..5a47da5845f99c9428e0e5b6e1e54757706c956f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.468498 0.691054 0.0123862 +H 0.50185 0.705298 0.954597 +H 0.40491 0.674244 0.993095 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..db77fe7ca0fd008c680200d92aa042f1001158f6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.7953 2 + 2 -12.7059 2 + 3 -8.9776 2 + 4 -6.633 2 + 5 0.884564 0 + 6 3.7282 0 + 7 11.1894 0 + 8 11.4285 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ebf9b8776f73e93b907047b6ab44ff874b997cc3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:13 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.117950804 19.3495094152 0.346814435739 0 0 0 0 + tauc_H1 14.0517922231 19.7483345094 26.728722413 0 0 0 0 + tauc_H2 11.337469773 18.8788352504 27.8066712542 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.104468418505 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.104842070939 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.122907410517 (SEC) + + DONE : INIT CHARGE Time : 0.166014779442 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448413 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 0 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000794 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00162 + + Density error is 0.211179688387 + + Energy Rydberg eV + E_KohnSham -34.1874313497 -465.143866339 + E_Harris -34.3708098029 -467.638858194 + E_Fermi -0.377200520899 -5.13207637279 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116986161321 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131068556661 + + Density error is 0.0995979144449 + + Energy Rydberg eV + E_KohnSham -34.2761216521 -466.35055981 + E_Harris -34.2835961379 -466.452255406 + E_Fermi -0.187615205163 -2.55263582166 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00112417310511 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121754671134 + + Density error is 0.0645519337593 + + Energy Rydberg eV + E_KohnSham -34.2767118863 -466.358590358 + E_Harris -34.2813962909 -466.422324952 + E_Fermi -0.183707220184 -2.49946495824 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107678244436 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102500596772 + + Density error is 0.00204417741159 + + Energy Rydberg eV + E_KohnSham -34.2765741224 -466.356715984 + E_Harris -34.2765790563 -466.356783114 + E_Fermi -0.148897027472 -2.02584798888 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010760496305 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102302137472 + + Density error is 0.00102103939666 + + Energy Rydberg eV + E_KohnSham -34.2765450044 -466.356319813 + E_Harris -34.2765452722 -466.356323457 + E_Fermi -0.148962552788 -2.02673950654 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107541262659 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101961290227 + + Density error is 0.000213702158017 + + Energy Rydberg eV + E_KohnSham -34.2765539491 -466.356441512 + E_Harris -34.2765539547 -466.356441589 + E_Fermi -0.148418543375 -2.01933787876 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107564310072 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101969668137 + + Density error is 2.78634799298e-05 + + Energy Rydberg eV + E_KohnSham -34.2765518012 -466.356412288 + E_Harris -34.2765518031 -466.356412315 + E_Fermi -0.148423205339 -2.01940130804 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107556584306 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101964420612 + + Density error is 1.15466768614e-05 + + Energy Rydberg eV + E_KohnSham -34.2765541048 -466.35644363 + E_Harris -34.2765541053 -466.356443637 + E_Fermi -0.148434238394 -2.01955142045 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107556611317 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101962108279 + + Density error is 1.75992424752e-06 + + Energy Rydberg eV + E_KohnSham -34.276553235 -466.356431796 + E_Harris -34.276553235 -466.356431796 + E_Fermi -0.148422778099 -2.01939549514 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00107556597346 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101961622307 + + Density error is 3.02569120862e-07 + + Energy Rydberg eV + E_KohnSham -34.2765533887 -466.356433888 + E_Harris -34.2765533887 -466.356433888 + E_Fermi -0.148421220246 -2.01937429946 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010755668017 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00101961649811 + + Density error is 4.32923417305e-08 + + Energy Rydberg eV + E_KohnSham -34.2765534055 -466.356434116 + E_Harris -34.2765534055 -466.356434116 + E_band -7.80728233401 -106.223525637 + E_one_elec -68.3105472124 -929.412675586 + E_Hartree +35.5808103697 +484.101760486 + E_xc -8.13597932236 -110.695677594 + E_Ewald +6.71546060263 +91.3685288903 + E_demet -3.90971565649e-52 -5.31944104881e-51 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193056439424 -2.62666761176 + E_Fermi -0.148421043849 -2.01937189945 + + charge density convergence is achieved + final etot is -466.356434116 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.7953 2.00000 + 2 -12.7059 2.00000 + 3 -8.97760 2.00000 + 4 -6.63300 2.00000 + 5 0.884564 0.00000 + 6 3.72820 0.00000 + 7 11.1894 0.00000 + 8 11.4285 0.00000 + + EFERMI = -2.019371899451929 eV + OUT.ABACUS/ final etot is -466.3564341163085 eV + correction force for each atom along direction 1 is -2.53586e-05 + correction force for each atom along direction 2 is -4.71523e-05 + correction force for each atom along direction 3 is -0.000105052 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.73395369 -0.093833682 -1.5059368 + H1 -0.92682926 -0.36270588 +1.2093382 + H2 +1.6607830 +0.45653956 +0.29659853 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3564341163085 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9815 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9715 1 7.0 1.e+02% + Potential init_pot 0.28326 2 0.14 4.1% + PW_Basis recip2real 0.26689 16 0.017 3.8% + PW_Basis gathers_scatterp 0.11975 16 0.0075 1.7% + Potential v_of_rho 0.97075 13 0.075 14.% + XC_Functional v_xc 0.29625 14 0.021 4.2% + H_Hartree_pw v_hartree 0.63153 13 0.049 9.0% + PW_Basis real2recip 0.68491 38 0.018 9.8% + PW_Basis gatherp_scatters 0.27314 38 0.0072 3.9% + ORB_control set_orb_tables 1.0946 1 1.1 16.% + ORB_gen_tables gen_tables 1.0946 1 1.1 16.% + ORB_table_phi init_Table 0.47371 1 0.47 6.8% + ORB_table_phi cal_ST_Phi12_R 0.46850 126 0.0037 6.7% + ORB_table_beta init_Table_Beta 0.18302 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18155 56 0.0032 2.6% + ORB_table_alpha init_Table_Alpha 0.24852 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24653 66 0.0037 3.5% + LOOP_ions opt_ions 5.3132 1 5.3 76.% + ESolver_KS_LCAO Run 4.7770 1 4.8 68.% + HSolverLCAO solve 2.3493 11 0.21 34.% + HamiltLCAO updateHk 1.2289 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2015 11 0.11 17.% + Gint_interface cal_gint 1.8893 23 0.082 27.% + Gint_Gamma distri_vl 2.2975 6 0.38 33.% + LCAO_Deepks cal_projected_DM 5.1592 13 0.40 74.% + LCAO_gen_fixedH add_v_delta 2.1497 6 0.36 31.% + LCAO_DESCRIPTOR add_v_delta 2.1497 6 0.36 31.% + ElecStateLCAO psiToRho 1.1009 11 0.10 16.% + Charge mix_rho 0.90484 10 0.090 13.% + LOOP_ions force_stress 0.53594 1 0.54 7.7% + Force_Stress_LCAO getForceStress 0.53592 1 0.54 7.7% + Force_LCAO_gamma ftable_gamma 0.32389 1 0.32 4.6% + Force_LCAO_gamma cal_fvl_dphi 0.31575 1 0.32 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:13 2022 + Finish Time : Wed Sep 28 11:11:20 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..bf16fc92812675cbb027f2ffc2724cd744f8990c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123568 ima = 3.65503e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124096339268 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112356470135 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113255777782 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113438257996 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113431000873 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113437787844 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113434353989 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113436095175 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113435612848 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113435556089 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113435538106 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9d299e42970d6c72dbf22a34c7115c3c12946830 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.882049195974 19.349509415189 0.346814435718 0 0 0 +H +0.0 +2 +-13.948207776876 19.748334509401 -1.271277587012 0 0 0 +-16.662530227011 18.878835250353 -0.193328745813 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/conv new file mode 100644 index 0000000000000000000000000000000000000000..3fdf418b18b7377a14bfd36abb05fc4d7a2dc0ec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/conv @@ -0,0 +1 @@ +59 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..688cf8c600b899e3e9e376ca1cd646d3fafc629a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748971176 0.01224452207 1.233985852 1.329971301 1.467265544 0.008116945969 0.0181682496 0.03907835757 +2.211783117e-18 0.0008568535786 0.002243940817 0.01095761657 0.03929436231 3.546950467e-20 1.319798962e-06 4.26300664e-06 +0.001624040317 0.005708094215 + +H atom_index 1 n_descriptor 18 +1.184155922 0.03636140425 0.0863548331 0.1226055529 0.2993139638 0.01870997496 0.02456801312 0.04001459611 +-1.174463662e-17 3.127124121e-05 0.0808459235 0.1045024986 0.1132433793 -2.333378633e-18 6.050855706e-06 0.01449745481 +0.02263669976 0.02746633984 + +H atom_index 2 n_descriptor 18 +1.177163199 0.03656264969 0.08438752327 0.1198937598 0.296591823 0.0183954662 0.02416150299 0.04030281504 +8.936654507e-18 3.075237331e-05 0.07910441104 0.1020997829 0.1128664521 -2.979261776e-19 6.188105997e-06 0.01472791111 +0.02234198572 0.02708247834 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4567a6b950a3013dd5a64735660c2977c50e01ec Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:13 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.104492 SEC) : SETUP UNITCELL + DONE(0.104857 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.122926 SEC) : INIT PLANEWAVE + DONE(0.16615 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448476 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651439e+02 0.000000e+00 2.112e-01 5.265e-01 + GE2 -4.663506e+02 -1.206693e+00 9.960e-02 4.879e-01 + GE3 -4.663586e+02 -8.030548e-03 6.455e-02 5.591e-01 + GE4 -4.663567e+02 1.874374e-03 2.044e-03 4.160e-01 + GE5 -4.663563e+02 3.961712e-04 1.021e-03 4.151e-01 + GE6 -4.663564e+02 -1.216983e-04 2.137e-04 4.102e-01 + GE7 -4.663564e+02 2.922313e-05 2.786e-05 3.945e-01 + GE8 -4.663564e+02 -3.134167e-05 1.155e-05 3.922e-01 + GE9 -4.663564e+02 1.183411e-05 1.760e-06 3.943e-01 + GE10 -4.663564e+02 -2.091639e-06 3.026e-07 3.957e-01 + GE11 -4.663564e+02 -2.287178e-07 4.329e-08 3.225e-01 +E_delta_band = -6.67585963e-02 Ry = -9.08297300e-01 eV +E_delta_NN= -1.93056439e-01 Ry = -2.62666761e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9815 11 0.63 1e+02 % + Run_lcao lcao_line 6.9715 1 7 1e+02 % + Potential init_pot 0.28326 2 0.14 4.1 % + PW_Basis recip2real 0.26689 16 0.017 3.8 % + PW_Basis gathers_scatterp 0.11975 16 0.0075 1.7 % + Potential v_of_rho 0.97075 13 0.075 14 % + XC_Functional v_xc 0.29625 14 0.021 4.2 % + H_Hartree_pw v_hartree 0.63153 13 0.049 9 % + PW_Basis real2recip 0.68491 38 0.018 9.8 % + PW_Basis gatherp_scatters 0.27314 38 0.0072 3.9 % + ORB_control set_orb_tables 1.0946 1 1.1 16 % + ORB_gen_tables gen_tables 1.0946 1 1.1 16 % + ORB_table_phi init_Table 0.47371 1 0.47 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.4685 126 0.0037 6.7 % + ORB_table_beta init_Table_Beta 0.18302 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18155 56 0.0032 2.6 % + ORB_table_alpha init_Table_Alpha 0.24852 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24653 66 0.0037 3.5 % + LOOP_ions opt_ions 5.3132 1 5.3 76 % + ESolver_KS_LCAO Run 4.777 1 4.8 68 % + HSolverLCAO solve 2.3493 11 0.21 34 % + HamiltLCAO updateHk 1.2289 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.2015 11 0.11 17 % + Gint_interface cal_gint 1.8893 23 0.082 27 % + Gint_Gamma distri_vl 2.2975 6 0.38 33 % + LCAO_Deepks cal_projected_DM 5.1592 13 0.4 74 % + LCAO_gen_fixedH add_v_delta 2.1497 6 0.36 31 % + LCAO_DESCRIPTOR add_v_delta 2.1497 6 0.36 31 % + ElecStateLCAO psiToRho 1.1009 11 0.1 16 % + Charge mix_rho 0.90484 10 0.09 13 % + LOOP_ions force_stress 0.53594 1 0.54 7.7 % + Force_Stress_LCAO getForceStress 0.53592 1 0.54 7.7 % + Force_LCAO_gamma ftable_gamma 0.32389 1 0.32 4.6 % + Force_LCAO_gamma cal_fvl_dphi 0.31575 1 0.32 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:13 2022 + FINISH Time : Wed Sep 28 11:11:20 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/59/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..10906545563b6ee5001c252574ae248e584b90ad --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.522941 0.71042 0.286911 +H 0.561476 0.762655 0.305526 +H 0.470872 0.749707 0.266169 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..78757eea337955b993cfd0e5a65d20d07a56a320 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0786 2 + 2 -12.2148 2 + 3 -9.5768 2 + 4 -6.70727 2 + 5 0.886375 0 + 6 3.74936 0 + 7 11.1531 0 + 8 11.4462 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..43fd8eefdad9aae494bf01ff5c4bdc842ed3e666 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:16 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.6423464353 19.8917708514 8.03351788017 0 0 0 0 + tauc_H1 15.7213412078 21.3543408314 8.55472737996 0 0 0 0 + tauc_H2 13.184424687 20.991789661 7.45274066477 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0860935755312 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0967617522039 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.114983844028 (SEC) + + DONE : INIT CHARGE Time : 0.162790301467 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.442596 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00108 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00136 + + Density error is 0.20843913535 + + Energy Rydberg eV + E_KohnSham -34.187536171 -465.145292506 + E_Harris -34.3668227654 -467.584611766 + E_Fermi -0.381882731106 -5.19578111084 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00116035503871 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127159794683 + + Density error is 0.0983033174181 + + Energy Rydberg eV + E_KohnSham -34.274040434 -466.322243385 + E_Harris -34.2814521074 -466.423084375 + E_Fermi -0.195989955504 -2.66658014562 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00109399608862 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118869042207 + + Density error is 0.063562980631 + + Energy Rydberg eV + E_KohnSham -34.2745497439 -466.329172901 + E_Harris -34.2792636511 -466.3933089 + E_Fermi -0.1910153641 -2.59889735731 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000987969282517 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103818771343 + + Density error is 0.00184078258087 + + Energy Rydberg eV + E_KohnSham -34.2744100806 -466.327272685 + E_Harris -34.2744098373 -466.327269375 + E_Fermi -0.155624915409 -2.11738560033 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000988259541608 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010384205873 + + Density error is 0.00098848855911 + + Energy Rydberg eV + E_KohnSham -34.2743899437 -466.326998708 + E_Harris -34.2743905528 -466.327006995 + E_Fermi -0.156078863944 -2.12356188701 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000986688534933 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103599620502 + + Density error is 0.000116182647318 + + Energy Rydberg eV + E_KohnSham -34.2743941018 -466.327055282 + E_Harris -34.2743940981 -466.327055231 + E_Fermi -0.15543653485 -2.11482255134 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000986723683774 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103599031389 + + Density error is 2.17820286677e-05 + + Energy Rydberg eV + E_KohnSham -34.2743947853 -466.327064582 + E_Harris -34.274394786 -466.327064591 + E_Fermi -0.155424863598 -2.11466375581 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000986661392422 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103592895402 + + Density error is 6.84702638917e-06 + + Energy Rydberg eV + E_KohnSham -34.274395511 -466.327074455 + E_Harris -34.2743955112 -466.327074458 + E_Fermi -0.155426642946 -2.11468796507 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000986657236073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103592140543 + + Density error is 1.60311824485e-06 + + Energy Rydberg eV + E_KohnSham -34.2743949642 -466.327067015 + E_Harris -34.2743949642 -466.327067015 + E_Fermi -0.155420149174 -2.11459961278 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000986656769353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010359190976 + + Density error is 2.12666836819e-07 + + Energy Rydberg eV + E_KohnSham -34.2743950601 -466.32706832 + E_Harris -34.2743950601 -466.32706832 + E_Fermi -0.155418872203 -2.1145822387 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000986657202008 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103591944006 + + Density error is 4.16842934462e-08 + + Energy Rydberg eV + E_KohnSham -34.2743950739 -466.327068508 + E_Harris -34.2743950739 -466.327068508 + E_band -7.87574533492 -107.155012552 + E_one_elec -68.4996340855 -931.985334478 + E_Hartree +35.6481434465 +485.017873994 + E_xc -8.14664508588 -110.840792752 + E_Ewald +6.84959492072 +93.1935199136 + E_demet -1.706264992e-55 -2.32149261892e-54 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193485039944 -2.63249902099 + E_Fermi -0.155418751604 -2.11458059786 + + charge density convergence is achieved + final etot is -466.327068508 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0786 2.00000 + 2 -12.2148 2.00000 + 3 -9.57680 2.00000 + 4 -6.70727 2.00000 + 5 0.886375 0.00000 + 6 3.74936 0.00000 + 7 11.1531 0.00000 + 8 11.4462 0.00000 + + EFERMI = -2.114580597862155 eV + OUT.ABACUS/ final etot is -466.3270685078908 eV + correction force for each atom along direction 1 is 8.12258e-06 + correction force for each atom along direction 2 is 0.000112429 + correction force for each atom along direction 3 is 0.000147232 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.71634626 +2.4327956 -0.20241677 + H1 +0.019259395 -1.0840257 -0.038542572 + H2 +0.69708686 -1.3487699 +0.24095934 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3270685078908 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6981 11 0.52 1.0e+02% + Run_lcao lcao_line 5.6877 1 5.7 1.e+02% + Potential init_pot 0.28611 2 0.14 5.0% + PW_Basis recip2real 0.26577 16 0.017 4.7% + PW_Basis gathers_scatterp 0.11473 16 0.0072 2.0% + Potential v_of_rho 0.87431 13 0.067 15.% + XC_Functional v_xc 0.24516 14 0.018 4.3% + H_Hartree_pw v_hartree 0.59103 13 0.045 10.% + PW_Basis real2recip 0.55643 38 0.015 9.8% + PW_Basis gatherp_scatters 0.21613 38 0.0057 3.8% + ORB_control set_orb_tables 1.1154 1 1.1 20.% + ORB_gen_tables gen_tables 1.1154 1 1.1 20.% + ORB_table_phi init_Table 0.48450 1 0.48 8.5% + ORB_table_phi cal_ST_Phi12_R 0.47963 126 0.0038 8.4% + ORB_table_beta init_Table_Beta 0.19222 1 0.19 3.4% + ORB_table_beta VNL_PhiBeta_R 0.19067 56 0.0034 3.3% + ORB_table_alpha init_Table_Alpha 0.25765 1 0.26 4.5% + ORB_table_alpha S_PhiAlpha_R 0.25576 66 0.0039 4.5% + LOOP_ions opt_ions 4.0530 1 4.1 71.% + ESolver_KS_LCAO Run 3.5775 1 3.6 63.% + HSolverLCAO solve 1.6103 11 0.15 28.% + HamiltLCAO updateHk 0.88108 11 0.080 15.% + LCAO_Hamilt cal_Hgamma 0.84813 11 0.077 15.% + Gint_interface cal_gint 0.82627 23 0.036 15.% + Gint_Gamma distri_vl_value 0.20819 11 0.019 3.7% + Gint_Gamma distri_vl 1.7374 6 0.29 30.% + LCAO_Deepks cal_projected_DM 3.8393 13 0.30 67.% + LCAO_gen_fixedH add_v_delta 1.6049 6 0.27 28.% + LCAO_DESCRIPTOR add_v_delta 1.6049 6 0.27 28.% + ElecStateLCAO psiToRho 0.71184 11 0.065 12.% + Charge mix_rho 0.65617 10 0.066 12.% + LOOP_ions force_stress 0.47534 1 0.48 8.3% + Force_Stress_LCAO getForceStress 0.47531 1 0.48 8.3% + Force_LCAO_gamma ftable_gamma 0.26620 1 0.27 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.18190 1 0.18 3.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:16 2022 + Finish Time : Wed Sep 28 11:05:22 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..edea034b847dc74b78939016bc7606235589425b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123408 ima = 3.68527e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122929450457 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111338572528 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112238751346 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112441556934 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112439452074 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112440553433 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112439673365 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112440768103 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112440465936 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112440424173 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112440411172 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3090a8d44bc46ef6905267015807bc7b0583238a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.357653564693 19.891770851393 8.033517880162 0 0 0 +H +0.0 +2 +-12.278658792210 21.354340831409 8.554727379945 0 0 0 +-14.815575312984 20.991789660948 7.452740664783 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/conv new file mode 100644 index 0000000000000000000000000000000000000000..611599133f51f24f34360308a8d915ce0038219b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/conv @@ -0,0 +1 @@ +6 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..1c7c75c7a2d7d07165d5065e99bb5de3fe0c8dc9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.757621439 0.01254797495 1.23926601 1.315090509 1.468482692 0.009995285787 0.01504611503 0.03934866987 +6.622902063e-19 0.0006671285764 0.00268494251 0.01283664343 0.04274622573 1.170267106e-19 2.425236746e-06 6.9381122e-06 +0.001565958815 0.006041193134 + +H atom_index 1 n_descriptor 18 +1.207006815 0.03661986912 0.09858004835 0.1307388622 0.3042797616 0.02145724141 0.02569199874 0.03996674151 +-2.533216919e-17 3.8939327e-05 0.08985989719 0.1115067276 0.1139833575 -2.66449874e-18 3.905272086e-06 0.0142824249 +0.02488985351 0.02856041631 + +H atom_index 2 n_descriptor 18 +1.187079663 0.03719818315 0.09235601292 0.1226256908 0.2964687755 0.02045699945 0.02451318726 0.04076379031 +-1.249204693e-18 3.734318305e-05 0.0849021341 0.1043616709 0.1128115768 -2.276627486e-18 4.662178939e-06 0.0148910738 +0.02404755181 0.02747522951 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..b20364eebdda43e993c9743134117094b79a0ac2 Binary files /dev/null and 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0000000000000000000000000000000000000000..e8dbc332257567bed9c405cbe0be002871c25bae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:16 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0861203 SEC) : SETUP UNITCELL + DONE(0.0967794 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115003 SEC) : INIT PLANEWAVE + DONE(0.162916 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.442669 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651453e+02 0.000000e+00 2.084e-01 4.380e-01 + GE2 -4.663222e+02 -1.176951e+00 9.830e-02 3.654e-01 + GE3 -4.663292e+02 -6.929517e-03 6.356e-02 4.194e-01 + GE4 -4.663273e+02 1.900216e-03 1.841e-03 3.089e-01 + GE5 -4.663270e+02 2.739771e-04 9.885e-04 3.089e-01 + GE6 -4.663271e+02 -5.657387e-05 1.162e-04 3.035e-01 + GE7 -4.663271e+02 -9.299889e-06 2.178e-05 2.880e-01 + GE8 -4.663271e+02 -9.873905e-06 6.847e-06 2.860e-01 + GE9 -4.663271e+02 7.440225e-06 1.603e-06 2.862e-01 + GE10 -4.663271e+02 -1.305077e-06 2.127e-07 2.841e-01 + GE11 -4.663271e+02 -1.876036e-07 4.168e-08 2.278e-01 +E_delta_band = -6.76307702e-02 Ry = -9.20163835e-01 eV +E_delta_NN= -1.93485040e-01 Ry = -2.63249902e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.6981 11 0.52 1e+02 % + Run_lcao lcao_line 5.6877 1 5.7 1e+02 % + Potential init_pot 0.28611 2 0.14 5 % + PW_Basis recip2real 0.26577 16 0.017 4.7 % + PW_Basis gathers_scatterp 0.11473 16 0.0072 2 % + Potential v_of_rho 0.87431 13 0.067 15 % + XC_Functional v_xc 0.24516 14 0.018 4.3 % + H_Hartree_pw v_hartree 0.59103 13 0.045 10 % + PW_Basis real2recip 0.55643 38 0.015 9.8 % + PW_Basis gatherp_scatters 0.21613 38 0.0057 3.8 % + ORB_control set_orb_tables 1.1154 1 1.1 20 % + ORB_gen_tables gen_tables 1.1154 1 1.1 20 % + ORB_table_phi init_Table 0.4845 1 0.48 8.5 % + ORB_table_phi cal_ST_Phi12_R 0.47963 126 0.0038 8.4 % + ORB_table_beta init_Table_Beta 0.19222 1 0.19 3.4 % + ORB_table_beta VNL_PhiBeta_R 0.19067 56 0.0034 3.3 % + ORB_table_alpha init_Table_Alpha 0.25765 1 0.26 4.5 % + ORB_table_alpha S_PhiAlpha_R 0.25576 66 0.0039 4.5 % + LOOP_ions opt_ions 4.053 1 4.1 71 % + ESolver_KS_LCAO Run 3.5775 1 3.6 63 % + HSolverLCAO solve 1.6103 11 0.15 28 % + HamiltLCAO updateHk 0.88108 11 0.08 15 % + LCAO_Hamilt cal_Hgamma 0.84813 11 0.077 15 % + Gint_interface cal_gint 0.82627 23 0.036 15 % + Gint_Gamma distri_vl_value 0.20819 11 0.019 3.7 % + Gint_Gamma distri_vl 1.7374 6 0.29 30 % + LCAO_Deepks cal_projected_DM 3.8393 13 0.3 67 % + LCAO_gen_fixedH add_v_delta 1.6049 6 0.27 28 % + LCAO_DESCRIPTOR add_v_delta 1.6049 6 0.27 28 % + ElecStateLCAO psiToRho 0.71184 11 0.065 12 % + Charge mix_rho 0.65617 10 0.066 12 % + LOOP_ions force_stress 0.47534 1 0.48 8.3 % + Force_Stress_LCAO getForceStress 0.47531 1 0.48 8.3 % + Force_LCAO_gamma ftable_gamma 0.2662 1 0.27 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.1819 1 0.18 3.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:16 2022 + FINISH Time : Wed Sep 28 11:05:22 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/6/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..63fa9f45699642a60f4b74c06b36b91334f93987 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.473187 0.702534 0.0129533 +H 0.482986 0.671275 0.956959 +H 0.424578 0.667647 0.0354064 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c5e75fa44a59f43c949d42415979fce289f43f6c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.596 2 + 2 -12.9364 2 + 3 -9.41579 2 + 4 -6.81196 2 + 5 1.421 0 + 6 4.67693 0 + 7 11.0199 0 + 8 11.2983 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..87a6052266a5ad015ebaeed06ccb6b8f95546c9b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:27 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.2492434585 19.6709563925 0.362691006609 0 0 0 0 + tauc_H1 13.5236147014 18.7957120523 26.7948652972 0 0 0 0 + tauc_H2 11.888192062 18.6941276175 0.991380540327 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0870714425726 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0876955473627 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105723817251 (SEC) + + DONE : INIT CHARGE Time : 0.153656387114 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.429195 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 9 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00102 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00154 + + Density error is 0.216095889788 + + Energy Rydberg eV + E_KohnSham -34.1868966816 -465.136591807 + E_Harris -34.3819616885 -467.790587382 + E_Fermi -0.418305033141 -5.6913319528 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00121123554663 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0014685286607 + + Density error is 0.097291886213 + + Energy Rydberg eV + E_KohnSham -34.2774662444 -466.368853926 + E_Harris -34.2841960836 -466.460418086 + E_Fermi -0.226546583972 -3.08232440446 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00114305478444 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00136396222451 + + Density error is 0.0622017402413 + + Energy Rydberg eV + E_KohnSham -34.2777541071 -466.3727705 + E_Harris -34.2820953642 -466.431836333 + E_Fermi -0.213356705632 -2.9028669031 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00104269814999 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119409931798 + + Density error is 0.00199845014466 + + Energy Rydberg eV + E_KohnSham -34.2777784617 -466.373101861 + E_Harris -34.2777800469 -466.373123429 + E_Fermi -0.177338679735 -2.4128165202 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00104580286111 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119526529803 + + Density error is 0.000934641803622 + + Energy Rydberg eV + E_KohnSham -34.2777031592 -466.372077317 + E_Harris -34.2777058696 -466.372114194 + E_Fermi -0.176354637549 -2.39942793939 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0010440278946 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119309955724 + + Density error is 0.000103416466896 + + Energy Rydberg eV + E_KohnSham -34.2777559195 -466.372795158 + E_Harris -34.2777559368 -466.372795394 + E_Fermi -0.176552197526 -2.40211588077 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00104382800754 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119273961217 + + Density error is 4.32252278744e-05 + + Energy Rydberg eV + E_KohnSham -34.2777392088 -466.372567798 + E_Harris -34.277739219 -466.372567936 + E_Fermi -0.176432432025 -2.40048638753 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00104381585672 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119276377085 + + Density error is 1.93101687299e-05 + + Energy Rydberg eV + E_KohnSham -34.2777415157 -466.372599185 + E_Harris -34.2777415172 -466.372599205 + E_Fermi -0.176489953358 -2.40126900542 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0010438112964 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119273859769 + + Density error is 2.15195735446e-06 + + Energy Rydberg eV + E_KohnSham -34.2777399941 -466.372578483 + E_Harris -34.2777399942 -466.372578483 + E_Fermi -0.176469197878 -2.40098661263 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00104381011224 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119273567214 + + Density error is 2.58767006566e-07 + + Energy Rydberg eV + E_KohnSham -34.2777402483 -466.372581941 + E_Harris -34.2777402483 -466.372581941 + E_Fermi -0.176467233074 -2.40095988011 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00104381081464 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119273624613 + + Density error is 1.0569138282e-07 + + Energy Rydberg eV + E_KohnSham -34.2777402857 -466.37258245 + E_Harris -34.2777402857 -466.37258245 + E_Fermi -0.176467188475 -2.4009592733 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00104381084444 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119273614102 + + Density error is 1.04164818218e-08 + + Energy Rydberg eV + E_KohnSham -34.277740287 -466.372582467 + E_Harris -34.277740287 -466.372582467 + E_band -8.04957875463 -109.520137563 + E_one_elec -69.7069136737 -948.411215957 + E_Hartree +36.2262162297 +492.882957704 + E_xc -8.23963371384 -112.105967941 + E_Ewald +7.56602350217 +102.941030831 + E_demet -3.47820091369e-88 -4.7323351215e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195624532789 -2.66160831452 + E_Fermi -0.176467073964 -2.4009577153 + + charge density convergence is achieved + final etot is -466.372582467 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5960 2.00000 + 2 -12.9364 2.00000 + 3 -9.41579 2.00000 + 4 -6.81196 2.00000 + 5 1.42100 0.00000 + 6 4.67693 0.00000 + 7 11.0199 0.00000 + 8 11.2983 0.00000 + + EFERMI = -2.400957715302874 eV + OUT.ABACUS/ final etot is -466.3725824667466 eV + correction force for each atom along direction 1 is -4.02323e-05 + correction force for each atom along direction 2 is -2.41420e-05 + correction force for each atom along direction 3 is -3.09765e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.81294059 +0.75649941 -0.14378833 + H1 +0.51097239 -0.11168232 -0.87841337 + H2 -1.3239130 -0.64481709 +1.0222017 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3725824667466 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8438 11 0.53 1.0e+02% + Run_lcao lcao_line 5.8330 1 5.8 1.e+02% + Potential init_pot 0.28061 2 0.14 4.8% + PW_Basis recip2real 0.28323 17 0.017 4.8% + PW_Basis gathers_scatterp 0.12280 17 0.0072 2.1% + Potential v_of_rho 0.93235 14 0.067 16.% + XC_Functional v_xc 0.25526 15 0.017 4.4% + H_Hartree_pw v_hartree 0.63376 14 0.045 11.% + PW_Basis real2recip 0.60133 41 0.015 10.% + PW_Basis gatherp_scatters 0.23473 41 0.0057 4.0% + ORB_control set_orb_tables 1.1105 1 1.1 19.% + ORB_gen_tables gen_tables 1.1105 1 1.1 19.% + ORB_table_phi init_Table 0.48742 1 0.49 8.3% + ORB_table_phi cal_ST_Phi12_R 0.48234 126 0.0038 8.3% + ORB_table_beta init_Table_Beta 0.19012 1 0.19 3.3% + ORB_table_beta VNL_PhiBeta_R 0.18862 56 0.0034 3.2% + ORB_table_alpha init_Table_Alpha 0.25585 1 0.26 4.4% + ORB_table_alpha S_PhiAlpha_R 0.25389 66 0.0038 4.3% + LOOP_ions opt_ions 4.2158 1 4.2 72.% + ESolver_KS_LCAO Run 3.7591 1 3.8 64.% + HSolverLCAO solve 1.6252 12 0.14 28.% + HamiltLCAO updateHk 0.89705 12 0.075 15.% + LCAO_Hamilt cal_Hgamma 0.86027 12 0.072 15.% + Gint_interface cal_gint 1.3990 25 0.056 24.% + Gint_Gamma distri_vl 1.9760 6 0.33 34.% + LCAO_Deepks cal_projected_DM 4.0830 14 0.29 70.% + LCAO_gen_fixedH add_v_delta 1.8436 6 0.31 32.% + LCAO_DESCRIPTOR add_v_delta 1.8436 6 0.31 32.% + ElecStateLCAO psiToRho 0.71215 12 0.059 12.% + Charge mix_rho 0.71898 11 0.065 12.% + LOOP_ions force_stress 0.45658 1 0.46 7.8% + Force_Stress_LCAO getForceStress 0.45654 1 0.46 7.8% + Force_LCAO_gamma ftable_gamma 0.24706 1 0.25 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.24036 1 0.24 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:27 2022 + Finish Time : Wed Sep 28 11:09:33 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1641e9ebc35b15788a650f7553bbfe24d6b1cec5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/OUT.ABACUS/warning.log @@ -0,0 +1,77 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124166 ima = 3.66506e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122485712127 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111456205136 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111949386313 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112242850044 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112166523059 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001122086293 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112206110449 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112209127465 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011220835776 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112208262361 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112208254319 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112208249229 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/STRU new file mode 100644 index 0000000000000000000000000000000000000000..777ce76d7f31064c0a3f6e6027f11ab59bc93d62 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.750756541517 19.670956392477 0.362691006603 0 0 0 +H +0.0 +2 +-14.476385298569 18.795712052316 -1.205134702780 0 0 0 +-16.111807937982 18.694127617479 0.991380540345 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/conv new file mode 100644 index 0000000000000000000000000000000000000000..88982ba8520d4328e6650df4f95d2d39a177c78f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/conv @@ -0,0 +1 @@ +60 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..df8e40c77444488af4374af63b3ac9d5a7530112 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753406613 0.01289120054 1.2867856 1.367877096 1.470560547 0.009475461833 0.01739312497 0.0391330864 +-2.217532258e-18 0.001014998036 0.002951637889 0.01370928362 0.04886714134 4.689502189e-19 3.027897186e-06 7.77364768e-06 +0.00159809884 0.006151681154 + +H atom_index 1 n_descriptor 18 +1.262159084 0.03440127193 0.1154660237 0.1552183805 0.323303698 0.02383033425 0.02894048635 0.0375312158 +-2.652488391e-18 5.470536376e-05 0.1069667253 0.1164800803 0.1333031179 -2.483059836e-18 2.60937683e-06 0.01336010798 +0.02781171901 0.03130500705 + +H atom_index 2 n_descriptor 18 +1.283381949 0.03371729823 0.1235419801 0.165751119 0.329774789 0.02487849025 0.03016937442 0.03708164577 +-2.133931898e-17 5.67657745e-05 0.1086515667 0.1209266818 0.142280588 -1.603772772e-18 1.455224314e-06 0.01350475976 +0.02852747818 0.03217575234 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ef5323f385519908fa8150a996e2d4d16c5f7085 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/e_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..d554648e5da56dc21960a90f25fa3f7078cef06b Binary 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..c36917e1a7c2d8d104a88a8a5ce81066f59aa890 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..9a0d84c0821ec98404d85e111419321844951894 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:27 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0870955 SEC) : SETUP UNITCELL + DONE(0.0877083 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105743 SEC) : INIT PLANEWAVE + DONE(0.153793 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.429259 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651366e+02 0.000000e+00 2.161e-01 4.340e-01 + GE2 -4.663689e+02 -1.232262e+00 9.729e-02 3.556e-01 + GE3 -4.663728e+02 -3.916574e-03 6.220e-02 4.075e-01 + GE4 -4.663731e+02 -3.313608e-04 1.998e-03 2.992e-01 + GE5 -4.663721e+02 1.024543e-03 9.346e-04 2.957e-01 + GE6 -4.663728e+02 -7.178411e-04 1.034e-04 2.909e-01 + GE7 -4.663726e+02 2.273608e-04 4.323e-05 2.903e-01 + GE8 -4.663726e+02 -3.138722e-05 1.931e-05 2.725e-01 + GE9 -4.663726e+02 2.070198e-05 2.152e-06 2.746e-01 + GE10 -4.663726e+02 -3.457890e-06 2.588e-07 2.800e-01 + GE11 -4.663726e+02 -5.088514e-07 1.057e-07 2.771e-01 + GE12 -4.663726e+02 -1.707896e-08 1.042e-08 2.203e-01 +E_delta_band = -7.21919015e-02 Ry = -9.82221210e-01 eV +E_delta_NN= -1.95624533e-01 Ry = -2.66160831e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.8438 11 0.53 1e+02 % + Run_lcao lcao_line 5.833 1 5.8 1e+02 % + Potential init_pot 0.28061 2 0.14 4.8 % + PW_Basis recip2real 0.28323 17 0.017 4.8 % + PW_Basis gathers_scatterp 0.1228 17 0.0072 2.1 % + Potential v_of_rho 0.93235 14 0.067 16 % + XC_Functional v_xc 0.25526 15 0.017 4.4 % + H_Hartree_pw v_hartree 0.63376 14 0.045 11 % + PW_Basis real2recip 0.60133 41 0.015 10 % + PW_Basis gatherp_scatters 0.23473 41 0.0057 4 % + ORB_control set_orb_tables 1.1105 1 1.1 19 % + ORB_gen_tables gen_tables 1.1105 1 1.1 19 % + ORB_table_phi init_Table 0.48742 1 0.49 8.3 % + ORB_table_phi cal_ST_Phi12_R 0.48234 126 0.0038 8.3 % + ORB_table_beta init_Table_Beta 0.19012 1 0.19 3.3 % + ORB_table_beta VNL_PhiBeta_R 0.18862 56 0.0034 3.2 % + ORB_table_alpha init_Table_Alpha 0.25585 1 0.26 4.4 % + ORB_table_alpha S_PhiAlpha_R 0.25389 66 0.0038 4.3 % + LOOP_ions opt_ions 4.2158 1 4.2 72 % + ESolver_KS_LCAO Run 3.7591 1 3.8 64 % + HSolverLCAO solve 1.6252 12 0.14 28 % + HamiltLCAO updateHk 0.89705 12 0.075 15 % + LCAO_Hamilt cal_Hgamma 0.86027 12 0.072 15 % + Gint_interface cal_gint 1.399 25 0.056 24 % + Gint_Gamma distri_vl 1.976 6 0.33 34 % + LCAO_Deepks cal_projected_DM 4.083 14 0.29 70 % + LCAO_gen_fixedH add_v_delta 1.8436 6 0.31 32 % + LCAO_DESCRIPTOR add_v_delta 1.8436 6 0.31 32 % + ElecStateLCAO psiToRho 0.71215 12 0.059 12 % + Charge mix_rho 0.71898 11 0.065 12 % + LOOP_ions force_stress 0.45658 1 0.46 7.8 % + Force_Stress_LCAO getForceStress 0.45654 1 0.46 7.8 % + Force_LCAO_gamma ftable_gamma 0.24706 1 0.25 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.24036 1 0.24 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:27 2022 + FINISH Time : Wed Sep 28 11:09:33 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/60/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..bc4ff9436918eda4b0c7ad4c5a99088d70e90428 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.488133 0.706344 0.0137143 +H 0.517493 0.649417 0.0102565 +H 0.472568 0.718423 0.0754924 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..54a734d28c1e4874e6ee9f94c37dac0dee057879 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3595 2 + 2 -13.428 2 + 3 -8.89449 2 + 4 -6.75872 2 + 5 1.46018 0 + 6 4.69068 0 + 7 11.0425 0 + 8 11.2665 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3e48b0a86303865c8ae6b00abcc7da4f52465889 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:31 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 13.6677252454 19.7776350558 0.384001447746 0 0 0 0 + tauc_H1 14.4898049117 18.1836653373 0.287182268199 0 0 0 0 + tauc_H2 13.2319104165 20.1158497464 2.11378785293 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0863308769511 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0955344929961 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.113852281184 (SEC) + + DONE : INIT CHARGE Time : 0.163642611456 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443385 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 9 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000614 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000929 + + Density error is 0.217404570239 + + Energy Rydberg eV + E_KohnSham -34.1887577007 -465.161912271 + E_Harris -34.3852799364 -467.83573446 + E_Fermi -0.414108220774 -5.63423139116 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000907075690254 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121827019528 + + Density error is 0.097702459389 + + Energy Rydberg eV + E_KohnSham -34.278941022 -466.388919305 + E_Harris -34.2854973007 -466.478122053 + E_Fermi -0.22177848392 -3.01745107511 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000873620762072 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011715892053 + + Density error is 0.0623876364814 + + Energy Rydberg eV + E_KohnSham -34.2791412923 -466.391644123 + E_Harris -34.2833254214 -466.44857212 + E_Fermi -0.207856233311 -2.82802913785 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827601431184 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110617307187 + + Density error is 0.00209737500203 + + Energy Rydberg eV + E_KohnSham -34.2791787538 -466.392153813 + E_Harris -34.2791818346 -466.392195729 + E_Fermi -0.172508286475 -2.34709564828 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000828264880427 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110775357479 + + Density error is 0.000866023324834 + + Energy Rydberg eV + E_KohnSham -34.2791116051 -466.391240208 + E_Harris -34.279113338 -466.391263785 + E_Fermi -0.171324756403 -2.33099289554 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827434352813 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110656783026 + + Density error is 0.000204883501766 + + Energy Rydberg eV + E_KohnSham -34.2791580175 -466.39187168 + E_Harris -34.279158149 -466.39187347 + E_Fermi -0.171586625631 -2.33455580917 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827669405245 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110685952855 + + Density error is 4.371426705e-05 + + Energy Rydberg eV + E_KohnSham -34.2791395171 -466.391619969 + E_Harris -34.2791395273 -466.391620108 + E_Fermi -0.171379916506 -2.33174338725 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827607917224 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110677810904 + + Density error is 1.66510818178e-05 + + Energy Rydberg eV + E_KohnSham -34.279145281 -466.391698392 + E_Harris -34.2791452821 -466.391698406 + E_Fermi -0.171431530102 -2.33244562625 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827604205178 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110677107619 + + Density error is 1.63491511915e-06 + + Energy Rydberg eV + E_KohnSham -34.2791438357 -466.391678727 + E_Harris -34.2791438357 -466.391678728 + E_Fermi -0.171413435492 -2.33219943645 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827605387296 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110677153366 + + Density error is 1.71926123525e-07 + + Energy Rydberg eV + E_KohnSham -34.2791440485 -466.391681623 + E_Harris -34.2791440485 -466.391681623 + E_Fermi -0.171411886449 -2.33217836063 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000827605865262 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110677220876 + + Density error is 6.14414804107e-08 + + Energy Rydberg eV + E_KohnSham -34.2791440726 -466.391681951 + E_Harris -34.2791440726 -466.391681951 + E_band -8.00262814564 -108.881341756 + E_one_elec -69.6155666846 -947.168376409 + E_Hartree +36.2012757705 +492.543625348 + E_xc -8.2354579113 -112.049153233 + E_Ewald +7.49430014067 +101.965184435 + E_demet -5.11074887776e-87 -6.95353057846e-86 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195299917949 -2.65719170305 + E_Fermi -0.17141187388 -2.33217818963 + + charge density convergence is achieved + final etot is -466.391681951 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3595 2.00000 + 2 -13.4280 2.00000 + 3 -8.89449 2.00000 + 4 -6.75872 2.00000 + 5 1.46018 0.00000 + 6 4.69068 0.00000 + 7 11.0425 0.00000 + 8 11.2665 0.00000 + + EFERMI = -2.332178189631264 eV + OUT.ABACUS/ final etot is -466.3916819507665 eV + correction force for each atom along direction 1 is 1.91403e-05 + correction force for each atom along direction 2 is -0.000120528 + correction force for each atom along direction 3 is 0.000141660 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.50240911 +1.2651373 -0.91154371 + H1 +0.52903535 -1.1151361 +0.23822892 + H2 -0.026626233 -0.15000113 +0.67331479 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3916819507665 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5530 11 0.50 1.0e+02% + Run_lcao lcao_line 5.5437 1 5.5 1.e+02% + Potential init_pot 0.28419 2 0.14 5.1% + PW_Basis recip2real 0.26610 16 0.017 4.8% + PW_Basis gathers_scatterp 0.11190 16 0.0070 2.0% + Charge atomic_rho 0.10076 1 0.10 1.8% + Potential v_of_rho 0.88285 13 0.068 16.% + XC_Functional v_xc 0.25000 14 0.018 4.5% + H_Hartree_pw v_hartree 0.59623 13 0.046 11.% + PW_Basis real2recip 0.55806 38 0.015 10.% + PW_Basis gatherp_scatters 0.21304 38 0.0056 3.8% + ORB_control set_orb_tables 1.1112 1 1.1 20.% + ORB_gen_tables gen_tables 1.1112 1 1.1 20.% + ORB_table_phi init_Table 0.48819 1 0.49 8.8% + ORB_table_phi cal_ST_Phi12_R 0.48320 126 0.0038 8.7% + ORB_table_beta init_Table_Beta 0.19000 1 0.19 3.4% + ORB_table_beta VNL_PhiBeta_R 0.18854 56 0.0034 3.4% + ORB_table_alpha init_Table_Alpha 0.25472 1 0.25 4.6% + ORB_table_alpha S_PhiAlpha_R 0.25287 66 0.0038 4.6% + LOOP_ions opt_ions 3.9112 1 3.9 70.% + ESolver_KS_LCAO Run 3.4581 1 3.5 62.% + HSolverLCAO solve 1.4761 11 0.13 27.% + HamiltLCAO updateHk 0.82742 11 0.075 15.% + LCAO_Hamilt cal_Hgamma 0.78912 11 0.072 14.% + Gint_interface cal_gint 1.2543 23 0.055 23.% + Gint_Gamma distri_vl 1.6859 6 0.28 30.% + LCAO_Deepks cal_projected_DM 3.7796 13 0.29 68.% + LCAO_gen_fixedH add_v_delta 1.5546 6 0.26 28.% + LCAO_DESCRIPTOR add_v_delta 1.5546 6 0.26 28.% + ElecStateLCAO psiToRho 0.63524 11 0.058 11.% + Charge mix_rho 0.66050 10 0.066 12.% + LOOP_ions force_stress 0.45290 1 0.45 8.2% + Force_Stress_LCAO getForceStress 0.45287 1 0.45 8.2% + Force_LCAO_gamma ftable_gamma 0.23902 1 0.24 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.23233 1 0.23 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:31 2022 + Finish Time : Wed Sep 28 11:10:37 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..f8be0f039b83086270de43068c66e35ab9f369d2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123999 ima = 3.67573e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123300320274 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112606347594 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011300190689 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113256071232 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113194856076 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113232893954 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113221973576 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011322497186 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113224364949 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011322430389 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113224297442 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a4e410b00c47fab0c1ee9e02d715e4534e734b17 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-14.332274754641 19.777635055759 0.384001447732 0 0 0 +H +0.0 +2 +-13.510195088278 18.183665337309 0.287182268178 0 0 0 +-14.768089583475 20.115849746427 2.113787852949 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/conv new file mode 100644 index 0000000000000000000000000000000000000000..92850c2ebb60767825ececdb0dd1d56d1eecfdf4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/conv @@ -0,0 +1 @@ +61 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..c4e2c5e856f55cacf0a2138c565df4ee9692f3fb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.744874136 0.01271152941 1.290411441 1.379434887 1.469765118 0.007923372021 0.02034215055 0.03889587999 +6.401704823e-18 0.001210152854 0.002486800693 0.01273516782 0.04458050321 1.21196849e-19 1.724653893e-06 5.291532279e-06 +0.001763679663 0.00570353453 + +H atom_index 1 n_descriptor 18 +1.270596712 0.03298552541 0.1160000536 0.1608140478 0.3286613394 0.02288100622 0.02962556927 0.03634474021 +-5.854644512e-17 4.388526567e-05 0.1067970436 0.1167495568 0.1381906029 3.036890389e-18 3.218581649e-06 0.01296769529 +0.02710176721 0.0317343842 + +H atom_index 2 n_descriptor 18 +1.255000456 0.03352600811 0.1104131724 0.1533175623 0.3240392066 0.02220394538 0.02873239422 0.03671653353 +2.665985677e-17 4.253568815e-05 0.1040329882 0.1150642646 0.1317664141 2.023395034e-18 4.027723557e-06 0.0129286661 +0.02655540401 0.03108617736 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..26801a11575a0193c57d2b74c1fc22de61125e0f Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..263b3ac8588797cc668ae1712ecf358fb03c9086 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..d7e403e261a3d37aeb0c878eb739a972b95da134 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..2ddf4752ff0624a841f59c32eb4b6df6f11217df Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..2ddf17b1ccc7c6f13a77b92ec335e2fb74749503 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:31 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0863546 SEC) : SETUP UNITCELL + DONE(0.0955508 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.113871 SEC) : INIT PLANEWAVE + DONE(0.163779 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443448 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651619e+02 0.000000e+00 2.174e-01 4.262e-01 + GE2 -4.663889e+02 -1.227007e+00 9.770e-02 3.539e-01 + GE3 -4.663916e+02 -2.724817e-03 6.239e-02 4.079e-01 + GE4 -4.663922e+02 -5.096896e-04 2.097e-03 2.965e-01 + GE5 -4.663912e+02 9.136046e-04 8.660e-04 2.985e-01 + GE6 -4.663919e+02 -6.314721e-04 2.049e-04 2.904e-01 + GE7 -4.663916e+02 2.517110e-04 4.371e-05 2.860e-01 + GE8 -4.663917e+02 -7.842265e-05 1.665e-05 2.731e-01 + GE9 -4.663917e+02 1.966423e-05 1.635e-06 2.722e-01 + GE10 -4.663917e+02 -2.895196e-06 1.719e-07 2.751e-01 + GE11 -4.663917e+02 -3.281507e-07 6.144e-08 2.166e-01 +E_delta_band = -7.16045300e-02 Ry = -9.74229611e-01 eV +E_delta_NN= -1.95299918e-01 Ry = -2.65719170e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.553 11 0.5 1e+02 % + Run_lcao lcao_line 5.5437 1 5.5 1e+02 % + Potential init_pot 0.28419 2 0.14 5.1 % + PW_Basis recip2real 0.2661 16 0.017 4.8 % + PW_Basis gathers_scatterp 0.1119 16 0.007 2 % + Charge atomic_rho 0.10076 1 0.1 1.8 % + Potential v_of_rho 0.88285 13 0.068 16 % + XC_Functional v_xc 0.25 14 0.018 4.5 % + H_Hartree_pw v_hartree 0.59623 13 0.046 11 % + PW_Basis real2recip 0.55806 38 0.015 10 % + PW_Basis gatherp_scatters 0.21304 38 0.0056 3.8 % + ORB_control set_orb_tables 1.1112 1 1.1 20 % + ORB_gen_tables gen_tables 1.1112 1 1.1 20 % + ORB_table_phi init_Table 0.48819 1 0.49 8.8 % + ORB_table_phi cal_ST_Phi12_R 0.4832 126 0.0038 8.7 % + ORB_table_beta init_Table_Beta 0.19 1 0.19 3.4 % + ORB_table_beta VNL_PhiBeta_R 0.18854 56 0.0034 3.4 % + ORB_table_alpha init_Table_Alpha 0.25472 1 0.25 4.6 % + ORB_table_alpha S_PhiAlpha_R 0.25287 66 0.0038 4.6 % + LOOP_ions opt_ions 3.9112 1 3.9 70 % + ESolver_KS_LCAO Run 3.4581 1 3.5 62 % + HSolverLCAO solve 1.4761 11 0.13 27 % + HamiltLCAO updateHk 0.82742 11 0.075 15 % + LCAO_Hamilt cal_Hgamma 0.78912 11 0.072 14 % + Gint_interface cal_gint 1.2543 23 0.055 23 % + Gint_Gamma distri_vl 1.6859 6 0.28 30 % + LCAO_Deepks cal_projected_DM 3.7796 13 0.29 68 % + LCAO_gen_fixedH add_v_delta 1.5546 6 0.26 28 % + LCAO_DESCRIPTOR add_v_delta 1.5546 6 0.26 28 % + ElecStateLCAO psiToRho 0.63524 11 0.058 11 % + Charge mix_rho 0.6605 10 0.066 12 % + LOOP_ions force_stress 0.4529 1 0.45 8.2 % + Force_Stress_LCAO getForceStress 0.45287 1 0.45 8.2 % + Force_LCAO_gamma ftable_gamma 0.23902 1 0.24 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.23233 1 0.23 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:31 2022 + FINISH Time : Wed Sep 28 11:10:37 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/61/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..923ffee0b43f75d4e1a2851d9d53f1da24baaa34 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.503343 0.707137 0.0208158 +H 0.543673 0.652682 0.0317298 +H 0.535897 0.725676 0.961276 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..8749579e1d012a798064b3cac9315914808a346b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.8451 2 + 2 -12.0287 2 + 3 -9.54937 2 + 4 -6.65986 2 + 5 0.668289 0 + 6 3.38192 0 + 7 11.2033 0 + 8 11.4809 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..21b0f8fcd6f23be7d9cb16802dd710565cedc7a6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/running_scf.log @@ -0,0 +1,755 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:40 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.0936178272 19.7998249134 0.582841653304 0 0 0 0 + tauc_H1 15.2228415527 18.2751003882 0.888433209344 0 0 0 0 + tauc_H2 15.0051023721 20.3189318646 26.915722296 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0744783535501 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0883930732302 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.104201006469 (SEC) + + DONE : INIT CHARGE Time : 0.145372150909 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388412 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 4 9 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000663 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000865 + + Density error is 0.206350603789 + + Energy Rydberg eV + E_KohnSham -34.1828272007 -465.081223679 + E_Harris -34.3579026076 -467.463246792 + E_Fermi -0.369048443432 -5.02116166871 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00097577275664 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010078812321 + + Density error is 0.099032879071 + + Energy Rydberg eV + E_KohnSham -34.2685348016 -466.247335413 + E_Harris -34.2764215483 -466.354640106 + E_Fermi -0.183942341498 -2.50266394783 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000932996944433 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000956093947775 + + Density error is 0.0642444886794 + + Energy Rydberg eV + E_KohnSham -34.2692075911 -466.256489184 + E_Harris -34.2740610325 -466.322523642 + E_Fermi -0.18232536302 -2.48066382699 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000893849175816 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000897453627106 + + Density error is 0.00187770169374 + + Energy Rydberg eV + E_KohnSham -34.268998134 -466.253639374 + E_Harris -34.268999433 -466.253657048 + E_Fermi -0.147409484605 -2.00560892987 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000892769294477 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000897405223258 + + Density error is 0.00100135438269 + + Energy Rydberg eV + E_KohnSham -34.268999174 -466.253653523 + E_Harris -34.2690000751 -466.253665783 + E_Fermi -0.148179566321 -2.01608642914 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000892695718863 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000896998750177 + + Density error is 0.000165630149297 + + Energy Rydberg eV + E_KohnSham -34.2689854137 -466.253466305 + E_Harris -34.2689854265 -466.253466479 + E_Fermi -0.147340431686 -2.00466941671 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000892750654321 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00089706891504 + + Density error is 2.25981857764e-05 + + Energy Rydberg eV + E_KohnSham -34.2689933561 -466.253574367 + E_Harris -34.2689933562 -466.253574368 + E_Fermi -0.147405204331 -2.00555069375 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000892718706397 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000897045512292 + + Density error is 3.11157208837e-06 + + Energy Rydberg eV + E_KohnSham -34.2689925949 -466.253564011 + E_Harris -34.2689925949 -466.253564011 + E_Fermi -0.147387806904 -2.00531398961 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000892714098079 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000897041124766 + + Density error is 1.23639019394e-06 + + Energy Rydberg eV + E_KohnSham -34.2689926017 -466.253564103 + E_Harris -34.2689926017 -466.253564103 + E_Fermi -0.147386690857 -2.00529880502 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.000892715055981 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000897040598087 + + Density error is 9.40869623006e-08 + + Energy Rydberg eV + E_KohnSham -34.2689925838 -466.25356386 + E_Harris -34.2689925838 -466.25356386 + E_band -7.80305973849 -106.166074278 + E_one_elec -68.0124366747 -925.35667364 + E_Hartree +35.4168057335 +481.870362934 + E_xc -8.11012805245 -110.343953023 + E_Ewald +6.56354108149 +89.3015577653 + E_demet -1.34183115928e-44 -1.82565495202e-43 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.192725689863 -2.62216753311 + E_Fermi -0.147386436065 -2.00529533839 + + charge density convergence is achieved + final etot is -466.25356386 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.8451 2.00000 + 2 -12.0287 2.00000 + 3 -9.54937 2.00000 + 4 -6.65986 2.00000 + 5 0.668289 0.00000 + 6 3.38192 0.00000 + 7 11.2033 0.00000 + 8 11.4809 0.00000 + + EFERMI = -2.005295338393705 eV + OUT.ABACUS/ final etot is -466.2535638600679 eV + correction force for each atom along direction 1 is 8.95657e-05 + correction force for each atom along direction 2 is -5.89896e-05 + correction force for each atom along direction 3 is -2.04909e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +2.6324690 -0.89247560 -2.1979218 + H1 -1.1776904 +1.0462544 +0.27562207 + H2 -1.4547785 -0.15377877 +1.9222997 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.2535638600679 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.1608 11 0.47 1.0e+02% + Run_lcao lcao_line 5.1528 1 5.2 1.e+02% + Potential init_pot 0.24205 2 0.12 4.7% + PW_Basis recip2real 0.22986 15 0.015 4.5% + Potential v_of_rho 0.84233 12 0.070 16.% + XC_Functional v_xc 0.26856 13 0.021 5.2% + H_Hartree_pw v_hartree 0.53927 12 0.045 10.% + PW_Basis real2recip 0.54153 35 0.015 10.% + PW_Basis gatherp_scatters 0.20477 35 0.0059 4.0% + ORB_control set_orb_tables 0.89861 1 0.90 17.% + ORB_gen_tables gen_tables 0.89860 1 0.90 17.% + ORB_table_phi init_Table 0.37576 1 0.38 7.3% + ORB_table_phi cal_ST_Phi12_R 0.37152 126 0.0029 7.2% + ORB_table_beta init_Table_Beta 0.15535 1 0.16 3.0% + ORB_table_beta VNL_PhiBeta_R 0.15406 56 0.0028 3.0% + ORB_table_alpha init_Table_Alpha 0.20962 1 0.21 4.1% + ORB_table_alpha S_PhiAlpha_R 0.20794 66 0.0032 4.0% + LOOP_ions opt_ions 3.7966 1 3.8 74.% + ESolver_KS_LCAO Run 3.3690 1 3.4 65.% + HSolverLCAO solve 1.4121 10 0.14 27.% + HamiltLCAO updateHk 0.79934 10 0.080 15.% + LCAO_Hamilt cal_Hgamma 0.77159 10 0.077 15.% + Gint_interface cal_gint 1.1941 21 0.057 23.% + Gint_Gamma distri_vl 1.7787 5 0.36 34.% + LCAO_Deepks cal_projected_DM 3.6762 12 0.31 71.% + LCAO_gen_fixedH add_v_delta 1.6500 5 0.33 32.% + LCAO_DESCRIPTOR add_v_delta 1.6499 5 0.33 32.% + ElecStateLCAO psiToRho 0.59752 10 0.060 12.% + Charge mix_rho 0.67896 9 0.075 13.% + LOOP_ions force_stress 0.42726 1 0.43 8.3% + Force_Stress_LCAO getForceStress 0.42724 1 0.43 8.3% + Force_LCAO_gamma ftable_gamma 0.23104 1 0.23 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.22370 1 0.22 4.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:40 2022 + Finish Time : Wed Sep 28 11:07:45 2022 + Total Time : 0 h 0 mins 5 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..102cd0e1d43e8239e0e414cc8059fc952088eed3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/OUT.ABACUS/warning.log @@ -0,0 +1,69 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123983 ima = 3.68067e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 1 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123249018781 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111365778043 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112457766177 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112631857217 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112659702404 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112645489439 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112647565974 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112647552981 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112647592333 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112647591 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5c617893c7c1835d2db9c6726b8e3de4d50f86a3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.906382172819 19.799824913443 0.582841653298 0 0 0 +H +0.0 +2 +-12.777158447253 18.275100388180 0.888433209326 0 0 0 +-12.994897627856 20.318931864633 -1.084277704065 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/conv new file mode 100644 index 0000000000000000000000000000000000000000..ac85e6276c778fa632464adc3820305e311d510a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/conv @@ -0,0 +1 @@ +62 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ef0dd7d64bb8773b85db9fe14f22eaa06820c1b4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.75855343 0.01228522474 1.219820119 1.296692272 1.467838455 0.01002670921 0.0147428027 0.03946048639 +5.312735066e-18 0.000589975153 0.002505153073 0.01204385721 0.03996823202 6.576383655e-19 1.954925696e-06 5.969162414e-06 +0.001523564245 0.005865013307 + +H atom_index 1 n_descriptor 18 +1.183275392 0.03727785033 0.09068552355 0.1211794052 0.2953746189 0.02005993282 0.02429246947 0.0409408389 +-2.805667789e-17 3.338107962e-05 0.08173596826 0.1029806351 0.1129810452 3.025781651e-18 4.481286737e-06 0.0149864494 +0.02333759439 0.0272422682 + +H atom_index 2 n_descriptor 18 +1.146630036 0.03812442433 0.08024347457 0.1074267965 0.279921451 0.01827127363 0.02214626574 0.04229932028 +1.866015074e-17 3.07015739e-05 0.07310843675 0.0907641614 0.110003367 -7.315616175e-18 5.354232873e-06 0.01629081025 +0.02174654522 0.02513237678 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0c7e7e97f4185f8c6379805ac5d554de0dfed109 Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..1fe3b927e5dcc3d51140c21742a70e74a6a6b3c5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/log.scf @@ -0,0 +1,99 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:40 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0744944 SEC) : SETUP UNITCELL + DONE(0.0884059 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104215 SEC) : INIT PLANEWAVE + DONE(0.145473 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.38846 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650812e+02 0.000000e+00 2.064e-01 4.174e-01 + GE2 -4.662473e+02 -1.166112e+00 9.903e-02 3.788e-01 + GE3 -4.662565e+02 -9.153771e-03 6.424e-02 4.448e-01 + GE4 -4.662536e+02 2.849810e-03 1.878e-03 3.204e-01 + GE5 -4.662537e+02 -1.414912e-05 1.001e-03 3.182e-01 + GE6 -4.662535e+02 1.872184e-04 1.656e-04 3.119e-01 + GE7 -4.662536e+02 -1.080620e-04 2.260e-05 2.944e-01 + GE8 -4.662536e+02 1.035589e-05 3.112e-06 2.975e-01 + GE9 -4.662536e+02 -9.162925e-08 1.236e-06 2.999e-01 + GE10 -4.662536e+02 2.426449e-07 9.409e-08 2.318e-01 +E_delta_band = -6.59510182e-02 Ry = -8.97309637e-01 eV +E_delta_NN= -1.92725690e-01 Ry = -2.62216753e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.1608 11 0.47 1e+02 % + Run_lcao lcao_line 5.1528 1 5.2 1e+02 % + Potential init_pot 0.24205 2 0.12 4.7 % + PW_Basis recip2real 0.22986 15 0.015 4.5 % + Potential v_of_rho 0.84233 12 0.07 16 % + XC_Functional v_xc 0.26856 13 0.021 5.2 % + H_Hartree_pw v_hartree 0.53927 12 0.045 10 % + PW_Basis real2recip 0.54153 35 0.015 10 % + PW_Basis gatherp_scatters 0.20477 35 0.0059 4 % + ORB_control set_orb_tables 0.89861 1 0.9 17 % + ORB_gen_tables gen_tables 0.8986 1 0.9 17 % + ORB_table_phi init_Table 0.37576 1 0.38 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.37152 126 0.0029 7.2 % + ORB_table_beta init_Table_Beta 0.15535 1 0.16 3 % + ORB_table_beta VNL_PhiBeta_R 0.15406 56 0.0028 3 % + ORB_table_alpha init_Table_Alpha 0.20962 1 0.21 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.20794 66 0.0032 4 % + LOOP_ions opt_ions 3.7966 1 3.8 74 % + ESolver_KS_LCAO Run 3.369 1 3.4 65 % + HSolverLCAO solve 1.4121 10 0.14 27 % + HamiltLCAO updateHk 0.79934 10 0.08 15 % + LCAO_Hamilt cal_Hgamma 0.77159 10 0.077 15 % + Gint_interface cal_gint 1.1941 21 0.057 23 % + Gint_Gamma distri_vl 1.7787 5 0.36 34 % + LCAO_Deepks cal_projected_DM 3.6762 12 0.31 71 % + LCAO_gen_fixedH add_v_delta 1.65 5 0.33 32 % + LCAO_DESCRIPTOR add_v_delta 1.6499 5 0.33 32 % + ElecStateLCAO psiToRho 0.59752 10 0.06 12 % + Charge mix_rho 0.67896 9 0.075 13 % + LOOP_ions force_stress 0.42726 1 0.43 8.3 % + Force_Stress_LCAO getForceStress 0.42724 1 0.43 8.3 % + Force_LCAO_gamma ftable_gamma 0.23104 1 0.23 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.2237 1 0.22 4.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:40 2022 + FINISH Time : Wed Sep 28 11:07:45 2022 + TOTAL Time : 5 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/62/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..bcb93f621fe3166861c3dee0598393518ea069f2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.511109 0.700467 0.0282424 +H 0.51843 0.65936 0.0765785 +H 0.4521 0.691594 0.00893263 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..41dce9b6ca6dbbff483e1faec79ba1de85d1d4c7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.6717 2 + 2 -13.3866 2 + 3 -9.16088 2 + 4 -6.82881 2 + 5 1.60858 0 + 6 4.96312 0 + 7 10.9809 0 + 8 11.2233 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..9e6f3f088b6d94d24d0e0464f482f16edee7c67c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:38 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.3110645373 19.6130624147 0.790787158177 0 0 0 0 + tauc_H1 14.5160433402 18.4620771972 2.14419893486 0 0 0 0 + tauc_H2 12.6587899916 19.3646276781 0.250113775437 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0874396270568 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0967417939893 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.114856519952 (SEC) + + DONE : INIT CHARGE Time : 0.163079176205 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.441355 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 4 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000717 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00189 + + Density error is 0.219666009501 + + Energy Rydberg eV + E_KohnSham -34.1827618553 -465.08033461 + E_Harris -34.3850611984 -467.832758377 + E_Fermi -0.429677496505 -5.84606225484 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0011002495122 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00154370821994 + + Density error is 0.0972327174045 + + Energy Rydberg eV + E_KohnSham -34.275315428 -466.339590568 + E_Harris -34.2819021223 -466.429207142 + E_Fermi -0.234907225857 -3.19607677303 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105716860133 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00140956797616 + + Density error is 0.0618964295937 + + Energy Rydberg eV + E_KohnSham -34.2755881585 -466.343301257 + E_Harris -34.2797645507 -466.400123987 + E_Fermi -0.21905483558 -2.98039393834 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00100037992286 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118985788328 + + Density error is 0.00211089863906 + + Energy Rydberg eV + E_KohnSham -34.2756628316 -466.344317237 + E_Harris -34.2756659755 -466.344360012 + E_Fermi -0.183157207198 -2.49198164766 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00100534058314 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118725898725 + + Density error is 0.000957857323396 + + Energy Rydberg eV + E_KohnSham -34.2755745246 -466.343115759 + E_Harris -34.2755780767 -466.343164088 + E_Fermi -0.181635503638 -2.47127780858 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00100370778335 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118575738967 + + Density error is 0.000114047559783 + + Energy Rydberg eV + E_KohnSham -34.2756362885 -466.343956099 + E_Harris -34.2756363198 -466.343956525 + E_Fermi -0.1821127381 -2.47777091654 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00100356512576 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118530164986 + + Density error is 5.26888992276e-05 + + Energy Rydberg eV + E_KohnSham -34.2756158738 -466.343678343 + E_Harris -34.2756158881 -466.343678537 + E_Fermi -0.181950542029 -2.47556412578 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00100353489529 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118539589982 + + Density error is 1.42442221825e-05 + + Energy Rydberg eV + E_KohnSham -34.2756191479 -466.34372289 + E_Harris -34.2756191487 -466.3437229 + E_Fermi -0.182016022861 -2.47645503821 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00100354770414 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118536645688 + + Density error is 1.99907656954e-06 + + Energy Rydberg eV + E_KohnSham -34.2756177136 -466.343703375 + E_Harris -34.2756177136 -466.343703375 + E_Fermi -0.182000719961 -2.47624683158 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010035494525 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118536088101 + + Density error is 1.4859475368e-07 + + Energy Rydberg eV + E_KohnSham -34.2756178778 -466.343705608 + E_Harris -34.2756178778 -466.343705608 + E_Fermi -0.181998853825 -2.47622144148 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00100354965329 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118536108825 + + Density error is 9.27874452032e-08 + + Energy Rydberg eV + E_KohnSham -34.275617916 -466.343706128 + E_Harris -34.275617916 -466.343706128 + E_band -8.09189654843 -110.095900685 + E_one_elec -70.0699272017 -953.350268389 + E_Hartree +36.4059624757 +495.328530843 + E_xc -8.26901881173 -112.505772709 + E_Ewald +7.7800974621 +105.85365648 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.196297775308 -2.67076824891 + E_Fermi -0.181998906311 -2.4762221556 + + charge density convergence is achieved + final etot is -466.343706128 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.6717 2.00000 + 2 -13.3866 2.00000 + 3 -9.16088 2.00000 + 4 -6.82881 2.00000 + 5 1.60858 0.00000 + 6 4.96312 0.00000 + 7 10.9809 0.00000 + 8 11.2233 0.00000 + + EFERMI = -2.476222155597708 eV + OUT.ABACUS/ final etot is -466.3437061279820 eV + correction force for each atom along direction 1 is -0.000122687 + correction force for each atom along direction 2 is -1.16680e-05 + correction force for each atom along direction 3 is 0.000100277 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +2.2278505 +1.2823814 -0.29467598 + H1 +0.27629068 -0.97505833 +1.1931015 + H2 -2.5041411 -0.30732304 -0.89842550 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3437061279820 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5685 11 0.51 1.0e+02% + Run_lcao lcao_line 5.5585 1 5.6 1.e+02% + Potential init_pot 0.28335 2 0.14 5.1% + PW_Basis recip2real 0.26385 16 0.016 4.7% + PW_Basis gathers_scatterp 0.11121 16 0.0070 2.0% + Potential v_of_rho 0.87145 13 0.067 16.% + XC_Functional v_xc 0.24143 14 0.017 4.3% + H_Hartree_pw v_hartree 0.59238 13 0.046 11.% + PW_Basis real2recip 0.55646 38 0.015 10.% + PW_Basis gatherp_scatters 0.21456 38 0.0056 3.9% + ORB_control set_orb_tables 1.1074 1 1.1 20.% + ORB_gen_tables gen_tables 1.1074 1 1.1 20.% + ORB_table_phi init_Table 0.48112 1 0.48 8.6% + ORB_table_phi cal_ST_Phi12_R 0.47620 126 0.0038 8.6% + ORB_table_beta init_Table_Beta 0.19044 1 0.19 3.4% + ORB_table_beta VNL_PhiBeta_R 0.18894 56 0.0034 3.4% + ORB_table_alpha init_Table_Alpha 0.25685 1 0.26 4.6% + ORB_table_alpha S_PhiAlpha_R 0.25495 66 0.0039 4.6% + LOOP_ions opt_ions 3.9325 1 3.9 71.% + ESolver_KS_LCAO Run 3.4735 1 3.5 62.% + HSolverLCAO solve 1.4958 11 0.14 27.% + HamiltLCAO updateHk 0.84268 11 0.077 15.% + LCAO_Hamilt cal_Hgamma 0.80431 11 0.073 14.% + Gint_interface cal_gint 1.2769 23 0.056 23.% + Gint_Gamma distri_vl 1.6954 6 0.28 30.% + LCAO_Deepks cal_projected_DM 3.7913 13 0.29 68.% + LCAO_gen_fixedH add_v_delta 1.5618 6 0.26 28.% + LCAO_DESCRIPTOR add_v_delta 1.5618 6 0.26 28.% + ElecStateLCAO psiToRho 0.63940 11 0.058 11.% + Charge mix_rho 0.66551 10 0.067 12.% + LOOP_ions force_stress 0.45890 1 0.46 8.2% + Force_Stress_LCAO getForceStress 0.45887 1 0.46 8.2% + Force_LCAO_gamma ftable_gamma 0.24646 1 0.25 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.23976 1 0.24 4.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:38 2022 + Finish Time : Wed Sep 28 11:10:43 2022 + Total Time : 0 h 0 mins 5 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..fdc4a5a2bc38a9e8d4657e962dc169f16e65b1f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012444 ima = 3.68217e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122855344599 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112037582227 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112393660609 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011270592957 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112618390208 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112667137763 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112662240371 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112665305488 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112664785001 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112664699034 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112664700724 + charge after normalized = 7.99999999999998 + charge before normalized = 7.99999999999998 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/STRU new file mode 100644 index 0000000000000000000000000000000000000000..eb43660ce66f7344cb67bb34959702457d28473a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.688935462671 19.613062414680 0.790787158186 0 0 0 +H +0.0 +2 +-13.483956659802 18.462077197192 2.144198934847 0 0 0 +-15.341210008432 19.364627678098 0.250113775440 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/conv new file mode 100644 index 0000000000000000000000000000000000000000..8f1f88e847a3df7e1fa01b9024f0fd4e2fb9eb23 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/conv @@ -0,0 +1 @@ +63 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..2a4cc987880dc8b7bb647a258309349dd6a67661 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749178361 0.01286999484 1.304722682 1.38784343 1.471212342 0.008805536345 0.01942831023 0.03903055364 +1.409118521e-18 0.001243782413 0.002827084724 0.01350536684 0.04901131122 4.118632465e-19 2.491136242e-06 6.793174785e-06 +0.001656968318 0.00592411196 + +H atom_index 1 n_descriptor 18 +1.280426014 0.03315235027 0.1203692595 0.1645038496 0.3295914742 0.0239840333 0.03004091402 0.03651549201 +1.205089546e-17 5.542110329e-05 0.1088165028 0.1196943932 0.1415064864 3.227487963e-18 2.437604831e-06 0.01331374518 +0.02820299303 0.03208447372 + +H atom_index 2 n_descriptor 18 +1.305847032 0.03239652178 0.13046441 0.1778249181 0.3364925957 0.02514058678 0.03147623287 0.03634643468 +1.845254948e-17 5.790584997e-05 0.1083749635 0.1273916014 0.1527218934 7.074858356e-19 1.128446297e-06 0.0139274706 +0.02897167464 0.0329798218 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..cd2f906bc13a07fe049fd0b72c17a8fbdf8ead92 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:38 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874616 SEC) : SETUP UNITCELL + DONE(0.0967669 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.114875 SEC) : INIT PLANEWAVE + DONE(0.163218 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44142 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.650803e+02 0.000000e+00 2.197e-01 4.405e-01 + GE2 -4.663396e+02 -1.259256e+00 9.723e-02 3.521e-01 + GE3 -4.663433e+02 -3.710690e-03 6.190e-02 4.132e-01 + GE4 -4.663443e+02 -1.015979e-03 2.111e-03 2.986e-01 + GE5 -4.663431e+02 1.201478e-03 9.579e-04 2.957e-01 + GE6 -4.663440e+02 -8.403407e-04 1.140e-04 2.812e-01 + GE7 -4.663437e+02 2.777559e-04 5.269e-05 2.851e-01 + GE8 -4.663437e+02 -4.454642e-05 1.424e-05 2.793e-01 + GE9 -4.663437e+02 1.951520e-05 1.999e-06 2.760e-01 + GE10 -4.663437e+02 -2.233815e-06 1.486e-07 2.759e-01 + GE11 -4.663437e+02 -5.195270e-07 9.279e-08 2.145e-01 +E_delta_band = -7.35659350e-02 Ry = -1.00091590e+00 eV +E_delta_NN= -1.96297775e-01 Ry = -2.67076825e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5685 11 0.51 1e+02 % + Run_lcao lcao_line 5.5585 1 5.6 1e+02 % + Potential init_pot 0.28335 2 0.14 5.1 % + PW_Basis recip2real 0.26385 16 0.016 4.7 % + PW_Basis gathers_scatterp 0.11121 16 0.007 2 % + Potential v_of_rho 0.87145 13 0.067 16 % + XC_Functional v_xc 0.24143 14 0.017 4.3 % + H_Hartree_pw v_hartree 0.59238 13 0.046 11 % + PW_Basis real2recip 0.55646 38 0.015 10 % + PW_Basis gatherp_scatters 0.21456 38 0.0056 3.9 % + ORB_control set_orb_tables 1.1074 1 1.1 20 % + ORB_gen_tables gen_tables 1.1074 1 1.1 20 % + ORB_table_phi init_Table 0.48112 1 0.48 8.6 % + ORB_table_phi cal_ST_Phi12_R 0.4762 126 0.0038 8.6 % + ORB_table_beta init_Table_Beta 0.19044 1 0.19 3.4 % + ORB_table_beta VNL_PhiBeta_R 0.18894 56 0.0034 3.4 % + ORB_table_alpha init_Table_Alpha 0.25685 1 0.26 4.6 % + ORB_table_alpha S_PhiAlpha_R 0.25495 66 0.0039 4.6 % + LOOP_ions opt_ions 3.9325 1 3.9 71 % + ESolver_KS_LCAO Run 3.4735 1 3.5 62 % + HSolverLCAO solve 1.4958 11 0.14 27 % + HamiltLCAO updateHk 0.84268 11 0.077 15 % + LCAO_Hamilt cal_Hgamma 0.80431 11 0.073 14 % + Gint_interface cal_gint 1.2769 23 0.056 23 % + Gint_Gamma distri_vl 1.6954 6 0.28 30 % + LCAO_Deepks cal_projected_DM 3.7913 13 0.29 68 % + LCAO_gen_fixedH add_v_delta 1.5618 6 0.26 28 % + LCAO_DESCRIPTOR add_v_delta 1.5618 6 0.26 28 % + ElecStateLCAO psiToRho 0.6394 11 0.058 11 % + Charge mix_rho 0.66551 10 0.067 12 % + LOOP_ions force_stress 0.4589 1 0.46 8.2 % + Force_Stress_LCAO getForceStress 0.45887 1 0.46 8.2 % + Force_LCAO_gamma ftable_gamma 0.24646 1 0.25 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.23976 1 0.24 4.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:38 2022 + FINISH Time : Wed Sep 28 11:10:43 2022 + TOTAL Time : 5 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/63/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..108177e8e7e96c78df7d6b4d0741c6320548a615 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.513492 0.68638 0.0447151 +H 0.557853 0.729192 0.0674108 +H 0.462106 0.689097 0.0911641 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e92ec4b735014b9b86ba8400dd8158c0d68d583d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9713 2 + 2 -12.763 2 + 3 -9.06755 2 + 4 -6.67242 2 + 5 0.972714 0 + 6 3.96219 0 + 7 11.1511 0 + 8 11.3941 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..083c139f1b1c81f8992bbc3bdd13dc7fce6c594e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:29 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.3777753927 19.2186300858 1.25202419799 0 0 0 0 + tauc_H1 15.6198899911 20.417370849 1.88750284627 0 0 0 0 + tauc_H2 12.9389657069 19.2947066555 2.55259540762 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0890822598269 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.089490476145 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107895829343 (SEC) + + DONE : INIT CHARGE Time : 0.158581215985 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437701 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000577 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126 + + Density error is 0.212033512348 + + Energy Rydberg eV + E_KohnSham -34.1879133522 -465.15042432 + E_Harris -34.3737071827 -467.678279069 + E_Fermi -0.386150521248 -5.25384737464 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000932479802738 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011624866146 + + Density error is 0.0990747264041 + + Energy Rydberg eV + E_KohnSham -34.2768636652 -466.360655416 + E_Harris -34.2840811483 -466.458854312 + E_Fermi -0.19670562016 -2.6763172628 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000900806737108 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109144215148 + + Density error is 0.0639767235986 + + Energy Rydberg eV + E_KohnSham -34.2773448728 -466.367202581 + E_Harris -34.2819395109 -466.429715839 + E_Fermi -0.1905864362 -2.59306149384 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00087667830742 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000959274964293 + + Density error is 0.00199346493892 + + Energy Rydberg eV + E_KohnSham -34.2772411855 -466.365791843 + E_Harris -34.2772438613 -466.365828249 + E_Fermi -0.155381583456 -2.11407489926 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000876131621717 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000957037864928 + + Density error is 0.000965756057702 + + Energy Rydberg eV + E_KohnSham -34.2772061386 -466.365315005 + E_Harris -34.2772064204 -466.36531884 + E_Fermi -0.155323462161 -2.11328411847 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000875903040114 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954901613423 + + Density error is 0.000190256318401 + + Energy Rydberg eV + E_KohnSham -34.2772195959 -466.365498101 + E_Harris -34.2772196049 -466.365498223 + E_Fermi -0.154870494674 -2.10712117964 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000876131867745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954975303306 + + Density error is 3.09866328684e-05 + + Energy Rydberg eV + E_KohnSham -34.2772157119 -466.365445257 + E_Harris -34.2772157147 -466.365445295 + E_Fermi -0.154851152794 -2.10685801986 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000876048447899 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954911396841 + + Density error is 1.19881529314e-05 + + Energy Rydberg eV + E_KohnSham -34.2772184113 -466.365481984 + E_Harris -34.2772184119 -466.365481992 + E_Fermi -0.154864753564 -2.10704306784 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000876054645923 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954897637775 + + Density error is 1.62038303724e-06 + + Energy Rydberg eV + E_KohnSham -34.2772174175 -466.365468462 + E_Harris -34.2772174175 -466.365468462 + E_Fermi -0.154852395859 -2.10687493264 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000876056835357 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954896702682 + + Density error is 5.71973180525e-07 + + Energy Rydberg eV + E_KohnSham -34.2772176075 -466.365471048 + E_Harris -34.2772176075 -466.365471048 + E_Fermi -0.154851565786 -2.10686363891 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000876057672874 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954896952496 + + Density error is 1.78967075552e-07 + + Energy Rydberg eV + E_KohnSham -34.2772176106 -466.365471091 + E_Harris -34.2772176106 -466.365471091 + E_Fermi -0.154851267636 -2.10685958237 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000876057891611 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954896853667 + + Density error is 1.18884970269e-08 + + Energy Rydberg eV + E_KohnSham -34.2772176156 -466.365471158 + E_Harris -34.2772176156 -466.365471158 + E_band -7.86055844888 -106.948384367 + E_one_elec -68.6161491932 -933.570603846 + E_Hartree +35.7220718884 +486.023722048 + E_xc -8.15886802036 -111.007094307 + E_Ewald +6.90140935771 +93.8984914954 + E_demet -2.68114012867e-58 -3.64787828864e-57 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193646820311 -2.63470015581 + E_Fermi -0.154851093787 -2.10685721703 + + charge density convergence is achieved + final etot is -466.365471158 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9713 2.00000 + 2 -12.7630 2.00000 + 3 -9.06755 2.00000 + 4 -6.67242 2.00000 + 5 0.972714 0.00000 + 6 3.96219 0.00000 + 7 11.1511 0.00000 + 8 11.3941 0.00000 + + EFERMI = -2.106857217031572 eV + OUT.ABACUS/ final etot is -466.3654711575224 eV + correction force for each atom along direction 1 is 5.58461e-05 + correction force for each atom along direction 2 is 0.000124227 + correction force for each atom along direction 3 is 0.000191142 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.6786382 -0.071827803 +1.2971469 + H1 +0.053639423 +0.10960607 +0.10616246 + H2 +1.6249988 -0.037778264 -1.4033094 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3654711575224 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5686 11 0.60 1.0e+02% + Run_lcao lcao_line 6.5578 1 6.6 1.e+02% + Potential init_pot 0.28354 2 0.14 4.3% + PW_Basis recip2real 0.30169 17 0.018 4.6% + PW_Basis gathers_scatterp 0.12782 17 0.0075 1.9% + Potential v_of_rho 1.0605 14 0.076 16.% + XC_Functional v_xc 0.30171 15 0.020 4.6% + H_Hartree_pw v_hartree 0.71505 14 0.051 11.% + PW_Basis real2recip 0.70806 41 0.017 11.% + PW_Basis gatherp_scatters 0.26271 41 0.0064 4.0% + ORB_control set_orb_tables 1.1150 1 1.1 17.% + ORB_gen_tables gen_tables 1.1150 1 1.1 17.% + ORB_table_phi init_Table 0.48762 1 0.49 7.4% + ORB_table_phi cal_ST_Phi12_R 0.48236 126 0.0038 7.3% + ORB_table_beta init_Table_Beta 0.18807 1 0.19 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18648 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25384 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.25188 66 0.0038 3.8% + LOOP_ions opt_ions 4.9263 1 4.9 75.% + ESolver_KS_LCAO Run 4.4285 1 4.4 67.% + HSolverLCAO solve 1.9588 12 0.16 30.% + HamiltLCAO updateHk 1.0603 12 0.088 16.% + LCAO_Hamilt cal_Hgamma 1.0304 12 0.086 16.% + Gint_interface cal_gint 1.7147 25 0.069 26.% + Gint_Gamma distri_vl 2.3138 6 0.39 35.% + LCAO_Deepks cal_projected_DM 4.7813 14 0.34 73.% + LCAO_gen_fixedH add_v_delta 2.1698 6 0.36 33.% + LCAO_DESCRIPTOR add_v_delta 2.1698 6 0.36 33.% + ElecStateLCAO psiToRho 0.88107 12 0.073 13.% + Charge mix_rho 0.85430 11 0.078 13.% + LOOP_ions force_stress 0.49767 1 0.50 7.6% + Force_Stress_LCAO getForceStress 0.49764 1 0.50 7.6% + Force_LCAO_gamma ftable_gamma 0.28264 1 0.28 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.27479 1 0.27 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:29 2022 + Finish Time : Wed Sep 28 11:03:36 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2ca899a45d972fb97475d17b32e8df0df057f84f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123413 ima = 3.65678e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012370662755 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112206917673 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113002946779 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113205716748 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113190529153 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113200658475 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113196334359 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113198313796 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113197778011 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113197751951 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113197729854 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113197720415 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d4fc778661c049f964f0e0c3d38959aebd6d8769 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.622224607268 19.218630085787 1.252024197996 0 0 0 +H +0.0 +2 +-12.380110008914 20.417370849013 1.887502846284 0 0 0 +-15.061034293113 19.294706655543 2.552595407598 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/conv new file mode 100644 index 0000000000000000000000000000000000000000..e00faa53578e4680f3466b33acad3dabfee1e7ef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/conv @@ -0,0 +1 @@ +64 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9dced6aa10433e568f637480a7e0d08fdd58c792 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749872186 0.01238567338 1.241488016 1.342616659 1.468028725 0.008395245344 0.01803401283 0.03909853046 +-3.123857707e-18 0.000898619124 0.002390469278 0.01137389611 0.0415050938 3.949952861e-19 1.566004805e-06 4.943111983e-06 +0.001608982032 0.00580992976 + +H atom_index 1 n_descriptor 18 +1.241132542 0.03458511675 0.1043730439 0.1462627615 0.3190389474 0.02151342375 0.02784085862 0.03782349503 +2.789297958e-17 3.905577484e-05 0.09658580675 0.1150712437 0.1253160235 1.228337312e-17 4.324881856e-06 0.01321362407 +0.02524510562 0.03035130092 + +H atom_index 2 n_descriptor 18 +1.161211951 0.0370576862 0.08036796375 0.1135059378 0.2893044614 0.01785529098 0.02317550515 0.040979236 +1.844851446e-17 3.256197341e-05 0.07617397637 0.09650366658 0.1115783554 8.871682952e-18 6.80147617e-06 0.01536881536 +0.02195814176 0.02615461997 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..a2be513308182a123e07481e53a029ace3b275a2 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:29 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0891058 SEC) : SETUP UNITCELL + DONE(0.0895088 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107916 SEC) : INIT PLANEWAVE + DONE(0.158713 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.437772 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651504e+02 0.000000e+00 2.120e-01 4.839e-01 + GE2 -4.663607e+02 -1.210231e+00 9.907e-02 4.216e-01 + GE3 -4.663672e+02 -6.547165e-03 6.398e-02 4.865e-01 + GE4 -4.663658e+02 1.410738e-03 1.993e-03 3.517e-01 + GE5 -4.663653e+02 4.768379e-04 9.658e-04 3.520e-01 + GE6 -4.663655e+02 -1.830961e-04 1.903e-04 3.455e-01 + GE7 -4.663654e+02 5.284443e-05 3.099e-05 3.310e-01 + GE8 -4.663655e+02 -3.672714e-05 1.199e-05 3.294e-01 + GE9 -4.663655e+02 1.352150e-05 1.620e-06 3.302e-01 + GE10 -4.663655e+02 -2.585225e-06 5.720e-07 3.325e-01 + GE11 -4.663655e+02 -4.314352e-08 1.790e-07 3.335e-01 + GE12 -4.663655e+02 -6.682640e-08 1.189e-08 2.683e-01 +E_delta_band = -6.79651722e-02 Ry = -9.24713608e-01 eV +E_delta_NN= -1.93646820e-01 Ry = -2.63470016e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5686 11 0.6 1e+02 % + Run_lcao lcao_line 6.5578 1 6.6 1e+02 % + Potential init_pot 0.28354 2 0.14 4.3 % + PW_Basis recip2real 0.30169 17 0.018 4.6 % + PW_Basis gathers_scatterp 0.12782 17 0.0075 1.9 % + Potential v_of_rho 1.0605 14 0.076 16 % + XC_Functional v_xc 0.30171 15 0.02 4.6 % + H_Hartree_pw v_hartree 0.71505 14 0.051 11 % + PW_Basis real2recip 0.70806 41 0.017 11 % + PW_Basis gatherp_scatters 0.26271 41 0.0064 4 % + ORB_control set_orb_tables 1.115 1 1.1 17 % + ORB_gen_tables gen_tables 1.115 1 1.1 17 % + ORB_table_phi init_Table 0.48762 1 0.49 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.48236 126 0.0038 7.3 % + ORB_table_beta init_Table_Beta 0.18807 1 0.19 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18648 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.25384 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.25188 66 0.0038 3.8 % + LOOP_ions opt_ions 4.9263 1 4.9 75 % + ESolver_KS_LCAO Run 4.4285 1 4.4 67 % + HSolverLCAO solve 1.9588 12 0.16 30 % + HamiltLCAO updateHk 1.0603 12 0.088 16 % + LCAO_Hamilt cal_Hgamma 1.0304 12 0.086 16 % + Gint_interface cal_gint 1.7147 25 0.069 26 % + Gint_Gamma distri_vl 2.3138 6 0.39 35 % + LCAO_Deepks cal_projected_DM 4.7813 14 0.34 73 % + LCAO_gen_fixedH add_v_delta 2.1698 6 0.36 33 % + LCAO_DESCRIPTOR add_v_delta 2.1698 6 0.36 33 % + ElecStateLCAO psiToRho 0.88107 12 0.073 13 % + Charge mix_rho 0.8543 11 0.078 13 % + LOOP_ions force_stress 0.49767 1 0.5 7.6 % + Force_Stress_LCAO getForceStress 0.49764 1 0.5 7.6 % + Force_LCAO_gamma ftable_gamma 0.28264 1 0.28 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.27479 1 0.27 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:29 2022 + FINISH Time : Wed Sep 28 11:03:36 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/64/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..38deb42343849829ec4bb95b5010c0253eb67b9d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.519794 0.670413 0.0530082 +H 0.50619 0.730213 0.0280709 +H 0.479168 0.668162 0.101085 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..fb1ab91f32af1c03f4457863183907a6241e0be2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5285 2 + 2 -13.0063 2 + 3 -9.3123 2 + 4 -6.79586 2 + 5 1.38117 0 + 6 4.64954 0 + 7 11.0294 0 + 8 11.2902 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..91c3d717fcb14f74eb8c9ccac336561fc19ccf44 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:38 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.5542303741 18.7715607598 1.48422972169 0 0 0 0 + tauc_H1 14.1733325693 20.4459579625 0.785985509254 0 0 0 0 + tauc_H2 13.4166962582 18.7085331566 2.83039162833 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.100357943864 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.100742506456 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118860696311 (SEC) + + DONE : INIT CHARGE Time : 0.161809165098 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445424 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 100 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00062 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00137 + + Density error is 0.215852161131 + + Energy Rydberg eV + E_KohnSham -34.1869785747 -465.13770602 + E_Harris -34.3813146076 -467.781783394 + E_Fermi -0.416483341205 -5.66654656246 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000955008583321 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138318300815 + + Density error is 0.0974029324575 + + Energy Rydberg eV + E_KohnSham -34.2768599756 -466.360605216 + E_Harris -34.2835669608 -466.451858431 + E_Fermi -0.225096357614 -3.0625930626 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000915757311037 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129492238886 + + Density error is 0.0622421235284 + + Energy Rydberg eV + E_KohnSham -34.2770748172 -466.363528287 + E_Harris -34.2813886473 -466.422220955 + E_Fermi -0.211772777982 -2.88131646184 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000868139132598 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115965241119 + + Density error is 0.00200379991054 + + Energy Rydberg eV + E_KohnSham -34.2770989422 -466.363856523 + E_Harris -34.2771006115 -466.363879236 + E_Fermi -0.175885624585 -2.39304669064 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000872354644072 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116254164203 + + Density error is 0.000867670225824 + + Energy Rydberg eV + E_KohnSham -34.2770320223 -466.362946031 + E_Harris -34.2770339609 -466.362972407 + E_Fermi -0.174911232428 -2.37978940522 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000871017644207 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116052638029 + + Density error is 0.000128632468528 + + Energy Rydberg eV + E_KohnSham -34.2770789566 -466.363584605 + E_Harris -34.2770789997 -466.363585192 + E_Fermi -0.175090718356 -2.38223143655 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000870981531865 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116033321467 + + Density error is 4.2143307035e-05 + + Energy Rydberg eV + E_KohnSham -34.2770624611 -466.363360172 + E_Harris -34.27706247 -466.363360294 + E_Fermi -0.174957798768 -2.38042297279 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000870929780889 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116031596525 + + Density error is 1.83513582734e-05 + + Energy Rydberg eV + E_KohnSham -34.2770661821 -466.3634108 + E_Harris -34.2770661834 -466.363410818 + E_Fermi -0.175004996741 -2.38106513416 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000870935778994 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116029880407 + + Density error is 2.2380361204e-06 + + Energy Rydberg eV + E_KohnSham -34.2770646717 -466.36339025 + E_Harris -34.2770646717 -466.36339025 + E_Fermi -0.174984981348 -2.38079281075 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00087093897632 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116029758586 + + Density error is 1.74392903803e-07 + + Energy Rydberg eV + E_KohnSham -34.2770649025 -466.36339339 + E_Harris -34.2770649025 -466.36339339 + E_Fermi -0.174983028709 -2.38076624374 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000870939088472 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116029779162 + + Density error is 9.09514340563e-08 + + Energy Rydberg eV + E_KohnSham -34.2770649468 -466.363393993 + E_Harris -34.2770649468 -466.363393993 + E_band -8.03235958606 -109.285858755 + E_one_elec -69.6319970692 -947.391923261 + E_Hartree +36.1941447097 +492.446602289 + E_xc -8.23474147406 -112.039405604 + E_Ewald +7.51914874692 +102.303267068 + E_demet -1.11636736557e-85 -1.51889572331e-84 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19551411155 -2.66010595649 + E_Fermi -0.174983006624 -2.38076594326 + + charge density convergence is achieved + final etot is -466.363393993 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5285 2.00000 + 2 -13.0063 2.00000 + 3 -9.31230 2.00000 + 4 -6.79586 2.00000 + 5 1.38117 0.00000 + 6 4.64954 0.00000 + 7 11.0294 0.00000 + 8 11.2902 0.00000 + + EFERMI = -2.380765943262687 eV + OUT.ABACUS/ final etot is -466.3633939931633 eV + correction force for each atom along direction 1 is -9.68805e-05 + correction force for each atom along direction 2 is 0.000128277 + correction force for each atom along direction 3 is 0.000105994 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.2576410 +0.62055717 -1.8571062 + H1 +0.26584727 -0.21639348 -0.16002432 + H2 -1.5234883 -0.40416368 +2.0171305 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3633939931633 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6287 11 0.69 1.0e+02% + Run_lcao lcao_line 7.6197 1 7.6 1.e+02% + Potential init_pot 0.28557 2 0.14 3.7% + PW_Basis recip2real 0.28340 16 0.018 3.7% + PW_Basis gathers_scatterp 0.12412 16 0.0078 1.6% + Potential v_of_rho 1.0282 13 0.079 13.% + XC_Functional v_xc 0.31499 14 0.022 4.1% + H_Hartree_pw v_hartree 0.67026 13 0.052 8.8% + PW_Basis real2recip 0.70971 38 0.019 9.3% + PW_Basis gatherp_scatters 0.28042 38 0.0074 3.7% + ORB_control set_orb_tables 1.0934 1 1.1 14.% + ORB_gen_tables gen_tables 1.0934 1 1.1 14.% + ORB_table_phi init_Table 0.47329 1 0.47 6.2% + ORB_table_phi cal_ST_Phi12_R 0.46805 126 0.0037 6.1% + ORB_table_beta init_Table_Beta 0.18223 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18073 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24825 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24624 66 0.0037 3.2% + LOOP_ions opt_ions 6.0028 1 6.0 79.% + ESolver_KS_LCAO Run 5.4155 1 5.4 71.% + HSolverLCAO solve 2.9271 11 0.27 38.% + HamiltLCAO updateHk 1.4986 11 0.14 20.% + LCAO_Hamilt cal_Hgamma 1.4710 11 0.13 19.% + Gint_interface cal_gint 2.7615 23 0.12 36.% + Gint_Gamma distri_vl 2.5988 6 0.43 34.% + LCAO_Deepks cal_projected_DM 5.8290 13 0.45 76.% + LCAO_gen_fixedH add_v_delta 2.4510 6 0.41 32.% + LCAO_DESCRIPTOR add_v_delta 2.4511 6 0.41 32.% + ElecStateLCAO psiToRho 1.4117 11 0.13 19.% + Charge mix_rho 0.90662 10 0.091 12.% + LOOP_ions force_stress 0.58709 1 0.59 7.7% + Force_Stress_LCAO getForceStress 0.58706 1 0.59 7.7% + Force_LCAO_gamma ftable_gamma 0.36842 1 0.37 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.36001 1 0.36 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:38 2022 + Finish Time : Wed Sep 28 11:09:45 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..62dab2ec15f087dc4be682b2e0e7148eccd2bae7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123994 ima = 3.65364e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012263505109 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111718372766 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112190935803 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112466651321 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112400493238 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112438835521 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112432816782 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112435854999 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112435132509 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112435026598 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112435024726 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9fe56a0104391897c324c460cac947fd438efbbb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.445769625888 18.771560759826 1.484229721712 0 0 0 +H +0.0 +2 +-13.826667430707 20.445957962532 0.785985509234 0 0 0 +-14.583303741828 18.708533156574 2.830391628347 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/conv new file mode 100644 index 0000000000000000000000000000000000000000..063f6c6db3db6e1aa21c5478dd6f508d0b3dbbde --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/conv @@ -0,0 +1 @@ +65 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..348eb4e6d1feca3a63108997b756abf0194027e9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752065695 0.01280662023 1.280942192 1.371875963 1.470356343 0.009178069473 0.01792657178 0.03911109336 +4.82698479e-19 0.001048220758 0.002849521261 0.01321516003 0.04801313577 -1.925162001e-19 2.647944383e-06 7.112824729e-06 +0.001601546342 0.006058962526 + +H atom_index 1 n_descriptor 18 +1.231701172 0.03520545639 0.1035583287 0.1412577312 0.3137306409 0.02195647874 0.02717803362 0.03830958529 +-1.876176582e-18 4.973896999e-05 0.09920202012 0.1141102622 0.1212569457 -8.612220723e-18 4.768253445e-06 0.01356155359 +0.0262927045 0.02989673836 + +H atom_index 2 n_descriptor 18 +1.302631984 0.03291940774 0.1298692087 0.1759361419 0.3355649867 0.02536625228 0.03127764364 0.03673692775 +-3.127298718e-17 5.662061166e-05 0.1082797321 0.1255244834 0.1508804111 8.466982112e-18 9.115001454e-07 0.01386966871 +0.02873556461 0.03285778582 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5c29674518df585c64d008041f6af64cc06625bd Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:38 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.100382 SEC) : SETUP UNITCELL + DONE(0.100758 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118882 SEC) : INIT PLANEWAVE + DONE(0.161942 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445496 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651377e+02 0.000000e+00 2.159e-01 5.806e-01 + GE2 -4.663606e+02 -1.222899e+00 9.740e-02 5.466e-01 + GE3 -4.663635e+02 -2.923071e-03 6.224e-02 6.159e-01 + GE4 -4.663639e+02 -3.282363e-04 2.004e-03 4.747e-01 + GE5 -4.663629e+02 9.104920e-04 8.677e-04 4.736e-01 + GE6 -4.663636e+02 -6.385740e-04 1.286e-04 4.696e-01 + GE7 -4.663634e+02 2.244327e-04 4.214e-05 4.641e-01 + GE8 -4.663634e+02 -5.062730e-05 1.835e-05 4.503e-01 + GE9 -4.663634e+02 2.055012e-05 2.238e-06 4.504e-01 + GE10 -4.663634e+02 -3.140009e-06 1.744e-07 4.499e-01 + GE11 -4.663634e+02 -6.034746e-07 9.095e-08 3.765e-01 +E_delta_band = -7.18942513e-02 Ry = -9.78171472e-01 eV +E_delta_NN= -1.95514112e-01 Ry = -2.66010596e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.6287 11 0.69 1e+02 % + Run_lcao lcao_line 7.6197 1 7.6 1e+02 % + Potential init_pot 0.28557 2 0.14 3.7 % + PW_Basis recip2real 0.2834 16 0.018 3.7 % + PW_Basis gathers_scatterp 0.12412 16 0.0078 1.6 % + Potential v_of_rho 1.0282 13 0.079 13 % + XC_Functional v_xc 0.31499 14 0.022 4.1 % + H_Hartree_pw v_hartree 0.67026 13 0.052 8.8 % + PW_Basis real2recip 0.70971 38 0.019 9.3 % + PW_Basis gatherp_scatters 0.28042 38 0.0074 3.7 % + ORB_control set_orb_tables 1.0934 1 1.1 14 % + ORB_gen_tables gen_tables 1.0934 1 1.1 14 % + ORB_table_phi init_Table 0.47329 1 0.47 6.2 % + ORB_table_phi cal_ST_Phi12_R 0.46805 126 0.0037 6.1 % + ORB_table_beta init_Table_Beta 0.18223 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18073 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24825 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24624 66 0.0037 3.2 % + LOOP_ions opt_ions 6.0028 1 6 79 % + ESolver_KS_LCAO Run 5.4155 1 5.4 71 % + HSolverLCAO solve 2.9271 11 0.27 38 % + HamiltLCAO updateHk 1.4986 11 0.14 20 % + LCAO_Hamilt cal_Hgamma 1.471 11 0.13 19 % + Gint_interface cal_gint 2.7615 23 0.12 36 % + Gint_Gamma distri_vl 2.5988 6 0.43 34 % + LCAO_Deepks cal_projected_DM 5.829 13 0.45 76 % + LCAO_gen_fixedH add_v_delta 2.451 6 0.41 32 % + LCAO_DESCRIPTOR add_v_delta 2.4511 6 0.41 32 % + ElecStateLCAO psiToRho 1.4117 11 0.13 19 % + Charge mix_rho 0.90662 10 0.091 12 % + LOOP_ions force_stress 0.58709 1 0.59 7.7 % + Force_Stress_LCAO getForceStress 0.58706 1 0.59 7.7 % + Force_LCAO_gamma ftable_gamma 0.36842 1 0.37 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.36001 1 0.36 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:38 2022 + FINISH Time : Wed Sep 28 11:09:45 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/65/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4cdf533063494b9d2cc95d7f5b4c819e3073067b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.544567 0.656322 0.0566744 +H 0.509415 0.68643 0.0102895 +H 0.539427 0.694856 0.11088 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..78f615094ab9fe9fa6441153b8ee4d24540ea53a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1553 2 + 2 -13.0259 2 + 3 -9.02672 2 + 4 -6.71396 2 + 5 1.21631 0 + 6 4.28004 0 + 7 11.1031 0 + 8 11.3476 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a0a7843403a552c4032b85b758b789df1a736e6c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:29 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.2478711761 18.3770241324 1.58688306143 0 0 0 0 + tauc_H1 14.2636071651 19.2200401261 0.28810721029 0 0 0 0 + tauc_H2 15.1039577454 19.4559597408 3.10464782515 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105272668883 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105633693125 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123643974027 (SEC) + + DONE : INIT CHARGE Time : 0.166760226275 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448035 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 100 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000929 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000762 + + Density error is 0.213943100198 + + Energy Rydberg eV + E_KohnSham -34.191996429 -465.20597743 + E_Harris -34.381229817 -467.780629759 + E_Fermi -0.398383360741 -5.42028369446 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00106822191724 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106159843738 + + Density error is 0.0982747565964 + + Energy Rydberg eV + E_KohnSham -34.2808216267 -466.414506245 + E_Harris -34.287644014 -466.507329586 + E_Fermi -0.207964371 -2.82950042658 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00101256150444 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102625896048 + + Density error is 0.0631438269503 + + Energy Rydberg eV + E_KohnSham -34.281131815 -466.418726573 + E_Harris -34.2855313201 -466.478584911 + E_Fermi -0.198149697817 -2.69596494729 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000930395263868 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989714801037 + + Density error is 0.00200793041124 + + Energy Rydberg eV + E_KohnSham -34.2810945373 -466.418219383 + E_Harris -34.2810965654 -466.418246978 + E_Fermi -0.162827629284 -2.21538355009 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000930348685391 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000990065027924 + + Density error is 0.000870492910397 + + Energy Rydberg eV + E_KohnSham -34.2810471836 -466.417575104 + E_Harris -34.281047797 -466.41758345 + E_Fermi -0.162301918662 -2.20823089014 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000929298981944 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989508482925 + + Density error is 0.000182407744119 + + Energy Rydberg eV + E_KohnSham -34.2810746598 -466.417948937 + E_Harris -34.2810748711 -466.417951811 + E_Fermi -0.162139980378 -2.20602760675 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000929526146956 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989843053321 + + Density error is 3.4529227481e-05 + + Energy Rydberg eV + E_KohnSham -34.2810641513 -466.417805961 + E_Harris -34.2810641568 -466.417806036 + E_Fermi -0.162044257075 -2.2047252244 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000929464090727 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989746628121 + + Density error is 1.539787739e-05 + + Energy Rydberg eV + E_KohnSham -34.2810683996 -466.417863763 + E_Harris -34.2810684006 -466.417863776 + E_Fermi -0.162076337642 -2.20516170291 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000929459095034 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989749869173 + + Density error is 2.2148719453e-06 + + Energy Rydberg eV + E_KohnSham -34.2810671425 -466.417846658 + E_Harris -34.2810671425 -466.417846659 + E_Fermi -0.162060861174 -2.20495113475 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000929459019074 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989752228936 + + Density error is 3.95851881327e-07 + + Energy Rydberg eV + E_KohnSham -34.2810673475 -466.417849447 + E_Harris -34.2810673475 -466.417849447 + E_Fermi -0.162058738572 -2.20492225527 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000929459150975 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989752763412 + + Density error is 1.50775374125e-07 + + Energy Rydberg eV + E_KohnSham -34.2810673738 -466.417849806 + E_Harris -34.2810673738 -466.417849806 + E_Fermi -0.162058605905 -2.20492045025 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00092945912441 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989752928718 + + Density error is 1.0251583853e-08 + + Energy Rydberg eV + E_KohnSham -34.2810673757 -466.417849831 + E_Harris -34.2810673757 -466.417849831 + E_band -7.92637176946 -107.843820531 + E_one_elec -69.0693362499 -939.736530076 + E_Hartree +35.9383979444 +488.966989036 + E_xc -8.19319056004 -111.474076416 + E_Ewald +7.1678643617 +97.5237978103 + E_demet -2.51969071506e-71 -3.42821509225e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194366562974 -2.64449275712 + E_Fermi -0.162058460498 -2.20491847188 + + charge density convergence is achieved + final etot is -466.417849831 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1553 2.00000 + 2 -13.0259 2.00000 + 3 -9.02672 2.00000 + 4 -6.71396 2.00000 + 5 1.21631 0.00000 + 6 4.28004 0.00000 + 7 11.1031 0.00000 + 8 11.3476 0.00000 + + EFERMI = -2.204918471883428 eV + OUT.ABACUS/ final etot is -466.4178498311842 eV + correction force for each atom along direction 1 is 5.20741e-05 + correction force for each atom along direction 2 is 6.03480e-05 + correction force for each atom along direction 3 is -4.03706e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.16439055 +0.11231724 +0.65337511 + H1 -0.14242464 +0.18494455 -0.066945392 + H2 -0.021965911 -0.29726178 -0.58642972 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4178498311842 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9157 11 0.72 1.0e+02% + Run_lcao lcao_line 7.9056 1 7.9 1.e+02% + Potential init_pot 0.28296 2 0.14 3.6% + PW_Basis recip2real 0.30411 17 0.018 3.8% + PW_Basis gathers_scatterp 0.13276 17 0.0078 1.7% + Potential v_of_rho 1.0951 14 0.078 14.% + XC_Functional v_xc 0.31412 15 0.021 4.0% + H_Hartree_pw v_hartree 0.73464 14 0.052 9.3% + PW_Basis real2recip 0.75399 41 0.018 9.5% + PW_Basis gatherp_scatters 0.28133 41 0.0069 3.6% + ORB_control set_orb_tables 1.0967 1 1.1 14.% + ORB_gen_tables gen_tables 1.0967 1 1.1 14.% + ORB_table_phi init_Table 0.47513 1 0.48 6.0% + ORB_table_phi cal_ST_Phi12_R 0.46974 126 0.0037 5.9% + ORB_table_beta init_Table_Beta 0.18426 1 0.18 2.3% + ORB_table_beta VNL_PhiBeta_R 0.18274 56 0.0033 2.3% + ORB_table_alpha init_Table_Alpha 0.24810 1 0.25 3.1% + ORB_table_alpha S_PhiAlpha_R 0.24611 66 0.0037 3.1% + LOOP_ions opt_ions 6.2846 1 6.3 79.% + ESolver_KS_LCAO Run 5.7077 1 5.7 72.% + HSolverLCAO solve 3.0196 12 0.25 38.% + HamiltLCAO updateHk 1.5423 12 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.5125 12 0.13 19.% + Gint_interface cal_gint 2.8297 25 0.11 36.% + Gint_Gamma distri_vl 2.9691 6 0.49 38.% + LCAO_Deepks cal_projected_DM 6.1162 14 0.44 77.% + LCAO_gen_fixedH add_v_delta 2.8213 6 0.47 36.% + LCAO_DESCRIPTOR add_v_delta 2.8213 6 0.47 36.% + ElecStateLCAO psiToRho 1.4575 12 0.12 18.% + Charge mix_rho 0.99372 11 0.090 13.% + LOOP_ions force_stress 0.57670 1 0.58 7.3% + Force_Stress_LCAO getForceStress 0.57667 1 0.58 7.3% + Force_LCAO_gamma ftable_gamma 0.35579 1 0.36 4.5% + Force_LCAO_gamma cal_fvl_dphi 0.34757 1 0.35 4.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:29 2022 + Finish Time : Wed Sep 28 11:11:37 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..cc7205e87d3329130b395408860357d7dd0ba710 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123466 ima = 3.66767e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123395428243 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112326885439 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112921247756 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113138573379 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011310373386 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113125944012 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113118229076 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113120782506 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113120162458 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113120086973 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113120074437 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113120066842 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/STRU new file mode 100644 index 0000000000000000000000000000000000000000..12c0261ee71c67a14ffceaa138f46daaf11abd31 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.752128823855 18.377024132413 1.586883061423 0 0 0 +H +0.0 +2 +-13.736392834949 19.220040126100 0.288107210314 0 0 0 +-12.896042254608 19.455959740784 3.104647825147 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/conv new file mode 100644 index 0000000000000000000000000000000000000000..b12adeb34400dcb73d876e4ae82f77245cd9386c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/conv @@ -0,0 +1 @@ +66 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b0df104619cef79bbfcba03363e8f7532aa9b928 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748056581 0.01258405793 1.264908117 1.356836493 1.468722433 0.008216487778 0.01879025313 0.03899767113 +-3.75171632e-18 0.001026625696 0.00246903749 0.01201901646 0.04330824577 7.480270667e-19 1.748311014e-06 5.301140577e-06 +0.001670711 0.00586226597 + +H atom_index 1 n_descriptor 18 +1.243398102 0.03433542246 0.1055960595 0.1473693696 0.3197402308 0.02169633807 0.02798682968 0.03751910393 +-2.587543721e-17 4.142585526e-05 0.09902804054 0.1148255421 0.1264224482 9.130481588e-18 4.448462335e-06 0.0131410704 +0.02572773892 0.03048731041 + +H atom_index 2 n_descriptor 18 +1.217213693 0.03523627503 0.09706297611 0.1358204779 0.3108339796 0.02050019752 0.02645945657 0.03847735231 +-3.316767794e-17 3.916387035e-05 0.09214516233 0.1140646759 0.116365981 4.323086866e-20 5.61450969e-06 0.01358408178 +0.02470519895 0.02922031224 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..c4a7f0a097b90cb63da8bb6a8f7aa114bcb0632f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:29 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105297 SEC) : SETUP UNITCELL + DONE(0.105649 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123666 SEC) : INIT PLANEWAVE + DONE(0.166897 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448104 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652060e+02 0.000000e+00 2.139e-01 5.677e-01 + GE2 -4.664145e+02 -1.208529e+00 9.827e-02 5.319e-01 + GE3 -4.664187e+02 -4.220327e-03 6.314e-02 6.052e-01 + GE4 -4.664182e+02 5.071891e-04 2.008e-03 4.614e-01 + GE5 -4.664176e+02 6.442793e-04 8.705e-04 4.605e-01 + GE6 -4.664179e+02 -3.738331e-04 1.824e-04 4.547e-01 + GE7 -4.664178e+02 1.429758e-04 3.453e-05 4.432e-01 + GE8 -4.664179e+02 -5.780137e-05 1.540e-05 4.388e-01 + GE9 -4.664178e+02 1.710444e-05 2.215e-06 4.373e-01 + GE10 -4.664178e+02 -2.788755e-06 3.959e-07 4.397e-01 + GE11 -4.664178e+02 -3.586973e-07 1.508e-07 4.415e-01 + GE12 -4.664178e+02 -2.536038e-08 1.025e-08 3.635e-01 +E_delta_band = -6.95636910e-02 Ry = -9.46462572e-01 eV +E_delta_NN= -1.94366563e-01 Ry = -2.64449276e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.9157 11 0.72 1e+02 % + Run_lcao lcao_line 7.9056 1 7.9 1e+02 % + Potential init_pot 0.28296 2 0.14 3.6 % + PW_Basis recip2real 0.30411 17 0.018 3.8 % + PW_Basis gathers_scatterp 0.13276 17 0.0078 1.7 % + Potential v_of_rho 1.0951 14 0.078 14 % + XC_Functional v_xc 0.31412 15 0.021 4 % + H_Hartree_pw v_hartree 0.73464 14 0.052 9.3 % + PW_Basis real2recip 0.75399 41 0.018 9.5 % + PW_Basis gatherp_scatters 0.28133 41 0.0069 3.6 % + ORB_control set_orb_tables 1.0967 1 1.1 14 % + ORB_gen_tables gen_tables 1.0967 1 1.1 14 % + ORB_table_phi init_Table 0.47513 1 0.48 6 % + ORB_table_phi cal_ST_Phi12_R 0.46974 126 0.0037 5.9 % + ORB_table_beta init_Table_Beta 0.18426 1 0.18 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.18274 56 0.0033 2.3 % + ORB_table_alpha init_Table_Alpha 0.2481 1 0.25 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.24611 66 0.0037 3.1 % + LOOP_ions opt_ions 6.2846 1 6.3 79 % + ESolver_KS_LCAO Run 5.7077 1 5.7 72 % + HSolverLCAO solve 3.0196 12 0.25 38 % + HamiltLCAO updateHk 1.5423 12 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.5125 12 0.13 19 % + Gint_interface cal_gint 2.8297 25 0.11 36 % + Gint_Gamma distri_vl 2.9691 6 0.49 38 % + LCAO_Deepks cal_projected_DM 6.1162 14 0.44 77 % + LCAO_gen_fixedH add_v_delta 2.8213 6 0.47 36 % + LCAO_DESCRIPTOR add_v_delta 2.8213 6 0.47 36 % + ElecStateLCAO psiToRho 1.4575 12 0.12 18 % + Charge mix_rho 0.99372 11 0.09 13 % + LOOP_ions force_stress 0.5767 1 0.58 7.3 % + Force_Stress_LCAO getForceStress 0.57667 1 0.58 7.3 % + Force_LCAO_gamma ftable_gamma 0.35579 1 0.36 4.5 % + Force_LCAO_gamma cal_fvl_dphi 0.34757 1 0.35 4.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:29 2022 + FINISH Time : Wed Sep 28 11:11:37 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/66/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..942e5ca593d28864c7409cdb4233920ef58995aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.563325 0.641533 0.0591064 +H 0.56103 0.618967 0.997891 +H 0.581367 0.705937 0.0514391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2c7e4db1d8f2ed4920424665e49da6ae6782610c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1689 2 + 2 -12.9007 2 + 3 -9.12873 2 + 4 -6.71829 2 + 5 1.17538 0 + 6 4.22755 0 + 7 11.1057 0 + 8 11.3585 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..38ca5debc3193999d85ebff6f45ba87ddf9848aa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:14 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.7731052946 17.9629319873 1.65497849628 0 0 0 0 + tauc_H1 15.7088393977 17.331062251 27.9409483962 0 0 0 0 + tauc_H2 16.2782806587 19.7662492329 1.44029399221 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0886359835201 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0900623025467 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.108313623471 (SEC) + + DONE : INIT CHARGE Time : 0.157844371136 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.439604 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 100 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00154 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000912 + + Density error is 0.212533103642 + + Energy Rydberg eV + E_KohnSham -34.1930687042 -465.220566482 + E_Harris -34.3796284572 -467.758842141 + E_Fermi -0.39665778955 -5.39680609396 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00139830349963 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121989809585 + + Density error is 0.0981491865662 + + Energy Rydberg eV + E_KohnSham -34.2804110695 -466.408920327 + E_Harris -34.2872414482 -466.501852397 + E_Fermi -0.207954863789 -2.82937107435 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00128710818421 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117533667136 + + Density error is 0.0629766006861 + + Energy Rydberg eV + E_KohnSham -34.2806282292 -466.411874937 + E_Harris -34.2850381045 -466.471874369 + E_Fermi -0.197985024001 -2.69372444509 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00108148225248 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112285466795 + + Density error is 0.00196959600689 + + Energy Rydberg eV + E_KohnSham -34.2805872484 -466.411317364 + E_Harris -34.2805886811 -466.411336857 + E_Fermi -0.162646744853 -2.21292249115 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107825797197 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112241852311 + + Density error is 0.000795044210472 + + Energy Rydberg eV + E_KohnSham -34.2805485944 -466.41079145 + E_Harris -34.2805490731 -466.410797962 + E_Fermi -0.162187100804 -2.20666871303 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107596342412 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112183244143 + + Density error is 0.00016159029532 + + Energy Rydberg eV + E_KohnSham -34.2805724369 -466.411115843 + E_Harris -34.2805724691 -466.411116281 + E_Fermi -0.161996620701 -2.20407709827 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107596547604 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112215663654 + + Density error is 3.044062394e-05 + + Energy Rydberg eV + E_KohnSham -34.2805638603 -466.410999153 + E_Harris -34.2805638639 -466.410999202 + E_Fermi -0.161925510499 -2.20310959434 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107593059276 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011220438533 + + Density error is 1.55405461021e-05 + + Energy Rydberg eV + E_KohnSham -34.2805673276 -466.411046328 + E_Harris -34.2805673287 -466.411046343 + E_Fermi -0.161951296725 -2.20346043395 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107590885537 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112205392456 + + Density error is 2.49785793207e-06 + + Energy Rydberg eV + E_KohnSham -34.2805661177 -466.411029866 + E_Harris -34.2805661177 -466.411029866 + E_Fermi -0.161936750033 -2.20326251605 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107590159127 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112205463457 + + Density error is 4.94941022915e-07 + + Energy Rydberg eV + E_KohnSham -34.2805663737 -466.41103335 + E_Harris -34.2805663737 -466.41103335 + E_Fermi -0.16193443173 -2.20323097392 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107590143285 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112205527457 + + Density error is 1.70626366124e-07 + + Energy Rydberg eV + E_KohnSham -34.2805663928 -466.411033609 + E_Harris -34.2805663928 -466.411033609 + E_Fermi -0.16193421217 -2.20322798665 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00107590111543 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112205549541 + + Density error is 1.06027198744e-08 + + Energy Rydberg eV + E_KohnSham -34.2805663963 -466.411033657 + E_Harris -34.2805663963 -466.411033657 + E_band -7.92559986875 -107.833318283 + E_one_elec -69.0182886462 -939.041991797 + E_Hartree +35.9103790099 +488.585771874 + E_xc -8.18882664797 -111.414702347 + E_Ewald +7.14105739721 +97.1590703471 + E_demet -1.26341337645e-69 -1.71896208491e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194326222393 -2.64394389536 + E_Fermi -0.161934046957 -2.20322573882 + + charge density convergence is achieved + final etot is -466.411033657 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1689 2.00000 + 2 -12.9007 2.00000 + 3 -9.12873 2.00000 + 4 -6.71829 2.00000 + 5 1.17538 0.00000 + 6 4.22755 0.00000 + 7 11.1057 0.00000 + 8 11.3585 0.00000 + + EFERMI = -2.203225738815068 eV + OUT.ABACUS/ final etot is -466.4110336570689 eV + correction force for each atom along direction 1 is -8.15139e-05 + correction force for each atom along direction 2 is 1.27718e-05 + correction force for each atom along direction 3 is -0.000104701 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.28604568 +1.1298675 +0.27697237 + H1 -0.020899493 -0.18128751 -0.41753984 + H2 -0.26514618 -0.94857997 +0.14056747 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4110336570689 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0004 11 0.64 1.0e+02% + Run_lcao lcao_line 6.9896 1 7.0 1.e+02% + Potential init_pot 0.28439 2 0.14 4.1% + PW_Basis recip2real 0.30235 17 0.018 4.3% + PW_Basis gathers_scatterp 0.13319 17 0.0078 1.9% + Potential v_of_rho 1.0487 14 0.075 15.% + XC_Functional v_xc 0.29476 15 0.020 4.2% + H_Hartree_pw v_hartree 0.70822 14 0.051 10.% + PW_Basis real2recip 0.71251 41 0.017 10.% + PW_Basis gatherp_scatters 0.27640 41 0.0067 3.9% + ORB_control set_orb_tables 1.0940 1 1.1 16.% + ORB_gen_tables gen_tables 1.0940 1 1.1 16.% + ORB_table_phi init_Table 0.47374 1 0.47 6.8% + ORB_table_phi cal_ST_Phi12_R 0.46859 126 0.0037 6.7% + ORB_table_beta init_Table_Beta 0.18594 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18441 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.24903 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24709 66 0.0037 3.5% + LOOP_ions opt_ions 5.3779 1 5.4 77.% + ESolver_KS_LCAO Run 4.8195 1 4.8 69.% + HSolverLCAO solve 2.3522 12 0.20 34.% + HamiltLCAO updateHk 1.2350 12 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.2052 12 0.10 17.% + Gint_interface cal_gint 2.1681 25 0.087 31.% + Gint_Gamma distri_vl 2.5104 6 0.42 36.% + LCAO_Deepks cal_projected_DM 5.2246 14 0.37 75.% + LCAO_gen_fixedH add_v_delta 2.3669 6 0.39 34.% + LCAO_DESCRIPTOR add_v_delta 2.3670 6 0.39 34.% + ElecStateLCAO psiToRho 1.1000 12 0.092 16.% + Charge mix_rho 0.86377 11 0.079 12.% + LOOP_ions force_stress 0.55825 1 0.56 8.0% + Force_Stress_LCAO getForceStress 0.55822 1 0.56 8.0% + Force_LCAO_gamma ftable_gamma 0.34269 1 0.34 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.33474 1 0.33 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:14 2022 + Finish Time : Wed Sep 28 11:05:21 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..97292b12e4707fb7a253100fd3d58727853b9cbe --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123634 ima = 3.65447e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123104836182 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112126556477 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112718135681 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112923017992 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112893962098 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112912631599 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112906475619 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112908784779 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011290804703 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112907985643 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112907967668 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112907958899 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/STRU new file mode 100644 index 0000000000000000000000000000000000000000..61ea7e601a8eadc5d40586d3a66c8e24e95c5932 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.226894705370 17.962931987328 1.654978496291 0 0 0 +H +0.0 +2 +-12.291160602310 17.331062251066 -0.059051603801 0 0 0 +-11.721719341269 19.766249232870 1.440293992205 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/conv new file mode 100644 index 0000000000000000000000000000000000000000..eb8ebcea106b7d2356ca04e88bdd262839d39d7a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/conv @@ -0,0 +1 @@ +67 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..78abaea928338d76d6c66d888aa71ac8e3648ea0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749907258 0.01259071688 1.260606964 1.35266429 1.468802121 0.008524317474 0.01813597316 0.03906482463 +1.621682804e-18 0.0009760852161 0.002534207981 0.01206392314 0.04379868081 4.637505386e-20 1.906188143e-06 5.647713162e-06 +0.001628632351 0.005938633325 + +H atom_index 1 n_descriptor 18 +1.250549281 0.03429425411 0.1082866297 0.150311164 0.3214591255 0.02220885447 0.02835246732 0.03748914272 +1.20346674e-17 4.376310231e-05 0.1006597014 0.1152142017 0.1289347809 6.150453727e-18 3.953447389e-06 0.01316753419 +0.02606775384 0.03078263338 + +H atom_index 2 n_descriptor 18 +1.205410232 0.03581637135 0.09360651671 0.1305085856 0.3058235895 0.0201080271 0.02571221317 0.03915249936 +1.803510873e-17 3.975600775e-05 0.08895945847 0.1116757949 0.1136656405 4.382468838e-18 6.006569533e-06 0.01398608456 +0.02429268006 0.02856984903 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4b4038e97520bd1de8446bbd0344d21f3dfe5da8 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:14 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0886598 SEC) : SETUP UNITCELL + DONE(0.0900939 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.108335 SEC) : INIT PLANEWAVE + DONE(0.157976 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.439678 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652206e+02 0.000000e+00 2.125e-01 5.093e-01 + GE2 -4.664089e+02 -1.188354e+00 9.815e-02 4.555e-01 + GE3 -4.664119e+02 -2.954609e-03 6.298e-02 5.233e-01 + GE4 -4.664113e+02 5.575724e-04 1.970e-03 3.898e-01 + GE5 -4.664108e+02 5.259140e-04 7.950e-04 3.857e-01 + GE6 -4.664111e+02 -3.243927e-04 1.616e-04 3.828e-01 + GE7 -4.664110e+02 1.166897e-04 3.044e-05 3.655e-01 + GE8 -4.664110e+02 -4.717423e-05 1.554e-05 3.625e-01 + GE9 -4.664110e+02 1.646135e-05 2.498e-06 3.632e-01 + GE10 -4.664110e+02 -3.483770e-06 4.949e-07 3.627e-01 + GE11 -4.664110e+02 -2.592795e-07 1.706e-07 3.616e-01 + GE12 -4.664110e+02 -4.786770e-08 1.060e-08 2.958e-01 +E_delta_band = -6.94387131e-02 Ry = -9.44762160e-01 eV +E_delta_NN= -1.94326222e-01 Ry = -2.64394390e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0004 11 0.64 1e+02 % + Run_lcao lcao_line 6.9896 1 7 1e+02 % + Potential init_pot 0.28439 2 0.14 4.1 % + PW_Basis recip2real 0.30235 17 0.018 4.3 % + PW_Basis gathers_scatterp 0.13319 17 0.0078 1.9 % + Potential v_of_rho 1.0487 14 0.075 15 % + XC_Functional v_xc 0.29476 15 0.02 4.2 % + H_Hartree_pw v_hartree 0.70822 14 0.051 10 % + PW_Basis real2recip 0.71251 41 0.017 10 % + PW_Basis gatherp_scatters 0.2764 41 0.0067 3.9 % + ORB_control set_orb_tables 1.094 1 1.1 16 % + ORB_gen_tables gen_tables 1.094 1 1.1 16 % + ORB_table_phi init_Table 0.47374 1 0.47 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.46859 126 0.0037 6.7 % + ORB_table_beta init_Table_Beta 0.18594 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18441 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.24903 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24709 66 0.0037 3.5 % + LOOP_ions opt_ions 5.3779 1 5.4 77 % + ESolver_KS_LCAO Run 4.8195 1 4.8 69 % + HSolverLCAO solve 2.3522 12 0.2 34 % + HamiltLCAO updateHk 1.235 12 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.2052 12 0.1 17 % + Gint_interface cal_gint 2.1681 25 0.087 31 % + Gint_Gamma distri_vl 2.5104 6 0.42 36 % + LCAO_Deepks cal_projected_DM 5.2246 14 0.37 75 % + LCAO_gen_fixedH add_v_delta 2.3669 6 0.39 34 % + LCAO_DESCRIPTOR add_v_delta 2.367 6 0.39 34 % + ElecStateLCAO psiToRho 1.1 12 0.092 16 % + Charge mix_rho 0.86377 11 0.079 12 % + LOOP_ions force_stress 0.55825 1 0.56 8 % + Force_Stress_LCAO getForceStress 0.55822 1 0.56 8 % + Force_LCAO_gamma ftable_gamma 0.34269 1 0.34 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.33474 1 0.33 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:14 2022 + FINISH Time : Wed Sep 28 11:05:21 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/67/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9e3ead17171b3758c4bf33f1c161747aa842a3e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.584704 0.628325 0.0494305 +H 0.575132 0.567679 0.030006 +H 0.571146 0.665997 0.000290144 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3dcc6bef06d31abe8effffe753a5fd99d39c13d1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5064 2 + 2 -13.4275 2 + 3 -9.0103 2 + 4 -6.79264 2 + 5 1.54005 0 + 6 4.82675 0 + 7 11.0122 0 + 8 11.2436 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..60dec2cc7c6caf56e61e6eb789be5a34aef36ae6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:53 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.371720964 17.5931096468 1.38405504087 0 0 0 0 + tauc_H1 16.1037097759 15.895023269 0.840167775619 0 0 0 0 + tauc_H2 15.992093324 18.6479168469 0.00812403995224 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0994492479483 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.11005824985 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.128190353784 (SEC) + + DONE : INIT CHARGE Time : 0.171264513519 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.4536 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 337 ; sender_size of each process is: +144 49 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00102 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998 + + Density error is 0.217617238904 + + Energy Rydberg eV + E_KohnSham -34.1881803716 -465.154057306 + E_Harris -34.3856679763 -467.841014014 + E_Fermi -0.420929168861 -5.72703515091 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.0011094118274 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131709361222 + + Density error is 0.0972864507449 + + Energy Rydberg eV + E_KohnSham -34.2778322336 -466.373833465 + E_Harris -34.2843730188 -466.462825413 + E_Fermi -0.228945191948 -3.11495914019 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.00103392981122 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126597528178 + + Density error is 0.0619044170121 + + Energy Rydberg eV + E_KohnSham -34.2779444436 -466.37536016 + E_Harris -34.2820780074 -466.431600181 + E_Fermi -0.213140191951 -2.89992108335 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000911039245291 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119451234296 + + Density error is 0.00208730214372 + + Energy Rydberg eV + E_KohnSham -34.2780133962 -466.376298308 + E_Harris -34.2780164577 -466.376339963 + E_Fermi -0.177696268606 -2.41768176637 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000909472354379 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119831275294 + + Density error is 0.000886788122365 + + Energy Rydberg eV + E_KohnSham -34.2779378699 -466.37527072 + E_Harris -34.2779408667 -466.375311494 + E_Fermi -0.176187799952 -2.39715799742 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000908464465731 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119668545374 + + Density error is 0.000176006418174 + + Energy Rydberg eV + E_KohnSham -34.2779956084 -466.376056293 + E_Harris -34.2779957253 -466.376057883 + E_Fermi -0.176686593527 -2.40394443217 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000908353669033 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119684248393 + + Density error is 4.14716141064e-05 + + Energy Rydberg eV + E_KohnSham -34.2779736397 -466.375757394 + E_Harris -34.2779736484 -466.375757512 + E_Fermi -0.176477028077 -2.40109314795 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000908354938552 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119678704533 + + Density error is 1.45840156015e-05 + + Energy Rydberg eV + E_KohnSham -34.2779786303 -466.375825294 + E_Harris -34.277978631 -466.375825304 + E_Fermi -0.176528926985 -2.40179926882 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000908333976121 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119678566036 + + Density error is 2.30297580718e-06 + + Energy Rydberg eV + E_KohnSham -34.277977388 -466.375808392 + E_Harris -34.277977388 -466.375808392 + E_Fermi -0.176513821749 -2.40159375154 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000908332128318 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119678441087 + + Density error is 2.32592417764e-07 + + Energy Rydberg eV + E_KohnSham -34.2779775255 -466.375810263 + E_Harris -34.2779775255 -466.375810263 + E_Fermi -0.176511391567 -2.40156068722 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000908332587837 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119678516474 + + Density error is 1.01988436604e-07 + + Energy Rydberg eV + E_KohnSham -34.2779775641 -466.375810788 + E_Harris -34.2779775641 -466.375810788 + E_Fermi -0.176511361588 -2.40156027933 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 337 + sender_size = 337 + last sender_buffer = 0.000908332660578 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119678538624 + + Density error is 9.33809725411e-09 + + Energy Rydberg eV + E_KohnSham -34.277977565 -466.3758108 + E_Harris -34.277977565 -466.3758108 + E_band -8.04615620714 -109.473571415 + E_one_elec -69.8409523046 -950.234905088 + E_Hartree +36.3032563444 +493.931142238 + E_xc -8.25221153392 -112.277097963 + E_Ewald +7.63514548883 +103.881483707 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195793983779 -2.66391381352 + E_Fermi -0.176511280376 -2.40155917438 + + charge density convergence is achieved + final etot is -466.3758108 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5064 2.00000 + 2 -13.4275 2.00000 + 3 -9.01030 2.00000 + 4 -6.79264 2.00000 + 5 1.54005 0.00000 + 6 4.82675 0.00000 + 7 11.0122 0.00000 + 8 11.2436 0.00000 + + EFERMI = -2.401559174382771 eV + OUT.ABACUS/ final etot is -466.3758107995271 eV + correction force for each atom along direction 1 is 0.000104408 + correction force for each atom along direction 2 is -6.34063e-05 + correction force for each atom along direction 3 is -0.000190249 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.64595929 -0.12379337 +2.0224074 + H1 -0.19370415 -0.92973714 -0.43187288 + H2 -0.45225515 +1.0535305 -1.5905345 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3758107995271 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4034 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3940 1 7.4 1.e+02% + Potential init_pot 0.28293 2 0.14 3.8% + PW_Basis recip2real 0.29515 17 0.017 4.0% + PW_Basis gathers_scatterp 0.13484 17 0.0079 1.8% + Potential v_of_rho 1.0483 14 0.075 14.% + XC_Functional v_xc 0.29877 15 0.020 4.0% + H_Hartree_pw v_hartree 0.70429 14 0.050 9.5% + PW_Basis real2recip 0.74462 41 0.018 10.% + PW_Basis gatherp_scatters 0.28265 41 0.0069 3.8% + ORB_control set_orb_tables 1.0950 1 1.1 15.% + ORB_gen_tables gen_tables 1.0950 1 1.1 15.% + ORB_table_phi init_Table 0.47508 1 0.48 6.4% + ORB_table_phi cal_ST_Phi12_R 0.46984 126 0.0037 6.3% + ORB_table_beta init_Table_Beta 0.18281 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18130 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24895 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24697 66 0.0037 3.3% + LOOP_ions opt_ions 5.7666 1 5.8 78.% + ESolver_KS_LCAO Run 5.2318 1 5.2 71.% + HSolverLCAO solve 2.6024 12 0.22 35.% + HamiltLCAO updateHk 1.3575 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.3279 12 0.11 18.% + Gint_interface cal_gint 2.3728 25 0.095 32.% + Gint_Gamma distri_vl 2.7397 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.6111 14 0.40 76.% + LCAO_gen_fixedH add_v_delta 2.5901 6 0.43 35.% + LCAO_DESCRIPTOR add_v_delta 2.5901 6 0.43 35.% + ElecStateLCAO psiToRho 1.2231 12 0.10 17.% + Charge mix_rho 0.98464 11 0.090 13.% + LOOP_ions force_stress 0.53459 1 0.53 7.2% + Force_Stress_LCAO getForceStress 0.53456 1 0.53 7.2% + Force_LCAO_gamma ftable_gamma 0.31819 1 0.32 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.30990 1 0.31 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:53 2022 + Finish Time : Wed Sep 28 11:03:00 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d730ac90d73c6f348344841ee76a95d7bd987f2d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012407 ima = 3.65755e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122940900991 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112423783747 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112743683455 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113014532205 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112937158876 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112984641666 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112975078403 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112977684697 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112977238831 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112977142655 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112977135973 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112977131896 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/STRU new file mode 100644 index 0000000000000000000000000000000000000000..a28fa15093f33693be57070a1165d84960c1c8a8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.628279036057 17.593109646794 1.384055040894 0 0 0 +H +0.0 +2 +-11.896290224130 15.895023269004 0.840167775606 0 0 0 +-12.007906676013 18.647916846880 0.008124039946 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/conv new file mode 100644 index 0000000000000000000000000000000000000000..7bbdf7d5ef190d8e4ef9ae3631ef4321d2489ddf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/conv @@ -0,0 +1 @@ +68 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..492182fde3c29ffa8aa89a48b56cc6014480ca71 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746743105 0.01279273379 1.297821213 1.383982112 1.470486727 0.008300447902 0.01997946642 0.03896015261 +-3.160792365e-18 0.001238671243 0.002637386647 0.01305950089 0.04667186475 -9.380889891e-20 2.03343307e-06 5.940798015e-06 +0.001714809746 0.005808955309 + +H atom_index 1 n_descriptor 18 +1.266764785 0.03331076366 0.1147046062 0.1583165561 0.3266206225 0.0229613248 0.02932987035 0.03655612013 +1.24296239e-17 4.833512059e-05 0.1069286019 0.1163419461 0.1361549196 6.639483104e-19 3.422218929e-06 0.01305184825 +0.02728726615 0.03155502568 + +H atom_index 2 n_descriptor 18 +1.289207462 0.03257605345 0.1231522219 0.1695756895 0.3329933028 0.02395196287 0.03060788962 0.03619838529 +3.690012811e-17 5.042075968e-05 0.1083999076 0.1212678068 0.1457234244 -4.54350313e-18 2.188053176e-06 0.01333650565 +0.02802406986 0.03242050329 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..28f0936772d64826476d581675173f694346f0c7 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:53 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0994747 SEC) : SETUP UNITCELL + DONE(0.110076 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.128211 SEC) : INIT PLANEWAVE + DONE(0.171412 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.453664 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651541e+02 0.000000e+00 2.176e-01 5.332e-01 + GE2 -4.663738e+02 -1.219776e+00 9.729e-02 4.941e-01 + GE3 -4.663754e+02 -1.526695e-03 6.190e-02 5.661e-01 + GE4 -4.663763e+02 -9.381479e-04 2.087e-03 4.221e-01 + GE5 -4.663753e+02 1.027588e-03 8.868e-04 4.221e-01 + GE6 -4.663761e+02 -7.855729e-04 1.760e-04 4.031e-01 + GE7 -4.663758e+02 2.988990e-04 4.147e-05 4.089e-01 + GE8 -4.663758e+02 -6.790049e-05 1.458e-05 3.982e-01 + GE9 -4.663758e+02 1.690287e-05 2.303e-06 3.991e-01 + GE10 -4.663758e+02 -1.871046e-06 2.326e-07 3.977e-01 + GE11 -4.663758e+02 -5.253948e-07 1.020e-07 3.976e-01 + GE12 -4.663758e+02 -1.154736e-08 9.338e-09 3.269e-01 +E_delta_band = -7.25784241e-02 Ry = -9.87480120e-01 eV +E_delta_NN= -1.95793984e-01 Ry = -2.66391381e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4034 11 0.67 1e+02 % + Run_lcao lcao_line 7.394 1 7.4 1e+02 % + Potential init_pot 0.28293 2 0.14 3.8 % + PW_Basis recip2real 0.29515 17 0.017 4 % + PW_Basis gathers_scatterp 0.13484 17 0.0079 1.8 % + Potential v_of_rho 1.0483 14 0.075 14 % + XC_Functional v_xc 0.29877 15 0.02 4 % + H_Hartree_pw v_hartree 0.70429 14 0.05 9.5 % + PW_Basis real2recip 0.74462 41 0.018 10 % + PW_Basis gatherp_scatters 0.28265 41 0.0069 3.8 % + ORB_control set_orb_tables 1.095 1 1.1 15 % + ORB_gen_tables gen_tables 1.095 1 1.1 15 % + ORB_table_phi init_Table 0.47508 1 0.48 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.46984 126 0.0037 6.3 % + ORB_table_beta init_Table_Beta 0.18281 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.1813 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24895 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.24697 66 0.0037 3.3 % + LOOP_ions opt_ions 5.7666 1 5.8 78 % + ESolver_KS_LCAO Run 5.2318 1 5.2 71 % + HSolverLCAO solve 2.6024 12 0.22 35 % + HamiltLCAO updateHk 1.3575 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.3279 12 0.11 18 % + Gint_interface cal_gint 2.3728 25 0.095 32 % + Gint_Gamma distri_vl 2.7397 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.6111 14 0.4 76 % + LCAO_gen_fixedH add_v_delta 2.5901 6 0.43 35 % + LCAO_DESCRIPTOR add_v_delta 2.5901 6 0.43 35 % + ElecStateLCAO psiToRho 1.2231 12 0.1 17 % + Charge mix_rho 0.98464 11 0.09 13 % + LOOP_ions force_stress 0.53459 1 0.53 7.2 % + Force_Stress_LCAO getForceStress 0.53456 1 0.53 7.2 % + Force_LCAO_gamma ftable_gamma 0.31819 1 0.32 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.3099 1 0.31 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:53 2022 + FINISH Time : Wed Sep 28 11:03:00 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/68/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..8687dd57d63e4f9bfdfcf189761ce33c79eb4f1c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.590219 0.611565 0.0384377 +H 0.610061 0.547715 0.0434492 +H 0.61284 0.628724 0.977421 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b4377a57a316b13927ad3b73448de231d4f61c06 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0471 2 + 2 -12.7184 2 + 3 -9.17535 2 + 4 -6.69314 2 + 5 1.0582 0 + 6 3.99424 0 + 7 11.138 0 + 8 11.3971 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..487f44c57952c8c407ecf86f1bad53a13352af56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:11 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.526143996 17.1238241941 1.07625513466 0 0 0 0 + tauc_H1 17.0817096004 15.3360065801 1.21657843819 0 0 0 0 + tauc_H2 17.1595254857 17.604268078 27.3677830861 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0729813347886 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0837035027311 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0993724894635 (SEC) + + DONE : INIT CHARGE Time : 0.140703542936 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.387183 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 81 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000614 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000917 + + Density error is 0.210739595456 + + Energy Rydberg eV + E_KohnSham -34.1932973833 -465.223677821 + E_Harris -34.3762737425 -467.713198905 + E_Fermi -0.388188174908 -5.28157107496 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000865600893491 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116605336159 + + Density error is 0.0983793035746 + + Energy Rydberg eV + E_KohnSham -34.2799539736 -466.402701218 + E_Harris -34.2869711062 -466.498174206 + E_Fermi -0.200371957804 -2.72620034555 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00082990332906 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111664427754 + + Density error is 0.0633994989096 + + Energy Rydberg eV + E_KohnSham -34.2802448933 -466.406659385 + E_Harris -34.2847608727 -466.468102436 + E_Fermi -0.192572812977 -2.62008753638 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000785368565248 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010588516046 + + Density error is 0.00194859503203 + + Energy Rydberg eV + E_KohnSham -34.2801625669 -466.405539276 + E_Harris -34.2801639105 -466.405557557 + E_Fermi -0.157355869247 -2.1409364355 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000784908768343 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105983763826 + + Density error is 0.000824293604103 + + Energy Rydberg eV + E_KohnSham -34.2801356295 -466.405172774 + E_Harris -34.280135857 -466.405175869 + E_Fermi -0.157216792193 -2.13904419511 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0007844467542 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105915125505 + + Density error is 0.000159321335551 + + Energy Rydberg eV + E_KohnSham -34.2801483411 -466.405345725 + E_Harris -34.280148341 -466.405345723 + E_Fermi -0.156832558532 -2.13381642795 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000784566996941 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105929380429 + + Density error is 2.44264141094e-05 + + Energy Rydberg eV + E_KohnSham -34.2801452177 -466.405303228 + E_Harris -34.2801452191 -466.405303247 + E_Fermi -0.156804419997 -2.13343358355 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000784520139066 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105923670881 + + Density error is 1.09821568108e-05 + + Energy Rydberg eV + E_KohnSham -34.2801472228 -466.405330508 + E_Harris -34.2801472233 -466.405330516 + E_Fermi -0.156816597534 -2.13359926744 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000784524123527 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105924315025 + + Density error is 1.95700361402e-06 + + Energy Rydberg eV + E_KohnSham -34.2801463667 -466.405318861 + E_Harris -34.2801463667 -466.405318861 + E_Fermi -0.156806359269 -2.1334599687 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000784523359988 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105924014374 + + Density error is 4.59373275863e-07 + + Energy Rydberg eV + E_KohnSham -34.2801465561 -466.405321438 + E_Harris -34.2801465561 -466.405321438 + E_Fermi -0.15680484511 -2.1334393675 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00078452405267 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105924099978 + + Density error is 1.32578941797e-07 + + Energy Rydberg eV + E_KohnSham -34.2801465635 -466.405321538 + E_Harris -34.2801465635 -466.405321538 + E_Fermi -0.156804581092 -2.13343577536 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000784524275631 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105924123017 + + Density error is 1.19205444257e-08 + + Energy Rydberg eV + E_KohnSham -34.2801465689 -466.405321612 + E_Harris -34.2801465689 -466.405321612 + E_band -7.88405544742 -107.268077433 + E_one_elec -68.7264142529 -935.070836947 + E_Hartree +35.7703562276 +486.680664185 + E_xc -8.16630635908 -111.108298097 + E_Ewald +6.967691187 +94.8003020476 + E_demet -2.02517504953e-62 -2.75539201211e-61 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193820543739 -2.63706378431 + E_Fermi -0.156804471776 -2.13343428804 + + charge density convergence is achieved + final etot is -466.405321612 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0471 2.00000 + 2 -12.7184 2.00000 + 3 -9.17535 2.00000 + 4 -6.69314 2.00000 + 5 1.05820 0.00000 + 6 3.99424 0.00000 + 7 11.1380 0.00000 + 8 11.3971 0.00000 + + EFERMI = -2.133434288036075 eV + OUT.ABACUS/ final etot is -466.4053216118169 eV + correction force for each atom along direction 1 is 0.000134485 + correction force for each atom along direction 2 is -0.000121076 + correction force for each atom along direction 3 is -3.00369e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.61201405 -0.57296467 -0.87365450 + H1 -0.26493278 +0.72815304 +0.021495358 + H2 -0.34708128 -0.15518837 +0.85215914 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4053216118169 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6561 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6484 1 6.6 1.e+02% + Potential init_pot 0.24497 2 0.12 3.7% + PW_Basis recip2real 0.28521 17 0.017 4.3% + PW_Basis gathers_scatterp 0.11544 17 0.0068 1.7% + Potential v_of_rho 0.99865 14 0.071 15.% + XC_Functional v_xc 0.28374 15 0.019 4.3% + H_Hartree_pw v_hartree 0.67291 14 0.048 10.% + PW_Basis real2recip 0.65523 41 0.016 9.8% + PW_Basis gatherp_scatters 0.24818 41 0.0061 3.7% + ORB_control set_orb_tables 0.89559 1 0.90 13.% + ORB_gen_tables gen_tables 0.89558 1 0.90 13.% + ORB_table_phi init_Table 0.37380 1 0.37 5.6% + ORB_table_phi cal_ST_Phi12_R 0.36961 126 0.0029 5.6% + ORB_table_beta init_Table_Beta 0.15487 1 0.15 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15359 56 0.0027 2.3% + ORB_table_alpha init_Table_Alpha 0.20855 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20687 66 0.0031 3.1% + LOOP_ions opt_ions 5.2963 1 5.3 80.% + ESolver_KS_LCAO Run 4.7708 1 4.8 72.% + HSolverLCAO solve 2.3939 12 0.20 36.% + HamiltLCAO updateHk 1.2419 12 0.10 19.% + LCAO_Hamilt cal_Hgamma 1.2064 12 0.10 18.% + Gint_interface cal_gint 2.2424 25 0.090 34.% + Gint_Gamma distri_vl 2.4855 6 0.41 37.% + LCAO_Deepks cal_projected_DM 5.1552 14 0.37 77.% + LCAO_gen_fixedH add_v_delta 2.3560 6 0.39 35.% + LCAO_DESCRIPTOR add_v_delta 2.3560 6 0.39 35.% + ElecStateLCAO psiToRho 1.1337 12 0.094 17.% + Charge mix_rho 0.83725 11 0.076 13.% + LOOP_ions force_stress 0.52536 1 0.53 7.9% + Force_Stress_LCAO getForceStress 0.52534 1 0.53 7.9% + Force_LCAO_gamma ftable_gamma 0.32799 1 0.33 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.32045 1 0.32 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:11 2022 + Finish Time : Wed Sep 28 11:10:18 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..7df6dd9b93a39ca8521aa8976d00b55c5f3f3687 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123583 ima = 3.69252e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123190429134 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112010011321 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112714186654 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112902562356 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112889550461 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112897879474 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112894778607 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112896409308 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112895871429 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112895836415 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112895816612 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112895810872 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0af95e6dcf956a3f35d2470fa7be86258931193c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.473856004011 17.123824194066 1.076255134664 0 0 0 +H +0.0 +2 +-10.918290399647 15.336006580085 1.216578438215 0 0 0 +-10.840474514250 17.604268077992 -0.632216913911 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/conv new file mode 100644 index 0000000000000000000000000000000000000000..0a9433e632435a99fc3a53ca8fe4415c326dfcd3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/conv @@ -0,0 +1 @@ +69 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..447e89de43e33c247eac2ba15f7cef6d0ffd52b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751188582 0.01250368464 1.249794603 1.338715294 1.468272261 0.008651396235 0.01750520664 0.03911507305 +-2.027948218e-18 0.0008878913036 0.002486428396 0.01179750475 0.04257276089 -3.741916937e-19 1.845243263e-06 5.489338547e-06 +0.001599490072 0.005948377682 + +H atom_index 1 n_descriptor 18 +1.212648554 0.03571425946 0.09584309077 0.1334304431 0.3082985478 0.02046603301 0.02611731141 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:11 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0729966 SEC) : SETUP UNITCELL + DONE(0.0837163 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0993848 SEC) : INIT PLANEWAVE + DONE(0.14081 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.387226 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652237e+02 0.000000e+00 2.107e-01 4.809e-01 + GE2 -4.664027e+02 -1.179023e+00 9.838e-02 4.431e-01 + GE3 -4.664067e+02 -3.958167e-03 6.340e-02 5.073e-01 + GE4 -4.664055e+02 1.120109e-03 1.949e-03 3.871e-01 + GE5 -4.664052e+02 3.665022e-04 8.243e-04 3.858e-01 + GE6 -4.664053e+02 -1.729507e-04 1.593e-04 3.828e-01 + GE7 -4.664053e+02 4.249722e-05 2.443e-05 3.687e-01 + GE8 -4.664053e+02 -2.728079e-05 1.098e-05 3.645e-01 + GE9 -4.664053e+02 1.164763e-05 1.957e-06 3.642e-01 + GE10 -4.664053e+02 -2.577322e-06 4.594e-07 3.691e-01 + GE11 -4.664053e+02 -1.003303e-07 1.326e-07 3.667e-01 + GE12 -4.664053e+02 -7.350466e-08 1.192e-08 2.968e-01 +E_delta_band = -6.83471722e-02 Ry = -9.29910984e-01 eV +E_delta_NN= -1.93820544e-01 Ry = -2.63706378e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6561 11 0.61 1e+02 % + Run_lcao lcao_line 6.6484 1 6.6 1e+02 % + Potential init_pot 0.24497 2 0.12 3.7 % + PW_Basis recip2real 0.28521 17 0.017 4.3 % + PW_Basis gathers_scatterp 0.11544 17 0.0068 1.7 % + Potential v_of_rho 0.99865 14 0.071 15 % + XC_Functional v_xc 0.28374 15 0.019 4.3 % + H_Hartree_pw v_hartree 0.67291 14 0.048 10 % + PW_Basis real2recip 0.65523 41 0.016 9.8 % + PW_Basis gatherp_scatters 0.24818 41 0.0061 3.7 % + ORB_control set_orb_tables 0.89559 1 0.9 13 % + ORB_gen_tables gen_tables 0.89558 1 0.9 13 % + ORB_table_phi init_Table 0.3738 1 0.37 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.36961 126 0.0029 5.6 % + ORB_table_beta init_Table_Beta 0.15487 1 0.15 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15359 56 0.0027 2.3 % + ORB_table_alpha init_Table_Alpha 0.20855 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20687 66 0.0031 3.1 % + LOOP_ions opt_ions 5.2963 1 5.3 80 % + ESolver_KS_LCAO Run 4.7708 1 4.8 72 % + HSolverLCAO solve 2.3939 12 0.2 36 % + HamiltLCAO updateHk 1.2419 12 0.1 19 % + LCAO_Hamilt cal_Hgamma 1.2064 12 0.1 18 % + Gint_interface cal_gint 2.2424 25 0.09 34 % + Gint_Gamma distri_vl 2.4855 6 0.41 37 % + LCAO_Deepks cal_projected_DM 5.1552 14 0.37 77 % + LCAO_gen_fixedH add_v_delta 2.356 6 0.39 35 % + LCAO_DESCRIPTOR add_v_delta 2.356 6 0.39 35 % + ElecStateLCAO psiToRho 1.1337 12 0.094 17 % + Charge mix_rho 0.83725 11 0.076 13 % + LOOP_ions force_stress 0.52536 1 0.53 7.9 % + Force_Stress_LCAO getForceStress 0.52534 1 0.53 7.9 % + Force_LCAO_gamma ftable_gamma 0.32799 1 0.33 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.32045 1 0.32 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:11 2022 + FINISH Time : Wed Sep 28 11:10:18 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/69/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..6ae877417e4e241a56481b288dcdec5928734759 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.517825 0.696471 0.282339 +H 0.568263 0.734958 0.284199 +H 0.480078 0.720205 0.236306 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f1179aee0e0d1770ec1b52d51439e9ff8420c434 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5629 2 + 2 -13.3576 2 + 3 -9.10262 2 + 4 -6.80534 2 + 5 1.55007 0 + 6 4.84601 0 + 7 11.0042 0 + 8 11.2452 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3406bf33d0bade63db00738f3f794a793ef7b594 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.4990899626 19.5011773885 7.90548820674 0 0 0 0 + tauc_H1 15.9113720153 20.5788236165 7.95756318433 0 0 0 0 + tauc_H2 13.4421740619 20.1657379649 6.61655639386 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0734986790783 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.073817013297 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0896539018693 (SEC) + + DONE : INIT CHARGE Time : 0.132136229863 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375418 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 144 81 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00155 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116 + + Density error is 0.218700400283 + + Energy Rydberg eV + E_KohnSham -34.185699044 -465.120297112 + E_Harris -34.3856928295 -467.841352159 + E_Fermi -0.42342838351 -5.76103871066 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00142007020811 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119517449703 + + Density error is 0.0973932671639 + + Energy Rydberg eV + E_KohnSham -34.2776164927 -466.37089816 + E_Harris -34.2842032933 -466.460516179 + E_Fermi -0.229649174714 -3.12453731711 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00131187282831 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112097128521 + + Density error is 0.0621188645923 + + Energy Rydberg eV + E_KohnSham -34.2779052822 -466.374827342 + E_Harris -34.2821055775 -466.431975291 + E_Fermi -0.214866515103 -2.9234089148 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011314727345 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100048902163 + + Density error is 0.00207838514558 + + Energy Rydberg eV + E_KohnSham -34.2779605818 -466.375579732 + E_Harris -34.2779629685 -466.375612205 + E_Fermi -0.179090800971 -2.43665535259 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112955625261 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010001459636 + + Density error is 0.00093645281427 + + Energy Rydberg eV + E_KohnSham -34.2778776683 -466.374451636 + E_Harris -34.2778807327 -466.37449333 + E_Fermi -0.177740773923 -2.41828729229 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011280060848 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998777904763 + + Density error is 0.000121675929716 + + Energy Rydberg eV + E_KohnSham -34.2779345587 -466.37522567 + E_Harris -34.2779345929 -466.375226135 + E_Fermi -0.178116067591 -2.4233934246 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112772807321 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998642905667 + + Density error is 4.98322666039e-05 + + Energy Rydberg eV + E_KohnSham -34.2779152111 -466.374962432 + E_Harris -34.2779152244 -466.374962613 + E_Fermi -0.177951539159 -2.42115490044 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112775197968 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00099862610935 + + Density error is 1.21040728955e-05 + + Energy Rydberg eV + E_KohnSham -34.2779188704 -466.375012219 + E_Harris -34.277918871 -466.375012227 + E_Fermi -0.178011414993 -2.42196955294 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112772863272 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998613459392 + + Density error is 1.08402870036e-06 + + Energy Rydberg eV + E_KohnSham -34.277917453 -466.374992935 + E_Harris -34.277917453 -466.374992935 + E_Fermi -0.177997809539 -2.42178444125 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112772723181 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00099861411919 + + Density error is 1.49761219007e-07 + + Energy Rydberg eV + E_KohnSham -34.2779176339 -466.374995396 + E_Harris -34.2779176339 -466.374995396 + E_Fermi -0.177996809412 -2.42177083383 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00112772774055 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000998614506988 + + Density error is 3.59313866438e-08 + + Energy Rydberg eV + E_KohnSham -34.277917655 -466.374995683 + E_Harris -34.277917655 -466.374995683 + E_band -8.05962798103 -109.656864302 + E_one_elec -69.8893278242 -950.893087799 + E_Hartree +36.3228457569 +494.197669869 + E_xc -8.25545499868 -112.321227565 + E_Ewald +7.6671209405 +104.316532046 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195921260835 -2.6656455067 + E_Fermi -0.177996928454 -2.42177245347 + + charge density convergence is achieved + final etot is -466.374995683 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5629 2.00000 + 2 -13.3576 2.00000 + 3 -9.10262 2.00000 + 4 -6.80534 2.00000 + 5 1.55007 0.00000 + 6 4.84601 0.00000 + 7 11.0042 0.00000 + 8 11.2452 0.00000 + + EFERMI = -2.421772453472122 eV + OUT.ABACUS/ final etot is -466.3749956831992 eV + correction force for each atom along direction 1 is -4.70385e-05 + correction force for each atom along direction 2 is -1.27566e-05 + correction force for each atom along direction 3 is -0.000119844 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.72945115 -1.6611420 +0.90664653 + H1 +1.5293997 +1.1624746 +0.062822812 + H2 -0.79994856 +0.49866741 -0.96946934 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3749956831992 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5636 11 0.51 1.0e+02% + Run_lcao lcao_line 5.5563 1 5.6 1.e+02% + Potential init_pot 0.24064 2 0.12 4.3% + PW_Basis recip2real 0.24427 16 0.015 4.4% + PW_Basis gathers_scatterp 0.10744 16 0.0067 1.9% + Potential v_of_rho 0.88539 13 0.068 16.% + XC_Functional v_xc 0.26543 14 0.019 4.8% + H_Hartree_pw v_hartree 0.58472 13 0.045 11.% + PW_Basis real2recip 0.58973 38 0.016 11.% + PW_Basis gatherp_scatters 0.21537 38 0.0057 3.9% + ORB_control set_orb_tables 0.89773 1 0.90 16.% + ORB_gen_tables gen_tables 0.89773 1 0.90 16.% + ORB_table_phi init_Table 0.37470 1 0.37 6.7% + ORB_table_phi cal_ST_Phi12_R 0.37039 126 0.0029 6.7% + ORB_table_beta init_Table_Beta 0.15484 1 0.15 2.8% + ORB_table_beta VNL_PhiBeta_R 0.15346 56 0.0027 2.8% + ORB_table_alpha init_Table_Alpha 0.21007 1 0.21 3.8% + ORB_table_alpha S_PhiAlpha_R 0.20839 66 0.0032 3.7% + LOOP_ions opt_ions 4.1998 1 4.2 75.% + ESolver_KS_LCAO Run 3.7619 1 3.8 68.% + HSolverLCAO solve 1.5958 11 0.15 29.% + HamiltLCAO updateHk 0.87923 11 0.080 16.% + LCAO_Hamilt cal_Hgamma 0.85576 11 0.078 15.% + Gint_interface cal_gint 0.97401 23 0.042 18.% + Gint_Gamma distri_vl_value 0.14705 11 0.013 2.6% + Gint_Gamma distri_vl 1.8348 6 0.31 33.% + LCAO_Deepks cal_projected_DM 4.0255 13 0.31 72.% + LCAO_gen_fixedH add_v_delta 1.7068 6 0.28 31.% + LCAO_DESCRIPTOR add_v_delta 1.7068 6 0.28 31.% + ElecStateLCAO psiToRho 0.69646 11 0.063 13.% + Charge mix_rho 0.75455 10 0.075 14.% + LOOP_ions force_stress 0.43772 1 0.44 7.9% + Force_Stress_LCAO getForceStress 0.43769 1 0.44 7.9% + Force_LCAO_gamma ftable_gamma 0.24073 1 0.24 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.18170 1 0.18 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:48 2022 + Finish Time : Wed Sep 28 11:12:53 2022 + Total Time : 0 h 0 mins 5 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b589ae77bfa0efbd5d12b9f7c93282aed14331e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123909 ima = 3.70175e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 2 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122986488533 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112164940396 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112556952383 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112852654888 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773613426 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112818506626 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112812539388 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112815585563 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112815089725 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112815044116 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112815044942 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/STRU new file mode 100644 index 0000000000000000000000000000000000000000..fe6934a8b1755be6f0f76dbac63e22aea7b2491c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.500910037451 19.501177388495 7.905488206733 0 0 0 +H +0.0 +2 +-12.088627984713 20.578823616511 7.957563184324 0 0 0 +-14.557825938133 20.165737964882 6.616556393864 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/conv new file mode 100644 index 0000000000000000000000000000000000000000..63d901d384af02fb48239fcf6a1d6c3f5a2b0e56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/conv @@ -0,0 +1 @@ +7 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..5fa3bf0aa6ba8474ffd326cdfe66e7b0bdfbe718 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748287666 0.01283046175 1.298586987 1.382914193 1.470691566 0.008572911684 0.01949456695 0.03900051107 +-5.144268024e-19 0.001218386061 0.002730328591 0.01320173718 0.04770353025 -9.834449564e-19 2.270667904e-06 6.387795911e-06 +0.001677596823 0.005901895363 + +H atom_index 1 n_descriptor 18 +1.288703525 0.03279269144 0.1231610058 0.168949634 0.3323451079 0.0241574626 0.03053790307 0.03635198201 +-3.5211797e-17 5.32884413e-05 0.1085722781 0.1213683647 0.145201328 -2.716385103e-18 2.082876351e-06 0.01339723743 +0.02818627682 0.03239063854 + +H atom_index 2 n_descriptor 18 +1.275095294 0.03322764047 0.117960468 0.162045837 0.3284903526 0.02354242917 0.02976269781 0.03654557756 +1.366543637e-17 5.197929325e-05 0.1080773013 0.1179762545 0.1393467294 -5.580171059e-18 2.840529701e-06 0.01319234196 +0.02774707907 0.03187383155 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d4c7caeda870b9e78bd390d43e26623c7c562798 Binary files /dev/null and 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0000000000000000000000000000000000000000..863b4012531442e6c666d44804ad97e3f32d5827 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0735141 SEC) : SETUP UNITCELL + DONE(0.0738264 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0896663 SEC) : INIT PLANEWAVE + DONE(0.132245 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.375465 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651203e+02 0.000000e+00 2.187e-01 4.334e-01 + GE2 -4.663709e+02 -1.250601e+00 9.739e-02 3.884e-01 + GE3 -4.663748e+02 -3.929182e-03 6.212e-02 4.511e-01 + GE4 -4.663756e+02 -7.523903e-04 2.078e-03 3.278e-01 + GE5 -4.663745e+02 1.128096e-03 9.365e-04 3.284e-01 + GE6 -4.663752e+02 -7.740338e-04 1.217e-04 3.030e-01 + GE7 -4.663750e+02 2.632376e-04 4.983e-05 3.145e-01 + GE8 -4.663750e+02 -4.978652e-05 1.210e-05 3.048e-01 + GE9 -4.663750e+02 1.928413e-05 1.084e-06 3.087e-01 + GE10 -4.663750e+02 -2.461852e-06 1.498e-07 3.079e-01 + GE11 -4.663750e+02 -2.868356e-07 3.593e-08 2.404e-01 +E_delta_band = -7.28197313e-02 Ry = -9.90763272e-01 eV +E_delta_NN= -1.95921261e-01 Ry = -2.66564551e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.5636 11 0.51 1e+02 % + Run_lcao lcao_line 5.5563 1 5.6 1e+02 % + Potential init_pot 0.24064 2 0.12 4.3 % + PW_Basis recip2real 0.24427 16 0.015 4.4 % + PW_Basis gathers_scatterp 0.10744 16 0.0067 1.9 % + Potential v_of_rho 0.88539 13 0.068 16 % + XC_Functional v_xc 0.26543 14 0.019 4.8 % + H_Hartree_pw v_hartree 0.58472 13 0.045 11 % + PW_Basis real2recip 0.58973 38 0.016 11 % + PW_Basis gatherp_scatters 0.21537 38 0.0057 3.9 % + ORB_control set_orb_tables 0.89773 1 0.9 16 % + ORB_gen_tables gen_tables 0.89773 1 0.9 16 % + ORB_table_phi init_Table 0.3747 1 0.37 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.37039 126 0.0029 6.7 % + ORB_table_beta init_Table_Beta 0.15484 1 0.15 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.15346 56 0.0027 2.8 % + ORB_table_alpha init_Table_Alpha 0.21007 1 0.21 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.20839 66 0.0032 3.7 % + LOOP_ions opt_ions 4.1998 1 4.2 75 % + ESolver_KS_LCAO Run 3.7619 1 3.8 68 % + HSolverLCAO solve 1.5958 11 0.15 29 % + HamiltLCAO updateHk 0.87923 11 0.08 16 % + LCAO_Hamilt cal_Hgamma 0.85576 11 0.078 15 % + Gint_interface cal_gint 0.97401 23 0.042 18 % + Gint_Gamma distri_vl_value 0.14705 11 0.013 2.6 % + Gint_Gamma distri_vl 1.8348 6 0.31 33 % + LCAO_Deepks cal_projected_DM 4.0255 13 0.31 72 % + LCAO_gen_fixedH add_v_delta 1.7068 6 0.28 31 % + LCAO_DESCRIPTOR add_v_delta 1.7068 6 0.28 31 % + ElecStateLCAO psiToRho 0.69646 11 0.063 13 % + Charge mix_rho 0.75455 10 0.075 14 % + LOOP_ions force_stress 0.43772 1 0.44 7.9 % + Force_Stress_LCAO getForceStress 0.43769 1 0.44 7.9 % + Force_LCAO_gamma ftable_gamma 0.24073 1 0.24 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.1817 1 0.18 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:48 2022 + FINISH Time : Wed Sep 28 11:12:53 2022 + TOTAL Time : 5 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/7/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..dccba854c2e263aadc6c036cb1b3a8a02f7c9669 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.577012 0.598589 0.0416874 +H 0.611495 0.568475 0.0881005 +H 0.619983 0.632674 0.00779371 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..470880d426df5b66d57f2cc2ab89c33c062bc02a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3749 2 + 2 -13.2044 2 + 3 -9.06893 2 + 4 -6.7634 2 + 5 1.40285 0 + 6 4.58979 0 + 7 11.0501 0 + 8 11.2942 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1b69d52e780ebf1854605f0e1e88ac2ba1290830 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:26 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.1563326149 16.7604898047 1.16724845924 0 0 0 0 + tauc_H1 17.1218477786 15.9172991073 2.46681450328 0 0 0 0 + tauc_H2 17.359520142 17.7148606723 0.218223982461 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0733962408952 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0736780960813 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0899205006977 (SEC) + + DONE : INIT CHARGE Time : 0.131753056917 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.374487 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 81 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00109 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114 + + Density error is 0.216424315526 + + Energy Rydberg eV + E_KohnSham -34.1896830875 -465.174502804 + E_Harris -34.3846595703 -467.827293946 + E_Fermi -0.412530893052 -5.61277074653 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00132142834902 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108183541588 + + Density error is 0.0978626993735 + + Energy Rydberg eV + E_KohnSham -34.280319357 -466.407672515 + E_Harris -34.2869797544 -466.49829187 + E_Fermi -0.219530329949 -2.98686337113 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00125010692464 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001014378712 + + Density error is 0.0626706126966 + + Energy Rydberg eV + E_KohnSham -34.2806006111 -466.411499173 + E_Harris -34.2848937184 -466.469909894 + E_Fermi -0.207096966257 -2.81769877961 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113801597502 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000910516187863 + + Density error is 0.00202794230152 + + Energy Rydberg eV + E_KohnSham -34.2806131114 -466.411669249 + E_Harris -34.2806147001 -466.411690864 + E_Fermi -0.171499533905 -2.33337086545 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113880979087 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000911213547619 + + Density error is 0.000914146626708 + + Energy Rydberg eV + E_KohnSham -34.2805440446 -466.410729547 + E_Harris -34.2805457658 -466.410752965 + E_Fermi -0.170554086289 -2.32050739071 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113723314791 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909883582404 + + Density error is 0.000152855416943 + + Energy Rydberg eV + E_KohnSham -34.2805891193 -466.411342819 + E_Harris -34.2805891733 -466.411343554 + E_Fermi -0.17068532268 -2.32229295341 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113729815218 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909922043454 + + Density error is 4.19879100614e-05 + + Energy Rydberg eV + E_KohnSham -34.2805727409 -466.41111998 + E_Harris -34.2805727509 -466.411120116 + E_Fermi -0.170534896146 -2.32024629542 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113724438203 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909905553814 + + Density error is 1.7010103131e-05 + + Energy Rydberg eV + E_KohnSham -34.280577141 -466.411179846 + E_Harris -34.2805771422 -466.411179862 + E_Fermi -0.170585821214 -2.32093916652 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113723033414 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909895530689 + + Density error is 1.45132061418e-06 + + Energy Rydberg eV + E_KohnSham -34.2805756284 -466.411159266 + E_Harris -34.2805756284 -466.411159266 + E_Fermi -0.170566908534 -2.3206818463 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113722994516 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909893420302 + + Density error is 2.12690470331e-07 + + Energy Rydberg eV + E_KohnSham -34.2805758798 -466.411162686 + E_Harris -34.2805758798 -466.411162686 + E_Fermi -0.170565809856 -2.32066689803 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00113723069317 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000909893843634 + + Density error is 5.49931066987e-08 + + Energy Rydberg eV + E_KohnSham -34.2805759 -466.411162962 + E_Harris -34.2805759 -466.411162962 + E_band -7.99836216033 -108.823300048 + E_one_elec -69.5140377961 -945.787005015 + E_Hartree +36.146964506 +491.804682685 + E_xc -8.22685879386 -111.932156238 + E_Ewald +7.4372321086 +101.188734025 + E_demet -5.42176374003e-84 -7.37668800742e-83 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195191832567 -2.65572112598 + E_Fermi -0.170565762142 -2.32066624884 + + charge density convergence is achieved + final etot is -466.411162962 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3749 2.00000 + 2 -13.2044 2.00000 + 3 -9.06893 2.00000 + 4 -6.76340 2.00000 + 5 1.40285 0.00000 + 6 4.58979 0.00000 + 7 11.0501 0.00000 + 8 11.2942 0.00000 + + EFERMI = -2.320666248843331 eV + OUT.ABACUS/ final etot is -466.4111629616054 eV + correction force for each atom along direction 1 is 0.000145341 + correction force for each atom along direction 2 is 8.02890e-05 + correction force for each atom along direction 3 is -4.29086e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.0038790 -0.34366386 +0.21325716 + H1 +0.27626634 -0.18535856 +0.29946152 + H2 +0.72761267 +0.52902242 -0.51271868 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4111629616054 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4195 11 0.58 1.0e+02% + Run_lcao lcao_line 6.4117 1 6.4 1.e+02% + Potential init_pot 0.24327 2 0.12 3.8% + PW_Basis recip2real 0.26382 16 0.016 4.1% + PW_Basis gathers_scatterp 0.10622 16 0.0066 1.7% + Potential v_of_rho 0.92832 13 0.071 14.% + XC_Functional v_xc 0.28254 14 0.020 4.4% + H_Hartree_pw v_hartree 0.60777 13 0.047 9.5% + PW_Basis real2recip 0.59867 38 0.016 9.3% + PW_Basis gatherp_scatters 0.22406 38 0.0059 3.5% + ORB_control set_orb_tables 0.89621 1 0.90 14.% + ORB_gen_tables gen_tables 0.89621 1 0.90 14.% + ORB_table_phi init_Table 0.37536 1 0.38 5.8% + ORB_table_phi cal_ST_Phi12_R 0.37117 126 0.0029 5.8% + ORB_table_beta init_Table_Beta 0.15531 1 0.16 2.4% + ORB_table_beta VNL_PhiBeta_R 0.15395 56 0.0027 2.4% + ORB_table_alpha init_Table_Alpha 0.20794 1 0.21 3.2% + ORB_table_alpha S_PhiAlpha_R 0.20630 66 0.0031 3.2% + LOOP_ions opt_ions 5.0716 1 5.1 79.% + ESolver_KS_LCAO Run 4.5331 1 4.5 71.% + HSolverLCAO solve 2.3533 11 0.21 37.% + HamiltLCAO updateHk 1.2165 11 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.1847 11 0.11 18.% + Gint_interface cal_gint 2.2315 23 0.097 35.% + Gint_Gamma distri_vl 2.1790 6 0.36 34.% + LCAO_Deepks cal_projected_DM 4.9281 13 0.38 77.% + LCAO_gen_fixedH add_v_delta 2.0495 6 0.34 32.% + LCAO_DESCRIPTOR add_v_delta 2.0494 6 0.34 32.% + ElecStateLCAO psiToRho 1.1212 11 0.10 17.% + Charge mix_rho 0.76084 10 0.076 12.% + LOOP_ions force_stress 0.53833 1 0.54 8.4% + Force_Stress_LCAO getForceStress 0.53830 1 0.54 8.4% + Force_LCAO_gamma ftable_gamma 0.34276 1 0.34 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.33550 1 0.34 5.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:26 2022 + Finish Time : Wed Sep 28 11:06:33 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..66d111aed94afff0dd670df96ee4700cde8db929 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123842 ima = 3.68361e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123110556854 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112107595159 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112594932802 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112856383478 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112794918667 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112831330526 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112823590119 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112826678824 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112825980075 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112825925181 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112825915282 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5da2d981835e1453c429017d9d340118fde7aa01 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.843667385078 16.760489804692 1.167248459219 0 0 0 +H +0.0 +2 +-10.878152221431 15.917299107337 2.466814503275 0 0 0 +-10.640479857987 17.714860672292 0.218223982471 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/conv new file mode 100644 index 0000000000000000000000000000000000000000..4b6b5a4989de547e681637a526b61711e1261860 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/conv @@ -0,0 +1 @@ +70 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..0120a965d99387b8870ed97000163c08cbcb2021 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748086165 0.01273786685 1.283353985 1.371019818 1.469737241 0.008384380386 0.01914406313 0.03898721116 +-1.603136346e-18 0.001128639969 0.00261095887 0.0126655753 0.04571129548 -1.408288373e-20 2.034057945e-06 5.915268484e-06 +0.001679386282 0.005906305374 + +H atom_index 1 n_descriptor 18 +1.250697195 0.03406741006 0.1086689331 0.1504973886 0.3215306879 0.02224226111 0.02838002647 0.03721123223 +-1.371361991e-17 4.605103075e-05 0.1026506306 0.1149059708 0.1292876896 8.469295519e-18 4.19578063e-06 0.01311539054 +0.02647213614 0.03082858049 + +H atom_index 2 n_descriptor 18 +1.266640579 0.03351861029 0.1143317861 0.1580805251 0.3264616895 0.02296923099 0.02930172639 0.03678137701 +-4.653426214e-17 4.752778205e-05 0.1059160409 0.1162196571 0.1358040862 1.232445445e-17 3.314069311e-06 0.01309267493 +0.02704246731 0.03151720686 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ff0a9776be8407b9fb7f4d711c86f6501de42686 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:26 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0734112 SEC) : SETUP UNITCELL + DONE(0.0736865 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0899333 SEC) : INIT PLANEWAVE + DONE(0.131858 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.374533 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651745e+02 0.000000e+00 2.164e-01 4.909e-01 + GE2 -4.664077e+02 -1.233170e+00 9.786e-02 4.611e-01 + GE3 -4.664115e+02 -3.826658e-03 6.267e-02 5.211e-01 + GE4 -4.664117e+02 -1.700764e-04 2.028e-03 3.994e-01 + GE5 -4.664107e+02 9.397021e-04 9.141e-04 3.961e-01 + GE6 -4.664113e+02 -6.132717e-04 1.529e-04 3.855e-01 + GE7 -4.664111e+02 2.228388e-04 4.199e-05 3.845e-01 + GE8 -4.664112e+02 -5.986616e-05 1.701e-05 3.809e-01 + GE9 -4.664112e+02 2.057986e-05 1.451e-06 3.754e-01 + GE10 -4.664112e+02 -3.419799e-06 2.127e-07 3.763e-01 + GE11 -4.664112e+02 -2.756088e-07 5.499e-08 3.089e-01 +E_delta_band = -7.13159080e-02 Ry = -9.70302707e-01 eV +E_delta_NN= -1.95191833e-01 Ry = -2.65572113e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4195 11 0.58 1e+02 % + Run_lcao lcao_line 6.4117 1 6.4 1e+02 % + Potential init_pot 0.24327 2 0.12 3.8 % + PW_Basis recip2real 0.26382 16 0.016 4.1 % + PW_Basis gathers_scatterp 0.10622 16 0.0066 1.7 % + Potential v_of_rho 0.92832 13 0.071 14 % + XC_Functional v_xc 0.28254 14 0.02 4.4 % + H_Hartree_pw v_hartree 0.60777 13 0.047 9.5 % + PW_Basis real2recip 0.59867 38 0.016 9.3 % + PW_Basis gatherp_scatters 0.22406 38 0.0059 3.5 % + ORB_control set_orb_tables 0.89621 1 0.9 14 % + ORB_gen_tables gen_tables 0.89621 1 0.9 14 % + ORB_table_phi init_Table 0.37536 1 0.38 5.8 % + ORB_table_phi cal_ST_Phi12_R 0.37117 126 0.0029 5.8 % + ORB_table_beta init_Table_Beta 0.15531 1 0.16 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.15395 56 0.0027 2.4 % + ORB_table_alpha init_Table_Alpha 0.20794 1 0.21 3.2 % + ORB_table_alpha S_PhiAlpha_R 0.2063 66 0.0031 3.2 % + LOOP_ions opt_ions 5.0716 1 5.1 79 % + ESolver_KS_LCAO Run 4.5331 1 4.5 71 % + HSolverLCAO solve 2.3533 11 0.21 37 % + HamiltLCAO updateHk 1.2165 11 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.1847 11 0.11 18 % + Gint_interface cal_gint 2.2315 23 0.097 35 % + Gint_Gamma distri_vl 2.179 6 0.36 34 % + LCAO_Deepks cal_projected_DM 4.9281 13 0.38 77 % + LCAO_gen_fixedH add_v_delta 2.0495 6 0.34 32 % + LCAO_DESCRIPTOR add_v_delta 2.0494 6 0.34 32 % + ElecStateLCAO psiToRho 1.1212 11 0.1 17 % + Charge mix_rho 0.76084 10 0.076 12 % + LOOP_ions force_stress 0.53833 1 0.54 8.4 % + Force_Stress_LCAO getForceStress 0.5383 1 0.54 8.4 % + Force_LCAO_gamma ftable_gamma 0.34276 1 0.34 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.3355 1 0.34 5.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:26 2022 + FINISH Time : Wed Sep 28 11:06:33 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/70/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..529c617805f644178e8239e4b39f16b9e51863ef --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.570954 0.586824 0.043645 +H 0.569361 0.633785 0.0889086 +H 0.553941 0.625857 0.992413 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..7567e99267014055b3958ba35a5da9d83f1fac96 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3872 2 + 2 -12.5732 2 + 3 -9.52689 2 + 4 -6.76926 2 + 5 1.1834 0 + 6 4.27979 0 + 7 11.0785 0 + 8 11.3721 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..fc3473cb5069495ade852baebeb83edbfc0648bc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:14 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 15.9867091823 16.4310748165 1.22206008016 0 0 0 0 + tauc_H1 15.9421147543 17.7459780915 2.48943942486 0 0 0 0 + tauc_H2 15.5103544226 17.5240055597 27.7875566771 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0916295577933 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0995172032679 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.118663630853 (SEC) + + DONE : INIT CHARGE Time : 0.167427640187 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.454945 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 81 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000888 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000948 + + Density error is 0.211969788631 + + Energy Rydberg eV + E_KohnSham -34.1899835526 -465.178590841 + E_Harris -34.3764895408 -467.716134992 + E_Fermi -0.401749326242 -5.46608000455 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000995921984036 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128524080244 + + Density error is 0.0975720836798 + + Energy Rydberg eV + E_KohnSham -34.2777099229 -466.372169343 + E_Harris -34.2846267335 -466.466277378 + E_Fermi -0.213770474477 -2.90849651705 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000936337135383 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123164393103 + + Density error is 0.0626229528782 + + Energy Rydberg eV + E_KohnSham -34.2780013874 -466.376134921 + E_Harris -34.2824835316 -466.437117621 + E_Fermi -0.203708304254 -2.77159366777 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000850544263353 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116972676341 + + Density error is 0.00189590383488 + + Energy Rydberg eV + E_KohnSham -34.2779604885 -466.375578462 + E_Harris -34.2779604089 -466.375577379 + E_Fermi -0.167904051913 -2.2844518233 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000852059132085 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117312283825 + + Density error is 0.000861747100085 + + Energy Rydberg eV + E_KohnSham -34.2779110178 -466.374905379 + E_Harris -34.2779122786 -466.374922533 + E_Fermi -0.167544082446 -2.27955418745 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000850764406906 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117154975596 + + Density error is 8.73400120703e-05 + + Energy Rydberg eV + E_KohnSham -34.2779455088 -466.375374653 + E_Harris -34.2779455135 -466.375374716 + E_Fermi -0.167394165762 -2.27751446632 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000850730188773 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117142097453 + + Density error is 3.30701323059e-05 + + Energy Rydberg eV + E_KohnSham -34.2779350266 -466.375232036 + E_Harris -34.2779350326 -466.375232117 + E_Fermi -0.16730239019 -2.27626579561 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000850698300377 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117135361337 + + Density error is 1.04474806432e-05 + + Energy Rydberg eV + E_KohnSham -34.2779365218 -466.375252378 + E_Harris -34.2779365222 -466.375252384 + E_Fermi -0.167338514844 -2.27675729674 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00085070042079 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117136578775 + + Density error is 2.34347999751e-06 + + Energy Rydberg eV + E_KohnSham -34.2779354357 -466.375237602 + E_Harris -34.2779354357 -466.375237602 + E_Fermi -0.167329925492 -2.27664043261 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000850700666781 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117136858453 + + Density error is 2.44510924207e-07 + + Energy Rydberg eV + E_KohnSham -34.2779355668 -466.375239385 + E_Harris -34.2779355668 -466.375239385 + E_Fermi -0.167327556286 -2.27660819791 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000850700801984 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117136900112 + + Density error is 5.42001214723e-08 + + Energy Rydberg eV + E_KohnSham -34.2779356077 -466.375239941 + E_Harris -34.2779356077 -466.375239941 + E_band -7.97557042082 -108.513202523 + E_one_elec -69.1844041055 -941.30210857 + E_Hartree +35.9751538156 +489.467078319 + E_xc -8.19899890715 -111.553103033 + E_Ewald +7.25480713302 +98.7067149002 + E_demet -6.85977782282e-73 -9.33320654044e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194661786179 -2.64850947489 + E_Fermi -0.167327444111 -2.27660667169 + + charge density convergence is achieved + final etot is -466.375239941 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3872 2.00000 + 2 -12.5732 2.00000 + 3 -9.52689 2.00000 + 4 -6.76926 2.00000 + 5 1.18340 0.00000 + 6 4.27979 0.00000 + 7 11.0785 0.00000 + 8 11.3721 0.00000 + + EFERMI = -2.276606671692539 eV + OUT.ABACUS/ final etot is -466.3752399413082 eV + correction force for each atom along direction 1 is -8.87672e-05 + correction force for each atom along direction 2 is 4.47141e-05 + correction force for each atom along direction 3 is 2.01857e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.27259242 +0.63673107 -0.78372401 + H1 +0.15773240 +0.057352072 +0.94757461 + H2 +0.11486002 -0.69408314 -0.16385060 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3752399413082 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8276 11 0.62 1.0e+02% + Run_lcao lcao_line 6.8177 1 6.8 1.e+02% + Potential init_pot 0.28972 2 0.14 4.2% + PW_Basis recip2real 0.25208 16 0.016 3.7% + PW_Basis gathers_scatterp 0.11245 16 0.0070 1.6% + Potential v_of_rho 0.80822 13 0.062 12.% + XC_Functional v_xc 0.19363 14 0.014 2.8% + H_Hartree_pw v_hartree 0.57599 13 0.044 8.4% + PW_Basis real2recip 0.65876 38 0.017 9.6% + PW_Basis gatherp_scatters 0.26553 38 0.0070 3.9% + ORB_control set_orb_tables 1.1216 1 1.1 16.% + ORB_gen_tables gen_tables 1.1216 1 1.1 16.% + ORB_table_phi init_Table 0.48614 1 0.49 7.1% + ORB_table_phi cal_ST_Phi12_R 0.48072 126 0.0038 7.0% + ORB_table_beta init_Table_Beta 0.18924 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18766 56 0.0034 2.7% + ORB_table_alpha init_Table_Alpha 0.25427 1 0.25 3.7% + ORB_table_alpha S_PhiAlpha_R 0.25227 66 0.0038 3.7% + LOOP_ions opt_ions 5.1539 1 5.2 75.% + ESolver_KS_LCAO Run 4.5918 1 4.6 67.% + HSolverLCAO solve 2.4212 11 0.22 35.% + HamiltLCAO updateHk 1.2871 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.2496 11 0.11 18.% + Gint_interface cal_gint 2.2593 23 0.098 33.% + Gint_Gamma distri_vl 2.2026 6 0.37 32.% + LCAO_Deepks cal_projected_DM 4.9804 13 0.38 73.% + LCAO_gen_fixedH add_v_delta 2.0626 6 0.34 30.% + LCAO_DESCRIPTOR add_v_delta 2.0627 6 0.34 30.% + ElecStateLCAO psiToRho 1.1178 11 0.10 16.% + Charge mix_rho 0.80637 10 0.081 12.% + LOOP_ions force_stress 0.56197 1 0.56 8.2% + Force_Stress_LCAO getForceStress 0.56195 1 0.56 8.2% + Force_LCAO_gamma ftable_gamma 0.36484 1 0.36 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.35978 1 0.36 5.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:14 2022 + Finish Time : Wed Sep 28 11:05:21 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..86695d554e8dfd2369e8ac63add52ae6b109d599 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123749 ima = 3.6919e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122481195839 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111325743022 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111962303783 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112205380379 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112158019977 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112184858683 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112183259376 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112185573643 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112185113783 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112185003706 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112184990727 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3414fb622f35db8ecc6c524a783b41742dc3c838 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-12.013290817735 16.431074816475 1.222060080168 0 0 0 +H +0.0 +2 +-12.057885245676 17.745978091486 2.489439424857 0 0 0 +-12.489645577347 17.524005559646 -0.212443322917 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/conv new file mode 100644 index 0000000000000000000000000000000000000000..1a7ffd39191026460d4ec5fd1f2e73c46b4deb56 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/conv @@ -0,0 +1 @@ +71 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..550a486697092a22282e74d473aa1cb8a7bfd2b8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.755646817 0.01279243839 1.265055915 1.344949812 1.469605464 0.009778284436 0.01608174766 0.03922222421 +-1.751095205e-18 0.0008305668292 0.002878131559 0.01349851035 0.04648444046 3.649713151e-20 2.919972997e-06 7.7344914e-06 +0.001588137346 0.006171043924 + +H atom_index 1 n_descriptor 18 +1.255758685 0.03490512102 0.1145708977 0.15229419 0.3212932541 0.02384509213 0.02856738667 0.03802814373 +5.183903986e-17 4.946499139e-05 0.1041988933 0.1162472608 0.130507455 8.486859002e-19 2.251915461e-06 0.01341895331 +0.02735038515 0.03100057524 + +H atom_index 2 n_descriptor 18 +1.225652978 0.03590023804 0.1040065225 0.1385676717 0.310909889 0.02232190724 0.02679291279 0.03905670494 +-3.239592077e-17 4.674268248e-05 0.09726941142 0.1142706296 0.118619775 9.086754857e-18 3.840069806e-06 0.01382091317 +0.02620107989 0.02956080532 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..2b1e999e11b3928ef57ea3f0bddc134d0687f91c Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..7dcc63b8d9b5b56beb1178a82b863e0039c1aacd Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..8c7619365d60e4b798be04571fe898b7ce5b75dc Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..789b2dafb0905d5a2b7aebd59785ad2b4345f6fd Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..7affa94744594d19425046c087eaa439b185842c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:14 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0916524 SEC) : SETUP UNITCELL + DONE(0.0995343 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.118684 SEC) : INIT PLANEWAVE + DONE(0.167559 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.45501 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651786e+02 0.000000e+00 2.120e-01 5.395e-01 + GE2 -4.663722e+02 -1.193579e+00 9.757e-02 4.674e-01 + GE3 -4.663761e+02 -3.965578e-03 6.262e-02 5.252e-01 + GE4 -4.663756e+02 5.564584e-04 1.896e-03 3.945e-01 + GE5 -4.663749e+02 6.730832e-04 8.617e-04 3.942e-01 + GE6 -4.663754e+02 -4.692740e-04 8.734e-05 3.851e-01 + GE7 -4.663752e+02 1.426172e-04 3.307e-05 3.782e-01 + GE8 -4.663753e+02 -2.034261e-05 1.045e-05 3.787e-01 + GE9 -4.663752e+02 1.477648e-05 2.343e-06 3.735e-01 + GE10 -4.663752e+02 -1.782899e-06 2.445e-07 3.738e-01 + GE11 -4.663752e+02 -5.565085e-07 5.420e-08 3.173e-01 +E_delta_band = -7.01682425e-02 Ry = -9.54687917e-01 eV +E_delta_NN= -1.94661786e-01 Ry = -2.64850947e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.8276 11 0.62 1e+02 % + Run_lcao lcao_line 6.8177 1 6.8 1e+02 % + Potential init_pot 0.28972 2 0.14 4.2 % + PW_Basis recip2real 0.25208 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.11245 16 0.007 1.6 % + Potential v_of_rho 0.80822 13 0.062 12 % + XC_Functional v_xc 0.19363 14 0.014 2.8 % + H_Hartree_pw v_hartree 0.57599 13 0.044 8.4 % + PW_Basis real2recip 0.65876 38 0.017 9.6 % + PW_Basis gatherp_scatters 0.26553 38 0.007 3.9 % + ORB_control set_orb_tables 1.1216 1 1.1 16 % + ORB_gen_tables gen_tables 1.1216 1 1.1 16 % + ORB_table_phi init_Table 0.48614 1 0.49 7.1 % + ORB_table_phi cal_ST_Phi12_R 0.48072 126 0.0038 7 % + ORB_table_beta init_Table_Beta 0.18924 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18766 56 0.0034 2.7 % + ORB_table_alpha init_Table_Alpha 0.25427 1 0.25 3.7 % + ORB_table_alpha S_PhiAlpha_R 0.25227 66 0.0038 3.7 % + LOOP_ions opt_ions 5.1539 1 5.2 75 % + ESolver_KS_LCAO Run 4.5918 1 4.6 67 % + HSolverLCAO solve 2.4212 11 0.22 35 % + HamiltLCAO updateHk 1.2871 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.2496 11 0.11 18 % + Gint_interface cal_gint 2.2593 23 0.098 33 % + Gint_Gamma distri_vl 2.2026 6 0.37 32 % + LCAO_Deepks cal_projected_DM 4.9804 13 0.38 73 % + LCAO_gen_fixedH add_v_delta 2.0626 6 0.34 30 % + LCAO_DESCRIPTOR add_v_delta 2.0627 6 0.34 30 % + ElecStateLCAO psiToRho 1.1178 11 0.1 16 % + Charge mix_rho 0.80637 10 0.081 12 % + LOOP_ions force_stress 0.56197 1 0.56 8.2 % + Force_Stress_LCAO getForceStress 0.56195 1 0.56 8.2 % + Force_LCAO_gamma ftable_gamma 0.36484 1 0.36 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.35978 1 0.36 5.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:14 2022 + FINISH Time : Wed Sep 28 11:05:21 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/71/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..bb1f83a467aab8772718b16cc323dfe27f722a33 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.598119 0.582757 0.0386289 +H 0.556981 0.627407 0.067135 +H 0.564048 0.538879 0.00900168 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e32e997570843a4ec972c28d4b8b919950380622 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2838 2 + 2 -13.3628 2 + 3 -8.86191 2 + 4 -6.7377 2 + 5 1.33574 0 + 6 4.60019 0 + 7 11.0613 0 + 8 11.2778 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..4065cc27d86fa342628ccc7ea3ce94b30a430ac2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:22 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 16.7473194638 16.3171941 1.08160997202 0 0 0 0 + tauc_H1 15.5954664214 17.5673892597 1.87977862513 0 0 0 0 + tauc_H2 15.7933439623 15.0886254386 0.252046960151 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0877999928782 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.102980226838 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.12132775657 (SEC) + + DONE : INIT CHARGE Time : 0.171275599922 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.455793 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 81 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00131 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000986 + + Density error is 0.216897590108 + + Energy Rydberg eV + E_KohnSham -34.1855386613 -465.118114992 + E_Harris -34.3815679267 -467.785229977 + E_Fermi -0.410834330554 -5.58968782956 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00135814092861 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00100621862137 + + Density error is 0.0981072970338 + + Energy Rydberg eV + E_KohnSham -34.2759625546 -466.348395178 + E_Harris -34.2825924631 -466.43859971 + E_Fermi -0.217827978069 -2.96370168556 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0012637198899 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000954170362227 + + Density error is 0.0627488142806 + + Energy Rydberg eV + E_KohnSham -34.2761719092 -466.351243592 + E_Harris -34.280421131 -466.409057221 + E_Fermi -0.205190882954 -2.79176518583 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110383873627 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000878899541306 + + Density error is 0.00210083167047 + + Energy Rydberg eV + E_KohnSham -34.2761863585 -466.351440185 + E_Harris -34.276189518 -466.351483172 + E_Fermi -0.169812964877 -2.3104239166 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110216213395 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00088025600688 + + Density error is 0.000861026396658 + + Energy Rydberg eV + E_KohnSham -34.2761281758 -466.35064857 + E_Harris -34.2761291366 -466.350661641 + E_Fermi -0.168885616672 -2.29780669698 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.0011004275112 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000879245174997 + + Density error is 0.000204569430235 + + Energy Rydberg eV + E_KohnSham -34.2761648781 -466.351147929 + E_Harris -34.2761650129 -466.351149763 + E_Fermi -0.16895275048 -2.2987200993 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110043959631 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000879383981269 + + Density error is 4.48541143045e-05 + + Energy Rydberg eV + E_KohnSham -34.2761498551 -466.350943532 + E_Harris -34.2761498663 -466.350943683 + E_Fermi -0.168775892599 -2.29631382439 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110042425121 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000879366861965 + + Density error is 1.90932857023e-05 + + Energy Rydberg eV + E_KohnSham -34.2761558221 -466.351024716 + E_Harris -34.2761558234 -466.351024734 + E_Fermi -0.168826919782 -2.29700808483 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110039255736 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000879361219479 + + Density error is 2.8592772947e-06 + + Energy Rydberg eV + E_KohnSham -34.2761542359 -466.351003135 + E_Harris -34.2761542359 -466.351003136 + E_Fermi -0.168807395217 -2.29674243949 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110038644952 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000879357152707 + + Density error is 4.74668017324e-07 + + Energy Rydberg eV + E_KohnSham -34.2761544515 -466.351006068 + E_Harris -34.2761544515 -466.351006068 + E_Fermi -0.168804627886 -2.29670478802 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110038687538 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000879357387404 + + Density error is 1.83694290464e-07 + + Energy Rydberg eV + E_KohnSham -34.2761544925 -466.351006626 + E_Harris -34.2761544925 -466.351006626 + E_Fermi -0.168804455148 -2.2967024378 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.00110038677295 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000879357385659 + + Density error is 1.04761865068e-08 + + Energy Rydberg eV + E_KohnSham -34.276154494 -466.351006647 + E_Harris -34.276154494 -466.351006647 + E_band -7.97403196814 -108.492270801 + E_one_elec -69.4452249244 -944.850757863 + E_Hartree +36.1221668902 +491.467293813 + E_xc -8.22297064048 -111.879255197 + E_Ewald +7.39394600056 +100.599796312 + E_demet -4.60462287297e-80 -6.26491082135e-79 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195024466802 -2.65344399792 + E_Fermi -0.168804275634 -2.29669999539 + + charge density convergence is achieved + final etot is -466.351006647 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2838 2.00000 + 2 -13.3628 2.00000 + 3 -8.86191 2.00000 + 4 -6.73770 2.00000 + 5 1.33574 0.00000 + 6 4.60019 0.00000 + 7 11.0613 0.00000 + 8 11.2778 0.00000 + + EFERMI = -2.296699995385553 eV + OUT.ABACUS/ final etot is -466.3510066471972 eV + correction force for each atom along direction 1 is -0.000123141 + correction force for each atom along direction 2 is 3.57843e-05 + correction force for each atom along direction 3 is 2.92192e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.2207773 +2.3266466 +1.5587269 + H1 +0.35797626 -0.85642182 -0.55637379 + H2 -1.5787535 -1.4702248 -1.0023531 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3510066471972 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1207 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1108 1 7.1 1.e+02% + Potential init_pot 0.28780 2 0.14 4.0% + PW_Basis recip2real 0.30149 17 0.018 4.2% + PW_Basis gathers_scatterp 0.13343 17 0.0078 1.9% + Potential v_of_rho 1.0614 14 0.076 15.% + XC_Functional v_xc 0.30677 15 0.020 4.3% + H_Hartree_pw v_hartree 0.70844 14 0.051 9.9% + PW_Basis real2recip 0.70891 41 0.017 10.% + PW_Basis gatherp_scatters 0.27266 41 0.0067 3.8% + ORB_control set_orb_tables 1.1148 1 1.1 16.% + ORB_gen_tables gen_tables 1.1148 1 1.1 16.% + ORB_table_phi init_Table 0.48545 1 0.49 6.8% + ORB_table_phi cal_ST_Phi12_R 0.48022 126 0.0038 6.7% + ORB_table_beta init_Table_Beta 0.19078 1 0.19 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18919 56 0.0034 2.7% + ORB_table_alpha init_Table_Alpha 0.25369 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.25165 66 0.0038 3.5% + LOOP_ions opt_ions 5.4615 1 5.5 77.% + ESolver_KS_LCAO Run 4.8939 1 4.9 69.% + HSolverLCAO solve 2.4132 12 0.20 34.% + HamiltLCAO updateHk 1.2609 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.2313 12 0.10 17.% + Gint_interface cal_gint 2.2383 25 0.090 31.% + Gint_Gamma distri_vl 2.5593 6 0.43 36.% + LCAO_Deepks cal_projected_DM 5.3059 14 0.38 75.% + LCAO_gen_fixedH add_v_delta 2.4136 6 0.40 34.% + LCAO_DESCRIPTOR add_v_delta 2.4136 6 0.40 34.% + ElecStateLCAO psiToRho 1.1352 12 0.095 16.% + Charge mix_rho 0.86816 11 0.079 12.% + LOOP_ions force_stress 0.56746 1 0.57 8.0% + Force_Stress_LCAO getForceStress 0.56743 1 0.57 8.0% + Force_LCAO_gamma ftable_gamma 0.35295 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.34504 1 0.35 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:22 2022 + Finish Time : Wed Sep 28 11:05:29 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3fb9a483312485dfbb8199b642b738a45c372d93 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123924 ima = 3.66399e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123574771386 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756160804 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011321098724 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113452164172 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113403822518 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113434176314 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011342297805 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113426247668 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113425576417 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113425464553 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113425451266 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113425442169 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/STRU new file mode 100644 index 0000000000000000000000000000000000000000..5740d881480853da09fbbf7b9f4e5212d3c3d987 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-11.252680536162 16.317194100041 1.081609972026 0 0 0 +H +0.0 +2 +-12.404533578625 17.567389259711 1.879778625143 0 0 0 +-12.206656037719 15.088625438572 0.252046960163 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/conv new file mode 100644 index 0000000000000000000000000000000000000000..28499cb348955b5fb5d816b80c77919df1ebfeb4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/conv @@ -0,0 +1 @@ +72 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..52fe272ddbdcb0e6a9e614af7bfd4d50b13a33b8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74475232 0.01260096197 1.277928446 1.379773147 1.469449346 0.007880314306 0.02034849243 0.0389142856 +-7.504689811e-19 0.001169212249 0.002434028928 0.01235367684 0.0436922166 -1.273691673e-19 1.563777704e-06 4.995070849e-06 +0.001753106703 0.005621702326 + +H atom_index 1 n_descriptor 18 +1.204873442 0.03525734894 0.09384044531 0.1314528158 0.3078221258 0.01987457022 0.02585837504 0.03853025834 +-1.117774819e-17 3.642953312e-05 0.09028093881 0.112665365 0.1135133363 9.863781363e-19 6.058023373e-06 0.01367252958 +0.02439406551 0.02870843416 + +H atom_index 2 n_descriptor 18 +1.296734036 0.03212893486 0.1256852645 0.1743839768 0.3361587044 0.02385444111 0.03112721131 0.03607853977 +-2.902347426e-17 4.404217255e-05 0.1078614664 0.122310703 0.149602857 4.488232768e-18 1.912344498e-06 0.01339760057 +0.02772347925 0.03269752703 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..10690ee8e886f52acc08517606a781a318401f38 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:22 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0878223 SEC) : SETUP UNITCELL + DONE(0.103 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.121353 SEC) : INIT PLANEWAVE + DONE(0.171402 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.455857 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651181e+02 0.000000e+00 2.169e-01 5.146e-01 + GE2 -4.663484e+02 -1.230280e+00 9.811e-02 4.600e-01 + GE3 -4.663512e+02 -2.848415e-03 6.275e-02 5.258e-01 + GE4 -4.663514e+02 -1.965927e-04 2.101e-03 3.912e-01 + GE5 -4.663506e+02 7.916154e-04 8.610e-04 3.910e-01 + GE6 -4.663511e+02 -4.993597e-04 2.046e-04 3.843e-01 + GE7 -4.663509e+02 2.043978e-04 4.485e-05 3.883e-01 + GE8 -4.663510e+02 -8.118450e-05 1.909e-05 3.674e-01 + GE9 -4.663510e+02 2.158090e-05 2.859e-06 3.674e-01 + GE10 -4.663510e+02 -2.932817e-06 4.747e-07 3.686e-01 + GE11 -4.663510e+02 -5.578043e-07 1.837e-07 3.682e-01 + GE12 -4.663510e+02 -2.147436e-08 1.048e-08 3.048e-01 +E_delta_band = -7.09526469e-02 Ry = -9.65360286e-01 eV +E_delta_NN= -1.95024467e-01 Ry = -2.65344400e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1207 11 0.65 1e+02 % + Run_lcao lcao_line 7.1108 1 7.1 1e+02 % + Potential init_pot 0.2878 2 0.14 4 % + PW_Basis recip2real 0.30149 17 0.018 4.2 % + PW_Basis gathers_scatterp 0.13343 17 0.0078 1.9 % + Potential v_of_rho 1.0614 14 0.076 15 % + XC_Functional v_xc 0.30677 15 0.02 4.3 % + H_Hartree_pw v_hartree 0.70844 14 0.051 9.9 % + PW_Basis real2recip 0.70891 41 0.017 10 % + PW_Basis gatherp_scatters 0.27266 41 0.0067 3.8 % + ORB_control set_orb_tables 1.1148 1 1.1 16 % + ORB_gen_tables gen_tables 1.1148 1 1.1 16 % + ORB_table_phi init_Table 0.48545 1 0.49 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.48022 126 0.0038 6.7 % + ORB_table_beta init_Table_Beta 0.19078 1 0.19 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18919 56 0.0034 2.7 % + ORB_table_alpha init_Table_Alpha 0.25369 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.25165 66 0.0038 3.5 % + LOOP_ions opt_ions 5.4615 1 5.5 77 % + ESolver_KS_LCAO Run 4.8939 1 4.9 69 % + HSolverLCAO solve 2.4132 12 0.2 34 % + HamiltLCAO updateHk 1.2609 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.2313 12 0.1 17 % + Gint_interface cal_gint 2.2383 25 0.09 31 % + Gint_Gamma distri_vl 2.5593 6 0.43 36 % + LCAO_Deepks cal_projected_DM 5.3059 14 0.38 75 % + LCAO_gen_fixedH add_v_delta 2.4136 6 0.4 34 % + LCAO_DESCRIPTOR add_v_delta 2.4136 6 0.4 34 % + ElecStateLCAO psiToRho 1.1352 12 0.095 16 % + Charge mix_rho 0.86816 11 0.079 12 % + LOOP_ions force_stress 0.56746 1 0.57 8 % + Force_Stress_LCAO getForceStress 0.56743 1 0.57 8 % + Force_LCAO_gamma ftable_gamma 0.35295 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.34504 1 0.35 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:22 2022 + FINISH Time : Wed Sep 28 11:05:29 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/72/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..53e49a56600b7eaf13ed9b51b851231eda3424b6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.624679 0.570233 0.0333814 +H 0.619362 0.634616 0.0233719 +H 0.577197 0.559929 0.0851659 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..f6f7bf8f9deb92e1fe9fdf8f87a0751ac3c3532b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9329 2 + 2 -12.5536 2 + 3 -9.18277 2 + 4 -6.66418 2 + 5 0.807547 0 + 6 3.82942 0 + 7 11.1668 0 + 8 11.4081 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e484b4bcb1503d86007efdddfa1f9a5fc4a68046 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:01:48 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.4910067336 15.9665294632 0.93468049755 0 0 0 0 + tauc_H1 17.3421468842 17.7692609547 0.654413787772 0 0 0 0 + tauc_H2 16.1615257416 15.6780000219 2.38464438708 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0737499094091 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0740579540941 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0902955869722 (SEC) + + DONE : INIT CHARGE Time : 0.131766510998 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375455 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 100 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000454 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112 + + Density error is 0.210093939559 + + Energy Rydberg eV + E_KohnSham -34.1847481844 -465.107360003 + E_Harris -34.3671901795 -467.58961069 + E_Fermi -0.381159742578 -5.18594434728 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000712094434055 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114475566853 + + Density error is 0.0990307020485 + + Energy Rydberg eV + E_KohnSham -34.2721906823 -466.297076222 + E_Harris -34.2795623834 -466.397373361 + E_Fermi -0.194004078388 -2.63956090132 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00068775014148 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108120064435 + + Density error is 0.064009084891 + + Energy Rydberg eV + E_KohnSham -34.2726171303 -466.302878345 + E_Harris -34.2772850267 -466.366388333 + E_Fermi -0.188777766435 -2.56845327923 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000670529487861 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098242195013 + + Density error is 0.00197576070785 + + Energy Rydberg eV + E_KohnSham -34.2724832574 -466.30105691 + E_Harris -34.272485386 -466.301085871 + E_Fermi -0.153512244314 -2.08864123544 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000669037856802 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000981483263766 + + Density error is 0.000907555441501 + + Energy Rydberg eV + E_KohnSham -34.272468433 -466.300855214 + E_Harris -34.2724687437 -466.300859442 + E_Fermi -0.153731205767 -2.09162035885 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.0006689879186 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980197919175 + + Density error is 0.000180500058458 + + Energy Rydberg eV + E_KohnSham -34.2724682274 -466.300852417 + E_Harris -34.2724682209 -466.300852328 + E_Fermi -0.153147730139 -2.08368176565 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000669065074221 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980272618571 + + Density error is 2.42208673183e-05 + + Energy Rydberg eV + E_KohnSham -34.2724707355 -466.300886541 + E_Harris -34.2724707358 -466.300886546 + E_Fermi -0.153164544495 -2.0839105367 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000669028323642 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980203680533 + + Density error is 4.91477992795e-06 + + Energy Rydberg eV + E_KohnSham -34.2724713364 -466.300894717 + E_Harris -34.2724713366 -466.300894719 + E_Fermi -0.153155271234 -2.08378436752 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000669031077621 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980203494938 + + Density error is 1.29225136004e-06 + + Energy Rydberg eV + E_KohnSham -34.2724709419 -466.30088935 + E_Harris -34.2724709419 -466.30088935 + E_Fermi -0.153150291327 -2.0837166124 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000669032482375 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980204913599 + + Density error is 4.41244573891e-07 + + Energy Rydberg eV + E_KohnSham -34.2724710536 -466.300890869 + E_Harris -34.2724710536 -466.300890869 + E_Fermi -0.153151137641 -2.0837281271 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000669033030878 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098020498162 + + Density error is 1.17467619101e-07 + + Energy Rydberg eV + E_KohnSham -34.2724710323 -466.300890579 + E_Harris -34.2724710323 -466.300890579 + E_Fermi -0.153150791853 -2.08372342241 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000669033153226 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980204839074 + + Density error is 1.39029627327e-08 + + Energy Rydberg eV + E_KohnSham -34.2724710392 -466.300890673 + E_Harris -34.2724710392 -466.300890673 + E_band -7.83986749279 -106.666869467 + E_one_elec -68.4175910582 -930.869081826 + E_Hartree +35.6230647401 +484.676660688 + E_xc -8.14359353784 -110.799274311 + E_Ewald +6.79168105225 +92.4055613093 + E_demet -1.05365815196e-51 -1.43357546108e-50 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193426125549 -2.63169744953 + E_Fermi -0.153150737243 -2.0837226794 + + charge density convergence is achieved + final etot is -466.300890673 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9329 2.00000 + 2 -12.5536 2.00000 + 3 -9.18277 2.00000 + 4 -6.66418 2.00000 + 5 0.807547 0.00000 + 6 3.82942 0.00000 + 7 11.1668 0.00000 + 8 11.4081 0.00000 + + EFERMI = -2.083722679399436 eV + OUT.ABACUS/ final etot is -466.3008906726854 eV + correction force for each atom along direction 1 is -1.85155e-05 + correction force for each atom along direction 2 is 5.78120e-05 + correction force for each atom along direction 3 is -3.83267e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.9585652 -0.79594436 +2.2230973 + H1 +0.022286420 +0.45821772 -0.13258629 + H2 +1.9362788 +0.33772664 -2.0905110 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3008906726854 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9049 11 0.63 1.0e+02% + Run_lcao lcao_line 6.8964 1 6.9 1.e+02% + Potential init_pot 0.24395 2 0.12 3.5% + PW_Basis recip2real 0.28106 17 0.017 4.1% + PW_Basis gathers_scatterp 0.11159 17 0.0066 1.6% + Potential v_of_rho 0.98715 14 0.071 14.% + XC_Functional v_xc 0.28616 15 0.019 4.1% + H_Hartree_pw v_hartree 0.66011 14 0.047 9.6% + PW_Basis real2recip 0.65119 41 0.016 9.4% + PW_Basis gatherp_scatters 0.24096 41 0.0059 3.5% + ORB_control set_orb_tables 0.90357 1 0.90 13.% + ORB_gen_tables gen_tables 0.90357 1 0.90 13.% + ORB_table_phi init_Table 0.38084 1 0.38 5.5% + ORB_table_phi cal_ST_Phi12_R 0.37656 126 0.0030 5.5% + ORB_table_beta init_Table_Beta 0.15531 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15395 56 0.0027 2.2% + ORB_table_alpha init_Table_Alpha 0.20934 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20766 66 0.0031 3.0% + LOOP_ions opt_ions 5.5492 1 5.5 80.% + ESolver_KS_LCAO Run 5.0025 1 5.0 72.% + HSolverLCAO solve 2.6407 12 0.22 38.% + HamiltLCAO updateHk 1.3521 12 0.11 20.% + LCAO_Hamilt cal_Hgamma 1.3165 12 0.11 19.% + Gint_interface cal_gint 2.5000 25 0.10 36.% + Gint_Gamma distri_vl 2.6039 6 0.43 38.% + LCAO_Deepks cal_projected_DM 5.4029 14 0.39 78.% + LCAO_gen_fixedH add_v_delta 2.4699 6 0.41 36.% + LCAO_DESCRIPTOR add_v_delta 2.4700 6 0.41 36.% + ElecStateLCAO psiToRho 1.2707 12 0.11 18.% + Charge mix_rho 0.84037 11 0.076 12.% + LOOP_ions force_stress 0.54653 1 0.55 7.9% + Force_Stress_LCAO getForceStress 0.54651 1 0.55 7.9% + Force_LCAO_gamma ftable_gamma 0.34548 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.33826 1 0.34 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:01:48 2022 + Finish Time : Wed Sep 28 11:01:55 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..3f955a9feb28aa4892d33e6e3f44b1c9f4ba06fb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012348 ima = 3.67967e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012352202766 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112056914287 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112917546691 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113098718565 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113104954696 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113102834895 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113102530437 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113103253677 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113102999769 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113103039925 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011310301937 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113103016623 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/STRU new file mode 100644 index 0000000000000000000000000000000000000000..37198c70858d0d446724af6603096220367c8c47 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.508993266418 15.966529463185 0.934680497560 0 0 0 +H +0.0 +2 +-10.657853115773 17.769260954666 0.654413787771 0 0 0 +-11.838474258384 15.678000021914 2.384644387097 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/conv new file mode 100644 index 0000000000000000000000000000000000000000..ea875d4a82159426096e3e4bc752035a6137297a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/conv @@ -0,0 +1 @@ +73 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f5066137da4d3eb22e15c99422cba09c4a486ccd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.752493442 0.01228749709 1.226346401 1.336838471 1.468029968 0.00884475088 0.0172157334 0.03922353893 +2.065065638e-18 0.0008082274782 0.002423714715 0.01119178877 0.04131921361 1.114543157e-19 1.595570182e-06 5.13300922e-06 +0.001542235886 0.00579912716 + +H atom_index 1 n_descriptor 18 +1.250237058 0.03451280324 0.1077886716 0.1501612907 0.3215692062 0.02211455527 0.0283248247 0.03777963721 +-2.01194628e-18 4.014898625e-05 0.09805942221 0.1156379375 0.1286063917 2.662038326e-18 3.604053196e-06 0.01321585238 +0.02551546167 0.03073888946 + +H atom_index 2 n_descriptor 18 +1.127143101 0.03793915784 0.07177474172 0.101121605 0.2738812552 0.01642820393 0.02115489981 0.04239705969 +1.911333481e-17 3.026184629e-05 0.06776013036 0.08536978561 0.1085513695 -1.652344902e-18 6.985323028e-06 0.01671646488 +0.02042543172 0.02410924706 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e4e4b319c6f2a7359e6070d9947ac2ca4b09f80e Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:01:48 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0737645 SEC) : SETUP UNITCELL + DONE(0.0740662 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.090308 SEC) : INIT PLANEWAVE + DONE(0.131875 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.375503 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651074e+02 0.000000e+00 2.101e-01 5.038e-01 + GE2 -4.662971e+02 -1.189716e+00 9.903e-02 4.686e-01 + GE3 -4.663029e+02 -5.802123e-03 6.401e-02 5.289e-01 + GE4 -4.663011e+02 1.821434e-03 1.976e-03 4.066e-01 + GE5 -4.663009e+02 2.016967e-04 9.076e-04 4.053e-01 + GE6 -4.663009e+02 2.796523e-06 1.805e-04 4.041e-01 + GE7 -4.663009e+02 -3.412411e-05 2.422e-05 3.796e-01 + GE8 -4.663009e+02 -8.175997e-06 4.915e-06 3.853e-01 + GE9 -4.663009e+02 5.367845e-06 1.292e-06 3.896e-01 + GE10 -4.663009e+02 -1.519576e-06 4.412e-07 3.811e-01 + GE11 -4.663009e+02 2.902509e-07 1.175e-07 3.812e-01 + GE12 -4.663009e+02 -9.383729e-08 1.390e-08 3.151e-01 +E_delta_band = -6.73938901e-02 Ry = -9.16940916e-01 eV +E_delta_NN= -1.93426126e-01 Ry = -2.63169745e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9049 11 0.63 1e+02 % + Run_lcao lcao_line 6.8964 1 6.9 1e+02 % + Potential init_pot 0.24395 2 0.12 3.5 % + PW_Basis recip2real 0.28106 17 0.017 4.1 % + PW_Basis gathers_scatterp 0.11159 17 0.0066 1.6 % + Potential v_of_rho 0.98715 14 0.071 14 % + XC_Functional v_xc 0.28616 15 0.019 4.1 % + H_Hartree_pw v_hartree 0.66011 14 0.047 9.6 % + PW_Basis real2recip 0.65119 41 0.016 9.4 % + PW_Basis gatherp_scatters 0.24096 41 0.0059 3.5 % + ORB_control set_orb_tables 0.90357 1 0.9 13 % + ORB_gen_tables gen_tables 0.90357 1 0.9 13 % + ORB_table_phi init_Table 0.38084 1 0.38 5.5 % + ORB_table_phi cal_ST_Phi12_R 0.37656 126 0.003 5.5 % + ORB_table_beta init_Table_Beta 0.15531 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15395 56 0.0027 2.2 % + ORB_table_alpha init_Table_Alpha 0.20934 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20766 66 0.0031 3 % + LOOP_ions opt_ions 5.5492 1 5.5 80 % + ESolver_KS_LCAO Run 5.0025 1 5 72 % + HSolverLCAO solve 2.6407 12 0.22 38 % + HamiltLCAO updateHk 1.3521 12 0.11 20 % + LCAO_Hamilt cal_Hgamma 1.3165 12 0.11 19 % + Gint_interface cal_gint 2.5 25 0.1 36 % + Gint_Gamma distri_vl 2.6039 6 0.43 38 % + LCAO_Deepks cal_projected_DM 5.4029 14 0.39 78 % + LCAO_gen_fixedH add_v_delta 2.4699 6 0.41 36 % + LCAO_DESCRIPTOR add_v_delta 2.47 6 0.41 36 % + ElecStateLCAO psiToRho 1.2707 12 0.11 18 % + Charge mix_rho 0.84037 11 0.076 12 % + LOOP_ions force_stress 0.54653 1 0.55 7.9 % + Force_Stress_LCAO getForceStress 0.54651 1 0.55 7.9 % + Force_LCAO_gamma ftable_gamma 0.34548 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.33826 1 0.34 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:01:48 2022 + FINISH Time : Wed Sep 28 11:01:55 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/73/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..547cc26ec2ce9c88ffe81100b9d9eb1ae04a470c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.641305 0.559891 0.0268169 +H 0.696726 0.527501 0.0382911 +H 0.657777 0.616884 0.00709118 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..bc37f346dba84dee54765a07d3e50b7333504bdc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5315 2 + 2 -13.4029 2 + 3 -9.03987 2 + 4 -6.79657 2 + 5 1.52368 0 + 6 4.84152 0 + 7 11.0087 0 + 8 11.2387 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..330881fd2b187020bbf3262025b356da37bb3535 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 17.9565452202 15.6769395875 0.750872013778 0 0 0 0 + tauc_H1 19.5083309113 14.7700156787 1.0721513196 0 0 0 0 + tauc_H2 18.4177574483 17.2727408896 0.19855315351 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.087569001364 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0978334266464 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116221184044 (SEC) + + DONE : INIT CHARGE Time : 0.165554982222 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448002 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 4 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00166 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000696 + + Density error is 0.218330316635 + + Energy Rydberg eV + E_KohnSham -34.1852653735 -465.114396722 + E_Harris -34.3844517671 -467.824466639 + E_Fermi -0.422919529255 -5.75411539335 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00153660162392 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000859165305626 + + Density error is 0.0974527457487 + + Energy Rydberg eV + E_KohnSham -34.2762159894 -466.351843334 + E_Harris -34.2827827569 -466.44118879 + E_Fermi -0.229492568758 -3.12240658376 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00140465956887 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000826609166407 + + Density error is 0.0620867651937 + + Energy Rydberg eV + E_KohnSham -34.2763910672 -466.354225391 + E_Harris -34.2805591487 -466.410935048 + E_Fermi -0.214200018673 -2.91434076565 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00118277976124 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000785842290934 + + Density error is 0.0020939147235 + + Energy Rydberg eV + E_KohnSham -34.2764530286 -466.355068418 + E_Harris -34.2764559022 -466.355107516 + E_Fermi -0.178569145624 -2.42955786748 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00117927248833 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000788037956159 + + Density error is 0.000902965882567 + + Energy Rydberg eV + E_KohnSham -34.2763756516 -466.35401565 + E_Harris -34.2763781997 -466.354050319 + E_Fermi -0.177186273336 -2.41074292475 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00117776163931 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787196184707 + + Density error is 0.000138337206399 + + Energy Rydberg eV + E_KohnSham -34.2764296981 -466.354750991 + E_Harris -34.2764297473 -466.35475166 + E_Fermi -0.177563612117 -2.41587688225 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00117737438552 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787337146031 + + Density error is 5.36028686594e-05 + + Energy Rydberg eV + E_KohnSham -34.2764108642 -466.354494742 + E_Harris -34.2764108806 -466.354494965 + E_Fermi -0.177381666017 -2.41340137857 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00117742900478 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787286103217 + + Density error is 1.46215051276e-05 + + Energy Rydberg eV + E_KohnSham -34.2764153177 -466.354555335 + E_Harris -34.2764153185 -466.354555346 + E_Fermi -0.177446484418 -2.41428327816 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00117738714093 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787290169246 + + Density error is 1.23615796934e-06 + + Energy Rydberg eV + E_KohnSham -34.2764136749 -466.354532984 + E_Harris -34.2764136749 -466.354532984 + E_Fermi -0.177429670632 -2.41405451486 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00117738532214 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787289945824 + + Density error is 1.5630161171e-07 + + Energy Rydberg eV + E_KohnSham -34.2764138857 -466.354535852 + E_Harris -34.2764138857 -466.354535852 + E_Fermi -0.177428878601 -2.41404373873 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00117738577925 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000787290267045 + + Density error is 6.30189607522e-08 + + Energy Rydberg eV + E_KohnSham -34.2764139063 -466.354536132 + E_Harris -34.2764139063 -466.354536132 + E_band -8.05116819804 -109.54176305 + E_one_elec -69.8590408285 -950.481012082 + E_Hartree +36.3106962128 +494.032366842 + E_xc -8.253576975 -112.295675742 + E_Ewald +7.64869725255 +104.065864912 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19586549994 -2.6648868408 + E_Fermi -0.177428932769 -2.41404447572 + + charge density convergence is achieved + final etot is -466.354536132 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5315 2.00000 + 2 -13.4029 2.00000 + 3 -9.03987 2.00000 + 4 -6.79657 2.00000 + 5 1.52368 0.00000 + 6 4.84152 0.00000 + 7 11.0087 0.00000 + 8 11.2387 0.00000 + + EFERMI = -2.414044475718672 eV + OUT.ABACUS/ final etot is -466.3545361322103 eV + correction force for each atom along direction 1 is 4.97760e-05 + correction force for each atom along direction 2 is 9.06980e-05 + correction force for each atom along direction 3 is -8.32593e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.2073669 -2.4488231 +0.84296496 + H1 +0.36781129 -0.11613444 +0.043324209 + H2 +0.83955566 +2.5649575 -0.88628917 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3545361322103 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1236 11 0.65 1.0e+02% + Run_lcao lcao_line 7.1137 1 7.1 1.e+02% + Potential init_pot 0.28349 2 0.14 4.0% + PW_Basis recip2real 0.28446 16 0.018 4.0% + PW_Basis gathers_scatterp 0.12401 16 0.0078 1.7% + Potential v_of_rho 0.97271 13 0.075 14.% + XC_Functional v_xc 0.27140 14 0.019 3.8% + H_Hartree_pw v_hartree 0.65941 13 0.051 9.3% + PW_Basis real2recip 0.64551 38 0.017 9.1% + PW_Basis gatherp_scatters 0.24753 38 0.0065 3.5% + ORB_control set_orb_tables 1.0946 1 1.1 15.% + ORB_gen_tables gen_tables 1.0946 1 1.1 15.% + ORB_table_phi init_Table 0.47906 1 0.48 6.7% + ORB_table_phi cal_ST_Phi12_R 0.47389 126 0.0038 6.7% + ORB_table_beta init_Table_Beta 0.18249 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18097 56 0.0032 2.5% + ORB_table_alpha init_Table_Alpha 0.24717 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24526 66 0.0037 3.4% + LOOP_ions opt_ions 5.4921 1 5.5 77.% + ESolver_KS_LCAO Run 4.9277 1 4.9 69.% + HSolverLCAO solve 2.6739 11 0.24 38.% + HamiltLCAO updateHk 1.3805 11 0.13 19.% + LCAO_Hamilt cal_Hgamma 1.3529 11 0.12 19.% + Gint_interface cal_gint 2.5107 23 0.11 35.% + Gint_Gamma distri_vl 2.3787 6 0.40 33.% + LCAO_Deepks cal_projected_DM 5.3244 13 0.41 75.% + LCAO_gen_fixedH add_v_delta 2.2333 6 0.37 31.% + LCAO_DESCRIPTOR add_v_delta 2.2333 6 0.37 31.% + ElecStateLCAO psiToRho 1.2767 11 0.12 18.% + Charge mix_rho 0.77772 10 0.078 11.% + LOOP_ions force_stress 0.56415 1 0.56 7.9% + Force_Stress_LCAO getForceStress 0.56412 1 0.56 7.9% + Force_LCAO_gamma ftable_gamma 0.34824 1 0.35 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.34027 1 0.34 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:17 2022 + Finish Time : Wed Sep 28 11:09:24 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4c8dffa4c20594ff36123796b6020548328bd835 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0124092 ima = 3.69158e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123027177367 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112322612402 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112679319045 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112961862241 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112886298032 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112928930436 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011292157719 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112925077116 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112924502606 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112924454117 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112924451761 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/STRU new file mode 100644 index 0000000000000000000000000000000000000000..bf7d487563444abbe310b43be55db6ec89141890 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-10.043454779846 15.676939587548 0.750872013761 0 0 0 +H +0.0 +2 +-8.491669088674 14.770015678702 1.072151319619 0 0 0 +-9.582242551761 17.272740889596 0.198553153522 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/conv new file mode 100644 index 0000000000000000000000000000000000000000..75fea200abd336629978861359d9a26604a54f1d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/conv @@ -0,0 +1 @@ +74 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..f382e856a3438d0648383650f12947a03b6388b1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747351363 0.01277950313 1.295627472 1.386037334 1.470589659 0.008419086657 0.01985752978 0.03898087934 +-1.371607261e-18 0.001231698509 0.002671926607 0.01304815535 0.04706878777 2.89496263e-19 2.085002397e-06 6.056217402e-06 +0.001694779821 0.005814691744 + +H atom_index 1 n_descriptor 18 +1.249127065 0.0339827943 0.1084349937 0.1498417993 0.3210356344 0.02221331111 0.02829824482 0.03708690337 +2.115037973e-17 4.75839411e-05 0.1035859431 0.1146475908 0.1288685661 3.90633322e-18 4.400428757e-06 0.01310164203 +0.02669449916 0.03078880302 + +H atom_index 2 n_descriptor 18 +1.308808168 0.03207701176 0.1310074399 0.1798985542 0.3379461188 0.02486195691 0.03168977098 0.03622455435 +-2.587651163e-17 5.316503749e-05 0.1079481567 0.1273128235 0.1543757903 -7.976270973e-18 1.209083384e-06 0.01393763873 +0.02863787729 0.03306836076 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..64da66d0a8d8306aa59296188dc6b09c62c19ceb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0875919 SEC) : SETUP UNITCELL + DONE(0.0978521 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.11624 SEC) : INIT PLANEWAVE + DONE(0.165688 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.448064 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651144e+02 0.000000e+00 2.183e-01 5.493e-01 + GE2 -4.663518e+02 -1.237447e+00 9.745e-02 4.973e-01 + GE3 -4.663542e+02 -2.382057e-03 6.209e-02 5.655e-01 + GE4 -4.663551e+02 -8.430273e-04 2.094e-03 4.304e-01 + GE5 -4.663540e+02 1.052768e-03 9.030e-04 4.280e-01 + GE6 -4.663548e+02 -7.353408e-04 1.383e-04 4.095e-01 + GE7 -4.663545e+02 2.562488e-04 5.360e-05 4.159e-01 + GE8 -4.663546e+02 -6.059212e-05 1.462e-05 4.073e-01 + GE9 -4.663545e+02 2.235058e-05 1.236e-06 4.113e-01 + GE10 -4.663545e+02 -2.867703e-06 1.563e-07 4.087e-01 + GE11 -4.663545e+02 -2.805388e-07 6.302e-08 3.417e-01 +E_delta_band = -7.26759317e-02 Ry = -9.88806779e-01 eV +E_delta_NN= -1.95865500e-01 Ry = -2.66488684e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.1236 11 0.65 1e+02 % + Run_lcao lcao_line 7.1137 1 7.1 1e+02 % + Potential init_pot 0.28349 2 0.14 4 % + PW_Basis recip2real 0.28446 16 0.018 4 % + PW_Basis gathers_scatterp 0.12401 16 0.0078 1.7 % + Potential v_of_rho 0.97271 13 0.075 14 % + XC_Functional v_xc 0.2714 14 0.019 3.8 % + H_Hartree_pw v_hartree 0.65941 13 0.051 9.3 % + PW_Basis real2recip 0.64551 38 0.017 9.1 % + PW_Basis gatherp_scatters 0.24753 38 0.0065 3.5 % + ORB_control set_orb_tables 1.0946 1 1.1 15 % + ORB_gen_tables gen_tables 1.0946 1 1.1 15 % + ORB_table_phi init_Table 0.47906 1 0.48 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.47389 126 0.0038 6.7 % + ORB_table_beta init_Table_Beta 0.18249 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18097 56 0.0032 2.5 % + ORB_table_alpha init_Table_Alpha 0.24717 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24526 66 0.0037 3.4 % + LOOP_ions opt_ions 5.4921 1 5.5 77 % + ESolver_KS_LCAO Run 4.9277 1 4.9 69 % + HSolverLCAO solve 2.6739 11 0.24 38 % + HamiltLCAO updateHk 1.3805 11 0.13 19 % + LCAO_Hamilt cal_Hgamma 1.3529 11 0.12 19 % + Gint_interface cal_gint 2.5107 23 0.11 35 % + Gint_Gamma distri_vl 2.3787 6 0.4 33 % + LCAO_Deepks cal_projected_DM 5.3244 13 0.41 75 % + LCAO_gen_fixedH add_v_delta 2.2333 6 0.37 31 % + LCAO_DESCRIPTOR add_v_delta 2.2333 6 0.37 31 % + ElecStateLCAO psiToRho 1.2767 11 0.12 18 % + Charge mix_rho 0.77772 10 0.078 11 % + LOOP_ions force_stress 0.56415 1 0.56 7.9 % + Force_Stress_LCAO getForceStress 0.56412 1 0.56 7.9 % + Force_LCAO_gamma ftable_gamma 0.34824 1 0.35 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.34027 1 0.34 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:17 2022 + FINISH Time : Wed Sep 28 11:09:24 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/74/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..0bba9bdc88b588b7df00c46d956d53c000235733 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.662808 0.550193 0.0287381 +H 0.61112 0.518126 0.0527205 +H 0.691214 0.501042 0.995749 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1d85efcb941dcf6052d4f5cc6a2873ed1fe95db4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.388 2 + 2 -12.7918 2 + 3 -9.3743 2 + 4 -6.76843 2 + 5 1.27291 0 + 6 4.3895 0 + 7 11.0676 0 + 8 11.3461 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7e41eb73ca0c781a5761d415eb4b17a9a8929179 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.5586347889 15.4054016051 0.804666836564 0 0 0 0 + tauc_H1 17.1113712125 14.5075198081 1.4761746318 0 0 0 0 + tauc_H2 19.3539817143 14.0291677587 27.8809693441 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0882196374763 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0979183279028 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.116162065797 (SEC) + + DONE : INIT CHARGE Time : 0.164563775377 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.443508 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 4 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00117 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000939 + + Density error is 0.21361783107 + + Energy Rydberg eV + E_KohnSham -34.1909651327 -465.191945924 + E_Harris -34.3804651636 -467.770226115 + E_Fermi -0.405589436973 -5.51832739145 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116214219902 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110597912611 + + Density error is 0.0976447682452 + + Energy Rydberg eV + E_KohnSham -34.2798606103 -466.401430945 + E_Harris -34.2866878978 -466.494320958 + E_Fermi -0.215825131397 -2.9364515586 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00108132819548 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105006959184 + + Density error is 0.0626752958566 + + Energy Rydberg eV + E_KohnSham -34.2801660572 -466.405586764 + E_Harris -34.2845924708 -466.465811211 + E_Fermi -0.205002052858 -2.78919602057 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000950056944938 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967989169568 + + Density error is 0.00192904402595 + + Energy Rydberg eV + E_KohnSham -34.2801450872 -466.405301453 + E_Harris -34.2801454204 -466.405305987 + E_Fermi -0.169239172598 -2.30261707214 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0009502808437 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000969183889189 + + Density error is 0.000911851698168 + + Energy Rydberg eV + E_KohnSham -34.2800850591 -466.404484729 + E_Harris -34.2800866544 -466.404506434 + E_Fermi -0.168647121114 -2.29456179844 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000948711168085 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967803841155 + + Density error is 9.5393337455e-05 + + Energy Rydberg eV + E_KohnSham -34.2801257695 -466.405038622 + E_Harris -34.280125773 -466.405038669 + E_Fermi -0.168612917404 -2.2940964331 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000948682829108 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967741339808 + + Density error is 3.55566575801e-05 + + Energy Rydberg eV + E_KohnSham -34.2801129882 -466.404864723 + E_Harris -34.2801129951 -466.404864817 + E_Fermi -0.168512640169 -2.29273209132 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000948659297694 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967687275678 + + Density error is 1.23535969137e-05 + + Energy Rydberg eV + E_KohnSham -34.280114994 -466.404892013 + E_Harris -34.2801149946 -466.404892022 + E_Fermi -0.168553327855 -2.29328567569 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000948650495092 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967688821612 + + Density error is 2.56416048249e-06 + + Energy Rydberg eV + E_KohnSham -34.2801137642 -466.404875282 + E_Harris -34.2801137643 -466.404875282 + E_Fermi -0.168542448306 -2.29313765184 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000948647880798 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967690300924 + + Density error is 1.22027910174e-07 + + Energy Rydberg eV + E_KohnSham -34.2801139233 -466.404877446 + E_Harris -34.2801139233 -466.404877446 + E_Fermi -0.168539631606 -2.29309932866 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000948648071379 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000967690516305 + + Density error is 3.53136507813e-08 + + Energy Rydberg eV + E_KohnSham -34.2801139738 -466.404878133 + E_Harris -34.2801139738 -466.404878133 + E_band -7.98526159755 -108.645057747 + E_one_elec -69.3067069796 -942.966124539 + E_Hartree +36.0382234465 +490.32518467 + E_xc -8.20924775111 -111.692545709 + E_Ewald +7.32187721061 +99.6192501206 + E_demet -2.93817293548e-77 -3.9975893632e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19487558604 -2.65141837124 + E_Fermi -0.168539632247 -2.29309933738 + + charge density convergence is achieved + final etot is -466.404878133 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3880 2.00000 + 2 -12.7918 2.00000 + 3 -9.37430 2.00000 + 4 -6.76843 2.00000 + 5 1.27291 0.00000 + 6 4.38950 0.00000 + 7 11.0676 0.00000 + 8 11.3461 0.00000 + + EFERMI = -2.293099337377082 eV + OUT.ABACUS/ final etot is -466.4048781333033 eV + correction force for each atom along direction 1 is 2.86304e-05 + correction force for each atom along direction 2 is -0.000173873 + correction force for each atom along direction 3 is 7.89192e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.092025058 -0.16918342 -0.10235800 + H1 -0.51531992 +0.11549279 +0.36465052 + H2 +0.42329487 +0.053690636 -0.26229252 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4048781333033 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3086 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2983 1 6.3 1.e+02% + Potential init_pot 0.28474 2 0.14 4.5% + PW_Basis recip2real 0.26959 16 0.017 4.3% + PW_Basis gathers_scatterp 0.11670 16 0.0073 1.8% + Potential v_of_rho 0.87748 13 0.067 14.% + XC_Functional v_xc 0.24197 14 0.017 3.8% + H_Hartree_pw v_hartree 0.59799 13 0.046 9.5% + PW_Basis real2recip 0.55804 38 0.015 8.8% + PW_Basis gatherp_scatters 0.21645 38 0.0057 3.4% + ORB_control set_orb_tables 1.0995 1 1.1 17.% + ORB_gen_tables gen_tables 1.0995 1 1.1 17.% + ORB_table_phi init_Table 0.48426 1 0.48 7.7% + ORB_table_phi cal_ST_Phi12_R 0.47922 126 0.0038 7.6% + ORB_table_beta init_Table_Beta 0.18325 1 0.18 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18179 56 0.0032 2.9% + ORB_table_alpha init_Table_Alpha 0.25556 1 0.26 4.1% + ORB_table_alpha S_PhiAlpha_R 0.25365 66 0.0038 4.0% + LOOP_ions opt_ions 4.6801 1 4.7 74.% + ESolver_KS_LCAO Run 4.1335 1 4.1 66.% + HSolverLCAO solve 2.1635 11 0.20 34.% + HamiltLCAO updateHk 1.1399 11 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1017 11 0.10 17.% + Gint_interface cal_gint 2.0316 23 0.088 32.% + Gint_Gamma distri_vl 1.9907 6 0.33 32.% + LCAO_Deepks cal_projected_DM 4.5177 13 0.35 72.% + LCAO_gen_fixedH add_v_delta 1.8592 6 0.31 29.% + LCAO_DESCRIPTOR add_v_delta 1.8592 6 0.31 29.% + ElecStateLCAO psiToRho 1.0096 11 0.092 16.% + Charge mix_rho 0.65442 10 0.065 10.% + LOOP_ions force_stress 0.54641 1 0.55 8.7% + Force_Stress_LCAO getForceStress 0.54638 1 0.55 8.7% + Force_LCAO_gamma ftable_gamma 0.33259 1 0.33 5.3% + Force_LCAO_gamma cal_fvl_dphi 0.32581 1 0.33 5.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:17 2022 + Finish Time : Wed Sep 28 11:12:23 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..852230222ebeccdfa77903c7868965c9c31c1a1b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123897 ima = 3.68105e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122685964944 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111552479762 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112140662223 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112395528673 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112339223572 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112371215868 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011236861236 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112371198161 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112370653081 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112370527651 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112370522473 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/STRU new file mode 100644 index 0000000000000000000000000000000000000000..8af2a11cb8e23f9c88351c72f492b1d3e137a6c0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.441365211125 15.405401605120 0.804666836578 0 0 0 +H +0.0 +2 +-10.888628787476 14.507519808068 1.476174631825 0 0 0 +-8.646018285719 14.029167758742 -0.119030655894 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/conv new file mode 100644 index 0000000000000000000000000000000000000000..e7557f9adf3ecef4705391264972791bf4b351be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/conv @@ -0,0 +1 @@ +75 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..1c873dd7387262637896578b56e5153df4032aa2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753234501 0.01278088763 1.271681602 1.3539583 1.46964183 0.009278398618 0.01708375101 0.03913925373 +-1.190081294e-19 0.0009381246729 0.002798913274 0.01307269273 0.04658170867 -1.245732016e-19 2.643449104e-06 7.106183957e-06 +0.001595483201 0.006132000865 + +H atom_index 1 n_descriptor 18 +1.251033272 0.03472603172 0.1107202841 0.1500316171 0.3201724176 0.02303242194 0.02830207444 0.03784670243 +-1.032054706e-17 4.9637921e-05 0.1028958551 0.1153885432 0.1287013388 -5.028962183e-18 3.302523539e-06 0.01335707841 +0.02687484709 0.03078601803 + +H atom_index 2 n_descriptor 18 +1.245008932 0.03492928429 0.1085993409 0.1472367305 0.3181653568 0.02273678717 0.02794861709 0.03804006987 +4.482509867e-17 4.906353814e-05 0.1015081085 0.1150128703 0.1262870855 3.052029882e-18 3.640465276e-06 0.01341281356 +0.02664998965 0.03050726732 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9a0db6528178fb1d2392695e8bd409a29b8b1976 Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..05c566d219f07fede4a808d1cbb6f81ecb24f654 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0882476 SEC) : SETUP UNITCELL + DONE(0.0979344 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116183 SEC) : INIT PLANEWAVE + DONE(0.164696 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.443576 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651919e+02 0.000000e+00 2.136e-01 4.900e-01 + GE2 -4.664014e+02 -1.209485e+00 9.764e-02 4.119e-01 + GE3 -4.664056e+02 -4.155818e-03 6.268e-02 4.687e-01 + GE4 -4.664053e+02 2.853104e-04 1.929e-03 3.609e-01 + GE5 -4.664045e+02 8.167246e-04 9.119e-04 3.593e-01 + GE6 -4.664050e+02 -5.538935e-04 9.539e-05 3.497e-01 + GE7 -4.664049e+02 1.738992e-04 3.556e-05 3.388e-01 + GE8 -4.664049e+02 -2.729037e-05 1.235e-05 3.377e-01 + GE9 -4.664049e+02 1.673144e-05 2.564e-06 3.380e-01 + GE10 -4.664049e+02 -2.163852e-06 1.220e-07 3.403e-01 + GE11 -4.664049e+02 -6.877350e-07 3.531e-08 2.767e-01 +E_delta_band = -7.06156858e-02 Ry = -9.60775695e-01 eV +E_delta_NN= -1.94875586e-01 Ry = -2.65141837e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3086 11 0.57 1e+02 % + Run_lcao lcao_line 6.2983 1 6.3 1e+02 % + Potential init_pot 0.28474 2 0.14 4.5 % + PW_Basis recip2real 0.26959 16 0.017 4.3 % + PW_Basis gathers_scatterp 0.1167 16 0.0073 1.8 % + Potential v_of_rho 0.87748 13 0.067 14 % + XC_Functional v_xc 0.24197 14 0.017 3.8 % + H_Hartree_pw v_hartree 0.59799 13 0.046 9.5 % + PW_Basis real2recip 0.55804 38 0.015 8.8 % + PW_Basis gatherp_scatters 0.21645 38 0.0057 3.4 % + ORB_control set_orb_tables 1.0995 1 1.1 17 % + ORB_gen_tables gen_tables 1.0995 1 1.1 17 % + ORB_table_phi init_Table 0.48426 1 0.48 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.47922 126 0.0038 7.6 % + ORB_table_beta init_Table_Beta 0.18325 1 0.18 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.18179 56 0.0032 2.9 % + ORB_table_alpha init_Table_Alpha 0.25556 1 0.26 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.25365 66 0.0038 4 % + LOOP_ions opt_ions 4.6801 1 4.7 74 % + ESolver_KS_LCAO Run 4.1335 1 4.1 66 % + HSolverLCAO solve 2.1635 11 0.2 34 % + HamiltLCAO updateHk 1.1399 11 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1017 11 0.1 17 % + Gint_interface cal_gint 2.0316 23 0.088 32 % + Gint_Gamma distri_vl 1.9907 6 0.33 32 % + LCAO_Deepks cal_projected_DM 4.5177 13 0.35 72 % + LCAO_gen_fixedH add_v_delta 1.8592 6 0.31 29 % + LCAO_DESCRIPTOR add_v_delta 1.8592 6 0.31 29 % + ElecStateLCAO psiToRho 1.0096 11 0.092 16 % + Charge mix_rho 0.65442 10 0.065 10 % + LOOP_ions force_stress 0.54641 1 0.55 8.7 % + Force_Stress_LCAO getForceStress 0.54638 1 0.55 8.7 % + Force_LCAO_gamma ftable_gamma 0.33259 1 0.33 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.32581 1 0.33 5.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:17 2022 + FINISH Time : Wed Sep 28 11:12:23 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/75/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..487f8ecac88b6a00ed2f2431bfc4260f1e9d986c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.678088 0.537134 0.0384447 +H 0.620063 0.552414 0.0626503 +H 0.680342 0.471632 0.0369256 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c6116b8ebd6737e2372f4918eff8842f7fc89585 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3123 2 + 2 -13.1882 2 + 3 -9.03164 2 + 4 -6.74937 2 + 5 1.36189 0 + 6 4.52119 0 + 7 11.0635 0 + 8 11.3054 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..368f1584a9f38626e3886df95c980fe3f4ceba8d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:02 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.9864683573 15.039749772 1.07645201391 0 0 0 0 + tauc_H1 17.3617638601 15.467586972 1.75420960133 0 0 0 0 + tauc_H2 19.0495821848 13.2056966742 1.03391654196 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0732675307178 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0869403724886 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.102670119635 (SEC) + + DONE : INIT CHARGE Time : 0.144057331903 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.388976 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00166 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000612 + + Density error is 0.215313576091 + + Energy Rydberg eV + E_KohnSham -34.1915572912 -465.200002653 + E_Harris -34.384051255 -467.819017392 + E_Fermi -0.408492531912 -5.55782602444 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00146911649597 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00083727413317 + + Density error is 0.0978326934687 + + Energy Rydberg eV + E_KohnSham -34.2807001835 -466.412853925 + E_Harris -34.2873530667 -466.503371044 + E_Fermi -0.217124614302 -2.95413193056 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00134300624375 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000811612555591 + + Density error is 0.0625930983693 + + Energy Rydberg eV + E_KohnSham -34.2809022831 -466.415603632 + E_Harris -34.2851858232 -466.473884184 + E_Fermi -0.20468921366 -2.78493962492 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111921897882 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00078312781696 + + Density error is 0.00203149846344 + + Energy Rydberg eV + E_KohnSham -34.2809119831 -466.415735607 + E_Harris -34.2809139704 -466.415762645 + E_Fermi -0.169258082959 -2.3028743608 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111533442785 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783276525146 + + Density error is 0.000852411045368 + + Energy Rydberg eV + E_KohnSham -34.2808529635 -466.414932604 + E_Harris -34.2808543594 -466.414951596 + E_Fermi -0.168363243887 -2.29069945062 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111339979831 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000782769115126 + + Density error is 0.000169767973485 + + Energy Rydberg eV + E_KohnSham -34.2808921275 -466.415465458 + E_Harris -34.2808921823 -466.415466203 + E_Fermi -0.168452012306 -2.29190720693 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111315208984 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000783059363913 + + Density error is 4.02083250852e-05 + + Energy Rydberg eV + E_KohnSham -34.2808776008 -466.415267812 + E_Harris -34.2808776096 -466.415267931 + E_Fermi -0.168302663823 -2.28987521657 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011131592814 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000782976693098 + + Density error is 1.94482937265e-05 + + Energy Rydberg eV + E_KohnSham -34.2808822022 -466.415330417 + E_Harris -34.280882204 -466.415330441 + E_Fermi -0.168349209656 -2.29050850512 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111312117768 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000782983987738 + + Density error is 2.59997045069e-06 + + Energy Rydberg eV + E_KohnSham -34.2808806068 -466.41530871 + E_Harris -34.2808806068 -466.41530871 + E_Fermi -0.168329940506 -2.29024633488 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111311336663 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00078298569771 + + Density error is 4.34075711574e-07 + + Energy Rydberg eV + E_KohnSham -34.2808809087 -466.415312818 + E_Harris -34.2808809087 -466.415312818 + E_Fermi -0.168327319975 -2.29021068073 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011131131808 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000782986171419 + + Density error is 1.58804173764e-07 + + Energy Rydberg eV + E_KohnSham -34.2808809381 -466.415313218 + E_Harris -34.2808809381 -466.415313218 + E_Fermi -0.168327149388 -2.29020835978 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111311281324 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000782986393729 + + Density error is 1.03910530008e-08 + + Energy Rydberg eV + E_KohnSham -34.2808809411 -466.415313258 + E_Harris -34.2808809411 -466.415313258 + E_band -7.97923518514 -108.5630642 + E_one_elec -69.4076899743 -944.340068668 + E_Hartree +36.0981334847 +491.140302556 + E_xc -8.21894422612 -111.824473019 + E_Ewald +7.37172299408 +100.297436797 + E_demet -6.6625037745e-81 -9.06480142797e-80 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194978878426 -2.65282373625 + E_Fermi -0.168327001818 -2.29020635199 + + charge density convergence is achieved + final etot is -466.415313258 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3123 2.00000 + 2 -13.1882 2.00000 + 3 -9.03164 2.00000 + 4 -6.74937 2.00000 + 5 1.36189 0.00000 + 6 4.52119 0.00000 + 7 11.0635 0.00000 + 8 11.3054 0.00000 + + EFERMI = -2.290206351987138 eV + OUT.ABACUS/ final etot is -466.4153132583588 eV + correction force for each atom along direction 1 is -2.98935e-06 + correction force for each atom along direction 2 is -1.49566e-05 + correction force for each atom along direction 3 is 8.48398e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.87245517 +0.064308222 -0.35699702 + H1 -0.77643576 +0.090243296 +0.32067226 + H2 -0.096019410 -0.15455152 +0.036324759 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4153132583588 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3245 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3167 1 7.3 1.e+02% + Potential init_pot 0.24397 2 0.12 3.3% + PW_Basis recip2real 0.28446 17 0.017 3.9% + PW_Basis gathers_scatterp 0.11438 17 0.0067 1.6% + Potential v_of_rho 1.0030 14 0.072 14.% + XC_Functional v_xc 0.29759 15 0.020 4.1% + H_Hartree_pw v_hartree 0.66344 14 0.047 9.1% + PW_Basis real2recip 0.65858 41 0.016 9.0% + PW_Basis gatherp_scatters 0.24590 41 0.0060 3.4% + ORB_control set_orb_tables 0.90688 1 0.91 12.% + ORB_gen_tables gen_tables 0.90688 1 0.91 12.% + ORB_table_phi init_Table 0.37204 1 0.37 5.1% + ORB_table_phi cal_ST_Phi12_R 0.36782 126 0.0029 5.0% + ORB_table_beta init_Table_Beta 0.16716 1 0.17 2.3% + ORB_table_beta VNL_PhiBeta_R 0.16570 56 0.0030 2.3% + ORB_table_alpha init_Table_Alpha 0.20928 1 0.21 2.9% + ORB_table_alpha S_PhiAlpha_R 0.20760 66 0.0031 2.8% + LOOP_ions opt_ions 5.9513 1 6.0 81.% + ESolver_KS_LCAO Run 5.4047 1 5.4 74.% + HSolverLCAO solve 3.0203 12 0.25 41.% + HamiltLCAO updateHk 1.5145 12 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.4800 12 0.12 20.% + Gint_interface cal_gint 2.8936 25 0.12 40.% + Gint_Gamma distri_vl 2.8104 6 0.47 38.% + LCAO_Deepks cal_projected_DM 5.7895 14 0.41 79.% + LCAO_gen_fixedH add_v_delta 2.6820 6 0.45 37.% + LCAO_DESCRIPTOR add_v_delta 2.6819 6 0.45 37.% + ElecStateLCAO psiToRho 1.4880 12 0.12 20.% + Charge mix_rho 0.82803 11 0.075 11.% + LOOP_ions force_stress 0.54647 1 0.55 7.5% + Force_Stress_LCAO getForceStress 0.54645 1 0.55 7.5% + Force_LCAO_gamma ftable_gamma 0.35059 1 0.35 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.34332 1 0.34 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:02 2022 + Finish Time : Wed Sep 28 11:07:10 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4498fefbff43f276c09f089109a51d5d13def0ac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123657 ima = 3.66693e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012313341797 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112328132515 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112799865646 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113042795743 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112990653171 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113021869253 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113013921843 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113017040302 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113016172378 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113016088551 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113016073274 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113016065831 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/STRU new file mode 100644 index 0000000000000000000000000000000000000000..723cf3ba57df4c8cec7d25995a5a7070d4133586 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.013531642656 15.039749772035 1.076452013891 0 0 0 +H +0.0 +2 +-10.638236139861 15.467586971990 1.754209601328 0 0 0 +-8.950417815169 13.205696674184 1.033916541963 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/conv new file mode 100644 index 0000000000000000000000000000000000000000..0467b245d4858bd665752bb8b5fe6602e1ff0084 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/conv @@ -0,0 +1 @@ +76 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..9050c3e6030052f4c672bf768edd1cd5299d31d2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747588911 0.01269673156 1.279323983 1.368452217 1.469469187 0.008262555989 0.01921187716 0.03897864264 +-1.739837981e-19 0.001113367333 0.002554930004 0.01248549418 0.04492008805 -5.247425677e-19 1.910439476e-06 5.659553173e-06 +0.001689229986 0.005873201396 + +H atom_index 1 n_descriptor 18 +1.261180039 0.03365165594 0.1121787326 0.1556099483 0.3251109551 0.02261625654 0.02900806381 0.03688402877 +-8.227654405e-18 4.537717829e-05 0.1045124968 0.1156198149 0.1336540405 -2.479510404e-18 3.630933411e-06 0.01304876122 +0.02670237841 0.03129248737 + +H atom_index 2 n_descriptor 18 +1.24212858 0.03431357053 0.1055587884 0.1467149191 0.3190832151 0.02175130846 0.0279038076 0.03745109566 +2.210462996e-17 4.365325092e-05 0.1000645577 0.1145767626 0.1259835737 -3.846717214e-18 4.63745543e-06 0.01315462872 +0.02600378623 0.03044445959 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..bbf15b9c939f9082b69209d43c063bec56503e80 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:02 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0732827 SEC) : SETUP UNITCELL + DONE(0.0869542 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.102684 SEC) : INIT PLANEWAVE + DONE(0.14416 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.38902 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652000e+02 0.000000e+00 2.153e-01 5.240e-01 + GE2 -4.664129e+02 -1.212851e+00 9.783e-02 5.006e-01 + GE3 -4.664156e+02 -2.749707e-03 6.259e-02 5.643e-01 + GE4 -4.664157e+02 -1.319750e-04 2.031e-03 4.366e-01 + GE5 -4.664149e+02 8.030033e-04 8.524e-04 4.387e-01 + GE6 -4.664155e+02 -5.328543e-04 1.698e-04 4.313e-01 + GE7 -4.664153e+02 1.976460e-04 4.021e-05 4.251e-01 + GE8 -4.664153e+02 -6.260544e-05 1.945e-05 4.186e-01 + GE9 -4.664153e+02 2.170759e-05 2.600e-06 4.213e-01 + GE10 -4.664153e+02 -4.108554e-06 4.341e-07 4.172e-01 + GE11 -4.664153e+02 -4.000323e-07 1.588e-07 4.194e-01 + GE12 -4.664153e+02 -4.000934e-08 1.039e-08 3.493e-01 +E_delta_band = -7.08756590e-02 Ry = -9.64312812e-01 eV +E_delta_NN= -1.94978878e-01 Ry = -2.65282374e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3245 11 0.67 1e+02 % + Run_lcao lcao_line 7.3167 1 7.3 1e+02 % + Potential init_pot 0.24397 2 0.12 3.3 % + PW_Basis recip2real 0.28446 17 0.017 3.9 % + PW_Basis gathers_scatterp 0.11438 17 0.0067 1.6 % + Potential v_of_rho 1.003 14 0.072 14 % + XC_Functional v_xc 0.29759 15 0.02 4.1 % + H_Hartree_pw v_hartree 0.66344 14 0.047 9.1 % + PW_Basis real2recip 0.65858 41 0.016 9 % + PW_Basis gatherp_scatters 0.2459 41 0.006 3.4 % + ORB_control set_orb_tables 0.90688 1 0.91 12 % + ORB_gen_tables gen_tables 0.90688 1 0.91 12 % + ORB_table_phi init_Table 0.37204 1 0.37 5.1 % + ORB_table_phi cal_ST_Phi12_R 0.36782 126 0.0029 5 % + ORB_table_beta init_Table_Beta 0.16716 1 0.17 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.1657 56 0.003 2.3 % + ORB_table_alpha init_Table_Alpha 0.20928 1 0.21 2.9 % + ORB_table_alpha S_PhiAlpha_R 0.2076 66 0.0031 2.8 % + LOOP_ions opt_ions 5.9513 1 6 81 % + ESolver_KS_LCAO Run 5.4047 1 5.4 74 % + HSolverLCAO solve 3.0203 12 0.25 41 % + HamiltLCAO updateHk 1.5145 12 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.48 12 0.12 20 % + Gint_interface cal_gint 2.8936 25 0.12 40 % + Gint_Gamma distri_vl 2.8104 6 0.47 38 % + LCAO_Deepks cal_projected_DM 5.7895 14 0.41 79 % + LCAO_gen_fixedH add_v_delta 2.682 6 0.45 37 % + LCAO_DESCRIPTOR add_v_delta 2.6819 6 0.45 37 % + ElecStateLCAO psiToRho 1.488 12 0.12 20 % + Charge mix_rho 0.82803 11 0.075 11 % + LOOP_ions force_stress 0.54647 1 0.55 7.5 % + Force_Stress_LCAO getForceStress 0.54645 1 0.55 7.5 % + Force_LCAO_gamma ftable_gamma 0.35059 1 0.35 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.34332 1 0.34 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:02 2022 + FINISH Time : Wed Sep 28 11:07:10 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/76/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b3d9c998709145c33e2a2812d4495a0a05213dce --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.701826 0.532501 0.0437324 +H 0.64264 0.560264 0.0520094 +H 0.70357 0.49065 0.0949932 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b3b2c6d8b6920b4e206547e0cd8b5c43bd4b5246 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2557 2 + 2 -12.8193 2 + 3 -9.25894 2 + 4 -6.73944 2 + 5 1.21351 0 + 6 4.26678 0 + 7 11.092 0 + 8 11.3597 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f390093948bb3df278e4bebe2b2bd118d46eabd6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:52 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.6511413839 14.9100141472 1.22450619286 0 0 0 0 + tauc_H1 17.9939164918 15.6873792756 1.45626383864 0 0 0 0 + tauc_H2 19.6999535812 13.7382066281 2.65981001042 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.104953393575 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105308587368 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123268875551 (SEC) + + DONE : INIT CHARGE Time : 0.166486933259 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447263 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 144 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00116 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000629 + + Density error is 0.213218995642 + + Energy Rydberg eV + E_KohnSham -34.1918395035 -465.203842349 + E_Harris -34.3802358773 -467.767106515 + E_Fermi -0.400280274055 -5.44609252415 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00131486135231 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000871154442229 + + Density error is 0.0980945302266 + + Energy Rydberg eV + E_KohnSham -34.2808115186 -466.414368717 + E_Harris -34.287698545 -466.508071519 + E_Fermi -0.210038334319 -2.85771814516 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00123807527748 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000840209363446 + + Density error is 0.0630360497535 + + Energy Rydberg eV + E_KohnSham -34.2811568957 -466.419067814 + E_Harris -34.2856123108 -466.479686846 + E_Fermi -0.200507215942 -2.72804062692 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111285559577 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000810134160987 + + Density error is 0.00193561046653 + + Energy Rydberg eV + E_KohnSham -34.2811132653 -466.418474191 + E_Harris -34.2811138072 -466.418481565 + E_Fermi -0.1649313927 -2.24400671979 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111279088546 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000811113265341 + + Density error is 0.000923694440026 + + Energy Rydberg eV + E_KohnSham -34.2810597707 -466.41774636 + E_Harris -34.2810607572 -466.417759782 + E_Fermi -0.164508995374 -2.23825970934 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111106734295 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000810550301449 + + Density error is 0.000126446864252 + + Energy Rydberg eV + E_KohnSham -34.2810915782 -466.418179123 + E_Harris -34.2810915905 -466.418179291 + E_Fermi -0.164341810587 -2.23598504362 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111112702331 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00081074153466 + + Density error is 3.3069080128e-05 + + Energy Rydberg eV + E_KohnSham -34.281081144 -466.418037158 + E_Harris -34.2810811494 -466.418037232 + E_Fermi -0.164253921432 -2.23478925032 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.0011110614322 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000810667438004 + + Density error is 1.46949582835e-05 + + Energy Rydberg eV + E_KohnSham -34.2810840249 -466.418076356 + E_Harris -34.2810840259 -466.418076369 + E_Fermi -0.16428744868 -2.23524541192 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111105035296 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000810673580658 + + Density error is 2.23551437864e-06 + + Energy Rydberg eV + E_KohnSham -34.28108276 -466.418059146 + E_Harris -34.28108276 -466.418059146 + E_Fermi -0.164272907317 -2.23504756653 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111104908563 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000810676089588 + + Density error is 2.99817432202e-07 + + Energy Rydberg eV + E_KohnSham -34.2810829715 -466.418062024 + E_Harris -34.2810829715 -466.418062024 + E_Fermi -0.164270671474 -2.23501714633 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111104958662 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000810676561482 + + Density error is 1.0711236246e-07 + + Energy Rydberg eV + E_KohnSham -34.2810830042 -466.418062468 + E_Harris -34.2810830042 -466.418062468 + E_Fermi -0.164270581894 -2.23501592753 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.00111104959406 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000810676714458 + + Density error is 1.05620647029e-08 + + Energy Rydberg eV + E_KohnSham -34.281083007 -466.418062506 + E_Harris -34.281083007 -466.418062506 + E_band -7.94863487191 -108.146725579 + E_one_elec -69.1144516215 -940.350356197 + E_Hartree +35.9512118263 +489.141330842 + E_xc -8.19530327662 -111.5028214 + E_Ewald +7.20213414192 +97.9900620904 + E_demet -2.00324145575e-72 -2.7255498268e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194514811463 -2.64650978129 + E_Fermi -0.16427049457 -2.23501473943 + + charge density convergence is achieved + final etot is -466.418062506 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2557 2.00000 + 2 -12.8193 2.00000 + 3 -9.25894 2.00000 + 4 -6.73944 2.00000 + 5 1.21351 0.00000 + 6 4.26678 0.00000 + 7 11.0920 0.00000 + 8 11.3597 0.00000 + + EFERMI = -2.235014739432934 eV + OUT.ABACUS/ final etot is -466.4180625061412 eV + correction force for each atom along direction 1 is -8.64212e-06 + correction force for each atom along direction 2 is -8.41565e-05 + correction force for each atom along direction 3 is 0.000162982 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.19126442 -0.19101787 +0.38151493 + H1 -0.0096475911 +0.14970227 -0.18231276 + H2 +0.20091201 +0.041315600 -0.19920216 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4180625061412 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9314 11 0.63 1.0e+02% + Run_lcao lcao_line 6.9216 1 6.9 1.e+02% + Potential init_pot 0.28292 2 0.14 4.1% + PW_Basis recip2real 0.29520 17 0.017 4.3% + PW_Basis gathers_scatterp 0.13064 17 0.0077 1.9% + Potential v_of_rho 1.0761 14 0.077 16.% + XC_Functional v_xc 0.31332 15 0.021 4.5% + H_Hartree_pw v_hartree 0.71665 14 0.051 10.% + PW_Basis real2recip 0.76262 41 0.019 11.% + PW_Basis gatherp_scatters 0.29182 41 0.0071 4.2% + ORB_control set_orb_tables 1.0947 1 1.1 16.% + ORB_gen_tables gen_tables 1.0947 1 1.1 16.% + ORB_table_phi init_Table 0.47389 1 0.47 6.8% + ORB_table_phi cal_ST_Phi12_R 0.46872 126 0.0037 6.8% + ORB_table_beta init_Table_Beta 0.18267 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18112 56 0.0032 2.6% + ORB_table_alpha init_Table_Alpha 0.24900 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24701 66 0.0037 3.6% + LOOP_ions opt_ions 5.3035 1 5.3 77.% + ESolver_KS_LCAO Run 4.7933 1 4.8 69.% + HSolverLCAO solve 2.1259 12 0.18 31.% + HamiltLCAO updateHk 1.2496 12 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.2202 12 0.10 18.% + Gint_interface cal_gint 1.8637 25 0.075 27.% + Gint_Gamma distri_vl 2.5014 6 0.42 36.% + LCAO_Deepks cal_projected_DM 5.1419 14 0.37 74.% + LCAO_gen_fixedH add_v_delta 2.3550 6 0.39 34.% + LCAO_DESCRIPTOR add_v_delta 2.3551 6 0.39 34.% + ElecStateLCAO psiToRho 0.85274 12 0.071 12.% + Charge mix_rho 0.98676 11 0.090 14.% + LOOP_ions force_stress 0.51003 1 0.51 7.4% + Force_Stress_LCAO getForceStress 0.50999 1 0.51 7.4% + Force_LCAO_gamma ftable_gamma 0.28062 1 0.28 4.0% + Force_LCAO_gamma cal_fvl_dphi 0.27247 1 0.27 3.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:52 2022 + Finish Time : Wed Sep 28 11:13:59 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c5244850254f02fd0d75660987102532238b0667 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123667 ima = 3.67137e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123002828399 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111776697962 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112414694959 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112652660335 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112609638018 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112634542569 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112629873561 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112632425523 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011263178007 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112631691044 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112631678726 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112631674058 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/STRU new file mode 100644 index 0000000000000000000000000000000000000000..91cb1a0cd0ce60cef383c1fd6e1c78796bae9c5d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.348858616037 14.910014147213 1.224506192875 0 0 0 +H +0.0 +2 +-10.006083508196 15.687379275588 1.456263838649 0 0 0 +-8.300046418787 13.738206628099 2.659810010437 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/conv new file mode 100644 index 0000000000000000000000000000000000000000..c91d008a2acd80ad1cdc948bd5c72b258064bc82 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/conv @@ -0,0 +1 @@ +77 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..2a8278fa08b23896ad4a7a4570d31f62f0f333c8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.751761881 0.01268036435 1.264909561 1.350526861 1.469119085 0.008902994323 0.01749598504 0.03910765154 +2.406252601e-18 0.0009462675496 0.002655340835 0.01249051774 0.04501655482 9.422385762e-20 2.245914811e-06 6.32394049e-06 +0.001604984749 0.00605359628 + +H atom_index 1 n_descriptor 18 +1.238640052 0.03493811832 0.1051577338 0.1445180628 0.316716316 0.02201495176 0.02760644955 0.03808448215 +-3.795533852e-18 4.555688057e-05 0.09850224636 0.1147701351 0.1239137066 -1.012364166e-17 4.318679876e-06 0.01340065799 +0.02594926472 0.03020773821 + +H atom_index 2 n_descriptor 18 +1.231999873 0.03516253933 0.1029276471 0.1415411957 0.314426082 0.02169683143 0.02721625387 0.03832143129 +-6.754748001e-17 4.49398495e-05 0.09679824634 0.1145170523 0.1213272622 9.527142041e-18 4.661364351e-06 0.01350451425 +0.02569150026 0.02988664037 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0b1139e31eb80061101257eeeaa65c739d284482 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:52 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.104979 SEC) : SETUP UNITCELL + DONE(0.105324 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123289 SEC) : INIT PLANEWAVE + DONE(0.166624 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447329 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652038e+02 0.000000e+00 2.132e-01 5.094e-01 + GE2 -4.664144e+02 -1.210526e+00 9.809e-02 4.582e-01 + GE3 -4.664191e+02 -4.699097e-03 6.304e-02 5.237e-01 + GE4 -4.664185e+02 5.936226e-04 1.936e-03 3.830e-01 + GE5 -4.664177e+02 7.278319e-04 9.237e-04 3.826e-01 + GE6 -4.664182e+02 -4.327633e-04 1.264e-04 3.747e-01 + GE7 -4.664180e+02 1.419647e-04 3.307e-05 3.655e-01 + GE8 -4.664181e+02 -3.919770e-05 1.469e-05 3.607e-01 + GE9 -4.664181e+02 1.720984e-05 2.236e-06 3.621e-01 + GE10 -4.664181e+02 -2.877640e-06 2.998e-07 3.641e-01 + GE11 -4.664181e+02 -4.439583e-07 1.071e-07 3.597e-01 + GE12 -4.664181e+02 -3.857662e-08 1.056e-08 2.871e-01 +E_delta_band = -6.98407344e-02 Ry = -9.50231940e-01 eV +E_delta_NN= -1.94514811e-01 Ry = -2.64650978e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.9314 11 0.63 1e+02 % + Run_lcao lcao_line 6.9216 1 6.9 1e+02 % + Potential init_pot 0.28292 2 0.14 4.1 % + PW_Basis recip2real 0.2952 17 0.017 4.3 % + PW_Basis gathers_scatterp 0.13064 17 0.0077 1.9 % + Potential v_of_rho 1.0761 14 0.077 16 % + XC_Functional v_xc 0.31332 15 0.021 4.5 % + H_Hartree_pw v_hartree 0.71665 14 0.051 10 % + PW_Basis real2recip 0.76262 41 0.019 11 % + PW_Basis gatherp_scatters 0.29182 41 0.0071 4.2 % + ORB_control set_orb_tables 1.0947 1 1.1 16 % + ORB_gen_tables gen_tables 1.0947 1 1.1 16 % + ORB_table_phi init_Table 0.47389 1 0.47 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.46872 126 0.0037 6.8 % + ORB_table_beta init_Table_Beta 0.18267 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18112 56 0.0032 2.6 % + ORB_table_alpha init_Table_Alpha 0.249 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24701 66 0.0037 3.6 % + LOOP_ions opt_ions 5.3035 1 5.3 77 % + ESolver_KS_LCAO Run 4.7933 1 4.8 69 % + HSolverLCAO solve 2.1259 12 0.18 31 % + HamiltLCAO updateHk 1.2496 12 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.2202 12 0.1 18 % + Gint_interface cal_gint 1.8637 25 0.075 27 % + Gint_Gamma distri_vl 2.5014 6 0.42 36 % + LCAO_Deepks cal_projected_DM 5.1419 14 0.37 74 % + LCAO_gen_fixedH add_v_delta 2.355 6 0.39 34 % + LCAO_DESCRIPTOR add_v_delta 2.3551 6 0.39 34 % + ElecStateLCAO psiToRho 0.85274 12 0.071 12 % + Charge mix_rho 0.98676 11 0.09 14 % + LOOP_ions force_stress 0.51003 1 0.51 7.4 % + Force_Stress_LCAO getForceStress 0.50999 1 0.51 7.4 % + Force_LCAO_gamma ftable_gamma 0.28062 1 0.28 4 % + Force_LCAO_gamma cal_fvl_dphi 0.27247 1 0.27 3.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:52 2022 + FINISH Time : Wed Sep 28 11:13:59 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/77/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..af35cf5951b3fdb659ac415005028e0864b07669 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.711183 0.516021 0.0404248 +H 0.679587 0.570316 0.0221489 +H 0.733753 0.528945 0.101414 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ed0f72c51f37c1c10747df69abbfb33f7d305f62 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2069 2 + 2 -13.037 2 + 3 -9.0603 2 + 4 -6.7262 2 + 5 1.25386 0 + 6 4.33683 0 + 7 11.0918 0 + 8 11.3394 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..05b08e0aeef61d43103207c7698325724c541a4c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:49 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.9131108391 14.4485779658 1.13189535307 0 0 0 0 + tauc_H1 19.0284321387 15.9688479672 0.620168366695 0 0 0 0 + tauc_H2 20.5450725209 14.8104538056 2.83957997866 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0751459413054 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0754236372231 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.091148197964 (SEC) + + DONE : INIT CHARGE Time : 0.132754788505 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.379877 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 100 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000555 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000952 + + Density error is 0.214028051685 + + Energy Rydberg eV + E_KohnSham -34.1924163328 -465.211690514 + E_Harris -34.3820514058 -467.791808048 + E_Fermi -0.400704509895 -5.45186454887 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000831757634327 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119635254256 + + Density error is 0.0981339082422 + + Energy Rydberg eV + E_KohnSham -34.2811326379 -466.41873777 + E_Harris -34.2879048026 -466.510877797 + E_Fermi -0.210552203172 -2.86470968959 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000802758011735 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114547340789 + + Density error is 0.062988285915 + + Energy Rydberg eV + E_KohnSham -34.2814047894 -466.42244058 + E_Harris -34.2857797907 -466.481965527 + E_Fermi -0.200034881957 -2.72161419337 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000773389158602 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107596045911 + + Density error is 0.00199907459299 + + Energy Rydberg eV + E_KohnSham -34.2813798434 -466.422101173 + E_Harris -34.2813810285 -466.422117297 + E_Fermi -0.164655789859 -2.24025695077 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000774512266382 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107660569203 + + Density error is 0.000856867548139 + + Energy Rydberg eV + E_KohnSham -34.2813292449 -466.421412745 + E_Harris -34.2813306265 -466.421431542 + E_Fermi -0.164052105503 -2.23204340374 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000773982955942 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107554484212 + + Density error is 0.00017127779683 + + Energy Rydberg eV + E_KohnSham -34.2813599173 -466.421830064 + E_Harris -34.2813598022 -466.421828498 + E_Fermi -0.163952466568 -2.23068774648 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000774221148396 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107576844152 + + Density error is 3.61470800058e-05 + + Energy Rydberg eV + E_KohnSham -34.2813485484 -466.421675382 + E_Harris -34.2813485548 -466.42167547 + E_Fermi -0.163842158438 -2.22918692738 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000774158340768 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107568391616 + + Density error is 1.54652969868e-05 + + Energy Rydberg eV + E_KohnSham -34.2813527631 -466.421732726 + E_Harris -34.2813527641 -466.42173274 + E_Fermi -0.163877690429 -2.22967036491 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000774164589654 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107568154664 + + Density error is 1.83977764331e-06 + + Energy Rydberg eV + E_KohnSham -34.2813514317 -466.421714612 + E_Harris -34.2813514317 -466.421714612 + E_Fermi -0.163861603193 -2.22945148684 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000774165677754 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107568205952 + + Density error is 2.1610295916e-07 + + Energy Rydberg eV + E_KohnSham -34.2813516506 -466.42171759 + E_Harris -34.2813516506 -466.42171759 + E_Fermi -0.163859852129 -2.22942766239 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000774166165357 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107568276932 + + Density error is 5.77659825154e-08 + + Energy Rydberg eV + E_KohnSham -34.2813516777 -466.421717958 + E_Harris -34.2813516777 -466.421717958 + E_band -7.94231373998 -108.060722167 + E_one_elec -69.1580714824 -940.943834851 + E_Hartree +35.9791396054 +489.521307771 + E_xc -8.19977713173 -111.563691322 + E_Ewald +7.22197247305 +98.2599764326 + E_demet -7.72926979564e-74 -1.051621106e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194536066061 -2.64679896494 + E_Fermi -0.163859786539 -2.22942677 + + charge density convergence is achieved + final etot is -466.421717958 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2069 2.00000 + 2 -13.0370 2.00000 + 3 -9.06030 2.00000 + 4 -6.72620 2.00000 + 5 1.25386 0.00000 + 6 4.33683 0.00000 + 7 11.0918 0.00000 + 8 11.3394 0.00000 + + EFERMI = -2.229426769997048 eV + OUT.ABACUS/ final etot is -466.4217179580496 eV + correction force for each atom along direction 1 is -2.86906e-05 + correction force for each atom along direction 2 is 3.58275e-05 + correction force for each atom along direction 3 is -1.09040e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.27678204 -0.27089026 +0.35070011 + H1 -0.12632354 +0.27622926 -0.018772114 + H2 -0.15045851 -0.0053390024 -0.33192799 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4217179580496 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0485 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0400 1 7.0 1.e+02% + Potential init_pot 0.24677 2 0.12 3.5% + PW_Basis recip2real 0.26741 16 0.017 3.8% + PW_Basis gathers_scatterp 0.10939 16 0.0068 1.6% + Potential v_of_rho 0.93346 13 0.072 13.% + XC_Functional v_xc 0.28301 14 0.020 4.0% + H_Hartree_pw v_hartree 0.61227 13 0.047 8.7% + PW_Basis real2recip 0.59975 38 0.016 8.5% + PW_Basis gatherp_scatters 0.22552 38 0.0059 3.2% + ORB_control set_orb_tables 0.90190 1 0.90 13.% + ORB_gen_tables gen_tables 0.90190 1 0.90 13.% + ORB_table_phi init_Table 0.37759 1 0.38 5.4% + ORB_table_phi cal_ST_Phi12_R 0.37329 126 0.0030 5.3% + ORB_table_beta init_Table_Beta 0.15553 1 0.16 2.2% + ORB_table_beta VNL_PhiBeta_R 0.15415 56 0.0028 2.2% + ORB_table_alpha init_Table_Alpha 0.21113 1 0.21 3.0% + ORB_table_alpha S_PhiAlpha_R 0.20943 66 0.0032 3.0% + LOOP_ions opt_ions 5.6900 1 5.7 81.% + ESolver_KS_LCAO Run 5.1361 1 5.1 73.% + HSolverLCAO solve 2.9555 11 0.27 42.% + HamiltLCAO updateHk 1.4773 11 0.13 21.% + LCAO_Hamilt cal_Hgamma 1.4458 11 0.13 21.% + Gint_interface cal_gint 2.8462 23 0.12 40.% + Gint_Gamma distri_vl 2.4605 6 0.41 35.% + LCAO_Deepks cal_projected_DM 5.5287 13 0.43 78.% + LCAO_gen_fixedH add_v_delta 2.3321 6 0.39 33.% + LCAO_DESCRIPTOR add_v_delta 2.3321 6 0.39 33.% + ElecStateLCAO psiToRho 1.4617 11 0.13 21.% + Charge mix_rho 0.76158 10 0.076 11.% + LOOP_ions force_stress 0.55380 1 0.55 7.9% + Force_Stress_LCAO getForceStress 0.55378 1 0.55 7.9% + Force_LCAO_gamma ftable_gamma 0.35484 1 0.35 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.34706 1 0.35 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:49 2022 + Finish Time : Wed Sep 28 11:10:56 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..e05b0b389b4f7853d2970a837db70479f3c8ea99 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123361 ima = 3.69382e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123275639353 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112297807353 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112859763236 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113083399689 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113044172036 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113068428123 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001130609224 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113063626202 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113062978766 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113062905489 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113062894993 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/STRU new file mode 100644 index 0000000000000000000000000000000000000000..28bdc58f5af49e5ec93840d30696a2721f22820e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.086889160930 14.448577965796 1.131895353087 0 0 0 +H +0.0 +2 +-8.971567861258 15.968847967222 0.620168366717 0 0 0 +-7.454927479098 14.810453805587 2.839579978676 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/conv new file mode 100644 index 0000000000000000000000000000000000000000..5c4cf96e6b47d891846421894fb2177b10dac58f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/conv @@ -0,0 +1 @@ +78 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e4ab4c2c41305fbede7787272e2abcf576c5469b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748461135 0.01262791959 1.268467942 1.358746719 1.468956584 0.008316726629 0.01870492501 0.03900845979 +2.923448472e-19 0.001037836395 0.002516508912 0.01217815795 0.04397453291 1.313215397e-19 1.854398743e-06 5.526675959e-06 +0.001664089446 0.005899996454 + +H atom_index 1 n_descriptor 18 +1.246077912 0.03428760852 0.1066764004 0.1484523869 0.3203364672 0.02190731063 0.02812316281 0.0374607806 +-9.107492476e-18 4.298084677e-05 0.1000783319 0.114888991 0.1273896466 -1.516890471e-18 4.325656279e-06 0.0131439171 +0.02595059956 0.03060416417 + +H atom_index 2 n_descriptor 18 +1.226560158 0.03496250648 0.1001914 0.1397031472 0.3137963963 0.02101034074 0.02698449335 0.03814692684 +-1.313509961e-17 4.124983753e-05 0.09500744156 0.1142769186 0.1197898105 -7.698351595e-18 5.2635701e-06 0.01342149124 +0.02519956257 0.02967696365 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..e657365ee191426b773132c6413e967f4907d5f2 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:49 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0751612 SEC) : SETUP UNITCELL + DONE(0.0754319 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.091163 SEC) : INIT PLANEWAVE + DONE(0.132886 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.379926 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652117e+02 0.000000e+00 2.140e-01 5.404e-01 + GE2 -4.664187e+02 -1.207047e+00 9.813e-02 5.154e-01 + GE3 -4.664224e+02 -3.702810e-03 6.299e-02 5.791e-01 + GE4 -4.664221e+02 3.394072e-04 1.999e-03 4.544e-01 + GE5 -4.664214e+02 6.884281e-04 8.569e-04 4.515e-01 + GE6 -4.664218e+02 -4.173193e-04 1.713e-04 4.468e-01 + GE7 -4.664217e+02 1.546822e-04 3.615e-05 4.373e-01 + GE8 -4.664217e+02 -5.734460e-05 1.547e-05 4.324e-01 + GE9 -4.664217e+02 1.811448e-05 1.840e-06 4.314e-01 + GE10 -4.664217e+02 -2.977740e-06 2.161e-07 4.332e-01 + GE11 -4.664217e+02 -3.684703e-07 5.777e-08 3.608e-01 +E_delta_band = -6.99209240e-02 Ry = -9.51322976e-01 eV +E_delta_NN= -1.94536066e-01 Ry = -2.64679896e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0485 11 0.64 1e+02 % + Run_lcao lcao_line 7.04 1 7 1e+02 % + Potential init_pot 0.24677 2 0.12 3.5 % + PW_Basis recip2real 0.26741 16 0.017 3.8 % + PW_Basis gathers_scatterp 0.10939 16 0.0068 1.6 % + Potential v_of_rho 0.93346 13 0.072 13 % + XC_Functional v_xc 0.28301 14 0.02 4 % + H_Hartree_pw v_hartree 0.61227 13 0.047 8.7 % + PW_Basis real2recip 0.59975 38 0.016 8.5 % + PW_Basis gatherp_scatters 0.22552 38 0.0059 3.2 % + ORB_control set_orb_tables 0.9019 1 0.9 13 % + ORB_gen_tables gen_tables 0.9019 1 0.9 13 % + ORB_table_phi init_Table 0.37759 1 0.38 5.4 % + ORB_table_phi cal_ST_Phi12_R 0.37329 126 0.003 5.3 % + ORB_table_beta init_Table_Beta 0.15553 1 0.16 2.2 % + ORB_table_beta VNL_PhiBeta_R 0.15415 56 0.0028 2.2 % + ORB_table_alpha init_Table_Alpha 0.21113 1 0.21 3 % + ORB_table_alpha S_PhiAlpha_R 0.20943 66 0.0032 3 % + LOOP_ions opt_ions 5.69 1 5.7 81 % + ESolver_KS_LCAO Run 5.1361 1 5.1 73 % + HSolverLCAO solve 2.9555 11 0.27 42 % + HamiltLCAO updateHk 1.4773 11 0.13 21 % + LCAO_Hamilt cal_Hgamma 1.4458 11 0.13 21 % + Gint_interface cal_gint 2.8462 23 0.12 40 % + Gint_Gamma distri_vl 2.4605 6 0.41 35 % + LCAO_Deepks cal_projected_DM 5.5287 13 0.43 78 % + LCAO_gen_fixedH add_v_delta 2.3321 6 0.39 33 % + LCAO_DESCRIPTOR add_v_delta 2.3321 6 0.39 33 % + ElecStateLCAO psiToRho 1.4617 11 0.13 21 % + Charge mix_rho 0.76158 10 0.076 11 % + LOOP_ions force_stress 0.5538 1 0.55 7.9 % + Force_Stress_LCAO getForceStress 0.55378 1 0.55 7.9 % + Force_LCAO_gamma ftable_gamma 0.35484 1 0.35 5 % + Force_LCAO_gamma cal_fvl_dphi 0.34706 1 0.35 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:49 2022 + FINISH Time : Wed Sep 28 11:10:56 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/78/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..72f1b8333e583d8b415c656822878bf79e9c6369 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.718687 0.49594 0.031721 +H 0.68582 0.554487 0.0308722 +H 0.767977 0.506463 0.0723521 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..2eec3a836e80e0f90d767aea18ec68b3d0a646ff --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2244 2 + 2 -12.9669 2 + 3 -9.12093 2 + 4 -6.72991 2 + 5 1.22316 0 + 6 4.32127 0 + 7 11.0915 0 + 8 11.3422 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e92e1719a1d93e5e3fe952bf76cd7c8707e6ebd4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:14:31 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 20.1232343654 13.8863144163 0.88818680925 0 0 0 0 + tauc_H1 19.2029694623 15.5256321613 0.864420740858 0 0 0 0 + tauc_H2 21.5033488054 14.180970575 2.02585756205 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.104906542456 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105325553731 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123495788452 (SEC) + + DONE : INIT CHARGE Time : 0.168009818682 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.449132 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 100 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000583 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0015 + + Density error is 0.213878025859 + + Energy Rydberg eV + E_KohnSham -34.1912541256 -465.195877874 + E_Harris -34.3807275178 -467.773795627 + E_Fermi -0.400833424671 -5.45361852437 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000860760254031 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138787901506 + + Density error is 0.0981680409518 + + Energy Rydberg eV + E_KohnSham -34.2801279063 -466.405067695 + E_Harris -34.2869457556 -466.497829294 + E_Fermi -0.210633122338 -2.86581065133 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000827995285214 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129114626571 + + Density error is 0.0629909317411 + + Energy Rydberg eV + E_KohnSham -34.2804242573 -466.409099757 + E_Harris -34.2848296492 -466.469038188 + E_Fermi -0.200435233311 -2.72706125299 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000792936562013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011235983267 + + Density error is 0.00198313357102 + + Energy Rydberg eV + E_KohnSham -34.2803925788 -466.408668749 + E_Harris -34.2803940671 -466.408688998 + E_Fermi -0.164961438334 -2.24441551162 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000795055598313 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112297949741 + + Density error is 0.000869203905535 + + Energy Rydberg eV + E_KohnSham -34.2803434188 -466.407999892 + E_Harris -34.280344132 -466.408009596 + E_Fermi -0.164434973773 -2.23725259379 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000794403440674 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112085614114 + + Density error is 0.000166190333964 + + Energy Rydberg eV + E_KohnSham -34.2803724166 -466.408394428 + E_Harris -34.2803724475 -466.408394849 + E_Fermi -0.164296965468 -2.23537489448 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000794570430517 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011208133344 + + Density error is 3.40212406843e-05 + + Energy Rydberg eV + E_KohnSham -34.280362028 -466.408253084 + E_Harris -34.280362033 -466.408253151 + E_Fermi -0.164199727455 -2.23405190344 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000794530083268 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112077573905 + + Density error is 1.80022493847e-05 + + Energy Rydberg eV + E_KohnSham -34.2803658368 -466.408304905 + E_Harris -34.2803658383 -466.408304926 + E_Fermi -0.164232028583 -2.23449138283 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000794542368783 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112076345426 + + Density error is 2.87708361107e-06 + + Energy Rydberg eV + E_KohnSham -34.2803644549 -466.408286103 + E_Harris -34.2803644549 -466.408286104 + E_Fermi -0.164215494257 -2.23426642178 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000794540310886 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112075514281 + + Density error is 4.84341715587e-07 + + Energy Rydberg eV + E_KohnSham -34.2803647374 -466.408289947 + E_Harris -34.2803647374 -466.408289947 + E_Fermi -0.164212603336 -2.23422708879 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000794541127066 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112075566514 + + Density error is 1.71887912601e-07 + + Energy Rydberg eV + E_KohnSham -34.2803647676 -466.408290358 + E_Harris -34.2803647676 -466.408290358 + E_Fermi -0.164212400711 -2.23422433192 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000794541332637 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112075554439 + + Density error is 1.05969452788e-08 + + Energy Rydberg eV + E_KohnSham -34.280364771 -466.408290404 + E_Harris -34.280364771 -466.408290404 + E_band -7.94404643607 -108.084296707 + E_one_elec -69.141085099 -940.712723249 + E_Hartree +35.9687724021 +489.380254734 + E_xc -8.19825124393 -111.542930553 + E_Ewald +7.21483889921 +98.1629191813 + E_demet -8.7710807328e-73 -1.19336675584e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194548329541 -2.64696581814 + E_Fermi -0.164212237186 -2.23422210706 + + charge density convergence is achieved + final etot is -466.408290404 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2244 2.00000 + 2 -12.9669 2.00000 + 3 -9.12093 2.00000 + 4 -6.72991 2.00000 + 5 1.22316 0.00000 + 6 4.32127 0.00000 + 7 11.0915 0.00000 + 8 11.3422 0.00000 + + EFERMI = -2.234222107060098 eV + OUT.ABACUS/ final etot is -466.4082904037337 eV + correction force for each atom along direction 1 is 2.39080e-05 + correction force for each atom along direction 2 is 0.000123514 + correction force for each atom along direction 3 is -9.75663e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -1.1045921 +0.66757683 -0.55259133 + H1 +0.42815359 -0.79191684 +0.00099078553 + H2 +0.67643856 +0.12434001 +0.55160054 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4082904037337 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0963 11 0.65 1.0e+02% + Run_lcao lcao_line 7.0857 1 7.1 1.e+02% + Potential init_pot 0.28305 2 0.14 4.0% + PW_Basis recip2real 0.29537 17 0.017 4.2% + PW_Basis gathers_scatterp 0.12836 17 0.0076 1.8% + Potential v_of_rho 1.0736 14 0.077 15.% + XC_Functional v_xc 0.31344 15 0.021 4.4% + H_Hartree_pw v_hartree 0.71409 14 0.051 10.% + PW_Basis real2recip 0.74791 41 0.018 11.% + PW_Basis gatherp_scatters 0.28207 41 0.0069 4.0% + ORB_control set_orb_tables 1.0897 1 1.1 15.% + ORB_gen_tables gen_tables 1.0897 1 1.1 15.% + ORB_table_phi init_Table 0.47265 1 0.47 6.7% + ORB_table_phi cal_ST_Phi12_R 0.46746 126 0.0037 6.6% + ORB_table_beta init_Table_Beta 0.18022 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.17870 56 0.0032 2.5% + ORB_table_alpha init_Table_Alpha 0.24811 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24613 66 0.0037 3.5% + LOOP_ions opt_ions 5.4712 1 5.5 77.% + ESolver_KS_LCAO Run 4.9463 1 4.9 70.% + HSolverLCAO solve 2.2973 12 0.19 32.% + HamiltLCAO updateHk 1.3466 12 0.11 19.% + LCAO_Hamilt cal_Hgamma 1.3172 12 0.11 19.% + Gint_interface cal_gint 2.0574 25 0.082 29.% + Gint_Gamma distri_vl 2.5768 6 0.43 36.% + LCAO_Deepks cal_projected_DM 5.3007 14 0.38 75.% + LCAO_gen_fixedH add_v_delta 2.4299 6 0.40 34.% + LCAO_DESCRIPTOR add_v_delta 2.4299 6 0.40 34.% + ElecStateLCAO psiToRho 0.92427 12 0.077 13.% + Charge mix_rho 0.98202 11 0.089 14.% + LOOP_ions force_stress 0.52469 1 0.52 7.4% + Force_Stress_LCAO getForceStress 0.52466 1 0.52 7.4% + Force_LCAO_gamma ftable_gamma 0.30470 1 0.30 4.3% + Force_LCAO_gamma cal_fvl_dphi 0.29628 1 0.30 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:14:31 2022 + Finish Time : Wed Sep 28 11:14:38 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2468a231285e38ec1d3e5281b656107f128afc51 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123596 ima = 3.6832e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012318022822 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112100460467 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112689617419 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112917014152 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112878963665 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112901918212 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112895410715 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112898052478 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112897215424 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112897126191 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112897108801 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112897100237 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/STRU new file mode 100644 index 0000000000000000000000000000000000000000..94768bcbaca1998735c5e40e730937e95c5f6769 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-7.876765634622 13.886314416346 0.888186809260 0 0 0 +H +0.0 +2 +-8.797030537666 15.525632161325 0.864420740842 0 0 0 +-6.496651194641 14.180970574968 2.025857562037 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/conv new file mode 100644 index 0000000000000000000000000000000000000000..c4a89aae5cdbf6518b68e75e34fcee9d929e5d50 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/conv @@ -0,0 +1 @@ +79 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..65445305e2c7114b9d4b9cc44af73f2eb28c5388 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749588308 0.01262595629 1.265142621 1.358001103 1.469040829 0.008515584735 0.01834510321 0.03904890615 +2.74263203e-19 0.001009775305 0.002561583464 0.01220038907 0.04436422211 3.461075327e-20 1.948669853e-06 5.747957784e-06 +0.00163681293 0.005934859399 + +H atom_index 1 n_descriptor 18 +1.2089246 0.03566654427 0.0947481162 0.1319739724 0.3071061276 0.02028887149 0.02592053508 0.03895770554 +9.125673901e-18 4.073383704e-05 0.09032889024 0.1130066252 0.1137149745 -8.914028657e-19 5.959421196e-06 0.01388154494 +0.02453783582 0.02876254827 + +H atom_index 2 n_descriptor 18 +1.262259904 0.03385382824 0.1124968558 0.1558660322 0.3251334641 0.0227660906 0.02903464402 0.03710634359 +4.080715127e-17 4.55383785e-05 0.1037657502 0.1158585245 0.1337563651 5.110804989e-18 3.383131874e-06 0.0131200596 +0.02659208706 0.03130544084 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..dcd82bb002e5ad73740efae453f51833ced8dad4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:14:31 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.104931 SEC) : SETUP UNITCELL + DONE(0.105343 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123515 SEC) : INIT PLANEWAVE + DONE(0.168141 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.449196 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651959e+02 0.000000e+00 2.139e-01 5.198e-01 + GE2 -4.664051e+02 -1.209190e+00 9.817e-02 4.671e-01 + GE3 -4.664091e+02 -4.032062e-03 6.299e-02 5.399e-01 + GE4 -4.664087e+02 4.310087e-04 1.983e-03 3.982e-01 + GE5 -4.664080e+02 6.688566e-04 8.692e-04 3.938e-01 + GE6 -4.664084e+02 -3.945362e-04 1.662e-04 3.907e-01 + GE7 -4.664083e+02 1.413441e-04 3.402e-05 3.780e-01 + GE8 -4.664083e+02 -5.182131e-05 1.800e-05 3.727e-01 + GE9 -4.664083e+02 1.880200e-05 2.877e-06 3.740e-01 + GE10 -4.664083e+02 -3.843262e-06 4.843e-07 3.734e-01 + GE11 -4.664083e+02 -4.117320e-07 1.719e-07 3.734e-01 + GE12 -4.664083e+02 -4.528737e-08 1.060e-08 3.024e-01 +E_delta_band = -6.99086001e-02 Ry = -9.51155301e-01 eV +E_delta_NN= -1.94548330e-01 Ry = -2.64696582e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0963 11 0.65 1e+02 % + Run_lcao lcao_line 7.0857 1 7.1 1e+02 % + Potential init_pot 0.28305 2 0.14 4 % + PW_Basis recip2real 0.29537 17 0.017 4.2 % + PW_Basis gathers_scatterp 0.12836 17 0.0076 1.8 % + Potential v_of_rho 1.0736 14 0.077 15 % + XC_Functional v_xc 0.31344 15 0.021 4.4 % + H_Hartree_pw v_hartree 0.71409 14 0.051 10 % + PW_Basis real2recip 0.74791 41 0.018 11 % + PW_Basis gatherp_scatters 0.28207 41 0.0069 4 % + ORB_control set_orb_tables 1.0897 1 1.1 15 % + ORB_gen_tables gen_tables 1.0897 1 1.1 15 % + ORB_table_phi init_Table 0.47265 1 0.47 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.46746 126 0.0037 6.6 % + ORB_table_beta init_Table_Beta 0.18022 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.1787 56 0.0032 2.5 % + ORB_table_alpha init_Table_Alpha 0.24811 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24613 66 0.0037 3.5 % + LOOP_ions opt_ions 5.4712 1 5.5 77 % + ESolver_KS_LCAO Run 4.9463 1 4.9 70 % + HSolverLCAO solve 2.2973 12 0.19 32 % + HamiltLCAO updateHk 1.3466 12 0.11 19 % + LCAO_Hamilt cal_Hgamma 1.3172 12 0.11 19 % + Gint_interface cal_gint 2.0574 25 0.082 29 % + Gint_Gamma distri_vl 2.5768 6 0.43 36 % + LCAO_Deepks cal_projected_DM 5.3007 14 0.38 75 % + LCAO_gen_fixedH add_v_delta 2.4299 6 0.4 34 % + LCAO_DESCRIPTOR add_v_delta 2.4299 6 0.4 34 % + ElecStateLCAO psiToRho 0.92427 12 0.077 13 % + Charge mix_rho 0.98202 11 0.089 14 % + LOOP_ions force_stress 0.52469 1 0.52 7.4 % + Force_Stress_LCAO getForceStress 0.52466 1 0.52 7.4 % + Force_LCAO_gamma ftable_gamma 0.3047 1 0.3 4.3 % + Force_LCAO_gamma cal_fvl_dphi 0.29628 1 0.3 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:14:31 2022 + FINISH Time : Wed Sep 28 11:14:38 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/79/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..1f9ec65e63c74f7dfb716e006aeb27eb0cc98d70 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.50961 0.678312 0.27154 +H 0.56309 0.676128 0.315712 +H 0.534199 0.699167 0.214633 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c8dcca71e24663aa1eefbc40a35fec91219eb1bc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9571 2 + 2 -12.8604 2 + 3 -8.97634 2 + 4 -6.66651 2 + 5 0.981355 0 + 6 4.0094 0 + 7 11.1504 0 + 8 11.3846 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e8d016b0db8fe1f888765cc818f537e11c2391e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:02 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.2690908315 18.9927430679 7.60311259625 0 0 0 0 + tauc_H1 15.7665278742 18.9315811102 8.83993089358 0 0 0 0 + tauc_H2 14.9575714128 19.5766720061 6.00973041178 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.110586754914 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.11096480849 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.129555130103 (SEC) + + DONE : INIT CHARGE Time : 0.172871234209 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451948 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 301 ; sender_size of each process is: +144 144 4 9 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00094 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000774 + + Density error is 0.213007213941 + + Energy Rydberg eV + E_KohnSham -34.1863694329 -465.129418221 + E_Harris -34.374101807 -467.683648208 + E_Fermi -0.388024486069 -5.27934397406 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00129097082481 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000875709736095 + + Density error is 0.0992424834904 + + Energy Rydberg eV + E_KohnSham -34.2762555798 -466.35238199 + E_Harris -34.2834657555 -466.450481462 + E_Fermi -0.196771114292 -2.67720835618 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00123633251662 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000839029168893 + + Density error is 0.0641186121104 + + Energy Rydberg eV + E_KohnSham -34.2767534237 -466.359155503 + E_Harris -34.2813355713 -466.42149882 + E_Fermi -0.190638375075 -2.59376815849 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116614450215 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00079459214998 + + Density error is 0.00203041875059 + + Energy Rydberg eV + E_KohnSham -34.2766540848 -466.357803928 + E_Harris -34.2766577435 -466.357853707 + E_Fermi -0.155481253162 -2.11543097518 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116688851337 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000795390609873 + + Density error is 0.000992564680402 + + Energy Rydberg eV + E_KohnSham -34.2766145187 -466.357265604 + E_Harris -34.2766148499 -466.35727011 + E_Fermi -0.155349795369 -2.11364240015 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116585606265 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000794798052364 + + Density error is 0.000197629381195 + + Energy Rydberg eV + E_KohnSham -34.2766306132 -466.357484581 + E_Harris -34.2766306333 -466.357484854 + E_Fermi -0.154919626607 -2.10778965388 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116614301386 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000795002935574 + + Density error is 3.34913723086e-05 + + Energy Rydberg eV + E_KohnSham -34.2766254383 -466.357414173 + E_Harris -34.2766254418 -466.357414221 + E_Fermi -0.154892944249 -2.10742662179 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116607512272 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000794974540395 + + Density error is 1.31543217468e-05 + + Energy Rydberg eV + E_KohnSham -34.2766285973 -466.357457153 + E_Harris -34.276628598 -466.357457163 + E_Fermi -0.154910398942 -2.10766410506 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116607136807 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000794974463759 + + Density error is 1.67807235499e-06 + + Energy Rydberg eV + E_KohnSham -34.2766275216 -466.357442517 + E_Harris -34.2766275216 -466.357442517 + E_Fermi -0.154896477737 -2.10747469736 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116606622063 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00079497128232 + + Density error is 6.20808090897e-07 + + Energy Rydberg eV + E_KohnSham -34.2766277306 -466.357445361 + E_Harris -34.2766277306 -466.357445361 + E_Fermi -0.154895723214 -2.10746443154 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.00116606707871 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000794971753723 + + Density error is 1.97595110554e-07 + + Energy Rydberg eV + E_KohnSham -34.2766277268 -466.35744531 + E_Harris -34.2766277268 -466.35744531 + E_Fermi -0.154895395774 -2.10745997649 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 301 + sender_size = 301 + last sender_buffer = 0.0011660672972 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000794971887042 + + Density error is 1.15152614658e-08 + + Energy Rydberg eV + E_KohnSham -34.276627732 -466.35744538 + E_Harris -34.276627732 -466.35744538 + E_band -7.85851758009 -106.920616922 + E_one_elec -68.6453779742 -933.968281812 + E_Hartree +35.7395180904 +486.261089804 + E_xc -8.16161093046 -111.044413513 + E_Ewald +6.91647797912 +94.1035106076 + E_demet -1.24160252444e-58 -1.68928689835e-57 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193664567674 -2.63494162108 + E_Fermi -0.15489520238 -2.10745734523 + + charge density convergence is achieved + final etot is -466.35744538 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9571 2.00000 + 2 -12.8604 2.00000 + 3 -8.97634 2.00000 + 4 -6.66651 2.00000 + 5 0.981355 0.00000 + 6 4.00940 0.00000 + 7 11.1504 0.00000 + 8 11.3846 0.00000 + + EFERMI = -2.107457345231432 eV + OUT.ABACUS/ final etot is -466.3574453797521 eV + correction force for each atom along direction 1 is 3.71984e-05 + correction force for each atom along direction 2 is 0.000153970 + correction force for each atom along direction 3 is 2.80545e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.2914522 -0.24218571 +1.7635903 + H1 -1.6024009 +0.12957619 -1.5642498 + H2 +0.31094865 +0.11260952 -0.19934045 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3574453797521 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3402 11 0.67 1.0e+02% + Run_lcao lcao_line 7.3306 1 7.3 1.e+02% + Potential init_pot 0.27989 2 0.14 3.8% + PW_Basis recip2real 0.27832 17 0.016 3.8% + PW_Basis gathers_scatterp 0.12449 17 0.0073 1.7% + Potential v_of_rho 0.98441 14 0.070 13.% + XC_Functional v_xc 0.29312 15 0.020 4.0% + H_Hartree_pw v_hartree 0.64840 14 0.046 8.8% + PW_Basis real2recip 0.73610 41 0.018 10.% + PW_Basis gatherp_scatters 0.28738 41 0.0070 3.9% + ORB_control set_orb_tables 1.0959 1 1.1 15.% + ORB_gen_tables gen_tables 1.0959 1 1.1 15.% + ORB_table_phi init_Table 0.47692 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47159 126 0.0037 6.4% + ORB_table_beta init_Table_Beta 0.18161 1 0.18 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18004 56 0.0032 2.5% + ORB_table_alpha init_Table_Alpha 0.24967 1 0.25 3.4% + ORB_table_alpha S_PhiAlpha_R 0.24770 66 0.0038 3.4% + LOOP_ions opt_ions 5.7070 1 5.7 78.% + ESolver_KS_LCAO Run 5.1585 1 5.2 70.% + HSolverLCAO solve 2.5748 12 0.21 35.% + HamiltLCAO updateHk 1.3405 12 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.3107 12 0.11 18.% + Gint_interface cal_gint 1.9760 25 0.079 27.% + Gint_Gamma distri_vl_value 0.14884 12 0.012 2.0% + Gint_Gamma distri_vl 2.6843 6 0.45 37.% + LCAO_Deepks cal_projected_DM 5.5016 14 0.39 75.% + LCAO_gen_fixedH add_v_delta 2.5384 6 0.42 35.% + LCAO_DESCRIPTOR add_v_delta 2.5385 6 0.42 35.% + ElecStateLCAO psiToRho 1.2148 12 0.10 17.% + Charge mix_rho 0.98301 11 0.089 13.% + LOOP_ions force_stress 0.54833 1 0.55 7.5% + Force_Stress_LCAO getForceStress 0.54831 1 0.55 7.5% + Force_LCAO_gamma ftable_gamma 0.34224 1 0.34 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.28470 1 0.28 3.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:02 2022 + Finish Time : Wed Sep 28 11:12:10 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..2565b117eeca93748503a9b71dc3d9991d16d118 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/OUT.ABACUS/warning.log @@ -0,0 +1,77 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123426 ima = 3.65637e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 3 + 3 1 + 4 1 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123908571707 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112358035261 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113148251772 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113355699744 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113336630508 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113349282695 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113343969049 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113346129306 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113345561351 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113345550744 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113345526923 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113345516472 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/STRU new file mode 100644 index 0000000000000000000000000000000000000000..baf23a7ce99db5fde7a916c04573e4bc979d68ca --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.730909168533 18.992743067916 7.603112596261 0 0 0 +H +0.0 +2 +-12.233472125803 18.931581110197 8.839930893599 0 0 0 +-13.042428587204 19.576672006131 6.009730411805 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/conv new file mode 100644 index 0000000000000000000000000000000000000000..a0934d4c925ea9ef460f18b40ef16e90e1d8bb31 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/conv @@ -0,0 +1 @@ +8 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..37eef7c2070e8066d79cb9eda21211ed42038eb6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748301025 0.01236046008 1.242784758 1.347520893 1.467959309 0.008142559621 0.01860009486 0.0390483618 +1.687262404e-18 0.0009342595779 0.002336775222 0.01128922238 0.04106156919 -2.9840948e-19 1.434422187e-06 4.656947883e-06 +0.001642054963 0.005726907798 + +H atom_index 1 n_descriptor 18 +1.157720596 0.03700942787 0.07934370635 0.1125941201 0.2887688076 0.01760064756 0.02303779402 0.04097236402 +2.112535429e-17 3.092997305e-05 0.07535181725 0.09570361281 0.1114516205 -4.045142334e-18 6.755666006e-06 0.01538715739 +0.02175149091 0.02601423298 + +H atom_index 2 n_descriptor 18 +1.245995023 0.03424760695 0.105832792 0.1488569471 0.3212185436 0.02158089095 0.02817591992 0.03750615672 +-1.463728976e-18 3.787881998e-05 0.097966597 0.1151219861 0.1275791664 -3.946497796e-18 4.167857139e-06 0.01308148296 +0.02536179833 0.03060981972 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..5b35c1350a726bbb140a8a11225721aa4ba36b68 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/e_base.npy 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/dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..eca8abd23aa78043aef56c698875d55788c1411b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..fa072f71000aebb7673b9e976f7795e14d9f57e8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:02 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.110621 SEC) : SETUP UNITCELL + DONE(0.110981 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.129576 SEC) : INIT PLANEWAVE + DONE(0.173007 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.452015 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651294e+02 0.000000e+00 2.130e-01 5.266e-01 + GE2 -4.663524e+02 -1.222964e+00 9.924e-02 4.845e-01 + GE3 -4.663592e+02 -6.773514e-03 6.412e-02 5.536e-01 + GE4 -4.663578e+02 1.351575e-03 2.030e-03 4.149e-01 + GE5 -4.663573e+02 5.383238e-04 9.926e-04 4.143e-01 + GE6 -4.663575e+02 -2.189769e-04 1.976e-04 4.119e-01 + GE7 -4.663574e+02 7.040823e-05 3.349e-05 3.969e-01 + GE8 -4.663575e+02 -4.298008e-05 1.315e-05 3.926e-01 + GE9 -4.663574e+02 1.463618e-05 1.678e-06 3.914e-01 + GE10 -4.663574e+02 -2.844055e-06 6.208e-07 3.918e-01 + GE11 -4.663574e+02 5.102576e-08 1.976e-07 3.912e-01 + GE12 -4.663574e+02 -6.992375e-08 1.152e-08 3.262e-01 +E_delta_band = -6.80296708e-02 Ry = -9.25591155e-01 eV +E_delta_NN= -1.93664568e-01 Ry = -2.63494162e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.3402 11 0.67 1e+02 % + Run_lcao lcao_line 7.3306 1 7.3 1e+02 % + Potential init_pot 0.27989 2 0.14 3.8 % + PW_Basis recip2real 0.27832 17 0.016 3.8 % + PW_Basis gathers_scatterp 0.12449 17 0.0073 1.7 % + Potential v_of_rho 0.98441 14 0.07 13 % + XC_Functional v_xc 0.29312 15 0.02 4 % + H_Hartree_pw v_hartree 0.6484 14 0.046 8.8 % + PW_Basis real2recip 0.7361 41 0.018 10 % + PW_Basis gatherp_scatters 0.28738 41 0.007 3.9 % + ORB_control set_orb_tables 1.0959 1 1.1 15 % + ORB_gen_tables gen_tables 1.0959 1 1.1 15 % + ORB_table_phi init_Table 0.47692 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.47159 126 0.0037 6.4 % + ORB_table_beta init_Table_Beta 0.18161 1 0.18 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18004 56 0.0032 2.5 % + ORB_table_alpha init_Table_Alpha 0.24967 1 0.25 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.2477 66 0.0038 3.4 % + LOOP_ions opt_ions 5.707 1 5.7 78 % + ESolver_KS_LCAO Run 5.1585 1 5.2 70 % + HSolverLCAO solve 2.5748 12 0.21 35 % + HamiltLCAO updateHk 1.3405 12 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.3107 12 0.11 18 % + Gint_interface cal_gint 1.976 25 0.079 27 % + Gint_Gamma distri_vl_value 0.14884 12 0.012 2 % + Gint_Gamma distri_vl 2.6843 6 0.45 37 % + LCAO_Deepks cal_projected_DM 5.5016 14 0.39 75 % + LCAO_gen_fixedH add_v_delta 2.5384 6 0.42 35 % + LCAO_DESCRIPTOR add_v_delta 2.5385 6 0.42 35 % + ElecStateLCAO psiToRho 1.2148 12 0.1 17 % + Charge mix_rho 0.98301 11 0.089 13 % + LOOP_ions force_stress 0.54833 1 0.55 7.5 % + Force_Stress_LCAO getForceStress 0.54831 1 0.55 7.5 % + Force_LCAO_gamma ftable_gamma 0.34224 1 0.34 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.2847 1 0.28 3.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:02 2022 + FINISH Time : Wed Sep 28 11:12:10 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/8/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..16dd8bb677d0bea045e508765fe349747ebdfdd0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.725527 0.480349 0.0269507 +H 0.673017 0.509863 0.0482838 +H 0.773718 0.51758 0.0487121 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..915d565cb26d2073e5e4e68fe98e7f296a69d55b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5117 2 + 2 -13.1923 2 + 3 -9.1801 2 + 4 -6.79385 2 + 5 1.47029 0 + 6 4.7156 0 + 7 11.0234 0 + 8 11.276 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ee2e2296030e3e3fe5d80b977ad7ac46d89311d0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:07:15 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 20.3147490081 13.4497811119 0.754618741223 0 0 0 0 + tauc_H1 18.8444679995 14.2761606481 1.35194623887 0 0 0 0 + tauc_H2 21.6640959121 14.4922437153 1.36393968429 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0867652725647 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0872590429712 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105315022906 (SEC) + + DONE : INIT CHARGE Time : 0.154645772156 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.437073 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 25 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000992 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134 + + Density error is 0.217363373798 + + Energy Rydberg eV + E_KohnSham -34.1876597472 -465.146973846 + E_Harris -34.384808458 -467.829319668 + E_Fermi -0.418277360759 -5.69095545073 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00114742917478 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123805574092 + + Density error is 0.0975464413419 + + Energy Rydberg eV + E_KohnSham -34.2789770623 -466.389409659 + E_Harris -34.2856258797 -466.47987146 + E_Fermi -0.225435932902 -3.06721322141 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00108350708268 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00114645837524 + + Density error is 0.0623507666382 + + Energy Rydberg eV + E_KohnSham -34.2792880022 -466.393640213 + E_Harris -34.2835623805 -466.451796113 + E_Fermi -0.211958614287 -2.88384489448 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000988283743984 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098923150981 + + Density error is 0.00202680246879 + + Energy Rydberg eV + E_KohnSham -34.2793196754 -466.394071149 + E_Harris -34.2793217764 -466.394099734 + E_Fermi -0.176143018985 -2.39654872112 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000989675812404 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000987442150336 + + Density error is 0.000943545319274 + + Energy Rydberg eV + E_KohnSham -34.2792414682 -466.393007085 + E_Harris -34.2792439987 -466.393041514 + E_Fermi -0.175022214848 -2.38129939851 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000988301469955 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000985883276131 + + Density error is 0.000111794386469 + + Energy Rydberg eV + E_KohnSham -34.2792946127 -466.393730153 + E_Harris -34.2792946332 -466.393730432 + E_Fermi -0.175272457736 -2.38470412768 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000988332038448 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000985655790162 + + Density error is 4.70182014577e-05 + + Energy Rydberg eV + E_KohnSham -34.2792768421 -466.393488372 + E_Harris -34.2792768543 -466.393488538 + E_Fermi -0.175129702021 -2.38276183652 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000988290970417 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000985662573534 + + Density error is 1.27085307075e-05 + + Energy Rydberg eV + E_KohnSham -34.2792800923 -466.393532593 + E_Harris -34.279280093 -466.393532602 + E_Fermi -0.175185746952 -2.38352436694 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000988283004662 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000985645495613 + + Density error is 2.13087413729e-06 + + Energy Rydberg eV + E_KohnSham -34.2792786816 -466.3935134 + E_Harris -34.2792786817 -466.393513401 + E_Fermi -0.175173056824 -2.38335170888 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000988283047589 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000985643420026 + + Density error is 1.33430943637e-07 + + Energy Rydberg eV + E_KohnSham -34.2792788329 -466.393515459 + E_Harris -34.2792788329 -466.393515459 + E_Fermi -0.175170631207 -2.38331870667 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000988283352534 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000985643772153 + + Density error is 4.69458640694e-08 + + Energy Rydberg eV + E_KohnSham -34.2792788773 -466.393516063 + E_Harris -34.2792788773 -466.393516063 + E_band -8.03750514114 -109.355867624 + E_one_elec -69.7181138493 -948.563602163 + E_Hartree +36.2393284055 +493.061358008 + E_xc -8.24186276395 -112.136295724 + E_Ewald +7.56480819121 +102.924495678 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195614201251 -2.66146774673 + E_Fermi -0.175170716736 -2.38331987036 + + charge density convergence is achieved + final etot is -466.393516063 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5117 2.00000 + 2 -13.1923 2.00000 + 3 -9.18010 2.00000 + 4 -6.79385 2.00000 + 5 1.47029 0.00000 + 6 4.71560 0.00000 + 7 11.0234 0.00000 + 8 11.2760 0.00000 + + EFERMI = -2.383319870355378 eV + OUT.ABACUS/ final etot is -466.3935160627500 eV + correction force for each atom along direction 1 is 2.38950e-05 + correction force for each atom along direction 2 is 0.000126164 + correction force for each atom along direction 3 is 5.80778e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.61001325 -1.0903454 -0.72949918 + H1 -1.3723296 +0.64157248 +0.47477253 + H2 +0.76231639 +0.44877289 +0.25472665 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3935160627500 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4459 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4369 1 7.4 1.e+02% + Potential init_pot 0.28551 2 0.14 3.8% + PW_Basis recip2real 0.28287 16 0.018 3.8% + PW_Basis gathers_scatterp 0.12537 16 0.0078 1.7% + Potential v_of_rho 0.96640 13 0.074 13.% + XC_Functional v_xc 0.28110 14 0.020 3.8% + H_Hartree_pw v_hartree 0.64576 13 0.050 8.7% + PW_Basis real2recip 0.64599 38 0.017 8.7% + PW_Basis gatherp_scatters 0.24745 38 0.0065 3.3% + ORB_control set_orb_tables 1.1040 1 1.1 15.% + ORB_gen_tables gen_tables 1.1040 1 1.1 15.% + ORB_table_phi init_Table 0.48282 1 0.48 6.5% + ORB_table_phi cal_ST_Phi12_R 0.47755 126 0.0038 6.4% + ORB_table_beta init_Table_Beta 0.18726 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18574 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24899 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24702 66 0.0037 3.3% + LOOP_ions opt_ions 5.8169 1 5.8 78.% + ESolver_KS_LCAO Run 5.2377 1 5.2 70.% + HSolverLCAO solve 2.9941 11 0.27 40.% + HamiltLCAO updateHk 1.5161 11 0.14 20.% + LCAO_Hamilt cal_Hgamma 1.4883 11 0.14 20.% + Gint_interface cal_gint 2.8433 23 0.12 38.% + Gint_Gamma distri_vl 2.5130 6 0.42 34.% + LCAO_Deepks cal_projected_DM 5.6378 13 0.43 76.% + LCAO_gen_fixedH add_v_delta 2.3676 6 0.39 32.% + LCAO_DESCRIPTOR add_v_delta 2.3677 6 0.39 32.% + ElecStateLCAO psiToRho 1.4615 11 0.13 20.% + Charge mix_rho 0.77678 10 0.078 10.% + LOOP_ions force_stress 0.57901 1 0.58 7.8% + Force_Stress_LCAO getForceStress 0.57898 1 0.58 7.8% + Force_LCAO_gamma ftable_gamma 0.36340 1 0.36 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.35550 1 0.36 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:07:15 2022 + Finish Time : Wed Sep 28 11:07:22 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..164180dd28ce1049845d3d488ad542a6dcb2e3cd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012418 ima = 3.66202e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122870649794 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011186283912 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112320436459 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112606534299 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112532024702 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112574347298 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112569275634 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112572350166 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112571851544 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011257174643 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112571745398 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b9a80a127aff3bd5c242fd6b3764c61c10c0540b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-7.685250991874 13.449781111938 0.754618741245 0 0 0 +H +0.0 +2 +-9.155532000475 14.276160648086 1.351946238872 0 0 0 +-6.335904087916 14.492243715233 1.363939684298 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/conv new file mode 100644 index 0000000000000000000000000000000000000000..cbb515072402d73ee68d91d7d6513e65c327a638 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/conv @@ -0,0 +1 @@ +80 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e563d52c52b80200619aff971539b3c9f8764858 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749731486 0.0128199748 1.290252641 1.37495439 1.470342655 0.008753745373 0.01877488635 0.03903344277 +-6.741216711e-19 0.001138163001 0.00275560038 0.01309086659 0.04751851005 -5.836289772e-19 2.388360838e-06 6.601119858e-06 +0.001646738396 0.005992872276 + +H atom_index 1 n_descriptor 18 +1.280670637 0.03325733938 0.1202135073 0.1646543208 0.3298582844 0.02394536 0.03005797073 0.03665116627 +9.069175149e-19 5.298973766e-05 0.1081575962 0.119117307 0.1414648653 -2.876275009e-18 2.347938512e-06 0.01330715204 +0.02789358593 0.03207228719 + +H atom_index 2 n_descriptor 18 +1.263709472 0.03381723342 0.1138975291 0.156273284 0.324803011 0.02315598015 0.02908171674 0.03700081273 +-4.1078542e-18 5.134123299e-05 0.1063412022 0.1160675063 0.1343159313 1.317864695e-18 3.322158864e-06 0.01318399798 +0.02731915204 0.03138393552 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..770e70ee786b38259a4300da59e7bdd7311d6935 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:07:15 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0867878 SEC) : SETUP UNITCELL + DONE(0.087273 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105336 SEC) : INIT PLANEWAVE + DONE(0.154775 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.437146 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651470e+02 0.000000e+00 2.174e-01 5.771e-01 + GE2 -4.663894e+02 -1.242436e+00 9.755e-02 5.304e-01 + GE3 -4.663936e+02 -4.230554e-03 6.235e-02 5.946e-01 + GE4 -4.663941e+02 -4.309358e-04 2.027e-03 4.568e-01 + GE5 -4.663930e+02 1.064064e-03 9.435e-04 4.562e-01 + GE6 -4.663937e+02 -7.230684e-04 1.118e-04 4.437e-01 + GE7 -4.663935e+02 2.417814e-04 4.702e-05 4.375e-01 + GE8 -4.663935e+02 -4.422112e-05 1.271e-05 4.350e-01 + GE9 -4.663935e+02 1.919294e-05 2.131e-06 4.361e-01 + GE10 -4.663935e+02 -2.058406e-06 1.334e-07 4.368e-01 + GE11 -4.663935e+02 -6.040348e-07 4.695e-08 3.707e-01 +E_delta_band = -7.21753404e-02 Ry = -9.81995885e-01 eV +E_delta_NN= -1.95614201e-01 Ry = -2.66146775e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4459 11 0.68 1e+02 % + Run_lcao lcao_line 7.4369 1 7.4 1e+02 % + Potential init_pot 0.28551 2 0.14 3.8 % + PW_Basis recip2real 0.28287 16 0.018 3.8 % + PW_Basis gathers_scatterp 0.12537 16 0.0078 1.7 % + Potential v_of_rho 0.9664 13 0.074 13 % + XC_Functional v_xc 0.2811 14 0.02 3.8 % + H_Hartree_pw v_hartree 0.64576 13 0.05 8.7 % + PW_Basis real2recip 0.64599 38 0.017 8.7 % + PW_Basis gatherp_scatters 0.24745 38 0.0065 3.3 % + ORB_control set_orb_tables 1.104 1 1.1 15 % + ORB_gen_tables gen_tables 1.104 1 1.1 15 % + ORB_table_phi init_Table 0.48282 1 0.48 6.5 % + ORB_table_phi cal_ST_Phi12_R 0.47755 126 0.0038 6.4 % + ORB_table_beta init_Table_Beta 0.18726 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18574 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.24899 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24702 66 0.0037 3.3 % + LOOP_ions opt_ions 5.8169 1 5.8 78 % + ESolver_KS_LCAO Run 5.2377 1 5.2 70 % + HSolverLCAO solve 2.9941 11 0.27 40 % + HamiltLCAO updateHk 1.5161 11 0.14 20 % + LCAO_Hamilt cal_Hgamma 1.4883 11 0.14 20 % + Gint_interface cal_gint 2.8433 23 0.12 38 % + Gint_Gamma distri_vl 2.513 6 0.42 34 % + LCAO_Deepks cal_projected_DM 5.6378 13 0.43 76 % + LCAO_gen_fixedH add_v_delta 2.3676 6 0.39 32 % + LCAO_DESCRIPTOR add_v_delta 2.3677 6 0.39 32 % + ElecStateLCAO psiToRho 1.4615 11 0.13 20 % + Charge mix_rho 0.77678 10 0.078 10 % + LOOP_ions force_stress 0.57901 1 0.58 7.8 % + Force_Stress_LCAO getForceStress 0.57898 1 0.58 7.8 % + Force_LCAO_gamma ftable_gamma 0.3634 1 0.36 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.3555 1 0.36 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:07:15 2022 + FINISH Time : Wed Sep 28 11:07:22 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/80/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b6bf57f34387f7e0716fdf7e5a419749c7767058 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.717213 0.465181 0.0271836 +H 0.652877 0.475853 0.0145608 +H 0.742848 0.523357 0.0365136 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..ca99a548527eb7997ea5cfc2b4e5ad6911754d32 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2899 2 + 2 -13.1378 2 + 3 -9.04699 2 + 4 -6.74331 2 + 5 1.31841 0 + 6 4.47592 0 + 7 11.071 0 + 8 11.3124 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..749764d11b45abc71f7f168a4b6282af52e31a60 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:59 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 20.0819752234 13.0250588003 0.761139772992 0 0 0 0 + tauc_H1 18.2805648496 13.3238716693 0.407701336808 0 0 0 0 + tauc_H2 20.7997514472 14.6539975004 1.0223816499 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.113701199048 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.114267437076 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.140370605421 (SEC) + + DONE : INIT CHARGE Time : 0.184046255799 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.465954 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 9 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0015 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000845 + + Density error is 0.215465963282 + + Energy Rydberg eV + E_KohnSham -34.1901671333 -465.181088586 + E_Harris -34.3828785703 -467.803062198 + E_Fermi -0.406595087154 -5.5320099641 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00135947367618 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000963834259327 + + Density error is 0.0979600985028 + + Energy Rydberg eV + E_KohnSham -34.2799970301 -466.403287033 + E_Harris -34.2867110502 -466.494635962 + E_Fermi -0.215277192663 -2.92899646966 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00125296395371 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000913736279304 + + Density error is 0.0628417091332 + + Energy Rydberg eV + E_KohnSham -34.2802767958 -466.40709344 + E_Harris -34.2846110386 -466.466063838 + E_Fermi -0.203763686387 -2.77234718035 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.0010686225466 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00083572402175 + + Density error is 0.0020214453239 + + Energy Rydberg eV + E_KohnSham -34.2802710173 -466.407014819 + E_Harris -34.2802732837 -466.407045656 + E_Fermi -0.168253018259 -2.28919975402 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00106710052235 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000835117579717 + + Density error is 0.000889203109496 + + Energy Rydberg eV + E_KohnSham -34.2802124393 -466.406217825 + E_Harris -34.2802134019 -466.406230921 + E_Fermi -0.167513320593 -2.27913565096 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00106511324628 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834178770455 + + Density error is 0.000162013325722 + + Energy Rydberg eV + E_KohnSham -34.2802477162 -466.406697791 + E_Harris -34.2802477508 -466.406698263 + E_Fermi -0.167493873311 -2.27887105713 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00106497902267 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834299044649 + + Density error is 4.09582327603e-05 + + Energy Rydberg eV + E_KohnSham -34.2802353155 -466.406529072 + E_Harris -34.2802353246 -466.406529195 + E_Fermi -0.167360355629 -2.27705445587 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00106497139068 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834245532154 + + Density error is 1.65719026875e-05 + + Energy Rydberg eV + E_KohnSham -34.2802395325 -466.406586447 + E_Harris -34.2802395338 -466.406586464 + E_Fermi -0.167404170635 -2.27765058959 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00106494452762 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834236307077 + + Density error is 1.68626575224e-06 + + Energy Rydberg eV + E_KohnSham -34.2802380291 -466.406565992 + E_Harris -34.2802380291 -466.406565992 + E_Fermi -0.167386674512 -2.27741254263 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00106494036767 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834237017149 + + Density error is 2.02254121858e-07 + + Energy Rydberg eV + E_KohnSham -34.2802382795 -466.406569399 + E_Harris -34.2802382795 -466.406569399 + E_Fermi -0.167385125017 -2.27739146068 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00106494064399 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000834237533144 + + Density error is 5.28357408515e-08 + + Energy Rydberg eV + E_KohnSham -34.2802383039 -466.406569731 + E_Harris -34.2802383039 -466.406569731 + E_band -7.96989491349 -108.435983285 + E_one_elec -69.3397592044 -943.415823128 + E_Hartree +36.0653951301 +490.694874391 + E_xc -8.21372339493 -111.753439967 + E_Ewald +7.33209365616 +99.7582519934 + E_demet -1.64658372864e-78 -2.24029209436e-77 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194876587901 -2.65143200226 + E_Fermi -0.167385081452 -2.27739086794 + + charge density convergence is achieved + final etot is -466.406569731 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2899 2.00000 + 2 -13.1378 2.00000 + 3 -9.04699 2.00000 + 4 -6.74331 2.00000 + 5 1.31841 0.00000 + 6 4.47592 0.00000 + 7 11.0710 0.00000 + 8 11.3124 0.00000 + + EFERMI = -2.277390867935068 eV + OUT.ABACUS/ final etot is -466.4065697309545 eV + correction force for each atom along direction 1 is -9.46094e-06 + correction force for each atom along direction 2 is 0.000146068 + correction force for each atom along direction 3 is -2.47717e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.88185744 -1.1619665 -0.26476551 + H1 +0.46962175 +0.0072238977 +0.098662396 + H2 +0.41223569 +1.1547426 +0.16610312 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4065697309545 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4861 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4762 1 6.5 1.e+02% + Potential init_pot 0.28224 2 0.14 4.4% + PW_Basis recip2real 0.27620 16 0.017 4.3% + PW_Basis gathers_scatterp 0.11927 16 0.0075 1.8% + Potential v_of_rho 1.0129 13 0.078 16.% + XC_Functional v_xc 0.30505 14 0.022 4.7% + H_Hartree_pw v_hartree 0.66414 13 0.051 10.% + PW_Basis real2recip 0.69717 38 0.018 11.% + PW_Basis gatherp_scatters 0.26539 38 0.0070 4.1% + ORB_control set_orb_tables 1.0941 1 1.1 17.% + ORB_gen_tables gen_tables 1.0941 1 1.1 17.% + ORB_table_phi init_Table 0.47360 1 0.47 7.3% + ORB_table_phi cal_ST_Phi12_R 0.46836 126 0.0037 7.2% + ORB_table_beta init_Table_Beta 0.18437 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18284 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.24674 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24475 66 0.0037 3.8% + LOOP_ions opt_ions 4.8342 1 4.8 75.% + ESolver_KS_LCAO Run 4.3423 1 4.3 67.% + HSolverLCAO solve 1.8776 11 0.17 29.% + HamiltLCAO updateHk 1.1329 11 0.10 17.% + LCAO_Hamilt cal_Hgamma 1.1054 11 0.10 17.% + Gint_interface cal_gint 1.6210 23 0.070 25.% + Gint_Gamma distri_vl 2.1028 6 0.35 32.% + LCAO_Deepks cal_projected_DM 4.6758 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9554 6 0.33 30.% + LCAO_DESCRIPTOR add_v_delta 1.9555 6 0.33 30.% + ElecStateLCAO psiToRho 0.72140 11 0.066 11.% + Charge mix_rho 0.90505 10 0.091 14.% + LOOP_ions force_stress 0.49173 1 0.49 7.6% + Force_Stress_LCAO getForceStress 0.49171 1 0.49 7.6% + Force_LCAO_gamma ftable_gamma 0.27201 1 0.27 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.26381 1 0.26 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:59 2022 + Finish Time : Wed Sep 28 11:09:06 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4052390edc7564d5043ae3a29c20030077127689 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123975 ima = 3.67874e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123223914416 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011220003482 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112723577224 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112965681438 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112917483687 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011294508033 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112937918303 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112941002642 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112940281911 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112940215877 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112940206244 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/STRU new file mode 100644 index 0000000000000000000000000000000000000000..0508da4258e1b7848d757d8ffd1328df83d71035 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-7.918024776644 13.025058800278 0.761139773007 0 0 0 +H +0.0 +2 +-9.719435150388 13.323871669269 0.407701336807 0 0 0 +-7.200248552797 14.653997500418 1.022381649919 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/conv new file mode 100644 index 0000000000000000000000000000000000000000..576344dc95b9b89b4b02889106cb4444879b6ac6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/conv @@ -0,0 +1 @@ +81 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..ec024c1b2423f3838c4eb870e219f2f6fd3b48f0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748013897 0.01266806655 1.274757394 1.367013248 1.469343174 0.00831505344 0.0190439512 0.03899087212 +4.789715103e-19 0.001089243394 0.002553217745 0.01237641169 0.04476067278 8.864918464e-20 1.897463111e-06 5.64919358e-06 +0.001675416252 0.00587537012 + +H atom_index 1 n_descriptor 18 +1.223231308 0.03501199311 0.09926402306 0.1382956841 0.3126655752 0.02088379345 0.02679615293 0.03818738793 +1.822211865e-18 4.18322433e-05 0.09480255764 0.1140599214 0.1186242277 -4.196661895e-18 5.505492804e-06 0.01346799442 +0.02521251045 0.02952887915 + +H atom_index 2 n_descriptor 18 +1.271482915 0.03334903105 0.1158279754 0.1605769675 0.328176939 0.02308238972 0.02959540376 0.03669793572 +-4.836200524e-19 4.61765739e-05 0.1060668473 0.1167398572 0.1378687886 -4.763010097e-19 3.041721412e-06 0.01309692611 +0.02700418575 0.0317129724 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..d4471d2caa489a854182bc53413e1c4985ca2a30 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:59 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.113738 SEC) : SETUP UNITCELL + DONE(0.114288 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.140392 SEC) : INIT PLANEWAVE + DONE(0.184184 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.466017 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651811e+02 0.000000e+00 2.155e-01 5.010e-01 + GE2 -4.664033e+02 -1.222198e+00 9.796e-02 4.458e-01 + GE3 -4.664071e+02 -3.806407e-03 6.284e-02 5.163e-01 + GE4 -4.664070e+02 7.862127e-05 2.021e-03 3.746e-01 + GE5 -4.664062e+02 7.969938e-04 8.892e-04 3.744e-01 + GE6 -4.664067e+02 -4.799662e-04 1.620e-04 3.681e-01 + GE7 -4.664065e+02 1.687196e-04 4.096e-05 3.600e-01 + GE8 -4.664066e+02 -5.737559e-05 1.657e-05 3.554e-01 + GE9 -4.664066e+02 2.045547e-05 1.686e-06 3.561e-01 + GE10 -4.664066e+02 -3.406854e-06 2.023e-07 3.535e-01 + GE11 -4.664066e+02 -3.323821e-07 5.284e-08 2.750e-01 +E_delta_band = -7.06320970e-02 Ry = -9.60998981e-01 eV +E_delta_NN= -1.94876588e-01 Ry = -2.65143200e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4861 11 0.59 1e+02 % + Run_lcao lcao_line 6.4762 1 6.5 1e+02 % + Potential init_pot 0.28224 2 0.14 4.4 % + PW_Basis recip2real 0.2762 16 0.017 4.3 % + PW_Basis gathers_scatterp 0.11927 16 0.0075 1.8 % + Potential v_of_rho 1.0129 13 0.078 16 % + XC_Functional v_xc 0.30505 14 0.022 4.7 % + H_Hartree_pw v_hartree 0.66414 13 0.051 10 % + PW_Basis real2recip 0.69717 38 0.018 11 % + PW_Basis gatherp_scatters 0.26539 38 0.007 4.1 % + ORB_control set_orb_tables 1.0941 1 1.1 17 % + ORB_gen_tables gen_tables 1.0941 1 1.1 17 % + ORB_table_phi init_Table 0.4736 1 0.47 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.46836 126 0.0037 7.2 % + ORB_table_beta init_Table_Beta 0.18437 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18284 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.24674 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24475 66 0.0037 3.8 % + LOOP_ions opt_ions 4.8342 1 4.8 75 % + ESolver_KS_LCAO Run 4.3423 1 4.3 67 % + HSolverLCAO solve 1.8776 11 0.17 29 % + HamiltLCAO updateHk 1.1329 11 0.1 17 % + LCAO_Hamilt cal_Hgamma 1.1054 11 0.1 17 % + Gint_interface cal_gint 1.621 23 0.07 25 % + Gint_Gamma distri_vl 2.1028 6 0.35 32 % + LCAO_Deepks cal_projected_DM 4.6758 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9554 6 0.33 30 % + LCAO_DESCRIPTOR add_v_delta 1.9555 6 0.33 30 % + ElecStateLCAO psiToRho 0.7214 11 0.066 11 % + Charge mix_rho 0.90505 10 0.091 14 % + LOOP_ions force_stress 0.49173 1 0.49 7.6 % + Force_Stress_LCAO getForceStress 0.49171 1 0.49 7.6 % + Force_LCAO_gamma ftable_gamma 0.27201 1 0.27 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.26381 1 0.26 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:59 2022 + FINISH Time : Wed Sep 28 11:09:06 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/81/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..7727c0fdaa2f00145d873bbfc814497aa2972ba4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.717906 0.439155 0.0266478 +H 0.663284 0.409185 0.0141301 +H 0.704275 0.499022 0.998751 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6819940c7734509645d8b13c3092d4bf912ab115 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4053 2 + 2 -12.8086 2 + 3 -9.3607 2 + 4 -6.76918 2 + 5 1.2323 0 + 6 4.43141 0 + 7 11.0635 0 + 8 11.3287 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b17f87d14929a05e8bf5a88421e2e78dae8f6d5d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:10:27 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 20.1013682684 12.2963278586 0.746139137984 0 0 0 0 + tauc_H1 18.5719658358 11.4571769146 0.395642808056 0 0 0 0 + tauc_H2 19.7197121411 13.9726299329 27.9650181261 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0731442689108 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0734846273176 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0892426196797 (SEC) + + DONE : INIT CHARGE Time : 0.131800848243 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375619 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00143 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000598 + + Density error is 0.213767880633 + + Energy Rydberg eV + E_KohnSham -34.1880364655 -465.152099363 + E_Harris -34.3782075136 -467.739509212 + E_Fermi -0.407711079475 -5.54719381859 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00136319043586 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000826282577417 + + Density error is 0.0976464347607 + + Energy Rydberg eV + E_KohnSham -34.2768605615 -466.360613188 + E_Harris -34.2836792453 -466.45338614 + E_Fermi -0.217676952545 -2.96164687789 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00125866564569 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000798031726692 + + Density error is 0.0626016580227 + + Energy Rydberg eV + E_KohnSham -34.2770994913 -466.363863994 + E_Harris -34.2815094356 -466.423864365 + E_Fermi -0.206381043447 -2.80795815006 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0010721198505 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000772484004771 + + Density error is 0.00194948347677 + + Energy Rydberg eV + E_KohnSham -34.2770824067 -466.363631547 + E_Harris -34.2770833787 -466.363644772 + E_Fermi -0.17053689193 -2.32027344946 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00106993037344 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000773331278987 + + Density error is 0.00083405882919 + + Energy Rydberg eV + E_KohnSham -34.2770293997 -466.362910349 + E_Harris -34.2770304794 -466.36292504 + E_Fermi -0.169954893318 -2.31235495211 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00106789948512 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000772815944097 + + Density error is 0.00012269176012 + + Energy Rydberg eV + E_KohnSham -34.2770641138 -466.363382659 + E_Harris -34.2770641398 -466.363383013 + E_Fermi -0.169894025244 -2.31152679948 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00106780680352 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000773047129138 + + Density error is 3.63934519014e-05 + + Energy Rydberg eV + E_KohnSham -34.2770523008 -466.363221935 + E_Harris -34.2770523066 -466.363222014 + E_Fermi -0.169802130377 -2.31027650566 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00106777390268 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000772956695107 + + Density error is 1.93562919839e-05 + + Energy Rydberg eV + E_KohnSham -34.2770554851 -466.36326526 + E_Harris -34.2770554868 -466.363265283 + E_Fermi -0.169837123421 -2.31075261045 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00106774998457 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000772976296254 + + Density error is 2.48932495261e-06 + + Energy Rydberg eV + E_KohnSham -34.277053972 -466.363244672 + E_Harris -34.277053972 -466.363244673 + E_Fermi -0.169818045573 -2.31049304302 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00106774695953 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00077298024564 + + Density error is 1.28577684447e-07 + + Energy Rydberg eV + E_KohnSham -34.277054265 -466.36324866 + E_Harris -34.277054265 -466.36324866 + E_Fermi -0.169815654031 -2.31046050442 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00106774705552 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000772980222614 + + Density error is 3.76816435294e-08 + + Energy Rydberg eV + E_KohnSham -34.2770543189 -466.363249393 + E_Harris -34.2770543189 -466.363249393 + E_band -7.98838500645 -108.687553906 + E_one_elec -69.3274672297 -943.248582232 + E_Hartree +36.0483624903 +490.463133438 + E_xc -8.21124437958 -111.719711233 + E_Ewald +7.33752817124 +99.8321923644 + E_demet -2.73832444792e-76 -3.72568154644e-75 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194973763559 -2.6527541449 + E_Fermi -0.169815658872 -2.31046057029 + + charge density convergence is achieved + final etot is -466.363249393 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4053 2.00000 + 2 -12.8086 2.00000 + 3 -9.36070 2.00000 + 4 -6.76918 2.00000 + 5 1.23230 0.00000 + 6 4.43141 0.00000 + 7 11.0635 0.00000 + 8 11.3287 0.00000 + + EFERMI = -2.310460570289666 eV + OUT.ABACUS/ final etot is -466.3632493926509 eV + correction force for each atom along direction 1 is -2.86524e-05 + correction force for each atom along direction 2 is -1.46036e-05 + correction force for each atom along direction 3 is -0.000152100 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +1.0762349 +2.0260438 -0.28848767 + H1 -1.6179357 -1.2990029 -0.21583380 + H2 +0.54170076 -0.72704085 +0.50432147 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3632493926509 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6377 11 0.60 1.0e+02% + Run_lcao lcao_line 6.6299 1 6.6 1.e+02% + Potential init_pot 0.24746 2 0.12 3.7% + PW_Basis recip2real 0.24806 16 0.016 3.7% + PW_Basis gathers_scatterp 0.10570 16 0.0066 1.6% + Potential v_of_rho 0.91777 13 0.071 14.% + XC_Functional v_xc 0.28136 14 0.020 4.2% + H_Hartree_pw v_hartree 0.59930 13 0.046 9.0% + PW_Basis real2recip 0.61635 38 0.016 9.3% + PW_Basis gatherp_scatters 0.23452 38 0.0062 3.5% + ORB_control set_orb_tables 0.89085 1 0.89 13.% + ORB_gen_tables gen_tables 0.89085 1 0.89 13.% + ORB_table_phi init_Table 0.37189 1 0.37 5.6% + ORB_table_phi cal_ST_Phi12_R 0.36774 126 0.0029 5.5% + ORB_table_beta init_Table_Beta 0.15457 1 0.15 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15327 56 0.0027 2.3% + ORB_table_alpha init_Table_Alpha 0.20670 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20506 66 0.0031 3.1% + LOOP_ions opt_ions 5.2937 1 5.3 80.% + ESolver_KS_LCAO Run 4.7204 1 4.7 71.% + HSolverLCAO solve 2.5606 11 0.23 39.% + HamiltLCAO updateHk 1.3059 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.2764 11 0.12 19.% + Gint_interface cal_gint 2.4227 23 0.11 36.% + Gint_Gamma distri_vl 2.2674 6 0.38 34.% + LCAO_Deepks cal_projected_DM 5.1458 13 0.40 78.% + LCAO_gen_fixedH add_v_delta 2.1373 6 0.36 32.% + LCAO_DESCRIPTOR add_v_delta 2.1373 6 0.36 32.% + ElecStateLCAO psiToRho 1.2401 11 0.11 19.% + Charge mix_rho 0.75851 10 0.076 11.% + LOOP_ions force_stress 0.57323 1 0.57 8.6% + Force_Stress_LCAO getForceStress 0.57320 1 0.57 8.6% + Force_LCAO_gamma ftable_gamma 0.32761 1 0.33 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.31986 1 0.32 4.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:10:27 2022 + Finish Time : Wed Sep 28 11:10:34 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..528aae0944e0d383bb98e56c10579493551adcc6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123916 ima = 3.69853e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122690431174 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111626442032 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112198497622 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112451742507 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112403341223 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112431353436 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112426401969 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112429266695 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112428361114 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112428230682 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112428227282 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/STRU new file mode 100644 index 0000000000000000000000000000000000000000..3625b79c4bfac9782cbc73261fbdb039a4ae46f1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-7.898631731577 12.296327858653 0.746139137990 0 0 0 +H +0.0 +2 +-9.428034164257 11.457176914628 0.395642808079 0 0 0 +-8.280287858924 13.972629932882 -0.034981873970 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/conv new file mode 100644 index 0000000000000000000000000000000000000000..f7b72241ec48e93af4278bf56122eac9d1944468 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/conv @@ -0,0 +1 @@ +82 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a9ab3929d9bfbfc9af0cbb0af9b42bffb863c6d1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753233177 0.01273071103 1.266361621 1.360992522 1.469781746 0.00930326283 0.0172553097 0.03915693757 +3.112036953e-18 0.0009459109001 0.002803327265 0.01294772976 0.04673534901 1.91836695e-19 2.560581197e-06 7.011014162e-06 +0.001582652936 0.006070161752 + +H atom_index 1 n_descriptor 18 +1.291199899 0.03339574239 0.1255664274 0.1699136414 0.332569713 0.02491817775 0.03063138739 0.03695630362 +6.785209236e-17 5.327659091e-05 0.107897354 0.1217226733 0.1456717787 -3.959055032e-18 1.240263895e-06 0.01357958138 +0.02818702526 0.03244861133 + +H atom_index 2 n_descriptor 18 +1.20558117 0.03619068087 0.09537969657 0.1300719759 0.3042367285 0.02075008035 0.02563406961 0.03949365909 +-1.778401094e-19 4.521294485e-05 0.09124948257 0.111323848 0.1133316761 8.783111747e-18 5.717810806e-06 0.01419198055 +0.02502294966 0.02854099059 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..06704047d2a186288c45d358db47e2c3a93dfb43 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:10:27 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0731601 SEC) : SETUP UNITCELL + DONE(0.0734961 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0892567 SEC) : INIT PLANEWAVE + DONE(0.131907 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.375664 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651521e+02 0.000000e+00 2.138e-01 4.981e-01 + GE2 -4.663606e+02 -1.208514e+00 9.765e-02 4.711e-01 + GE3 -4.663639e+02 -3.250806e-03 6.260e-02 5.388e-01 + GE4 -4.663636e+02 2.324471e-04 1.949e-03 4.115e-01 + GE5 -4.663629e+02 7.211978e-04 8.341e-04 4.130e-01 + GE6 -4.663634e+02 -4.723103e-04 1.227e-04 4.137e-01 + GE7 -4.663632e+02 1.607247e-04 3.639e-05 3.995e-01 + GE8 -4.663633e+02 -4.332537e-05 1.936e-05 3.917e-01 + GE9 -4.663632e+02 2.058767e-05 2.489e-06 4.027e-01 + GE10 -4.663632e+02 -3.987216e-06 1.286e-07 3.966e-01 + GE11 -4.663632e+02 -7.329998e-07 3.768e-08 3.305e-01 +E_delta_band = -7.07403924e-02 Ry = -9.62472415e-01 eV +E_delta_NN= -1.94973764e-01 Ry = -2.65275414e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6377 11 0.6 1e+02 % + Run_lcao lcao_line 6.6299 1 6.6 1e+02 % + Potential init_pot 0.24746 2 0.12 3.7 % + PW_Basis recip2real 0.24806 16 0.016 3.7 % + PW_Basis gathers_scatterp 0.1057 16 0.0066 1.6 % + Potential v_of_rho 0.91777 13 0.071 14 % + XC_Functional v_xc 0.28136 14 0.02 4.2 % + H_Hartree_pw v_hartree 0.5993 13 0.046 9 % + PW_Basis real2recip 0.61635 38 0.016 9.3 % + PW_Basis gatherp_scatters 0.23452 38 0.0062 3.5 % + ORB_control set_orb_tables 0.89085 1 0.89 13 % + ORB_gen_tables gen_tables 0.89085 1 0.89 13 % + ORB_table_phi init_Table 0.37189 1 0.37 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.36774 126 0.0029 5.5 % + ORB_table_beta init_Table_Beta 0.15457 1 0.15 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15327 56 0.0027 2.3 % + ORB_table_alpha init_Table_Alpha 0.2067 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20506 66 0.0031 3.1 % + LOOP_ions opt_ions 5.2937 1 5.3 80 % + ESolver_KS_LCAO Run 4.7204 1 4.7 71 % + HSolverLCAO solve 2.5606 11 0.23 39 % + HamiltLCAO updateHk 1.3059 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.2764 11 0.12 19 % + Gint_interface cal_gint 2.4227 23 0.11 36 % + Gint_Gamma distri_vl 2.2674 6 0.38 34 % + LCAO_Deepks cal_projected_DM 5.1458 13 0.4 78 % + LCAO_gen_fixedH add_v_delta 2.1373 6 0.36 32 % + LCAO_DESCRIPTOR add_v_delta 2.1373 6 0.36 32 % + ElecStateLCAO psiToRho 1.2401 11 0.11 19 % + Charge mix_rho 0.75851 10 0.076 11 % + LOOP_ions force_stress 0.57323 1 0.57 8.6 % + Force_Stress_LCAO getForceStress 0.5732 1 0.57 8.6 % + Force_LCAO_gamma ftable_gamma 0.32761 1 0.33 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.31986 1 0.32 4.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:10:27 2022 + FINISH Time : Wed Sep 28 11:10:34 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/82/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..f754101e366403257189a4f37baa8130ea050ff7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.722347 0.42089 0.0203009 +H 0.700467 0.388925 0.073745 +H 0.670723 0.438963 0.985347 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6b1f3fe717c3ebf7072f6a0f30ef55b1fb2c6f62 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2191 2 + 2 -13.2289 2 + 3 -8.92608 2 + 4 -6.72705 2 + 5 1.31628 0 + 6 4.45426 0 + 7 11.0807 0 + 8 11.3137 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..d2f28b95c4897641e285b7bccbf186036ea27f73 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:22 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 20.2257282923 11.7849237161 0.568425146412 0 0 0 0 + tauc_H1 19.6130683364 10.8899094704 2.06486020723 0 0 0 0 + tauc_H2 18.7802483685 12.2909539872 27.5897286595 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.104766867656 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105119195259 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123040970063 (SEC) + + DONE : INIT CHARGE Time : 0.166382615057 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446861 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 4 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000862 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138 + + Density error is 0.215991619772 + + Energy Rydberg eV + E_KohnSham -34.189662191 -465.174218493 + E_Harris -34.3833947346 -467.810084973 + E_Fermi -0.405583667468 -5.5182488933 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00121976295003 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00119539534346 + + Density error is 0.098285561535 + + Energy Rydberg eV + E_KohnSham -34.2802829476 -466.40717714 + E_Harris -34.2870049725 -466.49863498 + E_Fermi -0.212546659689 -2.89184566264 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00116893804725 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011122800071 + + Density error is 0.0630965367588 + + Energy Rydberg eV + E_KohnSham -34.2806125902 -466.411662158 + E_Harris -34.284943303 -466.470584527 + E_Fermi -0.201642424876 -2.74348593685 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010987938227 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000974796564412 + + Density error is 0.00205710279379 + + Energy Rydberg eV + E_KohnSham -34.2805992102 -466.411480114 + E_Harris -34.2806022184 -466.411521042 + E_Fermi -0.16626587602 -2.26216329683 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00110005792102 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000974808349205 + + Density error is 0.000921748800498 + + Energy Rydberg eV + E_KohnSham -34.2805392985 -466.410664972 + E_Harris -34.2805402682 -466.410678165 + E_Fermi -0.165528782968 -2.25213463137 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010989054767 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973029857212 + + Density error is 0.00019193076379 + + Energy Rydberg eV + E_KohnSham -34.2805746433 -466.411145863 + E_Harris -34.2805747199 -466.411146905 + E_Fermi -0.165491329665 -2.25162505304 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00109917581671 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973033357733 + + Density error is 3.93321128153e-05 + + Energy Rydberg eV + E_KohnSham -34.2805610434 -466.410960827 + E_Harris -34.2805610515 -466.410960938 + E_Fermi -0.165351060262 -2.2497165899 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00109909816813 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973026409993 + + Density error is 1.86339276599e-05 + + Energy Rydberg eV + E_KohnSham -34.2805660909 -466.411029501 + E_Harris -34.2805660923 -466.411029521 + E_Fermi -0.165395176269 -2.25031681897 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00109909732064 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973009552639 + + Density error is 2.38253046017e-06 + + Energy Rydberg eV + E_KohnSham -34.2805645959 -466.411009162 + E_Harris -34.2805645959 -466.411009162 + E_Fermi -0.165376128967 -2.25005766714 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00109909512383 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973003772266 + + Density error is 4.63215065849e-07 + + Energy Rydberg eV + E_KohnSham -34.2805648522 -466.411012649 + E_Harris -34.2805648522 -466.411012649 + E_Fermi -0.16537383059 -2.25002639611 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00109909615894 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973003977852 + + Density error is 1.57544618944e-07 + + Energy Rydberg eV + E_KohnSham -34.2805648799 -466.411013026 + E_Harris -34.2805648799 -466.411013026 + E_Fermi -0.16537363209 -2.25002369538 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00109909638544 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000973003841786 + + Density error is 9.88586012812e-09 + + Energy Rydberg eV + E_KohnSham -34.2805648834 -466.411013073 + E_Harris -34.2805648834 -466.411013074 + E_band -7.95271509387 -108.202239847 + E_one_elec -69.2843168259 -942.66149087 + E_Hartree +36.0438443557 +490.401661062 + E_xc -8.21005247625 -111.703494556 + E_Ewald +7.29433702412 +99.2445466604 + E_demet -2.85597103725e-77 -3.88574794295e-76 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194703358134 -2.64907509036 + E_Fermi -0.165373480175 -2.25002162847 + + charge density convergence is achieved + final etot is -466.411013073 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2191 2.00000 + 2 -13.2289 2.00000 + 3 -8.92608 2.00000 + 4 -6.72705 2.00000 + 5 1.31628 0.00000 + 6 4.45426 0.00000 + 7 11.0807 0.00000 + 8 11.3137 0.00000 + + EFERMI = -2.250021628465942 eV + OUT.ABACUS/ final etot is -466.4110130734978 eV + correction force for each atom along direction 1 is -0.000162509 + correction force for each atom along direction 2 is 6.80466e-05 + correction force for each atom along direction 3 is 6.70845e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.82197905 -0.20476978 +0.42325747 + H1 -0.16777345 +0.14442950 -0.26604691 + H2 -0.65420560 +0.060340285 -0.15721057 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4110130734978 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.7920 11 0.62 1.0e+02% + Run_lcao lcao_line 6.7824 1 6.8 1.e+02% + Potential init_pot 0.28199 2 0.14 4.2% + PW_Basis recip2real 0.29446 17 0.017 4.3% + PW_Basis gathers_scatterp 0.12558 17 0.0074 1.8% + Potential v_of_rho 1.0839 14 0.077 16.% + XC_Functional v_xc 0.31350 15 0.021 4.6% + H_Hartree_pw v_hartree 0.72543 14 0.052 11.% + PW_Basis real2recip 0.75202 41 0.018 11.% + PW_Basis gatherp_scatters 0.28998 41 0.0071 4.3% + ORB_control set_orb_tables 1.0993 1 1.1 16.% + ORB_gen_tables gen_tables 1.0993 1 1.1 16.% + ORB_table_phi init_Table 0.47738 1 0.48 7.0% + ORB_table_phi cal_ST_Phi12_R 0.47220 126 0.0037 7.0% + ORB_table_beta init_Table_Beta 0.18481 1 0.18 2.7% + ORB_table_beta VNL_PhiBeta_R 0.18323 56 0.0033 2.7% + ORB_table_alpha init_Table_Alpha 0.24786 1 0.25 3.6% + ORB_table_alpha S_PhiAlpha_R 0.24593 66 0.0037 3.6% + LOOP_ions opt_ions 5.1608 1 5.2 76.% + ESolver_KS_LCAO Run 4.6523 1 4.7 68.% + HSolverLCAO solve 1.9841 12 0.17 29.% + HamiltLCAO updateHk 1.1490 12 0.096 17.% + LCAO_Hamilt cal_Hgamma 1.1192 12 0.093 16.% + Gint_interface cal_gint 1.7332 25 0.069 26.% + Gint_Gamma distri_vl 2.4346 6 0.41 36.% + LCAO_Deepks cal_projected_DM 5.0082 14 0.36 74.% + LCAO_gen_fixedH add_v_delta 2.2883 6 0.38 34.% + LCAO_DESCRIPTOR add_v_delta 2.2883 6 0.38 34.% + ElecStateLCAO psiToRho 0.81191 12 0.068 12.% + Charge mix_rho 0.98792 11 0.090 15.% + LOOP_ions force_stress 0.50832 1 0.51 7.5% + Force_Stress_LCAO getForceStress 0.50829 1 0.51 7.5% + Force_LCAO_gamma ftable_gamma 0.28797 1 0.29 4.2% + Force_LCAO_gamma cal_fvl_dphi 0.28014 1 0.28 4.1% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:22 2022 + Finish Time : Wed Sep 28 11:02:29 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..ecbc1f69d84148e23837d721095713e4418309e7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123769 ima = 3.66054e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123534155746 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112443320406 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112985103931 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113223844703 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113176931712 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113205604259 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011319641845 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113199426928 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113198671574 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113198588386 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113198571414 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113198563729 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/STRU new file mode 100644 index 0000000000000000000000000000000000000000..80ddca1fb5a0c4bfc2e752c84c53a6d9900e33d2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-7.774271707672 11.784923716117 0.568425146421 0 0 0 +H +0.0 +2 +-8.386931663561 10.889909470367 2.064860207227 0 0 0 +-9.219751631439 12.290953987214 -0.410271340526 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/conv new file mode 100644 index 0000000000000000000000000000000000000000..b8e0b1423aba4f299d59e61ebf2dce2068b59617 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/conv @@ -0,0 +1 @@ +83 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..29a3f4011db7a0625c994f5d8a31687e63ffa9fb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.745920535 0.01262582485 1.275425899 1.367463118 1.469048341 0.007954004021 0.01967278157 0.03892902285 +1.698832761e-18 0.00111331651 0.002441370365 0.0122579928 0.04346145443 -1.542841951e-19 1.660333422e-06 5.126880473e-06 +0.001728996202 0.005761343307 + +H atom_index 1 n_descriptor 18 +1.230403471 0.03454485893 0.1015628639 0.1419734101 0.3160763885 0.02103826958 0.02729170537 0.0377087276 +-2.689576961e-17 3.929259231e-05 0.09652934278 0.114285584 0.1218205782 -6.596810624e-18 5.11712651e-06 0.01320937936 +0.02534201119 0.02992892031 + +H atom_index 2 n_descriptor 18 +1.254845834 0.03368590994 0.1098064464 0.1531111262 0.323943972 0.02212688249 0.0287079231 0.03690947418 +-5.677031708e-17 4.137174022e-05 0.1027282307 0.115139199 0.1314632154 -3.284860182e-18 3.966913571e-06 0.01296354587 +0.02626174454 0.031048916 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9bcb454a6f844e3669f790e8549cb270203040cd Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:22 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.10479 SEC) : SETUP UNITCELL + DONE(0.105135 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123061 SEC) : INIT PLANEWAVE + DONE(0.166521 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446932 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651742e+02 0.000000e+00 2.160e-01 4.936e-01 + GE2 -4.664072e+02 -1.232959e+00 9.829e-02 4.399e-01 + GE3 -4.664117e+02 -4.485018e-03 6.310e-02 5.106e-01 + GE4 -4.664115e+02 1.820442e-04 2.057e-03 3.690e-01 + GE5 -4.664107e+02 8.151416e-04 9.217e-04 3.673e-01 + GE6 -4.664111e+02 -4.808907e-04 1.919e-04 3.623e-01 + GE7 -4.664110e+02 1.850363e-04 3.933e-05 3.526e-01 + GE8 -4.664110e+02 -6.867472e-05 1.863e-05 3.452e-01 + GE9 -4.664110e+02 2.033952e-05 2.383e-06 3.571e-01 + GE10 -4.664110e+02 -3.487225e-06 4.632e-07 3.561e-01 + GE11 -4.664110e+02 -3.767895e-07 1.575e-07 3.556e-01 + GE12 -4.664110e+02 -4.778446e-08 9.886e-09 2.807e-01 +E_delta_band = -7.03263971e-02 Ry = -9.56839720e-01 eV +E_delta_NN= -1.94703358e-01 Ry = -2.64907509e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.792 11 0.62 1e+02 % + Run_lcao lcao_line 6.7824 1 6.8 1e+02 % + Potential init_pot 0.28199 2 0.14 4.2 % + PW_Basis recip2real 0.29446 17 0.017 4.3 % + PW_Basis gathers_scatterp 0.12558 17 0.0074 1.8 % + Potential v_of_rho 1.0839 14 0.077 16 % + XC_Functional v_xc 0.3135 15 0.021 4.6 % + H_Hartree_pw v_hartree 0.72543 14 0.052 11 % + PW_Basis real2recip 0.75202 41 0.018 11 % + PW_Basis gatherp_scatters 0.28998 41 0.0071 4.3 % + ORB_control set_orb_tables 1.0993 1 1.1 16 % + ORB_gen_tables gen_tables 1.0993 1 1.1 16 % + ORB_table_phi init_Table 0.47738 1 0.48 7 % + ORB_table_phi cal_ST_Phi12_R 0.4722 126 0.0037 7 % + ORB_table_beta init_Table_Beta 0.18481 1 0.18 2.7 % + ORB_table_beta VNL_PhiBeta_R 0.18323 56 0.0033 2.7 % + ORB_table_alpha init_Table_Alpha 0.24786 1 0.25 3.6 % + ORB_table_alpha S_PhiAlpha_R 0.24593 66 0.0037 3.6 % + LOOP_ions opt_ions 5.1608 1 5.2 76 % + ESolver_KS_LCAO Run 4.6523 1 4.7 68 % + HSolverLCAO solve 1.9841 12 0.17 29 % + HamiltLCAO updateHk 1.149 12 0.096 17 % + LCAO_Hamilt cal_Hgamma 1.1192 12 0.093 16 % + Gint_interface cal_gint 1.7332 25 0.069 26 % + Gint_Gamma distri_vl 2.4346 6 0.41 36 % + LCAO_Deepks cal_projected_DM 5.0082 14 0.36 74 % + LCAO_gen_fixedH add_v_delta 2.2883 6 0.38 34 % + LCAO_DESCRIPTOR add_v_delta 2.2883 6 0.38 34 % + ElecStateLCAO psiToRho 0.81191 12 0.068 12 % + Charge mix_rho 0.98792 11 0.09 15 % + LOOP_ions force_stress 0.50832 1 0.51 7.5 % + Force_Stress_LCAO getForceStress 0.50829 1 0.51 7.5 % + Force_LCAO_gamma ftable_gamma 0.28797 1 0.29 4.2 % + Force_LCAO_gamma cal_fvl_dphi 0.28014 1 0.28 4.1 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:22 2022 + FINISH Time : Wed Sep 28 11:02:29 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/83/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..a1df1b64cdb2f4d7af8797916acbd25043ad4960 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.716807 0.419754 0.0209646 +H 0.747097 0.424285 0.0776082 +H 0.659314 0.395113 0.0426653 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..05d4ac4a8b39a50f1a41594c18148d509292a50d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4468 2 + 2 -12.7831 2 + 3 -9.41851 2 + 4 -6.78039 2 + 5 1.28668 0 + 6 4.44986 0 + 7 11.0568 0 + 8 11.3366 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..3b48bf29a44394de8c2e8854d898bd0838e70130 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:54 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 20.0706002311 11.7531168188 0.587007612383 0 0 0 0 + tauc_H1 20.9187250194 11.8799719056 2.17302937629 0 0 0 0 + tauc_H2 18.4607856292 11.0631649493 1.19462917063 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101634321418 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.102056849602 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.120102782675 (SEC) + + DONE : INIT CHARGE Time : 0.163146029127 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.447462 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 25 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000932 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00161 + + Density error is 0.214791427773 + + Energy Rydberg eV + E_KohnSham -34.1875051506 -465.144870452 + E_Harris -34.3799457913 -467.763159693 + E_Fermi -0.409172672258 -5.56707980859 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00130482576504 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00139642242586 + + Density error is 0.0977652375689 + + Energy Rydberg eV + E_KohnSham -34.2784270355 -466.38192616 + E_Harris -34.2853133277 -466.475618972 + E_Fermi -0.217688724476 -2.96180704322 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00124529079129 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128911159465 + + Density error is 0.0628258931561 + + Energy Rydberg eV + E_KohnSham -34.2788454691 -466.387619241 + E_Harris -34.2833030157 -466.448267274 + E_Fermi -0.207252879101 -2.81982008267 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116692230245 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109794081935 + + Density error is 0.00194705865606 + + Energy Rydberg eV + E_KohnSham -34.2788219625 -466.387299417 + E_Harris -34.2788227073 -466.387309551 + E_Fermi -0.171288209013 -2.3304956428 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.0011702741304 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109761185285 + + Density error is 0.00103031178468 + + Energy Rydberg eV + E_KohnSham -34.2787514796 -466.386340449 + E_Harris -34.2787535144 -466.386368134 + E_Fermi -0.170736955464 -2.32299545348 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116850856872 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109503601572 + + Density error is 9.70603592319e-05 + + Energy Rydberg eV + E_KohnSham -34.2787951669 -466.386934845 + E_Harris -34.278795173 -466.386934927 + E_Fermi -0.170676185387 -2.32216863417 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116837209262 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109468171336 + + Density error is 4.1339160931e-05 + + Energy Rydberg eV + E_KohnSham -34.278782208 -466.38675853 + E_Harris -34.2787822177 -466.386758661 + E_Fermi -0.170564528234 -2.32064946067 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116830237127 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109471260396 + + Density error is 1.40109639535e-05 + + Energy Rydberg eV + E_KohnSham -34.2787840303 -466.386783324 + E_Harris -34.2787840311 -466.386783335 + E_Fermi -0.170616261771 -2.32135333155 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116830949184 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109469573489 + + Density error is 2.30893436604e-06 + + Energy Rydberg eV + E_KohnSham -34.278782665 -466.386764748 + E_Harris -34.2787826651 -466.386764748 + E_Fermi -0.170602748533 -2.32116947451 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116831264089 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109469331994 + + Density error is 3.28408952658e-07 + + Energy Rydberg eV + E_KohnSham -34.2787828605 -466.386767408 + E_Harris -34.2787828605 -466.386767408 + E_Fermi -0.170600740946 -2.32114215988 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00116831288688 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109469323563 + + Density error is 9.52808999762e-08 + + Energy Rydberg eV + E_KohnSham -34.2787828985 -466.386767924 + E_Harris -34.2787828985 -466.386767924 + E_band -8.00088383359 -108.857609173 + E_one_elec -69.3903424323 -944.10404325 + E_Hartree +36.0763123203 +490.843410383 + E_xc -8.21543280795 -111.776697724 + E_Ewald +7.37476628174 +100.33884285 + E_demet -5.11641463636e-79 -6.96123923851e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195043406977 -2.65370169223 + E_Fermi -0.170600561122 -2.32113971325 + + charge density convergence is achieved + final etot is -466.386767924 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4468 2.00000 + 2 -12.7831 2.00000 + 3 -9.41851 2.00000 + 4 -6.78039 2.00000 + 5 1.28668 0.00000 + 6 4.44986 0.00000 + 7 11.0568 0.00000 + 8 11.3366 0.00000 + + EFERMI = -2.321139713253144 eV + OUT.ABACUS/ final etot is -466.3867679244241 eV + correction force for each atom along direction 1 is 1.99148e-05 + correction force for each atom along direction 2 is 0.000111189 + correction force for each atom along direction 3 is 0.000179735 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.94533128 -0.30149481 -0.42675806 + H1 +1.0224551 +0.27277304 +0.92215898 + H2 -0.077123836 +0.028721779 -0.49540093 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3867679244241 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5420 11 0.59 1.0e+02% + Run_lcao lcao_line 6.5320 1 6.5 1.e+02% + Potential init_pot 0.28481 2 0.14 4.4% + PW_Basis recip2real 0.26915 16 0.017 4.1% + PW_Basis gathers_scatterp 0.12108 16 0.0076 1.9% + Potential v_of_rho 0.95966 13 0.074 15.% + XC_Functional v_xc 0.29026 14 0.021 4.4% + H_Hartree_pw v_hartree 0.62624 13 0.048 9.6% + PW_Basis real2recip 0.67779 38 0.018 10.% + PW_Basis gatherp_scatters 0.25791 38 0.0068 3.9% + ORB_control set_orb_tables 1.0965 1 1.1 17.% + ORB_gen_tables gen_tables 1.0965 1 1.1 17.% + ORB_table_phi init_Table 0.47681 1 0.48 7.3% + ORB_table_phi cal_ST_Phi12_R 0.47154 126 0.0037 7.2% + ORB_table_beta init_Table_Beta 0.18480 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18326 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.24807 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24609 66 0.0037 3.8% + LOOP_ions opt_ions 4.9044 1 4.9 75.% + ESolver_KS_LCAO Run 4.4079 1 4.4 67.% + HSolverLCAO solve 2.0017 11 0.18 31.% + HamiltLCAO updateHk 1.1978 11 0.11 18.% + LCAO_Hamilt cal_Hgamma 1.1705 11 0.11 18.% + Gint_interface cal_gint 1.7570 23 0.076 27.% + Gint_Gamma distri_vl 2.1325 6 0.36 33.% + LCAO_Deepks cal_projected_DM 4.7416 13 0.36 72.% + LCAO_gen_fixedH add_v_delta 1.9854 6 0.33 30.% + LCAO_DESCRIPTOR add_v_delta 1.9854 6 0.33 30.% + ElecStateLCAO psiToRho 0.78016 11 0.071 12.% + Charge mix_rho 0.90033 10 0.090 14.% + LOOP_ions force_stress 0.49634 1 0.50 7.6% + Force_Stress_LCAO getForceStress 0.49631 1 0.50 7.6% + Force_LCAO_gamma ftable_gamma 0.28484 1 0.28 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.27669 1 0.28 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:54 2022 + Finish Time : Wed Sep 28 11:10:01 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8493f62ee4032b71a593e5ef8afadeb70f749922 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123915 ima = 3.68095e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122754312784 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111411645143 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112039215608 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112320743428 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112256434116 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112290810591 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011228903888 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112291879673 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112291257008 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112291152805 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112291138338 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/STRU new file mode 100644 index 0000000000000000000000000000000000000000..d5b1dd08a584599c8eabbf9b808935093e66b48b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-7.929399768945 11.753116818820 0.587007612365 0 0 0 +H +0.0 +2 +-7.081274980616 11.879971905575 2.173029376304 0 0 0 +-9.539214370785 11.063164949265 1.194629170634 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/conv new file mode 100644 index 0000000000000000000000000000000000000000..f3a39e9847f08ce20fc7201971ce32bf61cf6905 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/conv @@ -0,0 +1 @@ +84 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..dc3d3199e529d199e08546012885b12c14d693d4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753825657 0.0128089683 1.273189936 1.357029684 1.469891313 0.009442697153 0.01695756424 0.03915673009 +2.073895745e-18 0.0009346665559 0.002860247701 0.01330954306 0.04723499055 -7.593650372e-19 2.801008654e-06 7.421330205e-06 +0.001591006614 0.006144424532 + +H atom_index 1 n_descriptor 18 +1.273161407 0.03407859213 0.1194419729 0.1606694835 0.326981526 0.02430344937 0.02958513381 0.03733270244 +-2.141717213e-17 5.277394335e-05 0.1071406276 0.1181794104 0.1378284342 6.655346189e-19 1.916006335e-06 0.01337523226 +0.02785431977 0.03175248584 + +H atom_index 2 n_descriptor 18 +1.233240909 0.03540739184 0.1051067822 0.1418799655 0.3138975269 0.02232822449 0.02724938013 0.03852203954 +8.158173856e-18 4.898567315e-05 0.099266774 0.1143988392 0.1216483773 5.083178306e-18 4.132463158e-06 0.01361178788 +0.02639431853 0.02994822159 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f1ca310ab91b42c10c72a2cbd67597344e24ae6f Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:54 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101672 SEC) : SETUP UNITCELL + DONE(0.102072 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.120124 SEC) : INIT PLANEWAVE + DONE(0.163283 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.447526 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651449e+02 0.000000e+00 2.148e-01 5.062e-01 + GE2 -4.663819e+02 -1.237056e+00 9.777e-02 4.548e-01 + GE3 -4.663876e+02 -5.693081e-03 6.283e-02 5.241e-01 + GE4 -4.663873e+02 3.198237e-04 1.947e-03 3.805e-01 + GE5 -4.663863e+02 9.589686e-04 1.030e-03 3.815e-01 + GE6 -4.663869e+02 -5.943960e-04 9.706e-05 3.638e-01 + GE7 -4.663868e+02 1.763150e-04 4.134e-05 3.654e-01 + GE8 -4.663868e+02 -2.479385e-05 1.401e-05 3.596e-01 + GE9 -4.663868e+02 1.857534e-05 2.309e-06 3.585e-01 + GE10 -4.663868e+02 -2.659967e-06 3.284e-07 3.610e-01 + GE11 -4.663868e+02 -5.162429e-07 9.528e-08 2.898e-01 +E_delta_band = -7.09571467e-02 Ry = -9.65421509e-01 eV +E_delta_NN= -1.95043407e-01 Ry = -2.65370169e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.542 11 0.59 1e+02 % + Run_lcao lcao_line 6.532 1 6.5 1e+02 % + Potential init_pot 0.28481 2 0.14 4.4 % + PW_Basis recip2real 0.26915 16 0.017 4.1 % + PW_Basis gathers_scatterp 0.12108 16 0.0076 1.9 % + Potential v_of_rho 0.95966 13 0.074 15 % + XC_Functional v_xc 0.29026 14 0.021 4.4 % + H_Hartree_pw v_hartree 0.62624 13 0.048 9.6 % + PW_Basis real2recip 0.67779 38 0.018 10 % + PW_Basis gatherp_scatters 0.25791 38 0.0068 3.9 % + ORB_control set_orb_tables 1.0965 1 1.1 17 % + ORB_gen_tables gen_tables 1.0965 1 1.1 17 % + ORB_table_phi init_Table 0.47681 1 0.48 7.3 % + ORB_table_phi cal_ST_Phi12_R 0.47154 126 0.0037 7.2 % + ORB_table_beta init_Table_Beta 0.1848 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18326 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.24807 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24609 66 0.0037 3.8 % + LOOP_ions opt_ions 4.9044 1 4.9 75 % + ESolver_KS_LCAO Run 4.4079 1 4.4 67 % + HSolverLCAO solve 2.0017 11 0.18 31 % + HamiltLCAO updateHk 1.1978 11 0.11 18 % + LCAO_Hamilt cal_Hgamma 1.1705 11 0.11 18 % + Gint_interface cal_gint 1.757 23 0.076 27 % + Gint_Gamma distri_vl 2.1325 6 0.36 33 % + LCAO_Deepks cal_projected_DM 4.7416 13 0.36 72 % + LCAO_gen_fixedH add_v_delta 1.9854 6 0.33 30 % + LCAO_DESCRIPTOR add_v_delta 1.9854 6 0.33 30 % + ElecStateLCAO psiToRho 0.78016 11 0.071 12 % + Charge mix_rho 0.90033 10 0.09 14 % + LOOP_ions force_stress 0.49634 1 0.5 7.6 % + Force_Stress_LCAO getForceStress 0.49631 1 0.5 7.6 % + Force_LCAO_gamma ftable_gamma 0.28484 1 0.28 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.27669 1 0.28 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:54 2022 + FINISH Time : Wed Sep 28 11:10:01 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/84/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b9d854fbf1cc29d82e1c98690332fdfe12639c9e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.70867 0.41405 0.0220625 +H 0.766153 0.444921 0.0336227 +H 0.705757 0.354561 0.0484518 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e51196ff73958a36ac391b8a76019da199d25f14 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.0765 2 + 2 -13.4245 2 + 3 -8.65417 2 + 4 -6.68959 2 + 5 1.27167 0 + 6 4.43427 0 + 7 11.102 0 + 8 11.3095 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..50896bb0c1fbfaa173e2f6dcec3a749bb72d2759 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:40 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.8427591681 11.5933959549 0.617748801429 0 0 0 0 + tauc_H1 21.4522942625 12.4577822198 0.941435543944 0 0 0 0 + tauc_H2 19.761208416 9.92769464062 1.35665068128 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0872619272684 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877180551411 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105879828605 (SEC) + + DONE : INIT CHARGE Time : 0.156271750571 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.438886 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 25 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00155 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000639 + + Density error is 0.21594584739 + + Energy Rydberg eV + E_KohnSham -34.1881738814 -465.153969002 + E_Harris -34.3813668555 -467.782494263 + E_Fermi -0.400995677059 -5.45582608138 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00143428838679 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000832723132295 + + Density error is 0.0984220635713 + + Energy Rydberg eV + E_KohnSham -34.2774483627 -466.368610634 + E_Harris -34.2840992658 -466.459100813 + E_Fermi -0.208973196007 -2.84322619497 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00132400630755 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000807788726895 + + Density error is 0.063080546687 + + Energy Rydberg eV + E_KohnSham -34.2776488987 -466.371339066 + E_Harris -34.2819047548 -466.429242959 + E_Fermi -0.197598548966 -2.68846618248 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00112618457106 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000777599567779 + + Density error is 0.00218183171258 + + Energy Rydberg eV + E_KohnSham -34.277642271 -466.371248892 + E_Harris -34.2776478021 -466.371324145 + E_Fermi -0.162654941155 -2.21303400756 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00112192283352 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000776664387656 + + Density error is 0.00084120424098 + + Energy Rydberg eV + E_KohnSham -34.2775957194 -466.370615524 + E_Harris -34.2775962828 -466.37062319 + E_Fermi -0.161809012154 -2.20152455304 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00111982027483 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000776280964388 + + Density error is 0.000213216264141 + + Energy Rydberg eV + E_KohnSham -34.2776260043 -466.371027571 + E_Harris -34.2776260876 -466.371028705 + E_Fermi -0.161771782942 -2.20101802363 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00111963144584 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000776544264975 + + Density error is 3.78846008299e-05 + + Energy Rydberg eV + E_KohnSham -34.2776139364 -466.370863379 + E_Harris -34.2776139441 -466.370863484 + E_Fermi -0.161617561971 -2.19891973967 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00111962339706 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000776484314102 + + Density error is 1.75507510901e-05 + + Energy Rydberg eV + E_KohnSham -34.2776192125 -466.370935165 + E_Harris -34.2776192139 -466.370935183 + E_Fermi -0.161659759734 -2.1994938697 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00111958400704 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000776484566911 + + Density error is 1.52979143328e-06 + + Energy Rydberg eV + E_KohnSham -34.2776177765 -466.370915627 + E_Harris -34.2776177766 -466.370915627 + E_Fermi -0.161640794146 -2.19923582963 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00111958047007 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000776485642023 + + Density error is 3.2204458191e-07 + + Energy Rydberg eV + E_KohnSham -34.2776180485 -466.370919327 + E_Harris -34.2776180485 -466.370919327 + E_Fermi -0.161639546619 -2.19921885616 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00111958064628 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000776486035283 + + Density error is 9.09254022187e-08 + + Energy Rydberg eV + E_KohnSham -34.2776180606 -466.370919492 + E_Harris -34.2776180606 -466.370919492 + E_band -7.91504035844 -107.689648775 + E_one_elec -69.1752773008 -941.177932022 + E_Hartree +36.0034993809 +489.852739519 + E_xc -8.20297389095 -111.607185462 + E_Ewald +7.22178932535 +98.2574845803 + E_demet -2.4774420105e-73 -3.37073278074e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19431779094 -2.64382917956 + E_Fermi -0.161639397123 -2.19921682215 + + charge density convergence is achieved + final etot is -466.370919492 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.0765 2.00000 + 2 -13.4245 2.00000 + 3 -8.65417 2.00000 + 4 -6.68959 2.00000 + 5 1.27167 0.00000 + 6 4.43427 0.00000 + 7 11.1020 0.00000 + 8 11.3095 0.00000 + + EFERMI = -2.199216822151963 eV + OUT.ABACUS/ final etot is -466.3709194916754 eV + correction force for each atom along direction 1 is 0.000170618 + correction force for each atom along direction 2 is -3.19080e-05 + correction force for each atom along direction 3 is 0.000168514 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.29900033 +0.95945960 -0.57778861 + H1 -0.26963988 -0.74579070 +0.22353126 + H2 +0.56864021 -0.21366890 +0.35425734 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3709194916754 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4373 11 0.68 1.0e+02% + Run_lcao lcao_line 7.4276 1 7.4 1.e+02% + Potential init_pot 0.28591 2 0.14 3.8% + PW_Basis recip2real 0.28961 16 0.018 3.9% + PW_Basis gathers_scatterp 0.11862 16 0.0074 1.6% + Charge atomic_rho 0.10050 1 0.10 1.4% + Potential v_of_rho 1.0065 13 0.077 14.% + XC_Functional v_xc 0.29801 14 0.021 4.0% + H_Hartree_pw v_hartree 0.66672 13 0.051 9.0% + PW_Basis real2recip 0.63874 38 0.017 8.6% + PW_Basis gatherp_scatters 0.24000 38 0.0063 3.2% + ORB_control set_orb_tables 1.0946 1 1.1 15.% + ORB_gen_tables gen_tables 1.0946 1 1.1 15.% + ORB_table_phi init_Table 0.47460 1 0.47 6.4% + ORB_table_phi cal_ST_Phi12_R 0.46942 126 0.0037 6.3% + ORB_table_beta init_Table_Beta 0.18507 1 0.19 2.5% + ORB_table_beta VNL_PhiBeta_R 0.18347 56 0.0033 2.5% + ORB_table_alpha init_Table_Alpha 0.24850 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24655 66 0.0037 3.3% + LOOP_ions opt_ions 5.8139 1 5.8 78.% + ESolver_KS_LCAO Run 5.2233 1 5.2 70.% + HSolverLCAO solve 2.9377 11 0.27 39.% + HamiltLCAO updateHk 1.4963 11 0.14 20.% + LCAO_Hamilt cal_Hgamma 1.4631 11 0.13 20.% + Gint_interface cal_gint 2.7875 23 0.12 37.% + Gint_Gamma distri_vl 2.5131 6 0.42 34.% + LCAO_Deepks cal_projected_DM 5.6385 13 0.43 76.% + LCAO_gen_fixedH add_v_delta 2.3680 6 0.39 32.% + LCAO_DESCRIPTOR add_v_delta 2.3680 6 0.39 32.% + ElecStateLCAO psiToRho 1.4259 11 0.13 19.% + Charge mix_rho 0.77549 10 0.078 10.% + LOOP_ions force_stress 0.59042 1 0.59 7.9% + Force_Stress_LCAO getForceStress 0.59039 1 0.59 7.9% + Force_LCAO_gamma ftable_gamma 0.36904 1 0.37 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.36094 1 0.36 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:40 2022 + Finish Time : Wed Sep 28 11:09:48 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..af08fbc32ba4244b4c740bb4942120273e5c3807 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123331 ima = 3.6737e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 2 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123987485158 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113212383777 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113691660702 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113894465158 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113857215289 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113881195218 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113871563499 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113874425565 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113873680096 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113873639293 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113873624873 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/STRU new file mode 100644 index 0000000000000000000000000000000000000000..83acdbc361c97593d8d792ca3c70ff5d7918b3ae --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.157240831848 11.593395954890 0.617748801449 0 0 0 +H +0.0 +2 +-6.547705737509 12.457782219757 0.941435543934 0 0 0 +-8.238791584052 9.927694640641 1.356650681256 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/conv new file mode 100644 index 0000000000000000000000000000000000000000..e21e998829ccd9524117e9526e440f8c0a2e6f03 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/conv @@ -0,0 +1 @@ +85 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..14f71def4ffec63d8ae80f08e733580a316cdbdb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.740911361 0.01250601111 1.274925174 1.372071958 1.468392863 0.007230108305 0.02118818836 0.03877618218 +1.093618579e-18 0.001134107698 0.002200059077 0.01226387229 0.04023701642 5.842976765e-20 1.226426386e-06 4.08297225e-06 +0.001871962181 0.005406600755 + +H atom_index 1 n_descriptor 18 +1.218600121 0.03446593081 0.09907304441 0.1386263596 0.3146846164 0.02037858528 0.02685024575 0.03767958902 +-1.893968502e-17 3.092380524e-05 0.09392623869 0.1140679386 0.1188159281 -3.938284052e-18 4.951344432e-06 0.01310465912 +0.02475488696 0.02952790577 + +H atom_index 2 n_descriptor 18 +1.243814574 0.03356085699 0.1073304862 0.1498005546 0.3227921102 0.02144955364 0.02830201453 0.03678715857 +-4.134225131e-17 3.269991327e-05 0.1006203601 0.1146435629 0.1285256415 -1.660907417e-18 4.067939302e-06 0.01275005692 +0.02572466464 0.03070369728 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..b3878c87053a1a9fb6c0fcd85d573acecb7010f2 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:40 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0872845 SEC) : SETUP UNITCELL + DONE(0.0877341 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105897 SEC) : INIT PLANEWAVE + DONE(0.1564 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.438948 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651540e+02 0.000000e+00 2.159e-01 5.766e-01 + GE2 -4.663686e+02 -1.214642e+00 9.842e-02 5.258e-01 + GE3 -4.663713e+02 -2.728432e-03 6.308e-02 5.926e-01 + GE4 -4.663712e+02 9.017415e-05 2.182e-03 4.558e-01 + GE5 -4.663706e+02 6.333674e-04 8.412e-04 4.547e-01 + GE6 -4.663710e+02 -4.120471e-04 2.132e-04 4.484e-01 + GE7 -4.663709e+02 1.641921e-04 3.788e-05 4.421e-01 + GE8 -4.663709e+02 -7.178533e-05 1.755e-05 4.319e-01 + GE9 -4.663709e+02 1.953742e-05 1.530e-06 4.327e-01 + GE10 -4.663709e+02 -3.700023e-06 3.220e-07 4.330e-01 + GE11 -4.663709e+02 -1.645293e-07 9.093e-08 3.675e-01 +E_delta_band = -6.96622160e-02 Ry = -9.47803072e-01 eV +E_delta_NN= -1.94317791e-01 Ry = -2.64382918e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.4373 11 0.68 1e+02 % + Run_lcao lcao_line 7.4276 1 7.4 1e+02 % + Potential init_pot 0.28591 2 0.14 3.8 % + PW_Basis recip2real 0.28961 16 0.018 3.9 % + PW_Basis gathers_scatterp 0.11862 16 0.0074 1.6 % + Charge atomic_rho 0.1005 1 0.1 1.4 % + Potential v_of_rho 1.0065 13 0.077 14 % + XC_Functional v_xc 0.29801 14 0.021 4 % + H_Hartree_pw v_hartree 0.66672 13 0.051 9 % + PW_Basis real2recip 0.63874 38 0.017 8.6 % + PW_Basis gatherp_scatters 0.24 38 0.0063 3.2 % + ORB_control set_orb_tables 1.0946 1 1.1 15 % + ORB_gen_tables gen_tables 1.0946 1 1.1 15 % + ORB_table_phi init_Table 0.4746 1 0.47 6.4 % + ORB_table_phi cal_ST_Phi12_R 0.46942 126 0.0037 6.3 % + ORB_table_beta init_Table_Beta 0.18507 1 0.19 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.18347 56 0.0033 2.5 % + ORB_table_alpha init_Table_Alpha 0.2485 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24655 66 0.0037 3.3 % + LOOP_ions opt_ions 5.8139 1 5.8 78 % + ESolver_KS_LCAO Run 5.2233 1 5.2 70 % + HSolverLCAO solve 2.9377 11 0.27 39 % + HamiltLCAO updateHk 1.4963 11 0.14 20 % + LCAO_Hamilt cal_Hgamma 1.4631 11 0.13 20 % + Gint_interface cal_gint 2.7875 23 0.12 37 % + Gint_Gamma distri_vl 2.5131 6 0.42 34 % + LCAO_Deepks cal_projected_DM 5.6385 13 0.43 76 % + LCAO_gen_fixedH add_v_delta 2.368 6 0.39 32 % + LCAO_DESCRIPTOR add_v_delta 2.368 6 0.39 32 % + ElecStateLCAO psiToRho 1.4259 11 0.13 19 % + Charge mix_rho 0.77549 10 0.078 10 % + LOOP_ions force_stress 0.59042 1 0.59 7.9 % + Force_Stress_LCAO getForceStress 0.59039 1 0.59 7.9 % + Force_LCAO_gamma ftable_gamma 0.36904 1 0.37 5 % + Force_LCAO_gamma cal_fvl_dphi 0.36094 1 0.36 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:40 2022 + FINISH Time : Wed Sep 28 11:09:48 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/85/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..47086439ec36edd61246eb13e4414aff2c31cb77 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.704481 0.392486 0.0263425 +H 0.740012 0.433002 0.989079 +H 0.735301 0.338524 0.00723582 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..af4df5d6d732ab27fc726584fb4f05f80aee0902 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.525 2 + 2 -12.6094 2 + 3 -9.59385 2 + 4 -6.79755 2 + 5 1.26719 0 + 6 4.44374 0 + 7 11.0509 0 + 8 11.3529 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7e148005c0b26bdcf8bb998f1c6aefecde7d1746 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:50 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.7254785332 10.9896061372 0.737590886092 0 0 0 0 + tauc_H1 20.7203235496 12.1240477914 27.6942060122 0 0 0 0 + tauc_H2 20.5884391412 9.47868513398 0.20260301479 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0868659927256 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0994710839248 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.1178467529 (SEC) + + DONE : INIT CHARGE Time : 0.168226853766 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451654 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00142 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102 + + Density error is 0.212836458524 + + Energy Rydberg eV + E_KohnSham -34.1885348204 -465.158879828 + E_Harris -34.377185083 -467.725598329 + E_Fermi -0.409301189039 -5.5688283691 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00138184680556 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117835491206 + + Density error is 0.0971348527591 + + Energy Rydberg eV + E_KohnSham -34.2765781586 -466.356770899 + E_Harris -34.2834116397 -466.449745179 + E_Fermi -0.220298514327 -2.99731505579 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00127183067468 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111748943423 + + Density error is 0.0622126283738 + + Energy Rydberg eV + E_KohnSham -34.2767893566 -466.359644396 + E_Harris -34.2812164728 -466.419878401 + E_Fermi -0.208614732957 -2.83834905496 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00108166007764 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010346779124 + + Density error is 0.00194269010444 + + Energy Rydberg eV + E_KohnSham -34.2767780637 -466.359490748 + E_Harris -34.2767787671 -466.359500318 + E_Fermi -0.172680328936 -2.34943640605 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00108176222603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103757748339 + + Density error is 0.000833428715895 + + Energy Rydberg eV + E_KohnSham -34.2767231852 -466.358744088 + E_Harris -34.2767246006 -466.358763345 + E_Fermi -0.172100467801 -2.34154699056 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00107946809616 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103608888105 + + Density error is 0.000106451647669 + + Energy Rydberg eV + E_KohnSham -34.2767626127 -466.359280525 + E_Harris -34.2767626304 -466.359280768 + E_Fermi -0.172083786494 -2.34132002973 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00107907102604 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103598164938 + + Density error is 3.52505693184e-05 + + Energy Rydberg eV + E_KohnSham -34.2767505027 -466.359115761 + E_Harris -34.2767505087 -466.359115842 + E_Fermi -0.171985417529 -2.3399816513 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00107907514558 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103592578404 + + Density error is 1.98445211739e-05 + + Energy Rydberg eV + E_KohnSham -34.2767525136 -466.35914312 + E_Harris -34.2767525152 -466.359143143 + E_Fermi -0.172027286991 -2.34055131456 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00107903612309 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103592688986 + + Density error is 1.92316430666e-06 + + Energy Rydberg eV + E_KohnSham -34.2767510451 -466.359123141 + E_Harris -34.2767510451 -466.359123141 + E_Fermi -0.172005177448 -2.3402504988 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00107903578877 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103592857211 + + Density error is 2.45357066817e-07 + + Energy Rydberg eV + E_KohnSham -34.27675134 -466.359127153 + E_Harris -34.27675134 -466.359127153 + E_Fermi -0.172003791015 -2.3402316354 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00107903636539 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103592908809 + + Density error is 4.3900020174e-08 + + Energy Rydberg eV + E_KohnSham -34.2767513737 -466.359127611 + E_Harris -34.2767513737 -466.359127611 + E_band -8.01514468942 -109.051638071 + E_one_elec -69.4194063224 -944.499477762 + E_Hartree +36.0843644644 +490.952965424 + E_xc -8.21642769222 -111.790233819 + E_Ewald +7.39871612543 +100.66469719 + E_demet -5.31647254852e-79 -7.23343199205e-78 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195071729683 -2.65408704241 + E_Fermi -0.172003714647 -2.34023059637 + + charge density convergence is achieved + final etot is -466.359127611 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5250 2.00000 + 2 -12.6094 2.00000 + 3 -9.59385 2.00000 + 4 -6.79755 2.00000 + 5 1.26719 0.00000 + 6 4.44374 0.00000 + 7 11.0509 0.00000 + 8 11.3529 0.00000 + + EFERMI = -2.340230596365763 eV + OUT.ABACUS/ final etot is -466.3591276112988 eV + correction force for each atom along direction 1 is -8.92703e-06 + correction force for each atom along direction 2 is -6.67889e-05 + correction force for each atom along direction 3 is -0.000177191 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.16888747 +0.25317779 -0.19576448 + H1 -0.13385702 +0.93000869 -0.015435781 + H2 -0.035030446 -1.1831865 +0.21120026 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3591276112988 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0850 11 0.64 1.0e+02% + Run_lcao lcao_line 7.0759 1 7.1 1.e+02% + Potential init_pot 0.28761 2 0.14 4.1% + PW_Basis recip2real 0.28731 16 0.018 4.1% + PW_Basis gathers_scatterp 0.12457 16 0.0078 1.8% + Potential v_of_rho 1.0080 13 0.078 14.% + XC_Functional v_xc 0.30108 14 0.022 4.2% + H_Hartree_pw v_hartree 0.66436 13 0.051 9.4% + PW_Basis real2recip 0.64858 38 0.017 9.2% + PW_Basis gatherp_scatters 0.24534 38 0.0065 3.5% + ORB_control set_orb_tables 1.0885 1 1.1 15.% + ORB_gen_tables gen_tables 1.0885 1 1.1 15.% + ORB_table_phi init_Table 0.47480 1 0.47 6.7% + ORB_table_phi cal_ST_Phi12_R 0.46972 126 0.0037 6.6% + ORB_table_beta init_Table_Beta 0.18123 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.17968 56 0.0032 2.5% + ORB_table_alpha init_Table_Alpha 0.24642 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24450 66 0.0037 3.5% + LOOP_ions opt_ions 5.4564 1 5.5 77.% + ESolver_KS_LCAO Run 4.8928 1 4.9 69.% + HSolverLCAO solve 2.6082 11 0.24 37.% + HamiltLCAO updateHk 1.3551 11 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.3176 11 0.12 19.% + Gint_interface cal_gint 2.4300 23 0.11 34.% + Gint_Gamma distri_vl 2.3590 6 0.39 33.% + LCAO_Deepks cal_projected_DM 5.2928 13 0.41 75.% + LCAO_gen_fixedH add_v_delta 2.2128 6 0.37 31.% + LCAO_DESCRIPTOR add_v_delta 2.2128 6 0.37 31.% + ElecStateLCAO psiToRho 1.2383 11 0.11 17.% + Charge mix_rho 0.77650 10 0.078 11.% + LOOP_ions force_stress 0.56342 1 0.56 8.0% + Force_Stress_LCAO getForceStress 0.56340 1 0.56 8.0% + Force_LCAO_gamma ftable_gamma 0.34450 1 0.34 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.33648 1 0.34 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:50 2022 + Finish Time : Wed Sep 28 11:06:57 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..4bb9f8948ad1586c9def25e05dc4f8d868a3e485 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123927 ima = 3.68868e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122196695733 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111160955562 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111730069476 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111994305616 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111936424056 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111967688494 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111965755469 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111968512452 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011196765733 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111967565542 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111967551837 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/STRU new file mode 100644 index 0000000000000000000000000000000000000000..b6b89c9dbe68ffe5a7992a1cc867e05a3c99a7b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.274521466802 10.989606137214 0.737590886088 0 0 0 +H +0.0 +2 +-7.279676450357 12.124047791374 -0.305793987838 0 0 0 +-7.411560858755 9.478685134002 0.202603014808 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/conv new file mode 100644 index 0000000000000000000000000000000000000000..916d02b5368edd676145a64cb8128fb48d027cc6 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/conv @@ -0,0 +1 @@ +86 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..a67ab56e8d0b9eca6a82825e8733638d54783533 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.756236741 0.01289152155 1.274589012 1.351042968 1.470107404 0.01001914844 0.01599565949 0.03921549731 +9.517346245e-18 0.0008469989793 0.003005358175 0.01412346986 0.04793895988 -4.916487383e-19 3.301856376e-06 8.439516168e-06 +0.001600603486 0.006211762047 + +H atom_index 1 n_descriptor 18 +1.249977775 0.03523504649 0.1137373233 0.1496048458 0.3190176444 0.02390551201 0.02822774726 0.03831790238 +2.004466275e-17 5.09704747e-05 0.1046997312 0.1157468548 0.1282245559 -5.807310932e-18 2.259058814e-06 0.01350994571 +0.02762592583 0.03075811572 + +H atom_index 2 n_descriptor 18 +1.261006006 0.03487165235 0.1178155152 0.1548418127 0.3226514491 0.02447306191 0.02887524123 0.03799220545 +-1.333274033e-17 5.19533667e-05 0.1065428309 0.1171400658 0.1327261306 -1.486087748e-18 1.692926542e-06 0.01345230625 +0.0280253387 0.03125556174 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..de6d93365576df943022a022fa0d25fd386b88e2 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..df0d6fda5870687cc96fd4fe2b3fbb69bd6ab354 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..6c4bb8baaf6cc968eb9ff606a0c134f72b09c6b4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..40c66e7f03cf73f583785bd1c8b9b3cdac5ede0f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:50 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.086889 SEC) : SETUP UNITCELL + DONE(0.0994905 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.117868 SEC) : INIT PLANEWAVE + DONE(0.168366 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451728 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651589e+02 0.000000e+00 2.128e-01 5.427e-01 + GE2 -4.663568e+02 -1.197891e+00 9.713e-02 4.947e-01 + GE3 -4.663596e+02 -2.873496e-03 6.221e-02 5.637e-01 + GE4 -4.663595e+02 1.536478e-04 1.943e-03 4.255e-01 + GE5 -4.663587e+02 7.466598e-04 8.334e-04 4.226e-01 + GE6 -4.663593e+02 -5.364374e-04 1.065e-04 4.191e-01 + GE7 -4.663591e+02 1.647646e-04 3.525e-05 4.169e-01 + GE8 -4.663591e+02 -2.735963e-05 1.984e-05 4.017e-01 + GE9 -4.663591e+02 1.997924e-05 1.923e-06 4.026e-01 + GE10 -4.663591e+02 -4.011745e-06 2.454e-07 4.025e-01 + GE11 -4.663591e+02 -4.583213e-07 4.390e-08 3.384e-01 +E_delta_band = -7.10737808e-02 Ry = -9.67008398e-01 eV +E_delta_NN= -1.95071730e-01 Ry = -2.65408704e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.085 11 0.64 1e+02 % + Run_lcao lcao_line 7.0759 1 7.1 1e+02 % + Potential init_pot 0.28761 2 0.14 4.1 % + PW_Basis recip2real 0.28731 16 0.018 4.1 % + PW_Basis gathers_scatterp 0.12457 16 0.0078 1.8 % + Potential v_of_rho 1.008 13 0.078 14 % + XC_Functional v_xc 0.30108 14 0.022 4.2 % + H_Hartree_pw v_hartree 0.66436 13 0.051 9.4 % + PW_Basis real2recip 0.64858 38 0.017 9.2 % + PW_Basis gatherp_scatters 0.24534 38 0.0065 3.5 % + ORB_control set_orb_tables 1.0885 1 1.1 15 % + ORB_gen_tables gen_tables 1.0885 1 1.1 15 % + ORB_table_phi init_Table 0.4748 1 0.47 6.7 % + ORB_table_phi cal_ST_Phi12_R 0.46972 126 0.0037 6.6 % + ORB_table_beta init_Table_Beta 0.18123 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.17968 56 0.0032 2.5 % + ORB_table_alpha init_Table_Alpha 0.24642 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.2445 66 0.0037 3.5 % + LOOP_ions opt_ions 5.4564 1 5.5 77 % + ESolver_KS_LCAO Run 4.8928 1 4.9 69 % + HSolverLCAO solve 2.6082 11 0.24 37 % + HamiltLCAO updateHk 1.3551 11 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.3176 11 0.12 19 % + Gint_interface cal_gint 2.43 23 0.11 34 % + Gint_Gamma distri_vl 2.359 6 0.39 33 % + LCAO_Deepks cal_projected_DM 5.2928 13 0.41 75 % + LCAO_gen_fixedH add_v_delta 2.2128 6 0.37 31 % + LCAO_DESCRIPTOR add_v_delta 2.2128 6 0.37 31 % + ElecStateLCAO psiToRho 1.2383 11 0.11 17 % + Charge mix_rho 0.7765 10 0.078 11 % + LOOP_ions force_stress 0.56342 1 0.56 8 % + Force_Stress_LCAO getForceStress 0.5634 1 0.56 8 % + Force_LCAO_gamma ftable_gamma 0.3445 1 0.34 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.33648 1 0.34 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:50 2022 + FINISH Time : Wed Sep 28 11:06:57 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/86/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9f2640606e881aa0e3cbeb1fb8b0786b6a2a8103 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.714545 0.370461 0.0144147 +H 0.693496 0.413329 0.968032 +H 0.692242 0.308951 0.000517732 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..e0a4d271706daa17f88474fdd49110fb23f9a528 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9691 2 + 2 -13.1363 2 + 3 -8.78553 2 + 4 -6.66713 2 + 5 1.12717 0 + 6 4.16414 0 + 7 11.1371 0 + 8 11.3614 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..a02dd3536fee16cf177e1fd1722f25faaf00ab9f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:05 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 20.0072538703 10.372906362 0.40361265243 0 0 0 0 + tauc_H1 19.4178829606 11.5732080723 27.1048957379 0 0 0 0 + tauc_H2 19.3827805127 8.650634627 0.0144965099535 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105730542176 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.106099139307 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.124179063446 (SEC) + + DONE : INIT CHARGE Time : 0.167523414844 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.451265 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 0 4 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00148 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000888 + + Density error is 0.212870082619 + + Energy Rydberg eV + E_KohnSham -34.1918678296 -465.204227745 + E_Harris -34.3786760866 -467.745884474 + E_Fermi -0.390876259026 -5.31814433568 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00133653381576 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111865709576 + + Density error is 0.0986381863884 + + Energy Rydberg eV + E_KohnSham -34.278892649 -466.388261157 + E_Harris -34.2857062445 -466.480964879 + E_Fermi -0.201508552367 -2.74166450792 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00123224372069 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107832241872 + + Density error is 0.0633605294514 + + Energy Rydberg eV + E_KohnSham -34.2790595246 -466.390531615 + E_Harris -34.2834363021 -466.450080728 + E_Fermi -0.192010087002 -2.6124312567 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00103530081317 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102911489993 + + Density error is 0.00211252169676 + + Energy Rydberg eV + E_KohnSham -34.2790132568 -466.38990211 + E_Harris -34.2790181458 -466.389968629 + E_Fermi -0.15711173876 -2.13761486982 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00103061027394 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102827063529 + + Density error is 0.000791844018636 + + Energy Rydberg eV + E_KohnSham -34.2789844865 -466.38951067 + E_Harris -34.2789846609 -466.389513042 + E_Fermi -0.156599931637 -2.13065137667 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102813153172 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102773475519 + + Density error is 0.000188660739906 + + Energy Rydberg eV + E_KohnSham -34.2790028251 -466.389760179 + E_Harris -34.2790028731 -466.389760833 + E_Fermi -0.15633924596 -2.12710456608 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010281913931 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102801885542 + + Density error is 2.89041397735e-05 + + Energy Rydberg eV + E_KohnSham -34.2789960523 -466.389668031 + E_Harris -34.2789960556 -466.389668076 + E_Fermi -0.156286489873 -2.12638678269 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102816122887 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102793804624 + + Density error is 1.40845689512e-05 + + Energy Rydberg eV + E_KohnSham -34.2789997473 -466.389718304 + E_Harris -34.2789997482 -466.389718316 + E_Fermi -0.156310061305 -2.12670748848 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102813115535 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102794064745 + + Density error is 1.69105493863e-06 + + Energy Rydberg eV + E_KohnSham -34.278998654 -466.389703429 + E_Harris -34.278998654 -466.389703429 + E_Fermi -0.156295355753 -2.12650740918 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102812729895 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102794171173 + + Density error is 4.30753656552e-07 + + Energy Rydberg eV + E_KohnSham -34.2789988787 -466.389706486 + E_Harris -34.2789988787 -466.389706486 + E_Fermi -0.156294046321 -2.12648959344 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102812726613 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102794213312 + + Density error is 1.3358290486e-07 + + Energy Rydberg eV + E_KohnSham -34.2789988887 -466.389706622 + E_Harris -34.2789988887 -466.389706622 + E_Fermi -0.156293834211 -2.12648670753 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00102812701374 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00102794219239 + + Density error is 9.85593465496e-09 + + Energy Rydberg eV + E_KohnSham -34.2789988926 -466.389706675 + E_Harris -34.2789988926 -466.389706675 + E_band -7.87288193632 -107.116054015 + E_one_elec -68.8386328722 -936.597649593 + E_Hartree +35.8389906884 +487.614483931 + E_xc -8.1768098631 -111.251205601 + E_Ewald +7.02276983212 +95.5496854593 + E_demet -9.16312697559e-65 -1.24670738366e-63 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.19382069763 -2.63706587811 + E_Fermi -0.156293705656 -2.12648495845 + + charge density convergence is achieved + final etot is -466.389706675 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9691 2.00000 + 2 -13.1363 2.00000 + 3 -8.78553 2.00000 + 4 -6.66713 2.00000 + 5 1.12717 0.00000 + 6 4.16414 0.00000 + 7 11.1371 0.00000 + 8 11.3614 0.00000 + + EFERMI = -2.126484958450219 eV + OUT.ABACUS/ final etot is -466.3897066747370 eV + correction force for each atom along direction 1 is -0.000127255 + correction force for each atom along direction 2 is -5.47274e-05 + correction force for each atom along direction 3 is -5.82801e-06 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.075158558 -0.19807284 -0.041700253 + H1 -0.0070990672 -0.75710664 +0.23444948 + H2 +0.082257626 +0.95517948 -0.19274922 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3897066747370 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5686 11 0.60 1.0e+02% + Run_lcao lcao_line 6.5583 1 6.6 1.e+02% + Potential init_pot 0.28474 2 0.14 4.3% + PW_Basis recip2real 0.28937 17 0.017 4.4% + PW_Basis gathers_scatterp 0.12972 17 0.0076 2.0% + Potential v_of_rho 1.0639 14 0.076 16.% + XC_Functional v_xc 0.31110 15 0.021 4.7% + H_Hartree_pw v_hartree 0.70445 14 0.050 11.% + PW_Basis real2recip 0.75462 41 0.018 11.% + PW_Basis gatherp_scatters 0.29951 41 0.0073 4.6% + ORB_control set_orb_tables 1.0971 1 1.1 17.% + ORB_gen_tables gen_tables 1.0971 1 1.1 17.% + ORB_table_phi init_Table 0.47449 1 0.47 7.2% + ORB_table_phi cal_ST_Phi12_R 0.46932 126 0.0037 7.1% + ORB_table_beta init_Table_Beta 0.18590 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18435 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.24737 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24538 66 0.0037 3.7% + LOOP_ions opt_ions 4.9332 1 4.9 75.% + ESolver_KS_LCAO Run 4.4716 1 4.5 68.% + HSolverLCAO solve 1.8128 12 0.15 28.% + HamiltLCAO updateHk 1.0507 12 0.088 16.% + LCAO_Hamilt cal_Hgamma 1.0211 12 0.085 16.% + Gint_interface cal_gint 1.3552 25 0.054 21.% + Gint_Gamma distri_vl 2.3370 6 0.39 36.% + LCAO_Deepks cal_projected_DM 4.7432 14 0.34 72.% + LCAO_gen_fixedH add_v_delta 2.1905 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.1906 6 0.37 33.% + ElecStateLCAO psiToRho 0.73667 12 0.061 11.% + Charge mix_rho 0.98728 11 0.090 15.% + LOOP_ions force_stress 0.46142 1 0.46 7.0% + Force_Stress_LCAO getForceStress 0.46139 1 0.46 7.0% + Force_LCAO_gamma ftable_gamma 0.24928 1 0.25 3.8% + Force_LCAO_gamma cal_fvl_dphi 0.19580 1 0.20 3.0% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:05 2022 + Finish Time : Wed Sep 28 11:11:12 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..1533019c5563fdd89a98d1eab07aa5b1c2b44d76 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123618 ima = 3.66342e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123775931688 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011289086891 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113465262091 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011363666599 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113617736212 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113631959552 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113625139908 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113627275108 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113626644935 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113626606091 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113626589141 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113626582418 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/STRU new file mode 100644 index 0000000000000000000000000000000000000000..68d0ee77c4944edb6609fd4bd5aa95db648b73b7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-7.992746129688 10.372906362043 0.403612652421 0 0 0 +H +0.0 +2 +-8.582117039402 11.573208072307 -0.895104262099 0 0 0 +-8.617219487347 8.650634626993 0.014496509944 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/conv new file mode 100644 index 0000000000000000000000000000000000000000..fc6d73796bb40615b24737519af488d1485c6e0d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/conv @@ -0,0 +1 @@ +87 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d8dbbed40c1d222c0e01088902202f82097a8b4a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.744168296 0.01242273515 1.258506506 1.355989972 1.467867795 0.00754290001 0.01992201083 0.0388807388 +-7.275679973e-18 0.001031476941 0.002234358108 0.01164557885 0.04020597436 1.10855437e-18 1.284277672e-06 4.211107744e-06 +0.001766829171 0.005586097922 + +H atom_index 1 n_descriptor 18 +1.215699344 0.03491068943 0.09674658767 0.1364675644 0.3124754229 0.02014390925 0.02655630178 0.03819120242 +-9.435296965e-18 3.242180311e-05 0.09129342733 0.1141876233 0.1168443502 -1.209993101e-18 5.240255318e-06 0.01336006566 +0.0243193985 0.02926701841 + +H atom_index 2 n_descriptor 18 +1.208688893 0.03514970388 0.09458386172 0.1335125197 0.3100207311 0.01983504104 0.02614887543 0.03847302974 +9.560553933e-18 3.190408419e-05 0.08942419717 0.1139980297 0.1142543073 -4.372776072e-18 5.451566916e-06 0.01352468304 +0.02403648195 0.0289137252 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..4785b49c126d0a00716b196ad5bdf0d07f72dcdb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/e_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/e_base.npy new file mode 100644 index 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ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:05 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.105755 SEC) : SETUP UNITCELL + DONE(0.106114 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.124201 SEC) : INIT PLANEWAVE + DONE(0.167656 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.451332 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652042e+02 0.000000e+00 2.129e-01 4.816e-01 + GE2 -4.663883e+02 -1.184033e+00 9.864e-02 4.297e-01 + GE3 -4.663905e+02 -2.270458e-03 6.336e-02 5.004e-01 + GE4 -4.663899e+02 6.295051e-04 2.113e-03 3.590e-01 + GE5 -4.663895e+02 3.914406e-04 7.918e-04 3.579e-01 + GE6 -4.663898e+02 -2.495094e-04 1.887e-04 3.513e-01 + GE7 -4.663897e+02 9.214774e-05 2.890e-05 3.414e-01 + GE8 -4.663897e+02 -5.027251e-05 1.408e-05 3.329e-01 + GE9 -4.663897e+02 1.487497e-05 1.691e-06 3.357e-01 + GE10 -4.663897e+02 -3.057312e-06 4.308e-07 3.368e-01 + GE11 -4.663897e+02 -1.353443e-07 1.336e-07 3.313e-01 + GE12 -4.663897e+02 -5.309749e-08 9.856e-09 2.513e-01 +E_delta_band = -6.85040199e-02 Ry = -9.32045006e-01 eV +E_delta_NN= -1.93820698e-01 Ry = -2.63706588e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5686 11 0.6 1e+02 % + Run_lcao lcao_line 6.5583 1 6.6 1e+02 % + Potential init_pot 0.28474 2 0.14 4.3 % + PW_Basis recip2real 0.28937 17 0.017 4.4 % + PW_Basis gathers_scatterp 0.12972 17 0.0076 2 % + Potential v_of_rho 1.0639 14 0.076 16 % + XC_Functional v_xc 0.3111 15 0.021 4.7 % + H_Hartree_pw v_hartree 0.70445 14 0.05 11 % + PW_Basis real2recip 0.75462 41 0.018 11 % + PW_Basis gatherp_scatters 0.29951 41 0.0073 4.6 % + ORB_control set_orb_tables 1.0971 1 1.1 17 % + ORB_gen_tables gen_tables 1.0971 1 1.1 17 % + ORB_table_phi init_Table 0.47449 1 0.47 7.2 % + ORB_table_phi cal_ST_Phi12_R 0.46932 126 0.0037 7.1 % + ORB_table_beta init_Table_Beta 0.1859 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18435 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.24737 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24538 66 0.0037 3.7 % + LOOP_ions opt_ions 4.9332 1 4.9 75 % + ESolver_KS_LCAO Run 4.4716 1 4.5 68 % + HSolverLCAO solve 1.8128 12 0.15 28 % + HamiltLCAO updateHk 1.0507 12 0.088 16 % + LCAO_Hamilt cal_Hgamma 1.0211 12 0.085 16 % + Gint_interface cal_gint 1.3552 25 0.054 21 % + Gint_Gamma distri_vl 2.337 6 0.39 36 % + LCAO_Deepks cal_projected_DM 4.7432 14 0.34 72 % + LCAO_gen_fixedH add_v_delta 2.1905 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.1906 6 0.37 33 % + ElecStateLCAO psiToRho 0.73667 12 0.061 11 % + Charge mix_rho 0.98728 11 0.09 15 % + LOOP_ions force_stress 0.46142 1 0.46 7 % + Force_Stress_LCAO getForceStress 0.46139 1 0.46 7 % + Force_LCAO_gamma ftable_gamma 0.24928 1 0.25 3.8 % + Force_LCAO_gamma cal_fvl_dphi 0.1958 1 0.2 3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:05 2022 + FINISH Time : Wed Sep 28 11:11:12 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/87/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..c3d6b92393efac76e976481a2c26b8a38b8f389d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.708902 0.347848 0.00262913 +H 0.684659 0.41071 0.992801 +H 0.656075 0.311596 0.0144047 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..d72d97a91616b52e6ef90ce49cc7b8540eaf9f01 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.102 2 + 2 -12.9071 2 + 3 -9.06646 2 + 4 -6.7015 2 + 5 1.1187 0 + 6 4.16926 0 + 7 11.1193 0 + 8 11.364 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..e5bbcd59c1113a25809a0d1fce02f3b8f06500da --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:38 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.8492505086 9.73975737057 0.0736155537234 0 0 0 0 + tauc_H1 19.1704573359 11.4998876159 27.7984254405 0 0 0 0 + tauc_H2 18.3700994335 8.7246909633 0.403332475602 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101323791511 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101689857371 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119732182088 (SEC) + + DONE : INIT CHARGE Time : 0.162933511372 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.445397 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000963 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00141 + + Density error is 0.212388399224 + + Energy Rydberg eV + E_KohnSham -34.1916374436 -465.201093184 + E_Harris -34.3780826171 -467.737809908 + E_Fermi -0.394639473463 -5.36934549482 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00106125337271 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00121309460738 + + Density error is 0.0983883135983 + + Energy Rydberg eV + E_KohnSham -34.2792256776 -466.392792243 + E_Harris -34.2861156449 -466.486535057 + E_Fermi -0.204966004357 -2.78870555555 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00099556245783 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00112769328125 + + Density error is 0.0632397819218 + + Energy Rydberg eV + E_KohnSham -34.2794671557 -466.396077721 + E_Harris -34.2839114783 -466.456545833 + E_Fermi -0.195800797626 -2.66400652066 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000883804226196 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098234953598 + + Density error is 0.00198977167267 + + Energy Rydberg eV + E_KohnSham -34.279412412 -466.395332894 + E_Harris -34.2794144559 -466.395360704 + E_Fermi -0.160517620041 -2.18395426195 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000882471212561 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000982719379619 + + Density error is 0.000823135551581 + + Energy Rydberg eV + E_KohnSham -34.2793773548 -466.394855917 + E_Harris -34.279377685 -466.394860411 + E_Fermi -0.160160864658 -2.17910035596 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000881120096729 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980709362727 + + Density error is 0.000169619932061 + + Energy Rydberg eV + E_KohnSham -34.2793967173 -466.395119358 + E_Harris -34.2793967454 -466.395119741 + E_Fermi -0.159879659353 -2.1752743615 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000881247139026 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980786154025 + + Density error is 2.89482923315e-05 + + Energy Rydberg eV + E_KohnSham -34.2793901123 -466.395029492 + E_Harris -34.2793901148 -466.395029526 + E_Fermi -0.15983282347 -2.17463712663 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000881206642561 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980778115983 + + Density error is 1.44139602017e-05 + + Energy Rydberg eV + E_KohnSham -34.2793932546 -466.395072245 + E_Harris -34.2793932555 -466.395072257 + E_Fermi -0.159853702675 -2.17492120278 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000881200614673 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980769059053 + + Density error is 2.60864217578e-06 + + Energy Rydberg eV + E_KohnSham -34.2793921715 -466.395057508 + E_Harris -34.2793921715 -466.395057509 + E_Fermi -0.159840338203 -2.17473936981 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000881194835243 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980760458328 + + Density error is 5.68181721195e-07 + + Energy Rydberg eV + E_KohnSham -34.2793924138 -466.395060806 + E_Harris -34.2793924138 -466.395060806 + E_Fermi -0.159838060883 -2.17470838528 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000881195419345 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098076050814 + + Density error is 1.85206468912e-07 + + Energy Rydberg eV + E_KohnSham -34.2793924243 -466.395060949 + E_Harris -34.2793924243 -466.395060949 + E_Fermi -0.159837777351 -2.17470452763 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000881195444218 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000980760268579 + + Density error is 1.05391823732e-08 + + Energy Rydberg eV + E_KohnSham -34.2793924288 -466.39506101 + E_Harris -34.2793924288 -466.39506101 + E_band -7.90507432117 -107.554053881 + E_one_elec -68.9102906754 -937.572604021 + E_Hartree +35.8615004365 +487.920744766 + E_xc -8.18102625907 -111.308572611 + E_Ewald +7.07553023578 +96.2675275779 + E_demet -2.72560712503e-66 -3.70837874099e-65 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194132287499 -2.64130527577 + E_Fermi -0.159837595465 -2.17470205294 + + charge density convergence is achieved + final etot is -466.39506101 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1020 2.00000 + 2 -12.9071 2.00000 + 3 -9.06646 2.00000 + 4 -6.70150 2.00000 + 5 1.11870 0.00000 + 6 4.16926 0.00000 + 7 11.1193 0.00000 + 8 11.3640 0.00000 + + EFERMI = -2.174702052942854 eV + OUT.ABACUS/ final etot is -466.3950610102917 eV + correction force for each atom along direction 1 is -5.12407e-05 + correction force for each atom along direction 2 is 5.08364e-05 + correction force for each atom along direction 3 is -0.000123318 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.016258504 +1.6478491 -0.32319057 + H1 +0.46844359 -1.3987726 +0.22804862 + H2 -0.48470210 -0.24907658 +0.095141943 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3950610102917 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4359 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4260 1 6.4 1.e+02% + Potential init_pot 0.28448 2 0.14 4.4% + PW_Basis recip2real 0.28815 17 0.017 4.5% + PW_Basis gathers_scatterp 0.13302 17 0.0078 2.1% + Potential v_of_rho 1.0390 14 0.074 16.% + XC_Functional v_xc 0.30649 15 0.020 4.8% + H_Hartree_pw v_hartree 0.68525 14 0.049 11.% + PW_Basis real2recip 0.73341 41 0.018 11.% + PW_Basis gatherp_scatters 0.27859 41 0.0068 4.3% + ORB_control set_orb_tables 1.1006 1 1.1 17.% + ORB_gen_tables gen_tables 1.1006 1 1.1 17.% + ORB_table_phi init_Table 0.47870 1 0.48 7.4% + ORB_table_phi cal_ST_Phi12_R 0.47340 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18358 1 0.18 2.9% + ORB_table_beta VNL_PhiBeta_R 0.18200 56 0.0032 2.8% + ORB_table_alpha init_Table_Alpha 0.25068 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.24868 66 0.0038 3.9% + LOOP_ions opt_ions 4.8005 1 4.8 75.% + ESolver_KS_LCAO Run 4.3555 1 4.4 68.% + HSolverLCAO solve 1.7385 12 0.14 27.% + HamiltLCAO updateHk 1.0387 12 0.087 16.% + LCAO_Hamilt cal_Hgamma 1.0091 12 0.084 16.% + Gint_interface cal_gint 1.4256 25 0.057 22.% + Gint_Gamma distri_vl 2.2830 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.6560 14 0.33 72.% + LCAO_gen_fixedH add_v_delta 2.1363 6 0.36 33.% + LCAO_DESCRIPTOR add_v_delta 2.1363 6 0.36 33.% + ElecStateLCAO psiToRho 0.67549 12 0.056 10.% + Charge mix_rho 0.98244 11 0.089 15.% + LOOP_ions force_stress 0.44486 1 0.44 6.9% + Force_Stress_LCAO getForceStress 0.44482 1 0.44 6.9% + Force_LCAO_gamma ftable_gamma 0.23073 1 0.23 3.6% + Force_LCAO_gamma cal_fvl_dphi 0.22240 1 0.22 3.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:38 2022 + Finish Time : Wed Sep 28 11:05:44 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..8ef578e69e85b44e1a0ce908ed144a05248f545d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123785 ima = 3.66423e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123314021733 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112242575089 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112872656499 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113073520191 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113050739938 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113065648961 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113060081233 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113062115078 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113061431408 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113061388058 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113061366702 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011306135705 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/STRU new file mode 100644 index 0000000000000000000000000000000000000000..cbdfcb0971dd19b2d87c4c1233a20a58ba31d931 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.150749491463 9.739757370578 0.073615553724 0 0 0 +H +0.0 +2 +-8.829542664123 11.499887615946 -0.201574559521 0 0 0 +-9.629900566467 8.724690963304 0.403332475578 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/conv new file mode 100644 index 0000000000000000000000000000000000000000..86f25324db91190a426ccb34fc8a4e4ca9d50aac --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/conv @@ -0,0 +1 @@ +88 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..bce39ee302d7a2a598e25cf27c54ada1384bb481 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749150481 0.01251635798 1.255177669 1.352215373 1.468521596 0.008359791998 0.01837905822 0.03904807088 +2.062236205e-19 0.0009713450162 0.002463112409 0.01179507063 0.04289650532 3.374728661e-19 1.722229307e-06 5.276139479e-06 +0.001637305148 0.005862031529 + +H atom_index 1 n_descriptor 18 +1.187655723 0.03627899751 0.08802049812 0.123572988 0.2996898028 0.01914605707 0.02471082655 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:38 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101348 SEC) : SETUP UNITCELL + DONE(0.101705 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119751 SEC) : INIT PLANEWAVE + DONE(0.163069 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.445471 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652011e+02 0.000000e+00 2.124e-01 4.724e-01 + GE2 -4.663928e+02 -1.191699e+00 9.839e-02 4.188e-01 + GE3 -4.663961e+02 -3.285478e-03 6.324e-02 4.891e-01 + GE4 -4.663953e+02 7.448267e-04 1.990e-03 3.489e-01 + GE5 -4.663949e+02 4.769776e-04 8.231e-04 3.462e-01 + GE6 -4.663951e+02 -2.634414e-04 1.696e-04 3.380e-01 + GE7 -4.663950e+02 8.986663e-05 2.895e-05 3.287e-01 + GE8 -4.663951e+02 -4.275297e-05 1.441e-05 3.219e-01 + GE9 -4.663951e+02 1.473628e-05 2.609e-06 3.280e-01 + GE10 -4.663951e+02 -3.297578e-06 5.682e-07 3.236e-01 + GE11 -4.663951e+02 -1.430566e-07 1.852e-07 3.242e-01 + GE12 -4.663951e+02 -6.128358e-08 1.054e-08 2.531e-01 +E_delta_band = -6.90261208e-02 Ry = -9.39148554e-01 eV +E_delta_NN= -1.94132287e-01 Ry = -2.64130528e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4359 11 0.59 1e+02 % + Run_lcao lcao_line 6.426 1 6.4 1e+02 % + Potential init_pot 0.28448 2 0.14 4.4 % + PW_Basis recip2real 0.28815 17 0.017 4.5 % + PW_Basis gathers_scatterp 0.13302 17 0.0078 2.1 % + Potential v_of_rho 1.039 14 0.074 16 % + XC_Functional v_xc 0.30649 15 0.02 4.8 % + H_Hartree_pw v_hartree 0.68525 14 0.049 11 % + PW_Basis real2recip 0.73341 41 0.018 11 % + PW_Basis gatherp_scatters 0.27859 41 0.0068 4.3 % + ORB_control set_orb_tables 1.1006 1 1.1 17 % + ORB_gen_tables gen_tables 1.1006 1 1.1 17 % + ORB_table_phi init_Table 0.4787 1 0.48 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.4734 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18358 1 0.18 2.9 % + ORB_table_beta VNL_PhiBeta_R 0.182 56 0.0032 2.8 % + ORB_table_alpha init_Table_Alpha 0.25068 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.24868 66 0.0038 3.9 % + LOOP_ions opt_ions 4.8005 1 4.8 75 % + ESolver_KS_LCAO Run 4.3555 1 4.4 68 % + HSolverLCAO solve 1.7385 12 0.14 27 % + HamiltLCAO updateHk 1.0387 12 0.087 16 % + LCAO_Hamilt cal_Hgamma 1.0091 12 0.084 16 % + Gint_interface cal_gint 1.4256 25 0.057 22 % + Gint_Gamma distri_vl 2.283 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.656 14 0.33 72 % + LCAO_gen_fixedH add_v_delta 2.1363 6 0.36 33 % + LCAO_DESCRIPTOR add_v_delta 2.1363 6 0.36 33 % + ElecStateLCAO psiToRho 0.67549 12 0.056 10 % + Charge mix_rho 0.98244 11 0.089 15 % + LOOP_ions force_stress 0.44486 1 0.44 6.9 % + Force_Stress_LCAO getForceStress 0.44482 1 0.44 6.9 % + Force_LCAO_gamma ftable_gamma 0.23073 1 0.23 3.6 % + Force_LCAO_gamma cal_fvl_dphi 0.2224 1 0.22 3.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:38 2022 + FINISH Time : Wed Sep 28 11:05:44 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/88/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4bf564ea623645bbe9183dbd9b083d88e67c2f83 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.710008 0.329748 0.994372 +H 0.714478 0.379902 0.0347535 +H 0.647159 0.313438 0.00862464 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..6a663669a8ccc547790bbd6255bfcc2043fb9861 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.4419 2 + 2 -12.6799 2 + 3 -9.48696 2 + 4 -6.77967 2 + 5 1.24393 0 + 6 4.39368 0 + 7 11.0628 0 + 8 11.3502 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..bcf649682777eeb0b128b20ef912a2eec4b48e87 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:06:00 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.8802199057 9.23295510062 27.842421634 0 0 0 0 + tauc_H1 20.0053756434 10.6372613033 0.97309850061 0 0 0 0 + tauc_H2 18.1204524649 8.77626324731 0.241489785607 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0847009049961 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.085193475453 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.103253967391 (SEC) + + DONE : INIT CHARGE Time : 0.15147144053 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.435234 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 4 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000697 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00176 + + Density error is 0.213507097024 + + Energy Rydberg eV + E_KohnSham -34.1882936556 -465.155598613 + E_Harris -34.3781509086 -467.738739061 + E_Fermi -0.406932313816 -5.53659816822 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010470624757 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00143255991197 + + Density error is 0.0976497047202 + + Energy Rydberg eV + E_KohnSham -34.2777142708 -466.372228498 + E_Harris -34.2846000332 -466.465914103 + E_Fermi -0.216940370029 -2.95162515862 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00100245876654 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00131497171153 + + Density error is 0.0626814155117 + + Energy Rydberg eV + E_KohnSham -34.2780481932 -466.376771747 + E_Harris -34.2825117781 -466.437501935 + E_Fermi -0.206416244819 -2.8084370893 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000949465887976 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110471651236 + + Density error is 0.00193043758068 + + Energy Rydberg eV + E_KohnSham -34.2780206351 -466.376396798 + E_Harris -34.2780208889 -466.376400252 + E_Fermi -0.170480244078 -2.31950271589 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000952652181399 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110427933113 + + Density error is 0.000936270530261 + + Energy Rydberg eV + E_KohnSham -34.2779609783 -466.375585126 + E_Harris -34.2779622936 -466.375603023 + E_Fermi -0.170017804902 -2.31321090812 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000951362554849 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110171940978 + + Density error is 0.00010120186596 + + Energy Rydberg eV + E_KohnSham -34.2779980424 -466.376089409 + E_Harris -34.2779982102 -466.376091693 + E_Fermi -0.169911191052 -2.31176035227 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000951068440681 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110128907005 + + Density error is 3.87966770325e-05 + + Energy Rydberg eV + E_KohnSham -34.2779880081 -466.375952886 + E_Harris -34.2779880162 -466.375952997 + E_Fermi -0.16980195788 -2.31027415873 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000951044355937 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110134882684 + + Density error is 1.3140352482e-05 + + Energy Rydberg eV + E_KohnSham -34.2779892349 -466.375969577 + E_Harris -34.2779892357 -466.375969588 + E_Fermi -0.169850818384 -2.31093893999 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000951068991072 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110134162276 + + Density error is 2.10393602871e-06 + + Energy Rydberg eV + E_KohnSham -34.2779879731 -466.37595241 + E_Harris -34.2779879731 -466.37595241 + E_Fermi -0.169839836739 -2.31078952704 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000951070494369 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110133598068 + + Density error is 4.03847382861e-07 + + Energy Rydberg eV + E_KohnSham -34.2779881948 -466.375955425 + E_Harris -34.2779881948 -466.375955425 + E_Fermi -0.169837928144 -2.31076355927 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00095107172357 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011013364622 + + Density error is 8.33570731506e-08 + + Energy Rydberg eV + E_KohnSham -34.2779882214 -466.375955787 + E_Harris -34.2779882214 -466.375955787 + E_band -7.99494185602 -108.776764421 + E_one_elec -69.3256727566 -943.224167173 + E_Hartree +36.0434000007 +490.395615303 + E_xc -8.21005915132 -111.703585375 + E_Ewald +7.33855450914 +99.8461564078 + E_demet -8.7281677298e-77 -1.18752814225e-75 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194926070522 -2.65210524785 + E_Fermi -0.169837752724 -2.31076117256 + + charge density convergence is achieved + final etot is -466.375955787 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4419 2.00000 + 2 -12.6799 2.00000 + 3 -9.48696 2.00000 + 4 -6.77967 2.00000 + 5 1.24393 0.00000 + 6 4.39368 0.00000 + 7 11.0628 0.00000 + 8 11.3502 0.00000 + + EFERMI = -2.310761172556854 eV + OUT.ABACUS/ final etot is -466.3759557874257 eV + correction force for each atom along direction 1 is -2.33322e-05 + correction force for each atom along direction 2 is -3.24734e-05 + correction force for each atom along direction 3 is -2.32217e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.92412027 -0.66553685 -0.15058992 + H1 +0.66269586 +1.0507454 +0.59248951 + H2 +0.26142441 -0.38520858 -0.44189959 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3759557874257 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2554 11 0.57 1.0e+02% + Run_lcao lcao_line 6.2467 1 6.2 1.e+02% + Potential init_pot 0.28851 2 0.14 4.6% + PW_Basis recip2real 0.27266 16 0.017 4.4% + PW_Basis gathers_scatterp 0.12163 16 0.0076 1.9% + Charge atomic_rho 0.10010 1 0.10 1.6% + Potential v_of_rho 0.86153 13 0.066 14.% + XC_Functional v_xc 0.22679 14 0.016 3.6% + H_Hartree_pw v_hartree 0.59441 13 0.046 9.5% + PW_Basis real2recip 0.56173 38 0.015 9.0% + PW_Basis gatherp_scatters 0.22191 38 0.0058 3.5% + ORB_control set_orb_tables 1.1195 1 1.1 18.% + ORB_gen_tables gen_tables 1.1195 1 1.1 18.% + ORB_table_phi init_Table 0.48677 1 0.49 7.8% + ORB_table_phi cal_ST_Phi12_R 0.48185 126 0.0038 7.7% + ORB_table_beta init_Table_Beta 0.19175 1 0.19 3.1% + ORB_table_beta VNL_PhiBeta_R 0.19018 56 0.0034 3.0% + ORB_table_alpha init_Table_Alpha 0.25988 1 0.26 4.2% + ORB_table_alpha S_PhiAlpha_R 0.25794 66 0.0039 4.1% + LOOP_ions opt_ions 4.6112 1 4.6 74.% + ESolver_KS_LCAO Run 4.0899 1 4.1 65.% + HSolverLCAO solve 2.1328 11 0.19 34.% + HamiltLCAO updateHk 1.1166 11 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.0830 11 0.098 17.% + Gint_interface cal_gint 1.9866 23 0.086 32.% + Gint_Gamma distri_vl 1.9722 6 0.33 32.% + LCAO_Deepks cal_projected_DM 4.4529 13 0.34 71.% + LCAO_gen_fixedH add_v_delta 1.8408 6 0.31 29.% + LCAO_DESCRIPTOR add_v_delta 1.8408 6 0.31 29.% + ElecStateLCAO psiToRho 1.0020 11 0.091 16.% + Charge mix_rho 0.66187 10 0.066 11.% + LOOP_ions force_stress 0.52109 1 0.52 8.3% + Force_Stress_LCAO getForceStress 0.52106 1 0.52 8.3% + Force_LCAO_gamma ftable_gamma 0.31073 1 0.31 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.30400 1 0.30 4.9% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:06:00 2022 + Finish Time : Wed Sep 28 11:06:06 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..44677582971c0db63904b88d394c42ffd6feccf1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123855 ima = 3.65851e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122577447642 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111339994909 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111962244552 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112227809923 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112172338217 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112200515361 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112199973476 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112202512785 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011220184679 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112201764634 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112201743641 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/STRU new file mode 100644 index 0000000000000000000000000000000000000000..1e695337f3125ffa8a64e1d06aedf4170f8120c3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.119780094328 9.232955100628 -0.157578365960 0 0 0 +H +0.0 +2 +-7.994624356640 10.637261303286 0.973098500604 0 0 0 +-9.879547535146 8.776263247289 0.241489785582 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/conv new file mode 100644 index 0000000000000000000000000000000000000000..a4c6b24663b535a0f8f1f3dacce48b2af2434894 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/conv @@ -0,0 +1 @@ +89 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..710c014576cebc0850f644933929d654eaa240c4 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.754913199 0.01281348159 1.269942352 1.352547293 1.469833599 0.009663601118 0.01648854952 0.03918992985 +-3.239354438e-19 0.0008829494171 0.002893815282 0.0134936486 0.0471459558 -1.363653951e-19 2.927879951e-06 7.701456531e-06 +0.001587760072 0.00616536583 + +H atom_index 1 n_descriptor 18 +1.270541718 0.03432269522 0.1194600937 0.1594078867 0.3260343233 0.02444466137 0.02943098365 0.03753999999 +2.445321724e-17 5.214971663e-05 0.1068526383 0.1180595331 0.1366803613 -8.152100043e-18 1.731298703e-06 0.01339830559 +0.02789485954 0.03164632696 + +H atom_index 2 n_descriptor 18 +1.228142033 0.0357256477 0.1042795559 0.1396332452 0.3118713358 0.02231564476 0.02694268013 0.03886152504 +2.994172613e-17 4.821247398e-05 0.09821455899 0.1142498294 0.1196253988 -2.348985683e-18 4.01932579e-06 0.0137500429 +0.02632342602 0.02969307525 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..08d1fd544d4456bafd812e543dfb3268470eef47 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/err b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/err.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/err.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/f_base.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/f_base.npy new file mode 100644 index 0000000000000000000000000000000000000000..bf2ada04d127b3fb47a7ddac266d6f3399c27f5c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/f_base.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..48fe63ecaa91cf775c01c8679c95a9ee94663f9b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..6ce33a4e35e70df76b30798d73a112c847098deb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..fac39807591c4a4e36127f6f5260a4f7378f1af0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:06:00 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0847238 SEC) : SETUP UNITCELL + DONE(0.0852086 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.103276 SEC) : INIT PLANEWAVE + DONE(0.151613 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.435298 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651556e+02 0.000000e+00 2.135e-01 4.843e-01 + GE2 -4.663722e+02 -1.216630e+00 9.765e-02 4.132e-01 + GE3 -4.663768e+02 -4.543249e-03 6.268e-02 4.676e-01 + GE4 -4.663764e+02 3.749483e-04 1.930e-03 3.569e-01 + GE5 -4.663756e+02 8.116723e-04 9.363e-04 3.550e-01 + GE6 -4.663761e+02 -5.042829e-04 1.012e-04 3.365e-01 + GE7 -4.663760e+02 1.365227e-04 3.880e-05 3.408e-01 + GE8 -4.663760e+02 -1.669091e-05 1.314e-05 3.387e-01 + GE9 -4.663760e+02 1.716751e-05 2.104e-06 3.267e-01 + GE10 -4.663760e+02 -3.015751e-06 4.038e-07 3.348e-01 + GE11 -4.663760e+02 -3.619400e-07 8.336e-08 2.744e-01 +E_delta_band = -7.07152472e-02 Ry = -9.62130297e-01 eV +E_delta_NN= -1.94926071e-01 Ry = -2.65210525e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2554 11 0.57 1e+02 % + Run_lcao lcao_line 6.2467 1 6.2 1e+02 % + Potential init_pot 0.28851 2 0.14 4.6 % + PW_Basis recip2real 0.27266 16 0.017 4.4 % + PW_Basis gathers_scatterp 0.12163 16 0.0076 1.9 % + Charge atomic_rho 0.1001 1 0.1 1.6 % + Potential v_of_rho 0.86153 13 0.066 14 % + XC_Functional v_xc 0.22679 14 0.016 3.6 % + H_Hartree_pw v_hartree 0.59441 13 0.046 9.5 % + PW_Basis real2recip 0.56173 38 0.015 9 % + PW_Basis gatherp_scatters 0.22191 38 0.0058 3.5 % + ORB_control set_orb_tables 1.1195 1 1.1 18 % + ORB_gen_tables gen_tables 1.1195 1 1.1 18 % + ORB_table_phi init_Table 0.48677 1 0.49 7.8 % + ORB_table_phi cal_ST_Phi12_R 0.48185 126 0.0038 7.7 % + ORB_table_beta init_Table_Beta 0.19175 1 0.19 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.19018 56 0.0034 3 % + ORB_table_alpha init_Table_Alpha 0.25988 1 0.26 4.2 % + ORB_table_alpha S_PhiAlpha_R 0.25794 66 0.0039 4.1 % + LOOP_ions opt_ions 4.6112 1 4.6 74 % + ESolver_KS_LCAO Run 4.0899 1 4.1 65 % + HSolverLCAO solve 2.1328 11 0.19 34 % + HamiltLCAO updateHk 1.1166 11 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.083 11 0.098 17 % + Gint_interface cal_gint 1.9866 23 0.086 32 % + Gint_Gamma distri_vl 1.9722 6 0.33 32 % + LCAO_Deepks cal_projected_DM 4.4529 13 0.34 71 % + LCAO_gen_fixedH add_v_delta 1.8408 6 0.31 29 % + LCAO_DESCRIPTOR add_v_delta 1.8408 6 0.31 29 % + ElecStateLCAO psiToRho 1.002 11 0.091 16 % + Charge mix_rho 0.66187 10 0.066 11 % + LOOP_ions force_stress 0.52109 1 0.52 8.3 % + Force_Stress_LCAO getForceStress 0.52106 1 0.52 8.3 % + Force_LCAO_gamma ftable_gamma 0.31073 1 0.31 5 % + Force_LCAO_gamma cal_fvl_dphi 0.304 1 0.3 4.9 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:06:00 2022 + FINISH Time : Wed Sep 28 11:06:06 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/89/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..0ffe3e98cee04b1fb4fae09709146476ec053ce0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.516002 0.65544 0.279223 +H 0.514774 0.612448 0.325794 +H 0.564257 0.637229 0.23502 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..7f2de120238a26244e51f920d9d9bb65edd14c5e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2051 2 + 2 -13.2057 2 + 3 -8.91132 2 + 4 -6.71965 2 + 5 1.22841 0 + 6 4.44786 0 + 7 11.0848 0 + 8 11.3075 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..172177bb36467b94ab5303085930a014bdaaebb7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:08:19 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.4480547643 18.3523255197 7.81823612381 0 0 0 0 + tauc_H1 14.4136710667 17.1485434517 9.12224586886 0 0 0 0 + tauc_H2 15.7991964033 17.8424129327 6.58055778147 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.101451795293 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.101803409482 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.119864186838 (SEC) + + DONE : INIT CHARGE Time : 0.163247640484 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.446056 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 292 ; sender_size of each process is: +144 144 4 0 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000806 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00126 + + Density error is 0.215981794317 + + Energy Rydberg eV + E_KohnSham -34.1857079709 -465.120418568 + E_Harris -34.3797401161 -467.760361338 + E_Fermi -0.404275458844 -5.50044980184 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00105061630619 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00125100667219 + + Density error is 0.0983868647781 + + Energy Rydberg eV + E_KohnSham -34.2762816679 -466.352736936 + E_Harris -34.2830454738 -466.444763237 + E_Fermi -0.212282097275 -2.88824610633 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.0010112476123 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117712560574 + + Density error is 0.0631420001786 + + Energy Rydberg eV + E_KohnSham -34.276590534 -466.356939275 + E_Harris -34.2809431542 -466.416159712 + E_Fermi -0.201566907671 -2.74245847256 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000962182719131 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105813192906 + + Density error is 0.00207562773176 + + Energy Rydberg eV + E_KohnSham -34.2765714786 -466.356680013 + E_Harris -34.2765744748 -466.356720779 + E_Fermi -0.166147005628 -2.26054598218 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000963401446332 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105682344886 + + Density error is 0.000890843990627 + + Energy Rydberg eV + E_KohnSham -34.2765188642 -466.355964158 + E_Harris -34.276519441 -466.355972006 + E_Fermi -0.165493586851 -2.25165576363 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000962737105137 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105531759262 + + Density error is 0.000187675934836 + + Energy Rydberg eV + E_KohnSham -34.2765479767 -466.356360253 + E_Harris -34.2765480337 -466.35636103 + E_Fermi -0.165379041845 -2.25009729887 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000963016827829 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105545303279 + + Density error is 4.08457517698e-05 + + Energy Rydberg eV + E_KohnSham -34.2765370846 -466.356212059 + E_Harris -34.276537093 -466.356212173 + E_Fermi -0.165255272439 -2.24841332971 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000962957926814 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105537895218 + + Density error is 1.64065564214e-05 + + Energy Rydberg eV + E_KohnSham -34.2765418386 -466.35627674 + E_Harris -34.2765418397 -466.356276755 + E_Fermi -0.165294102149 -2.24894163502 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000962957332143 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105536279823 + + Density error is 2.25460572087e-06 + + Energy Rydberg eV + E_KohnSham -34.2765404158 -466.356257382 + E_Harris -34.2765404158 -466.356257382 + E_Fermi -0.165277189994 -2.24871153335 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.00096295475415 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105536312161 + + Density error is 4.38654997808e-07 + + Energy Rydberg eV + E_KohnSham -34.2765406194 -466.356260153 + E_Harris -34.2765406194 -466.356260153 + E_Fermi -0.165275260757 -2.24868528473 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000962955454605 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010553632835 + + Density error is 1.84749988767e-07 + + Energy Rydberg eV + E_KohnSham -34.2765406504 -466.356260574 + E_Harris -34.2765406504 -466.356260574 + E_Fermi -0.165275140962 -2.24868365483 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 292 + sender_size = 292 + last sender_buffer = 0.000962955663064 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00105536322762 + + Density error is 1.16073097022e-08 + + Energy Rydberg eV + E_KohnSham -34.2765406506 -466.356260577 + E_Harris -34.2765406506 -466.356260577 + E_band -7.94397851684 -108.083372619 + E_one_elec -69.2301587666 -941.924632671 + E_Hartree +36.0187536841 +490.060284962 + E_xc -8.2064379916 -111.654316969 + E_Ewald +7.26578984992 +98.8561424295 + E_demet -1.38391059073e-73 -1.88290695565e-72 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194671592441 -2.64864289594 + E_Fermi -0.165274958587 -2.24868117349 + + charge density convergence is achieved + final etot is -466.356260577 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2051 2.00000 + 2 -13.2057 2.00000 + 3 -8.91132 2.00000 + 4 -6.71965 2.00000 + 5 1.22841 0.00000 + 6 4.44786 0.00000 + 7 11.0848 0.00000 + 8 11.3075 0.00000 + + EFERMI = -2.248681173490684 eV + OUT.ABACUS/ final etot is -466.3562605771174 eV + correction force for each atom along direction 1 is 1.44031e-05 + correction force for each atom along direction 2 is -1.87860e-07 + correction force for each atom along direction 3 is 7.92811e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.83320240 +1.3067500 -2.4537516 + H1 +0.18215926 -1.4892958 +1.3161604 + H2 -1.0153617 +0.18254577 +1.1375912 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3562605771174 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5435 11 0.69 1.0e+02% + Run_lcao lcao_line 7.5337 1 7.5 1.e+02% + Potential init_pot 0.28458 2 0.14 3.8% + PW_Basis recip2real 0.27490 17 0.016 3.6% + PW_Basis gathers_scatterp 0.12376 17 0.0073 1.6% + Potential v_of_rho 0.97603 14 0.070 13.% + XC_Functional v_xc 0.28977 15 0.019 3.8% + H_Hartree_pw v_hartree 0.64181 14 0.046 8.5% + PW_Basis real2recip 0.73241 41 0.018 9.7% + PW_Basis gatherp_scatters 0.29568 41 0.0072 3.9% + ORB_control set_orb_tables 1.0937 1 1.1 14.% + ORB_gen_tables gen_tables 1.0937 1 1.1 14.% + ORB_table_phi init_Table 0.47497 1 0.47 6.3% + ORB_table_phi cal_ST_Phi12_R 0.46969 126 0.0037 6.2% + ORB_table_beta init_Table_Beta 0.18274 1 0.18 2.4% + ORB_table_beta VNL_PhiBeta_R 0.18121 56 0.0032 2.4% + ORB_table_alpha init_Table_Alpha 0.24697 1 0.25 3.3% + ORB_table_alpha S_PhiAlpha_R 0.24499 66 0.0037 3.2% + LOOP_ions opt_ions 5.9185 1 5.9 78.% + ESolver_KS_LCAO Run 5.3600 1 5.4 71.% + HSolverLCAO solve 2.7894 12 0.23 37.% + HamiltLCAO updateHk 1.4433 12 0.12 19.% + LCAO_Hamilt cal_Hgamma 1.4136 12 0.12 19.% + Gint_interface cal_gint 1.8057 25 0.072 24.% + Gint_Gamma distri_vl_value 0.31301 12 0.026 4.1% + Gint_Gamma distri_vl 2.7893 6 0.46 37.% + LCAO_Deepks cal_projected_DM 5.6926 14 0.41 75.% + LCAO_gen_fixedH add_v_delta 2.6430 6 0.44 35.% + LCAO_DESCRIPTOR add_v_delta 2.6431 6 0.44 35.% + ElecStateLCAO psiToRho 1.3255 12 0.11 18.% + Charge mix_rho 0.98502 11 0.090 13.% + LOOP_ions force_stress 0.55834 1 0.56 7.4% + Force_Stress_LCAO getForceStress 0.55830 1 0.56 7.4% + Force_LCAO_gamma ftable_gamma 0.35453 1 0.35 4.7% + Force_LCAO_gamma cal_fvl_dphi 0.28318 1 0.28 3.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:08:19 2022 + Finish Time : Wed Sep 28 11:08:27 2022 + Total Time : 0 h 0 mins 8 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..980113e86c58e25374f1b718262b55bf3b13f1e0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123508 ima = 3.69e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 3 + 3 1 + 4 0 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123666281298 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112635635153 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113188789959 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113421919043 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113383459725 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113406493192 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011339808076 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113401030118 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113400407765 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113400324013 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113400313838 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113400304411 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/STRU new file mode 100644 index 0000000000000000000000000000000000000000..00fddb2484ac3d226fe4b42627e00172f9f8a2d9 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-13.551945235760 18.352325519680 7.818236123788 0 0 0 +H +0.0 +2 +-13.586328933365 17.148543451679 9.122245868841 0 0 0 +-12.200803596729 17.842412932683 6.580557781477 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/conv new file mode 100644 index 0000000000000000000000000000000000000000..8c9a13a2aabefc0887334ac8d8df3c2a36c41b85 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/conv @@ -0,0 +1 @@ +9 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..2770c0a5120bde9313f500bb41f8123466c3952f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.746031636 0.01254181562 1.26677722 1.372040778 1.469047213 0.007997401182 0.01975967311 0.03895546353 +2.154333558e-18 0.001099812167 0.002429400041 0.01201758331 0.04326574377 2.425544156e-20 1.559478635e-06 4.993527166e-06 +0.001711467739 0.005679363282 + +H atom_index 1 n_descriptor 18 +1.288436367 0.03254594662 0.1219420603 0.1698040888 0.3338624125 0.02351233073 0.03063830899 0.03627458919 +-7.603132205e-17 4.339992695e-05 0.1074286967 0.1195593827 0.1456681234 -4.374239113e-18 2.270486399e-06 0.01322303445 +0.02729480398 0.03239097884 + +H atom_index 2 n_descriptor 18 +1.187405501 0.03595902717 0.08823461917 0.1241631158 0.3009948597 0.01904914033 0.024806656 0.03943969998 +3.31999852e-17 3.501784717e-05 0.08479013228 0.1061590898 0.112946508 7.112785596e-18 6.53228726e-06 0.01425490379 +0.02348270124 0.02774220215 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f3cde828972863c8a1a59383c59fd15ccdfdca82 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/e_base.npy 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/dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..8e5f67264bf3962578cac42e6cc35e79a01fa9ff Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..509d0837c1e2c693808931aaf4c6ec73a878b359 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:19 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.101475 SEC) : SETUP UNITCELL + DONE(0.101818 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.119884 SEC) : INIT PLANEWAVE + DONE(0.163381 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.446129 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651204e+02 0.000000e+00 2.160e-01 5.408e-01 + GE2 -4.663527e+02 -1.232318e+00 9.839e-02 4.993e-01 + GE3 -4.663569e+02 -4.202339e-03 6.314e-02 5.705e-01 + GE4 -4.663567e+02 2.592620e-04 2.076e-03 4.312e-01 + GE5 -4.663560e+02 7.158544e-04 8.908e-04 4.296e-01 + GE6 -4.663564e+02 -3.960947e-04 1.877e-04 4.250e-01 + GE7 -4.663562e+02 1.481944e-04 4.085e-05 4.188e-01 + GE8 -4.663563e+02 -6.468180e-05 1.641e-05 4.097e-01 + GE9 -4.663563e+02 1.935830e-05 2.255e-06 4.098e-01 + GE10 -4.663563e+02 -2.770533e-06 4.387e-07 4.099e-01 + GE11 -4.663563e+02 -4.210641e-07 1.847e-07 4.079e-01 + GE12 -4.663563e+02 -3.515464e-09 1.161e-08 3.444e-01 +E_delta_band = -7.01841660e-02 Ry = -9.54904567e-01 eV +E_delta_NN= -1.94671592e-01 Ry = -2.64864290e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.5435 11 0.69 1e+02 % + Run_lcao lcao_line 7.5337 1 7.5 1e+02 % + Potential init_pot 0.28458 2 0.14 3.8 % + PW_Basis recip2real 0.2749 17 0.016 3.6 % + PW_Basis gathers_scatterp 0.12376 17 0.0073 1.6 % + Potential v_of_rho 0.97603 14 0.07 13 % + XC_Functional v_xc 0.28977 15 0.019 3.8 % + H_Hartree_pw v_hartree 0.64181 14 0.046 8.5 % + PW_Basis real2recip 0.73241 41 0.018 9.7 % + PW_Basis gatherp_scatters 0.29568 41 0.0072 3.9 % + ORB_control set_orb_tables 1.0937 1 1.1 14 % + ORB_gen_tables gen_tables 1.0937 1 1.1 14 % + ORB_table_phi init_Table 0.47497 1 0.47 6.3 % + ORB_table_phi cal_ST_Phi12_R 0.46969 126 0.0037 6.2 % + ORB_table_beta init_Table_Beta 0.18274 1 0.18 2.4 % + ORB_table_beta VNL_PhiBeta_R 0.18121 56 0.0032 2.4 % + ORB_table_alpha init_Table_Alpha 0.24697 1 0.25 3.3 % + ORB_table_alpha S_PhiAlpha_R 0.24499 66 0.0037 3.2 % + LOOP_ions opt_ions 5.9185 1 5.9 78 % + ESolver_KS_LCAO Run 5.36 1 5.4 71 % + HSolverLCAO solve 2.7894 12 0.23 37 % + HamiltLCAO updateHk 1.4433 12 0.12 19 % + LCAO_Hamilt cal_Hgamma 1.4136 12 0.12 19 % + Gint_interface cal_gint 1.8057 25 0.072 24 % + Gint_Gamma distri_vl_value 0.31301 12 0.026 4.1 % + Gint_Gamma distri_vl 2.7893 6 0.46 37 % + LCAO_Deepks cal_projected_DM 5.6926 14 0.41 75 % + LCAO_gen_fixedH add_v_delta 2.643 6 0.44 35 % + LCAO_DESCRIPTOR add_v_delta 2.6431 6 0.44 35 % + ElecStateLCAO psiToRho 1.3255 12 0.11 18 % + Charge mix_rho 0.98502 11 0.09 13 % + LOOP_ions force_stress 0.55834 1 0.56 7.4 % + Force_Stress_LCAO getForceStress 0.5583 1 0.56 7.4 % + Force_LCAO_gamma ftable_gamma 0.35453 1 0.35 4.7 % + Force_LCAO_gamma cal_fvl_dphi 0.28318 1 0.28 3.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:19 2022 + FINISH Time : Wed Sep 28 11:08:27 2022 + TOTAL Time : 8 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/9/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..b8fa3ad420808c530677e452e4a558463b4c4600 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.697944 0.321995 0.978414 +H 0.757085 0.299284 0.00250494 +H 0.651962 0.292898 0.0124139 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..5b686bd93d0d12e43e24d32800266b5d9973c0b5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1739 2 + 2 -13.0923 2 + 3 -8.97956 2 + 4 -6.71521 2 + 5 1.20335 0 + 6 4.34822 0 + 7 11.0964 0 + 8 11.3301 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..ec34a42fa51d4fb42faf00baad8f032702378e1f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:07 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.5424359304 9.01586103097 27.3955952507 0 0 0 0 + tauc_H1 21.1983732224 8.37996594048 0.0701383599589 0 0 0 0 + tauc_H2 18.2549421871 8.20115404525 0.347588894256 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.105587651082 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.105947654747 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.123930290101 (SEC) + + DONE : INIT CHARGE Time : 0.16705414536 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.448983 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000975 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00133 + + Density error is 0.215400200985 + + Energy Rydberg eV + E_KohnSham -34.187405995 -465.143521371 + E_Harris -34.3800783388 -467.764963094 + E_Fermi -0.401028438549 -5.45627182431 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00122113612251 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00120296970927 + + Density error is 0.0984991525534 + + Energy Rydberg eV + E_KohnSham -34.2782410481 -466.379395671 + E_Harris -34.2851058739 -466.472796419 + E_Fermi -0.209085943456 -2.84476020271 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00116349715415 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111551961853 + + Density error is 0.0633722832001 + + Energy Rydberg eV + E_KohnSham -34.2786489319 -466.384945215 + E_Harris -34.283066999 -466.445056102 + E_Fermi -0.199609771653 -2.71583027095 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0010815735228 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00095675006586 + + Density error is 0.00203573897664 + + Energy Rydberg eV + E_KohnSham -34.2786103499 -466.38442028 + E_Harris -34.2786128889 -466.384454825 + E_Fermi -0.164157998264 -2.23348414866 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.0010832319586 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00095477250039 + + Density error is 0.000949520668001 + + Energy Rydberg eV + E_KohnSham -34.2785551591 -466.383669371 + E_Harris -34.2785561231 -466.383682487 + E_Fermi -0.163647742444 -2.22654176208 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00108199070236 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000952693915272 + + Density error is 0.000187389279408 + + Energy Rydberg eV + E_KohnSham -34.2785838163 -466.384059272 + E_Harris -34.2785838642 -466.384059924 + E_Fermi -0.163464625111 -2.22405032294 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00108220945617 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000952707244365 + + Density error is 3.86128982928e-05 + + Energy Rydberg eV + E_KohnSham -34.2785732664 -466.383915734 + E_Harris -34.2785732735 -466.383915831 + E_Fermi -0.163360050903 -2.22262751785 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00108215538366 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00095267167741 + + Density error is 1.69068205081e-05 + + Energy Rydberg eV + E_KohnSham -34.2785777545 -466.383976797 + E_Harris -34.2785777556 -466.383976812 + E_Fermi -0.163395657908 -2.22311197601 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00108215284466 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009526481523 + + Density error is 2.82352507951e-06 + + Energy Rydberg eV + E_KohnSham -34.2785763602 -466.383957827 + E_Harris -34.2785763602 -466.383957827 + E_Fermi -0.163379413773 -2.22289096321 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00108214799663 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0009526424144 + + Density error is 5.11902236533e-07 + + Energy Rydberg eV + E_KohnSham -34.2785765692 -466.38396067 + E_Harris -34.2785765692 -466.38396067 + E_Fermi -0.163376648672 -2.22285334208 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00108214864054 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000952642807314 + + Density error is 1.86766470102e-07 + + Energy Rydberg eV + E_KohnSham -34.2785766041 -466.383961145 + E_Harris -34.2785766041 -466.383961145 + E_Fermi -0.163376440438 -2.22285050892 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00108214874992 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000952642689294 + + Density error is 1.09565794536e-08 + + Energy Rydberg eV + E_KohnSham -34.2785766068 -466.383961182 + E_Harris -34.2785766068 -466.383961182 + E_band -7.93211173164 -107.921916723 + E_one_elec -69.1241879427 -940.482825644 + E_Hartree +35.9660342509 +489.343000275 + E_xc -8.19785338968 -111.537517468 + E_Ewald +7.20211951993 +97.9898631481 + E_demet -1.59174006996e-71 -2.16567346864e-70 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194488096485 -2.64614630537 + E_Fermi -0.163376257945 -2.22284802597 + + charge density convergence is achieved + final etot is -466.383961182 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1739 2.00000 + 2 -13.0923 2.00000 + 3 -8.97956 2.00000 + 4 -6.71521 2.00000 + 5 1.20335 0.00000 + 6 4.34822 0.00000 + 7 11.0964 0.00000 + 8 11.3301 0.00000 + + EFERMI = -2.222848025972844 eV + OUT.ABACUS/ final etot is -466.3839611815422 eV + correction force for each atom along direction 1 is -2.18381e-05 + correction force for each atom along direction 2 is -0.000178552 + correction force for each atom along direction 3 is -2.32891e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +2.0875653 +0.32689653 -0.43397161 + H1 -1.2871897 +0.35750500 -0.36431075 + H2 -0.80037553 -0.68440153 +0.79828236 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3839611815422 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5254 11 0.59 1.0e+02% + Run_lcao lcao_line 6.5148 1 6.5 1.e+02% + Potential init_pot 0.28313 2 0.14 4.3% + PW_Basis recip2real 0.28017 17 0.016 4.3% + PW_Basis gathers_scatterp 0.12569 17 0.0074 1.9% + Potential v_of_rho 1.0218 14 0.073 16.% + XC_Functional v_xc 0.30644 15 0.020 4.7% + H_Hartree_pw v_hartree 0.66807 14 0.048 10.% + PW_Basis real2recip 0.73728 41 0.018 11.% + PW_Basis gatherp_scatters 0.28721 41 0.0070 4.4% + ORB_control set_orb_tables 1.0952 1 1.1 17.% + ORB_gen_tables gen_tables 1.0952 1 1.1 17.% + ORB_table_phi init_Table 0.47259 1 0.47 7.2% + ORB_table_phi cal_ST_Phi12_R 0.46734 126 0.0037 7.2% + ORB_table_beta init_Table_Beta 0.18451 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18296 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.24807 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.24608 66 0.0037 3.8% + LOOP_ions opt_ions 4.8940 1 4.9 75.% + ESolver_KS_LCAO Run 4.4323 1 4.4 68.% + HSolverLCAO solve 1.8234 12 0.15 28.% + HamiltLCAO updateHk 1.0736 12 0.089 16.% + LCAO_Hamilt cal_Hgamma 1.0441 12 0.087 16.% + Gint_interface cal_gint 1.4408 25 0.058 22.% + Gint_Gamma distri_vl 2.3192 6 0.39 36.% + LCAO_Deepks cal_projected_DM 4.7302 14 0.34 72.% + LCAO_gen_fixedH add_v_delta 2.1711 6 0.36 33.% + LCAO_DESCRIPTOR add_v_delta 2.1711 6 0.36 33.% + ElecStateLCAO psiToRho 0.72765 12 0.061 11.% + Charge mix_rho 0.98351 11 0.089 15.% + LOOP_ions force_stress 0.46157 1 0.46 7.1% + Force_Stress_LCAO getForceStress 0.46153 1 0.46 7.1% + Force_LCAO_gamma ftable_gamma 0.25098 1 0.25 3.8% + Force_LCAO_gamma cal_fvl_dphi 0.22501 1 0.23 3.4% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:07 2022 + Finish Time : Wed Sep 28 11:09:13 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..5bc08bd77030d25727de01a3030ecbed2be11e33 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123682 ima = 3.70323e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123623831941 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112373544827 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112996440326 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113234186514 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113195796608 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113218729063 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011321084336 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113213700394 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113213038526 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113212936981 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113212920425 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113212910909 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/STRU new file mode 100644 index 0000000000000000000000000000000000000000..19f09d23d94264b14d177c82eb67f833415e7e13 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.457564069547 9.015861030949 -0.604404749297 0 0 0 +H +0.0 +2 +-6.801626777620 8.379965940503 0.070138359956 0 0 0 +-9.745057812929 8.201154045268 0.347588894239 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/conv new file mode 100644 index 0000000000000000000000000000000000000000..212c707d29fa2ebac208365b1750566f7c62220c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/conv @@ -0,0 +1 @@ +90 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..286fd5195053c26b680e1ac80437f4f159d5ae8c --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.747318627 0.01255248162 1.263699242 1.364061316 1.468863502 0.008140209105 0.01918082755 0.03898839955 +-2.944170719e-18 0.001053853093 0.002453585688 0.01196278438 0.04330067853 -1.004565474e-18 1.653822209e-06 5.160903092e-06 +0.001681641063 0.005778402959 + +H atom_index 1 n_descriptor 18 +1.192410217 0.03594548641 0.08951520275 0.1258054062 0.302207361 0.01931043535 0.02504440717 0.03939017207 +2.613642039e-17 3.635020333e-05 0.08571793075 0.1075772938 0.1131623275 -2.045912819e-18 6.448152706e-06 0.01419247144 +0.02366020248 0.02795907586 + +H atom_index 2 n_descriptor 18 +1.272774079 0.03321964941 0.1158995515 0.1615470761 0.3291209805 0.02293021739 0.0297103443 0.03663806935 +-2.189979321e-17 4.317415878e-05 0.1055716166 0.1167021334 0.138626287 -8.995904672e-18 2.998689364e-06 0.01305071967 +0.02675635455 0.03177427888 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..ccc96c294cf17d470e433ecff53bdb9b5c9bc1fd Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/dm_eig.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/e_base.npy 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:07 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.10561 SEC) : SETUP UNITCELL + DONE(0.105963 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.123949 SEC) : INIT PLANEWAVE + DONE(0.167192 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.44905 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651435e+02 0.000000e+00 2.154e-01 4.769e-01 + GE2 -4.663794e+02 -1.235874e+00 9.850e-02 4.244e-01 + GE3 -4.663849e+02 -5.549544e-03 6.337e-02 4.969e-01 + GE4 -4.663844e+02 5.249352e-04 2.036e-03 3.531e-01 + GE5 -4.663837e+02 7.509094e-04 9.495e-04 3.539e-01 + GE6 -4.663841e+02 -3.899010e-04 1.874e-04 3.460e-01 + GE7 -4.663839e+02 1.435380e-04 3.861e-05 3.358e-01 + GE8 -4.663840e+02 -6.106305e-05 1.691e-05 3.307e-01 + GE9 -4.663840e+02 1.896998e-05 2.824e-06 3.297e-01 + GE10 -4.663840e+02 -2.842971e-06 5.119e-07 3.298e-01 + GE11 -4.663840e+02 -4.751385e-07 1.868e-07 3.309e-01 + GE12 -4.663840e+02 -3.654076e-08 1.096e-08 2.615e-01 +E_delta_band = -6.97990513e-02 Ry = -9.49664813e-01 eV +E_delta_NN= -1.94488096e-01 Ry = -2.64614631e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5254 11 0.59 1e+02 % + Run_lcao lcao_line 6.5148 1 6.5 1e+02 % + Potential init_pot 0.28313 2 0.14 4.3 % + PW_Basis recip2real 0.28017 17 0.016 4.3 % + PW_Basis gathers_scatterp 0.12569 17 0.0074 1.9 % + Potential v_of_rho 1.0218 14 0.073 16 % + XC_Functional v_xc 0.30644 15 0.02 4.7 % + H_Hartree_pw v_hartree 0.66807 14 0.048 10 % + PW_Basis real2recip 0.73728 41 0.018 11 % + PW_Basis gatherp_scatters 0.28721 41 0.007 4.4 % + ORB_control set_orb_tables 1.0952 1 1.1 17 % + ORB_gen_tables gen_tables 1.0952 1 1.1 17 % + ORB_table_phi init_Table 0.47259 1 0.47 7.2 % + ORB_table_phi cal_ST_Phi12_R 0.46734 126 0.0037 7.2 % + ORB_table_beta init_Table_Beta 0.18451 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18296 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.24807 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.24608 66 0.0037 3.8 % + LOOP_ions opt_ions 4.894 1 4.9 75 % + ESolver_KS_LCAO Run 4.4323 1 4.4 68 % + HSolverLCAO solve 1.8234 12 0.15 28 % + HamiltLCAO updateHk 1.0736 12 0.089 16 % + LCAO_Hamilt cal_Hgamma 1.0441 12 0.087 16 % + Gint_interface cal_gint 1.4408 25 0.058 22 % + Gint_Gamma distri_vl 2.3192 6 0.39 36 % + LCAO_Deepks cal_projected_DM 4.7302 14 0.34 72 % + LCAO_gen_fixedH add_v_delta 2.1711 6 0.36 33 % + LCAO_DESCRIPTOR add_v_delta 2.1711 6 0.36 33 % + ElecStateLCAO psiToRho 0.72765 12 0.061 11 % + Charge mix_rho 0.98351 11 0.089 15 % + LOOP_ions force_stress 0.46157 1 0.46 7.1 % + Force_Stress_LCAO getForceStress 0.46153 1 0.46 7.1 % + Force_LCAO_gamma ftable_gamma 0.25098 1 0.25 3.8 % + Force_LCAO_gamma cal_fvl_dphi 0.22501 1 0.23 3.4 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:07 2022 + FINISH Time : Wed Sep 28 11:09:13 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/90/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9bd76c7f7f6d55d223f8f806aca72eef61f884f5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.684444 0.305461 0.976411 +H 0.733247 0.266053 0.993082 +H 0.632662 0.284297 0.0121686 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..3a8b7a49eae4ba7c265cc82632c3da48ff8262ba --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.2509 2 + 2 -13.0535 2 + 3 -9.08131 2 + 4 -6.73596 2 + 5 1.27929 0 + 6 4.39058 0 + 7 11.0822 0 + 8 11.3303 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..da22d745e839b7aee837fafe53912221bf06ac6d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:11:35 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.1644257613 8.55289818306 27.3395025283 0 0 0 0 + tauc_H1 20.5309099339 7.44948113665 27.8062881221 0 0 0 0 + tauc_H2 17.7145411959 7.96031838687 0.340721401612 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0886202504349 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.102683220775 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.120847851762 (SEC) + + DONE : INIT CHARGE Time : 0.169128600648 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.450644 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000705 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00139 + + Density error is 0.215062968015 + + Energy Rydberg eV + E_KohnSham -34.1905646347 -465.186496869 + E_Harris -34.3824661517 -467.797450955 + E_Fermi -0.403598803607 -5.49124343504 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000995856720114 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00124158648398 + + Density error is 0.0981776847969 + + Energy Rydberg eV + E_KohnSham -34.280738909 -466.413380813 + E_Harris -34.287536527 -466.50586715 + E_Fermi -0.212161255581 -2.88660197074 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000956182994798 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00115334019512 + + Density error is 0.0630487499955 + + Energy Rydberg eV + E_KohnSham -34.2811024866 -466.418327539 + E_Harris -34.2854918485 -466.478047871 + E_Fermi -0.201808780805 -2.74574932538 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000909206722335 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000993914287762 + + Density error is 0.00199870081796 + + Energy Rydberg eV + E_KohnSham -34.2810779951 -466.417994315 + E_Harris -34.2810797894 -466.418018729 + E_Fermi -0.16628388805 -2.26240836308 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000910541007478 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000991640559595 + + Density error is 0.00093347662832 + + Energy Rydberg eV + E_KohnSham -34.2810189081 -466.417190395 + E_Harris -34.281019891 -466.417203769 + E_Fermi -0.165677383725 -2.25415644839 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000909709112679 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989640884281 + + Density error is 0.000167045032684 + + Energy Rydberg eV + E_KohnSham -34.2810532032 -466.417657005 + E_Harris -34.2810532473 -466.417657605 + E_Fermi -0.165586832519 -2.25292443604 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000909971414238 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989573051906 + + Density error is 3.88590616622e-05 + + Energy Rydberg eV + E_KohnSham -34.2810407134 -466.417487072 + E_Harris -34.2810407211 -466.417487177 + E_Fermi -0.165468886633 -2.25131969993 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000909891219111 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098954434726 + + Density error is 1.59500628787e-05 + + Energy Rydberg eV + E_KohnSham -34.2810449926 -466.417545293 + E_Harris -34.2810449936 -466.417545308 + E_Fermi -0.165508382194 -2.2518570646 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000909892430035 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00098951748164 + + Density error is 1.87040465527e-06 + + Energy Rydberg eV + E_KohnSham -34.2810436049 -466.417526413 + E_Harris -34.2810436049 -466.417526413 + E_Fermi -0.165491705269 -2.25163016339 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000909894550239 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989515928446 + + Density error is 2.53087976292e-07 + + Energy Rydberg eV + E_KohnSham -34.2810438143 -466.417529263 + E_Harris -34.2810438143 -466.417529263 + E_Fermi -0.165489998262 -2.25160693838 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000909894941913 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000989516338774 + + Density error is 7.29955186136e-08 + + Energy Rydberg eV + E_KohnSham -34.2810438435 -466.417529659 + E_Harris -34.2810438435 -466.417529659 + E_band -7.95573603304 -108.243341833 + E_one_elec -69.2349864433 -941.990316581 + E_Hartree +36.0147002304 +490.005134896 + E_xc -8.20555833788 -111.642348667 + E_Ewald +7.26925411505 +98.9032761746 + E_demet -8.50572270612e-76 -1.15726294411e-74 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194689103239 -2.64888114257 + E_Fermi -0.165489933817 -2.25160606155 + + charge density convergence is achieved + final etot is -466.417529659 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.2509 2.00000 + 2 -13.0535 2.00000 + 3 -9.08131 2.00000 + 4 -6.73596 2.00000 + 5 1.27929 0.00000 + 6 4.39058 0.00000 + 7 11.0822 0.00000 + 8 11.3303 0.00000 + + EFERMI = -2.251606061550463 eV + OUT.ABACUS/ final etot is -466.4175296587750 eV + correction force for each atom along direction 1 is 3.47562e-05 + correction force for each atom along direction 2 is -0.000114827 + correction force for each atom along direction 3 is 5.17729e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.85928702 +0.34297813 +0.0025871919 + H1 +0.51153215 -0.45079329 +0.20755011 + H2 +0.34775487 +0.10781516 -0.21013730 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4175296587750 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1855 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1753 1 6.2 1.e+02% + Potential init_pot 0.28511 2 0.14 4.6% + PW_Basis recip2real 0.26434 16 0.017 4.3% + PW_Basis gathers_scatterp 0.11369 16 0.0071 1.8% + Potential v_of_rho 0.87387 13 0.067 14.% + XC_Functional v_xc 0.24835 14 0.018 4.0% + H_Hartree_pw v_hartree 0.58774 13 0.045 9.5% + PW_Basis real2recip 0.55435 38 0.015 9.0% + PW_Basis gatherp_scatters 0.21255 38 0.0056 3.4% + ORB_control set_orb_tables 1.1102 1 1.1 18.% + ORB_gen_tables gen_tables 1.1102 1 1.1 18.% + ORB_table_phi init_Table 0.48859 1 0.49 7.9% + ORB_table_phi cal_ST_Phi12_R 0.48366 126 0.0038 7.8% + ORB_table_beta init_Table_Beta 0.18769 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18614 56 0.0033 3.0% + ORB_table_alpha init_Table_Alpha 0.25437 1 0.25 4.1% + ORB_table_alpha S_PhiAlpha_R 0.25249 66 0.0038 4.1% + LOOP_ions opt_ions 4.5388 1 4.5 73.% + ESolver_KS_LCAO Run 4.0159 1 4.0 65.% + HSolverLCAO solve 2.0549 11 0.19 33.% + HamiltLCAO updateHk 1.0771 11 0.098 17.% + LCAO_Hamilt cal_Hgamma 1.0392 11 0.094 17.% + Gint_interface cal_gint 1.7287 23 0.075 28.% + Gint_Gamma distri_vl 1.9374 6 0.32 31.% + LCAO_Deepks cal_projected_DM 4.3747 13 0.34 71.% + LCAO_gen_fixedH add_v_delta 1.8059 6 0.30 29.% + LCAO_DESCRIPTOR add_v_delta 1.8059 6 0.30 29.% + ElecStateLCAO psiToRho 0.96157 11 0.087 16.% + Charge mix_rho 0.65572 10 0.066 11.% + LOOP_ions force_stress 0.52273 1 0.52 8.5% + Force_Stress_LCAO getForceStress 0.52269 1 0.52 8.5% + Force_LCAO_gamma ftable_gamma 0.31045 1 0.31 5.0% + Force_LCAO_gamma cal_fvl_dphi 0.29228 1 0.29 4.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:11:35 2022 + Finish Time : Wed Sep 28 11:11:41 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..757aaf1c9038d4d2d70312c38d82886e7fece857 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123525 ima = 3.69434e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123316420515 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112179678534 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011276254412 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113006745731 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112960555224 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112987963586 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112980436101 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011298330315 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112982673073 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112982594948 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112982584718 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/STRU new file mode 100644 index 0000000000000000000000000000000000000000..73d792f49f8e187755f865b27dd353d12028ee21 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.835574238678 8.552898183071 -0.660497471711 0 0 0 +H +0.0 +2 +-7.469090066121 7.449481136662 -0.193711877958 0 0 0 +-10.285458804126 7.960318386872 0.340721401601 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/conv new file mode 100644 index 0000000000000000000000000000000000000000..5501b99aefd239673974cdf60d24b0da3a9e40f8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/conv @@ -0,0 +1 @@ +91 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..160ac16e38a00c7a1fb5445dd8a8167b93b8b44e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74871039 0.01265535895 1.270853959 1.361384241 1.469160995 0.008388062676 0.01869230859 0.03901599446 +-1.990155156e-18 0.001049901599 0.002552875635 0.01229491652 0.04450874438 -1.839120287e-19 1.927105163e-06 5.68914558e-06 +0.001659428759 0.005916626604 + +H atom_index 1 n_descriptor 18 +1.257818712 0.03390631861 0.1108803087 0.1538459784 0.3238867588 0.02250617932 0.02879213358 0.03712175226 +1.358143769e-17 4.50075501e-05 0.1031697033 0.1154521487 0.1320649382 -1.253405542e-17 3.71376216e-06 0.01309330724 +0.02647613072 0.03112598032 + +H atom_index 2 n_descriptor 18 +1.224807858 0.03504576841 0.0997393966 0.1388504082 0.3129929552 0.02098582709 0.02686917209 0.03822626201 +1.237632689e-17 4.203105464e-05 0.09486495014 0.1141705499 0.1190707266 3.053775944e-19 5.372519177e-06 0.01347446025 +0.0252241798 0.02958706742 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..9abae4dd8eabd6690badbd7a9e3a787e6fea5fea Binary files /dev/null and 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mode 100644 index 0000000000000000000000000000000000000000..ddbe17181faea2995b453d655c93fde973c4a75b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:11:35 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0886448 SEC) : SETUP UNITCELL + DONE(0.102701 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.120869 SEC) : INIT PLANEWAVE + DONE(0.16926 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.450715 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651865e+02 0.000000e+00 2.151e-01 4.784e-01 + GE2 -4.664134e+02 -1.226884e+00 9.818e-02 4.022e-01 + GE3 -4.664183e+02 -4.946727e-03 6.305e-02 4.564e-01 + GE4 -4.664180e+02 3.332239e-04 1.999e-03 3.497e-01 + GE5 -4.664172e+02 8.039199e-04 9.335e-04 3.509e-01 + GE6 -4.664177e+02 -4.666093e-04 1.670e-04 3.440e-01 + GE7 -4.664175e+02 1.699331e-04 3.886e-05 3.326e-01 + GE8 -4.664175e+02 -5.822177e-05 1.595e-05 3.204e-01 + GE9 -4.664175e+02 1.888086e-05 1.870e-06 3.250e-01 + GE10 -4.664175e+02 -2.850040e-06 2.531e-07 3.288e-01 + GE11 -4.664175e+02 -3.961807e-07 7.300e-08 2.667e-01 +E_delta_band = -7.02356955e-02 Ry = -9.55605661e-01 eV +E_delta_NN= -1.94689103e-01 Ry = -2.64888114e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1855 11 0.56 1e+02 % + Run_lcao lcao_line 6.1753 1 6.2 1e+02 % + Potential init_pot 0.28511 2 0.14 4.6 % + PW_Basis recip2real 0.26434 16 0.017 4.3 % + PW_Basis gathers_scatterp 0.11369 16 0.0071 1.8 % + Potential v_of_rho 0.87387 13 0.067 14 % + XC_Functional v_xc 0.24835 14 0.018 4 % + H_Hartree_pw v_hartree 0.58774 13 0.045 9.5 % + PW_Basis real2recip 0.55435 38 0.015 9 % + PW_Basis gatherp_scatters 0.21255 38 0.0056 3.4 % + ORB_control set_orb_tables 1.1102 1 1.1 18 % + ORB_gen_tables gen_tables 1.1102 1 1.1 18 % + ORB_table_phi init_Table 0.48859 1 0.49 7.9 % + ORB_table_phi cal_ST_Phi12_R 0.48366 126 0.0038 7.8 % + ORB_table_beta init_Table_Beta 0.18769 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18614 56 0.0033 3 % + ORB_table_alpha init_Table_Alpha 0.25437 1 0.25 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.25249 66 0.0038 4.1 % + LOOP_ions opt_ions 4.5388 1 4.5 73 % + ESolver_KS_LCAO Run 4.0159 1 4 65 % + HSolverLCAO solve 2.0549 11 0.19 33 % + HamiltLCAO updateHk 1.0771 11 0.098 17 % + LCAO_Hamilt cal_Hgamma 1.0392 11 0.094 17 % + Gint_interface cal_gint 1.7287 23 0.075 28 % + Gint_Gamma distri_vl 1.9374 6 0.32 31 % + LCAO_Deepks cal_projected_DM 4.3747 13 0.34 71 % + LCAO_gen_fixedH add_v_delta 1.8059 6 0.3 29 % + LCAO_DESCRIPTOR add_v_delta 1.8059 6 0.3 29 % + ElecStateLCAO psiToRho 0.96157 11 0.087 16 % + Charge mix_rho 0.65572 10 0.066 11 % + LOOP_ions force_stress 0.52273 1 0.52 8.5 % + Force_Stress_LCAO getForceStress 0.52269 1 0.52 8.5 % + Force_LCAO_gamma ftable_gamma 0.31045 1 0.31 5 % + Force_LCAO_gamma cal_fvl_dphi 0.29228 1 0.29 4.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:11:35 2022 + FINISH Time : Wed Sep 28 11:11:41 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/91/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..d81e54085562967510a86839986b5beb5e944429 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.672653 0.287682 0.968577 +H 0.709173 0.235222 0.965158 +H 0.616423 0.266612 0.994074 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0c3e228d1ddd3284267512cdc4ce04cef5e07cfc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.435 2 + 2 -13.1832 2 + 3 -9.12881 2 + 4 -6.77704 2 + 5 1.42502 0 + 6 4.63782 0 + 7 11.0389 0 + 8 11.2876 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..40decc91cd0375bec897e21a2ccf16f1afb16827 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:12:32 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.8342914343 8.055102259 27.1201614316 0 0 0 0 + tauc_H1 19.8568339521 6.58622668678 27.0244161664 0 0 0 0 + tauc_H2 17.2598564095 7.46514883595 27.8340801184 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0864869077751 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0974528117508 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.115481974292 (SEC) + + DONE : INIT CHARGE Time : 0.16364253382 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.444574 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 369 ; sender_size of each process is: +144 0 81 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000605 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00162 + + Density error is 0.216548086946 + + Energy Rydberg eV + E_KohnSham -34.1892962283 -465.169239315 + E_Harris -34.3845582558 -467.825915492 + E_Fermi -0.414194812868 -5.63540953705 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000841650219251 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00139563457591 + + Density error is 0.0976195081632 + + Energy Rydberg eV + E_KohnSham -34.2797377867 -466.399759845 + E_Harris -34.2863889233 -466.490253201 + E_Fermi -0.222200723959 -3.02319594556 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000807175634903 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128662073823 + + Density error is 0.0624397075628 + + Energy Rydberg eV + E_KohnSham -34.2800101518 -466.403465562 + E_Harris -34.2842912366 -466.461712709 + E_Fermi -0.209151962912 -2.84565844349 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000766456744826 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109687127651 + + Density error is 0.00202130242935 + + Energy Rydberg eV + E_KohnSham -34.2800328493 -466.403774377 + E_Harris -34.2800346542 -466.403798935 + E_Fermi -0.17347325053 -2.36022465779 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000768670139834 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109432536985 + + Density error is 0.000905859585275 + + Energy Rydberg eV + E_KohnSham -34.2799620986 -466.402811765 + E_Harris -34.2799640346 -466.402838106 + E_Fermi -0.172454091286 -2.34635828491 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000767732659936 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109253050974 + + Density error is 0.000132979060727 + + Energy Rydberg eV + E_KohnSham -34.2800095608 -466.403457521 + E_Harris -34.2800095938 -466.40345797 + E_Fermi -0.172634865854 -2.34881784908 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000767865430465 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109228844416 + + Density error is 4.50783484288e-05 + + Energy Rydberg eV + E_KohnSham -34.2799930648 -466.403233082 + E_Harris -34.2799930763 -466.403233238 + E_Fermi -0.172488148574 -2.34682165808 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000767807372691 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109229519817 + + Density error is 1.47064933719e-05 + + Energy Rydberg eV + E_KohnSham -34.2799969518 -466.403285967 + E_Harris -34.2799969527 -466.40328598 + E_Fermi -0.172540232926 -2.34753030204 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000767814278081 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109226701994 + + Density error is 1.6333595913e-06 + + Energy Rydberg eV + E_KohnSham -34.2799954519 -466.40326556 + E_Harris -34.2799954519 -466.40326556 + E_Fermi -0.172524609252 -2.34731773105 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000767814961942 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109226412739 + + Density error is 1.52909119345e-07 + + Energy Rydberg eV + E_KohnSham -34.2799956646 -466.403268454 + E_Harris -34.2799956646 -466.403268454 + E_Fermi -0.172523025289 -2.34729618013 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 369 + sender_size = 369 + last sender_buffer = 0.000767815291953 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00109226461028 + + Density error is 4.37232266844e-08 + + Energy Rydberg eV + E_KohnSham -34.2799956912 -466.403268815 + E_Harris -34.2799956912 -466.403268815 + E_band -8.0148735966 -109.047949663 + E_one_elec -69.5946188375 -946.883366328 + E_Hartree +36.1828904971 +492.293480871 + E_xc -8.2327556239 -112.012386727 + E_Ewald +7.48819102511 +101.882065654 + E_demet -3.88653711489e-86 -5.2879050251e-85 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195367732011 -2.65811436069 + E_Fermi -0.172523032271 -2.34729627512 + + charge density convergence is achieved + final etot is -466.403268815 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.4350 2.00000 + 2 -13.1832 2.00000 + 3 -9.12881 2.00000 + 4 -6.77704 2.00000 + 5 1.42502 0.00000 + 6 4.63782 0.00000 + 7 11.0389 0.00000 + 8 11.2876 0.00000 + + EFERMI = -2.347296275118819 eV + OUT.ABACUS/ final etot is -466.4032688152353 eV + correction force for each atom along direction 1 is -5.52475e-05 + correction force for each atom along direction 2 is -1.62873e-05 + correction force for each atom along direction 3 is 3.18113e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.48155898 +1.2860023 -0.072485184 + H1 +0.86969393 -1.1825138 -0.095029483 + H2 -0.38813495 -0.10348854 +0.16751467 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4032688152353 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3106 11 0.57 1.0e+02% + Run_lcao lcao_line 6.3011 1 6.3 1.e+02% + Potential init_pot 0.28565 2 0.14 4.5% + PW_Basis recip2real 0.26519 16 0.017 4.2% + PW_Basis gathers_scatterp 0.11434 16 0.0071 1.8% + Potential v_of_rho 0.87763 13 0.068 14.% + XC_Functional v_xc 0.24459 14 0.017 3.9% + H_Hartree_pw v_hartree 0.59372 13 0.046 9.4% + PW_Basis real2recip 0.55648 38 0.015 8.8% + PW_Basis gatherp_scatters 0.21594 38 0.0057 3.4% + ORB_control set_orb_tables 1.1233 1 1.1 18.% + ORB_gen_tables gen_tables 1.1233 1 1.1 18.% + ORB_table_phi init_Table 0.49379 1 0.49 7.8% + ORB_table_phi cal_ST_Phi12_R 0.48864 126 0.0039 7.7% + ORB_table_beta init_Table_Beta 0.19031 1 0.19 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18878 56 0.0034 3.0% + ORB_table_alpha init_Table_Alpha 0.25859 1 0.26 4.1% + ORB_table_alpha S_PhiAlpha_R 0.25671 66 0.0039 4.1% + LOOP_ions opt_ions 4.6550 1 4.7 74.% + ESolver_KS_LCAO Run 4.1246 1 4.1 65.% + HSolverLCAO solve 2.1585 11 0.20 34.% + HamiltLCAO updateHk 1.1328 11 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.0992 11 0.10 17.% + Gint_interface cal_gint 1.5443 23 0.067 24.% + Gint_Gamma distri_vl_value 0.18033 11 0.016 2.9% + Gint_Gamma distri_vl 1.9856 6 0.33 31.% + LCAO_Deepks cal_projected_DM 4.4488 13 0.34 70.% + LCAO_gen_fixedH add_v_delta 1.8526 6 0.31 29.% + LCAO_DESCRIPTOR add_v_delta 1.8526 6 0.31 29.% + ElecStateLCAO psiToRho 1.0083 11 0.092 16.% + Charge mix_rho 0.65690 10 0.066 10.% + LOOP_ions force_stress 0.53024 1 0.53 8.4% + Force_Stress_LCAO getForceStress 0.53021 1 0.53 8.4% + Force_LCAO_gamma ftable_gamma 0.32071 1 0.32 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.26774 1 0.27 4.2% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:12:32 2022 + Finish Time : Wed Sep 28 11:12:38 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..b50d591f3074fa28dc0c66a628a3e8d8a8f2bfb3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123612 ima = 3.71587e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 2 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123002943093 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112118464526 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112580201582 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112848211863 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112783035383 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112820566071 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112814148584 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112817297149 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112816687849 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.001128166207 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112816614033 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/STRU new file mode 100644 index 0000000000000000000000000000000000000000..e8b29d2f1ad5dd8afd131cc9aa1e2d9797ea919a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.165708565695 8.055102259013 -0.879838568427 0 0 0 +H +0.0 +2 +-8.143166047926 6.586226686785 -0.975583833632 0 0 0 +-10.740143590498 7.465148835930 -0.165919881635 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/conv new file mode 100644 index 0000000000000000000000000000000000000000..fe6779c9f9e9308eb1821edfcd6db750ed023a9b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/conv @@ -0,0 +1 @@ +92 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e4727be41b925289da1dff8342a2364e5727faf8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74901661 0.01277342244 1.28547454 1.372442671 1.470021395 0.008579691365 0.01890340183 0.03901971894 +2.41916923e-19 0.001126449416 0.002681518795 0.01283975509 0.04656218608 1.780175564e-19 2.202702064e-06 6.248685411e-06 +0.00165912525 0.005954115078 + +H atom_index 1 n_descriptor 18 +1.277730276 0.03326281214 0.1187124274 0.1633382168 0.3293560589 0.02363589288 0.02991061782 0.03664184442 +-3.349222989e-17 5.057836133e-05 0.1075919361 0.1181580507 0.140313297 -4.972328299e-18 2.608187017e-06 0.01322580913 +0.02758303615 0.03195836437 + +H atom_index 2 n_descriptor 18 +1.250555721 0.0341807828 0.1088684849 0.1502097146 0.321054744 0.02238242794 0.02834162424 0.03730565806 +-2.818608011e-18 4.799493658e-05 0.1030457518 0.1148955906 0.129065403 -8.052829476e-18 4.149981942e-06 0.01317182851 +0.02663069022 0.0308116814 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..afded614bbb3fc2f4e4e1b00b09db9c05edd9cc9 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..9184a8c4ba631cf0f29026cfd3926995870de507 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..30d1ad58d4fc4daaf8fd813206f2c25399abcab2 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..61645da6b522ea22a769ee4497a8e97929c30256 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:12:32 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.086509 SEC) : SETUP UNITCELL + DONE(0.0974702 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.115502 SEC) : INIT PLANEWAVE + DONE(0.163775 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.444642 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651692e+02 0.000000e+00 2.165e-01 4.882e-01 + GE2 -4.663998e+02 -1.230521e+00 9.762e-02 4.167e-01 + GE3 -4.664035e+02 -3.705718e-03 6.244e-02 4.689e-01 + GE4 -4.664038e+02 -3.088147e-04 2.021e-03 3.572e-01 + GE5 -4.664028e+02 9.626123e-04 9.059e-04 3.593e-01 + GE6 -4.664035e+02 -6.457559e-04 1.330e-04 3.484e-01 + GE7 -4.664032e+02 2.244390e-04 4.508e-05 3.412e-01 + GE8 -4.664033e+02 -5.288547e-05 1.471e-05 3.356e-01 + GE9 -4.664033e+02 2.040703e-05 1.633e-06 3.347e-01 + GE10 -4.664033e+02 -2.893910e-06 1.529e-07 3.352e-01 + GE11 -4.664033e+02 -3.612019e-07 4.372e-08 2.776e-01 +E_delta_band = -7.16649800e-02 Ry = -9.75052075e-01 eV +E_delta_NN= -1.95367732e-01 Ry = -2.65811436e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.3106 11 0.57 1e+02 % + Run_lcao lcao_line 6.3011 1 6.3 1e+02 % + Potential init_pot 0.28565 2 0.14 4.5 % + PW_Basis recip2real 0.26519 16 0.017 4.2 % + PW_Basis gathers_scatterp 0.11434 16 0.0071 1.8 % + Potential v_of_rho 0.87763 13 0.068 14 % + XC_Functional v_xc 0.24459 14 0.017 3.9 % + H_Hartree_pw v_hartree 0.59372 13 0.046 9.4 % + PW_Basis real2recip 0.55648 38 0.015 8.8 % + PW_Basis gatherp_scatters 0.21594 38 0.0057 3.4 % + ORB_control set_orb_tables 1.1233 1 1.1 18 % + ORB_gen_tables gen_tables 1.1233 1 1.1 18 % + ORB_table_phi init_Table 0.49379 1 0.49 7.8 % + ORB_table_phi cal_ST_Phi12_R 0.48864 126 0.0039 7.7 % + ORB_table_beta init_Table_Beta 0.19031 1 0.19 3 % + ORB_table_beta VNL_PhiBeta_R 0.18878 56 0.0034 3 % + ORB_table_alpha init_Table_Alpha 0.25859 1 0.26 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.25671 66 0.0039 4.1 % + LOOP_ions opt_ions 4.655 1 4.7 74 % + ESolver_KS_LCAO Run 4.1246 1 4.1 65 % + HSolverLCAO solve 2.1585 11 0.2 34 % + HamiltLCAO updateHk 1.1328 11 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.0992 11 0.1 17 % + Gint_interface cal_gint 1.5443 23 0.067 24 % + Gint_Gamma distri_vl_value 0.18033 11 0.016 2.9 % + Gint_Gamma distri_vl 1.9856 6 0.33 31 % + LCAO_Deepks cal_projected_DM 4.4488 13 0.34 70 % + LCAO_gen_fixedH add_v_delta 1.8526 6 0.31 29 % + LCAO_DESCRIPTOR add_v_delta 1.8526 6 0.31 29 % + ElecStateLCAO psiToRho 1.0083 11 0.092 16 % + Charge mix_rho 0.6569 10 0.066 10 % + LOOP_ions force_stress 0.53024 1 0.53 8.4 % + Force_Stress_LCAO getForceStress 0.53021 1 0.53 8.4 % + Force_LCAO_gamma ftable_gamma 0.32071 1 0.32 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.26774 1 0.27 4.2 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:12:32 2022 + FINISH Time : Wed Sep 28 11:12:38 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/92/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..4c4162bc68425d58be543d063b7e1cf1122ae053 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.665421 0.268422 0.955303 +H 0.684755 0.205171 0.956815 +H 0.600377 0.258497 0.950082 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..7117eb5f4cf1763f992339e5640a045c05d022dc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3075 2 + 2 -12.6765 2 + 3 -9.40029 2 + 4 -6.75179 2 + 5 1.19019 0 + 6 4.24508 0 + 7 11.089 0 + 8 11.3703 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..b7819aed0d35a94935178dfb409cb3f6b4872301 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:05:58 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.63177751 7.51582868543 26.7484730927 0 0 0 0 + tauc_H1 19.1731397838 5.74477950346 26.7908196277 0 0 0 0 + tauc_H2 16.8105427794 7.23791080504 26.6022994877 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.073381079081 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0736548123253 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0899521899658 (SEC) + + DONE : INIT CHARGE Time : 0.131156289517 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375458 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 432 ; sender_size of each process is: +144 0 144 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000532 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00187 + + Density error is 0.21232756957 + + Energy Rydberg eV + E_KohnSham -34.1914630213 -465.198720046 + E_Harris -34.3783565466 -467.74153691 + E_Fermi -0.400105210492 -5.44371066218 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000818582392059 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00146915488313 + + Density error is 0.0978089025309 + + Energy Rydberg eV + E_KohnSham -34.2796972873 -466.399208822 + E_Harris -34.2866150832 -466.493330264 + E_Fermi -0.211056269141 -2.87156785894 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000786346776243 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00134479197526 + + Density error is 0.0628944017114 + + Energy Rydberg eV + E_KohnSham -34.28001611 -466.403546627 + E_Harris -34.2845007868 -466.464563786 + E_Fermi -0.201481935768 -2.74130237051 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000756588736782 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111368245302 + + Density error is 0.00191040610543 + + Energy Rydberg eV + E_KohnSham -34.2799708124 -466.402930323 + E_Harris -34.2799706866 -466.402928611 + E_Fermi -0.165805726946 -2.2559026475 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000759285800206 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111263924637 + + Density error is 0.000903128625386 + + Energy Rydberg eV + E_KohnSham -34.2799214145 -466.402258229 + E_Harris -34.2799224421 -466.402272211 + E_Fermi -0.165478528589 -2.25145088547 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000758605949432 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110978064504 + + Density error is 0.000107727650258 + + Energy Rydberg eV + E_KohnSham -34.2799504918 -466.402653847 + E_Harris -34.2799504936 -466.402653871 + E_Fermi -0.165280767301 -2.24876020511 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000758525329483 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110942419682 + + Density error is 3.07226363141e-05 + + Energy Rydberg eV + E_KohnSham -34.2799426914 -466.402547717 + E_Harris -34.2799426956 -466.402547773 + E_Fermi -0.165195324983 -2.24759770273 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000758486593788 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110942068135 + + Density error is 1.61750636196e-05 + + Energy Rydberg eV + E_KohnSham -34.2799442929 -466.402569507 + E_Harris -34.2799442942 -466.402569523 + E_Fermi -0.165225612347 -2.24800978346 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000758505721416 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110940564423 + + Density error is 2.58816318929e-06 + + Energy Rydberg eV + E_KohnSham -34.2799430231 -466.40255223 + E_Harris -34.2799430231 -466.40255223 + E_Fermi -0.165212060191 -2.24782539692 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000758507714577 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011093975629 + + Density error is 2.8535338621e-07 + + Energy Rydberg eV + E_KohnSham -34.2799432792 -466.402555714 + E_Harris -34.2799432792 -466.402555714 + E_Fermi -0.165209458972 -2.24779000552 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 432 + sender_size = 432 + last sender_buffer = 0.000758508298547 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00110939766798 + + Density error is 6.22568096092e-08 + + Energy Rydberg eV + E_KohnSham -34.2799433204 -466.402556274 + E_Harris -34.2799433204 -466.402556274 + E_band -7.95784731504 -108.272067299 + E_one_elec -69.1176043596 -940.393251401 + E_Hartree +35.947760621 +489.094374786 + E_xc -8.19466892799 -111.494190644 + E_Ewald +7.20921664314 +98.0864244632 + E_demet -5.34310675936e-72 -7.26966969496e-71 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194537136751 -2.64681353242 + E_Fermi -0.165209288032 -2.24778767976 + + charge density convergence is achieved + final etot is -466.402556274 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3075 2.00000 + 2 -12.6765 2.00000 + 3 -9.40029 2.00000 + 4 -6.75179 2.00000 + 5 1.19019 0.00000 + 6 4.24508 0.00000 + 7 11.0890 0.00000 + 8 11.3703 0.00000 + + EFERMI = -2.247787679759517 eV + OUT.ABACUS/ final etot is -466.4025562738962 eV + correction force for each atom along direction 1 is -0.000100535 + correction force for each atom along direction 2 is -0.000165409 + correction force for each atom along direction 3 is -0.000173394 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.29706442 -0.63411934 -0.032459948 + H1 +0.41085958 +0.19400124 +0.037222473 + H2 -0.11379516 +0.44011811 -0.0047625251 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4025562738962 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6640 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6562 1 6.7 1.e+02% + Potential init_pot 0.24289 2 0.12 3.6% + PW_Basis recip2real 0.23288 16 0.015 3.5% + PW_Basis gathers_scatterp 0.11368 16 0.0071 1.7% + Potential v_of_rho 0.88093 13 0.068 13.% + XC_Functional v_xc 0.28962 14 0.021 4.3% + H_Hartree_pw v_hartree 0.56115 13 0.043 8.4% + PW_Basis real2recip 0.61705 38 0.016 9.3% + PW_Basis gatherp_scatters 0.27965 38 0.0074 4.2% + ORB_control set_orb_tables 0.89687 1 0.90 13.% + ORB_gen_tables gen_tables 0.89686 1 0.90 13.% + ORB_table_phi init_Table 0.37334 1 0.37 5.6% + ORB_table_phi cal_ST_Phi12_R 0.36906 126 0.0029 5.5% + ORB_table_beta init_Table_Beta 0.15653 1 0.16 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15517 56 0.0028 2.3% + ORB_table_alpha init_Table_Alpha 0.20950 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20789 66 0.0031 3.1% + LOOP_ions opt_ions 5.3134 1 5.3 80.% + ESolver_KS_LCAO Run 4.7838 1 4.8 72.% + HSolverLCAO solve 2.6239 11 0.24 39.% + HamiltLCAO updateHk 1.3313 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.3080 11 0.12 20.% + Gint_interface cal_gint 1.5292 23 0.066 23.% + Gint_Gamma distri_vl_value 0.36884 11 0.034 5.5% + Gint_Gamma distri_vl 2.2918 6 0.38 34.% + LCAO_Deepks cal_projected_DM 5.0801 13 0.39 76.% + LCAO_gen_fixedH add_v_delta 2.1643 6 0.36 32.% + LCAO_DESCRIPTOR add_v_delta 2.1645 6 0.36 32.% + ElecStateLCAO psiToRho 1.2766 11 0.12 19.% + Charge mix_rho 0.75236 10 0.075 11.% + LOOP_ions force_stress 0.52941 1 0.53 7.9% + Force_Stress_LCAO getForceStress 0.52939 1 0.53 7.9% + Force_LCAO_gamma ftable_gamma 0.33666 1 0.34 5.1% + Force_LCAO_gamma cal_fvl_dphi 0.24654 1 0.25 3.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:05:58 2022 + Finish Time : Wed Sep 28 11:06:04 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..418e092fb96066675d26bbeb3a65ae96ac910ae2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012375 ima = 3.6799e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 3 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122740272321 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111527813579 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112175246051 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112413864948 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112372524216 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011239396346 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112392300948 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112394728583 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112393937014 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112393824014 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112393808432 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/STRU new file mode 100644 index 0000000000000000000000000000000000000000..91caac36b9ea732f49def52c47ab2ad4d1ecebf1 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.368222489932 7.515828685414 -1.251526907307 0 0 0 +H +0.0 +2 +-8.826860216220 5.744779503476 -1.209180372276 0 0 0 +-11.189457220589 7.237910805042 -1.397700512299 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/conv new file mode 100644 index 0000000000000000000000000000000000000000..81900884056fec38151e599d298e712c840a9337 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/conv @@ -0,0 +1 @@ +93 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..763582b8289df96005f46a633759a922efc04b3a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.753898181 0.01273061007 1.264019426 1.345898164 1.469299358 0.009349860582 0.01669973765 0.03917037657 +-5.006108285e-20 0.0008803362432 0.00276155239 0.01292191407 0.04568532298 8.142937264e-21 2.571028004e-06 6.996333089e-06 +0.001586824886 0.006127917473 + +H atom_index 1 n_descriptor 18 +1.234559816 0.03535371276 0.1052203185 0.1425180669 0.3146173753 0.02226790988 0.02733249042 0.03849112703 +-1.473789054e-17 4.6658344e-05 0.09823639745 0.1146830884 0.1221113865 -1.705707004e-18 4.004828959e-06 0.01356910018 +0.02612199754 0.02999707055 + +H atom_index 2 n_descriptor 18 +1.23794736 0.03524026516 0.1063765295 0.1440421979 0.3157937974 0.02243490279 0.02753212507 0.03837041107 +-3.022825855e-18 4.697229555e-05 0.09908301913 0.1148377531 0.123434945 1.551378893e-18 3.824918246e-06 0.01351621983 +0.02625315335 0.03016135616 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..10e47283fcfd2f081eda9bd7152f07fdb0ea6c7c Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:05:58 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733965 SEC) : SETUP UNITCELL + DONE(0.0736642 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.0899653 SEC) : INIT PLANEWAVE + DONE(0.131287 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.375502 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651987e+02 0.000000e+00 2.123e-01 5.049e-01 + GE2 -4.663992e+02 -1.200489e+00 9.781e-02 4.830e-01 + GE3 -4.664035e+02 -4.337805e-03 6.289e-02 5.418e-01 + GE4 -4.664029e+02 6.163045e-04 1.910e-03 4.236e-01 + GE5 -4.664023e+02 6.720938e-04 9.031e-04 4.246e-01 + GE6 -4.664027e+02 -3.956181e-04 1.077e-04 4.164e-01 + GE7 -4.664025e+02 1.061303e-04 3.072e-05 4.030e-01 + GE8 -4.664026e+02 -2.178985e-05 1.618e-05 4.022e-01 + GE9 -4.664026e+02 1.727703e-05 2.588e-06 4.014e-01 + GE10 -4.664026e+02 -3.484286e-06 2.854e-07 3.978e-01 + GE11 -4.664026e+02 -5.600848e-07 6.226e-08 3.317e-01 +E_delta_band = -6.98898398e-02 Ry = -9.50900054e-01 eV +E_delta_NN= -1.94537137e-01 Ry = -2.64681353e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.664 11 0.61 1e+02 % + Run_lcao lcao_line 6.6562 1 6.7 1e+02 % + Potential init_pot 0.24289 2 0.12 3.6 % + PW_Basis recip2real 0.23288 16 0.015 3.5 % + PW_Basis gathers_scatterp 0.11368 16 0.0071 1.7 % + Potential v_of_rho 0.88093 13 0.068 13 % + XC_Functional v_xc 0.28962 14 0.021 4.3 % + H_Hartree_pw v_hartree 0.56115 13 0.043 8.4 % + PW_Basis real2recip 0.61705 38 0.016 9.3 % + PW_Basis gatherp_scatters 0.27965 38 0.0074 4.2 % + ORB_control set_orb_tables 0.89687 1 0.9 13 % + ORB_gen_tables gen_tables 0.89686 1 0.9 13 % + ORB_table_phi init_Table 0.37334 1 0.37 5.6 % + ORB_table_phi cal_ST_Phi12_R 0.36906 126 0.0029 5.5 % + ORB_table_beta init_Table_Beta 0.15653 1 0.16 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15517 56 0.0028 2.3 % + ORB_table_alpha init_Table_Alpha 0.2095 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20789 66 0.0031 3.1 % + LOOP_ions opt_ions 5.3134 1 5.3 80 % + ESolver_KS_LCAO Run 4.7838 1 4.8 72 % + HSolverLCAO solve 2.6239 11 0.24 39 % + HamiltLCAO updateHk 1.3313 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.308 11 0.12 20 % + Gint_interface cal_gint 1.5292 23 0.066 23 % + Gint_Gamma distri_vl_value 0.36884 11 0.034 5.5 % + Gint_Gamma distri_vl 2.2918 6 0.38 34 % + LCAO_Deepks cal_projected_DM 5.0801 13 0.39 76 % + LCAO_gen_fixedH add_v_delta 2.1643 6 0.36 32 % + LCAO_DESCRIPTOR add_v_delta 2.1645 6 0.36 32 % + ElecStateLCAO psiToRho 1.2766 11 0.12 19 % + Charge mix_rho 0.75236 10 0.075 11 % + LOOP_ions force_stress 0.52941 1 0.53 7.9 % + Force_Stress_LCAO getForceStress 0.52939 1 0.53 7.9 % + Force_LCAO_gamma ftable_gamma 0.33666 1 0.34 5.1 % + Force_LCAO_gamma cal_fvl_dphi 0.24654 1 0.25 3.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:05:58 2022 + FINISH Time : Wed Sep 28 11:06:04 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/93/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..9710c2316652d18fc13a114a912f696a70708f39 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.650834 0.251723 0.949723 +H 0.668123 0.192833 0.969189 +H 0.608085 0.250062 0.902124 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..491c573347563375433e9321e8a943cf68cafa37 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.3452 2 + 2 -13.6246 2 + 3 -8.73894 2 + 4 -6.75464 2 + 5 1.50594 0 + 6 4.77895 0 + 7 11.0357 0 + 8 11.2415 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..98f3bd6bb7be7360426fb2d4399016114b54071f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/running_scf.log @@ -0,0 +1,801 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:40 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.223354166 7.04823814126 26.5922474717 0 0 0 0 + tauc_H1 18.707437022 5.39932880773 27.137289806 0 0 0 0 + tauc_H2 17.0263804643 7.00174175348 25.2594670115 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.088067664911 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0884641717867 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.106532100493 (SEC) + + DONE : INIT CHARGE Time : 0.149755710917 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.432955 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 0 100 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000508 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00139 + + Density error is 0.218624392737 + + Energy Rydberg eV + E_KohnSham -34.18579076 -465.121544971 + E_Harris -34.385023362 -467.832243586 + E_Fermi -0.416687311783 -5.66932172455 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00078198115169 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00140503301123 + + Density error is 0.0976519645317 + + Energy Rydberg eV + E_KohnSham -34.2766545353 -466.357810057 + E_Harris -34.2831466851 -466.446140287 + E_Fermi -0.223246652712 -3.0374265363 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000757416475424 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013198929366 + + Density error is 0.0623135906379 + + Energy Rydberg eV + E_KohnSham -34.2768641741 -466.36066234 + E_Harris -34.2809732858 -466.416569672 + E_Fermi -0.20856610065 -2.83768737848 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000727575143225 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118336731118 + + Density error is 0.00217667211691 + + Energy Rydberg eV + E_KohnSham -34.2769161139 -466.361369018 + E_Harris -34.2769206078 -466.36143016 + E_Fermi -0.173381702148 -2.35897907815 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000728803620817 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118270084419 + + Density error is 0.000871674515049 + + Energy Rydberg eV + E_KohnSham -34.2768472686 -466.360432328 + E_Harris -34.2768490871 -466.360457071 + E_Fermi -0.172052048196 -2.34088820804 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000728124177204 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118126578496 + + Density error is 0.000246942739944 + + Energy Rydberg eV + E_KohnSham -34.2768953611 -466.36108666 + E_Harris -34.2768955774 -466.361089604 + E_Fermi -0.172389002368 -2.34547270473 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000728420008937 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118126822692 + + Density error is 4.72688246398e-05 + + Energy Rydberg eV + E_KohnSham -34.2768751037 -466.360811045 + E_Harris -34.2768751158 -466.360811209 + E_Fermi -0.172132630248 -2.3419845831 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000728366401801 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118124210182 + + Density error is 1.8398805101e-05 + + Energy Rydberg eV + E_KohnSham -34.2768820301 -466.360905283 + E_Harris -34.2768820314 -466.360905301 + E_Fermi -0.172189249753 -2.34275493098 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000728370014924 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118122083069 + + Density error is 2.2897428133e-06 + + Energy Rydberg eV + E_KohnSham -34.276880479 -466.360884179 + E_Harris -34.276880479 -466.360884179 + E_Fermi -0.172170195563 -2.34249568543 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000728369387439 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118121547332 + + Density error is 4.05101546517e-07 + + Energy Rydberg eV + E_KohnSham -34.2768807069 -466.36088728 + E_Harris -34.2768807069 -466.36088728 + E_Fermi -0.172167939229 -2.34246498644 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000728370063238 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118121608117 + + Density error is 1.6032273493e-07 + + Energy Rydberg eV + E_KohnSham -34.2768807331 -466.360887637 + E_Harris -34.2768807331 -466.360887637 + E_Fermi -0.172167786919 -2.34246291414 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000728370300097 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00118121609511 + + Density error is 9.29006174673e-09 + + Energy Rydberg eV + E_KohnSham -34.2768807348 -466.36088766 + E_Harris -34.2768807348 -466.36088766 + E_band -8.0059661401 -108.9267575 + E_one_elec -69.7063449578 -948.403478179 + E_Hartree +36.2500258309 +493.206903948 + E_xc -8.2430772582 -112.152819766 + E_Ewald +7.5460530242 +102.669318539 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195370232977 -2.65814838807 + E_Fermi -0.172167635001 -2.3424608472 + + charge density convergence is achieved + final etot is -466.36088766 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.3452 2.00000 + 2 -13.6246 2.00000 + 3 -8.73894 2.00000 + 4 -6.75464 2.00000 + 5 1.50594 0.00000 + 6 4.77895 0.00000 + 7 11.0357 0.00000 + 8 11.2415 0.00000 + + EFERMI = -2.342460847202683 eV + OUT.ABACUS/ final etot is -466.3608876599307 eV + correction force for each atom along direction 1 is -0.000133867 + correction force for each atom along direction 2 is -0.000150974 + correction force for each atom along direction 3 is -3.02209e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.90223638 +1.6028802 +1.0049218 + H1 -0.071805892 -1.0461176 -0.079106123 + H2 -0.83043049 -0.55676256 -0.92581568 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3608876599307 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0049 11 0.64 1.0e+02% + Run_lcao lcao_line 6.9950 1 7.0 1.e+02% + Potential init_pot 0.28487 2 0.14 4.1% + PW_Basis recip2real 0.28144 17 0.017 4.0% + PW_Basis gathers_scatterp 0.13060 17 0.0077 1.9% + Potential v_of_rho 1.0341 14 0.074 15.% + XC_Functional v_xc 0.30247 15 0.020 4.3% + H_Hartree_pw v_hartree 0.68552 14 0.049 9.8% + PW_Basis real2recip 0.74779 41 0.018 11.% + PW_Basis gatherp_scatters 0.32426 41 0.0079 4.6% + ORB_control set_orb_tables 1.0979 1 1.1 16.% + ORB_gen_tables gen_tables 1.0979 1 1.1 16.% + ORB_table_phi init_Table 0.47695 1 0.48 6.8% + ORB_table_phi cal_ST_Phi12_R 0.47171 126 0.0037 6.7% + ORB_table_beta init_Table_Beta 0.18362 1 0.18 2.6% + ORB_table_beta VNL_PhiBeta_R 0.18208 56 0.0033 2.6% + ORB_table_alpha init_Table_Alpha 0.24730 1 0.25 3.5% + ORB_table_alpha S_PhiAlpha_R 0.24533 66 0.0037 3.5% + LOOP_ions opt_ions 5.3866 1 5.4 77.% + ESolver_KS_LCAO Run 4.8605 1 4.9 69.% + HSolverLCAO solve 2.2132 12 0.18 32.% + HamiltLCAO updateHk 1.1798 12 0.098 17.% + LCAO_Hamilt cal_Hgamma 1.1504 12 0.096 16.% + Gint_interface cal_gint 1.0032 25 0.040 14.% + Gint_Gamma distri_vl_value 0.36393 12 0.030 5.2% + Gint_Gamma distri_vl 2.5413 6 0.42 36.% + LCAO_Deepks cal_projected_DM 5.1360 14 0.37 73.% + LCAO_gen_fixedH add_v_delta 2.3953 6 0.40 34.% + LCAO_DESCRIPTOR add_v_delta 2.3953 6 0.40 34.% + ElecStateLCAO psiToRho 1.0113 12 0.084 14.% + Charge mix_rho 0.98377 11 0.089 14.% + LOOP_ions force_stress 0.52593 1 0.53 7.5% + Force_Stress_LCAO getForceStress 0.52591 1 0.53 7.5% + Force_LCAO_gamma ftable_gamma 0.30807 1 0.31 4.4% + Force_LCAO_gamma cal_fvl_dphi 0.19326 1 0.19 2.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:40 2022 + Finish Time : Wed Sep 28 11:03:47 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..47a610382c242d875994d345db283342b437bad2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123906 ima = 3.68744e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 2 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123577521738 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112974074633 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011332117968 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113572780024 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113509954957 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113549875135 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113536466728 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011353968937 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113539026816 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113538952833 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113538940666 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113538933265 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/STRU new file mode 100644 index 0000000000000000000000000000000000000000..57330688fcd4e69ac72f66bb92a3460f5d53f179 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.776645834021 7.048238141275 -1.407752528316 0 0 0 +H +0.0 +2 +-9.292562978007 5.399328807702 -0.862710194013 0 0 0 +-10.973619535702 7.001741753501 -2.740532988521 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/conv new file mode 100644 index 0000000000000000000000000000000000000000..9cfc173a44fba6c2f2dc78064de9d7ffe419f403 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/conv @@ -0,0 +1 @@ +94 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..690bcf55a11839a663c037e794a42a7a5cdbfaec --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.741796406 0.01268939549 1.297317196 1.38661206 1.469802125 0.00753801864 0.02144543624 0.03881222342 +2.086048833e-18 0.001262161833 0.002368192318 0.01299677844 0.04322865578 1.52957103e-19 1.492303477e-06 4.772573199e-06 +0.001856440598 0.005480084329 + +H atom_index 1 n_descriptor 18 +1.261571421 0.0329311849 0.1137715938 0.1574423143 0.3271704685 0.02239410731 0.02922903422 0.03621849555 +-6.134527911e-17 3.89672259e-05 0.1059532056 0.1157476924 0.1353260189 -2.905002808e-18 3.561859023e-06 0.0127733654 +0.02682431625 0.03144233838 + +H atom_index 2 n_descriptor 18 +1.270305018 0.03262682259 0.1169351654 0.1616763885 0.3296520185 0.02275466043 0.02972454368 0.03603693749 +6.078372663e-17 3.965926621e-05 0.1071634647 0.1170156648 0.1389455817 8.0551727e-18 3.145272296e-06 0.01282574253 +0.02712429943 0.03179218639 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..3961b1b37dfd92b7db3b758cf3f7969f99e96bd0 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/log.scf @@ -0,0 +1,103 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:40 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0880901 SEC) : SETUP UNITCELL + DONE(0.0884798 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.106553 SEC) : INIT PLANEWAVE + DONE(0.149894 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.433021 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651215e+02 0.000000e+00 2.186e-01 4.884e-01 + GE2 -4.663578e+02 -1.236265e+00 9.765e-02 4.358e-01 + GE3 -4.663607e+02 -2.852282e-03 6.231e-02 5.077e-01 + GE4 -4.663614e+02 -7.066778e-04 2.177e-03 3.680e-01 + GE5 -4.663604e+02 9.366896e-04 8.717e-04 4.097e-01 + GE6 -4.663611e+02 -6.543321e-04 2.469e-04 3.893e-01 + GE7 -4.663608e+02 2.756155e-04 4.727e-05 3.886e-01 + GE8 -4.663609e+02 -9.423868e-05 1.840e-05 3.761e-01 + GE9 -4.663609e+02 2.110449e-05 2.290e-06 3.791e-01 + GE10 -4.663609e+02 -3.101076e-06 4.051e-07 3.778e-01 + GE11 -4.663609e+02 -3.567052e-07 1.603e-07 3.764e-01 + GE12 -4.663609e+02 -2.331117e-08 9.290e-09 3.012e-01 +E_delta_band = -7.18328590e-02 Ry = -9.77336186e-01 eV +E_delta_NN= -1.95370233e-01 Ry = -2.65814839e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 7.0049 11 0.64 1e+02 % + Run_lcao lcao_line 6.995 1 7 1e+02 % + Potential init_pot 0.28487 2 0.14 4.1 % + PW_Basis recip2real 0.28144 17 0.017 4 % + PW_Basis gathers_scatterp 0.1306 17 0.0077 1.9 % + Potential v_of_rho 1.0341 14 0.074 15 % + XC_Functional v_xc 0.30247 15 0.02 4.3 % + H_Hartree_pw v_hartree 0.68552 14 0.049 9.8 % + PW_Basis real2recip 0.74779 41 0.018 11 % + PW_Basis gatherp_scatters 0.32426 41 0.0079 4.6 % + ORB_control set_orb_tables 1.0979 1 1.1 16 % + ORB_gen_tables gen_tables 1.0979 1 1.1 16 % + ORB_table_phi init_Table 0.47695 1 0.48 6.8 % + ORB_table_phi cal_ST_Phi12_R 0.47171 126 0.0037 6.7 % + ORB_table_beta init_Table_Beta 0.18362 1 0.18 2.6 % + ORB_table_beta VNL_PhiBeta_R 0.18208 56 0.0033 2.6 % + ORB_table_alpha init_Table_Alpha 0.2473 1 0.25 3.5 % + ORB_table_alpha S_PhiAlpha_R 0.24533 66 0.0037 3.5 % + LOOP_ions opt_ions 5.3866 1 5.4 77 % + ESolver_KS_LCAO Run 4.8605 1 4.9 69 % + HSolverLCAO solve 2.2132 12 0.18 32 % + HamiltLCAO updateHk 1.1798 12 0.098 17 % + LCAO_Hamilt cal_Hgamma 1.1504 12 0.096 16 % + Gint_interface cal_gint 1.0032 25 0.04 14 % + Gint_Gamma distri_vl_value 0.36393 12 0.03 5.2 % + Gint_Gamma distri_vl 2.5413 6 0.42 36 % + LCAO_Deepks cal_projected_DM 5.136 14 0.37 73 % + LCAO_gen_fixedH add_v_delta 2.3953 6 0.4 34 % + LCAO_DESCRIPTOR add_v_delta 2.3953 6 0.4 34 % + ElecStateLCAO psiToRho 1.0113 12 0.084 14 % + Charge mix_rho 0.98377 11 0.089 14 % + LOOP_ions force_stress 0.52593 1 0.53 7.5 % + Force_Stress_LCAO getForceStress 0.52591 1 0.53 7.5 % + Force_LCAO_gamma ftable_gamma 0.30807 1 0.31 4.4 % + Force_LCAO_gamma cal_fvl_dphi 0.19326 1 0.19 2.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:40 2022 + FINISH Time : Wed Sep 28 11:03:47 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/94/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..62a874348f4fe78203ccac856809a2064fb8ff49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.655294 0.245421 0.957373 +H 0.684125 0.197403 0.994587 +H 0.602999 0.214474 0.932923 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c73bbefe7d13493c5c72821ae966988fdd30df4a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.182 2 + 2 -12.8289 2 + 3 -9.19356 2 + 4 -6.7221 2 + 5 1.16377 0 + 6 4.19946 0 + 7 11.1063 0 + 8 11.3659 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..1f44b3276adbbb0f86ecd7c5fb4ccf4e4958a2cf --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/running_scf.log @@ -0,0 +1,802 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:02:28 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.3482253882 6.87179030195 26.8064561206 0 0 0 0 + tauc_H1 19.155499482 5.52728165883 27.848449719 0 0 0 0 + tauc_H2 16.8839712002 6.0052678175 26.1218516367 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.087432440401 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0980747231832 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.1166615746 (SEC) + + DONE : INIT CHARGE Time : 0.164847986303 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.442636 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 388 ; sender_size of each process is: +144 0 100 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000794 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00153 + + Density error is 0.212781584539 + + Energy Rydberg eV + E_KohnSham -34.1919197201 -465.204933752 + E_Harris -34.3791798157 -467.752738061 + E_Fermi -0.396538353528 -5.39518108352 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000956762389636 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0013906400836 + + Density error is 0.0982268202837 + + Energy Rydberg eV + E_KohnSham -34.2803383281 -466.40793063 + E_Harris -34.2872562945 -466.502054391 + E_Fermi -0.207110810741 -2.81788714348 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000908875464512 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129245152906 + + Density error is 0.0632031088102 + + Energy Rydberg eV + E_KohnSham -34.2806841327 -466.412635543 + E_Harris -34.2851521323 -466.473425797 + E_Fermi -0.198059495009 -2.69473767513 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000844864786462 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111909509705 + + Density error is 0.00194656998577 + + Energy Rydberg eV + E_KohnSham -34.2806306397 -466.411907733 + E_Harris -34.2806317944 -466.411923443 + E_Fermi -0.162597067118 -2.2122465909 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000846527894193 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111842633195 + + Density error is 0.00089008278487 + + Energy Rydberg eV + E_KohnSham -34.2805855267 -466.411293939 + E_Harris -34.2805861542 -466.411302478 + E_Fermi -0.162252864204 -2.20756346999 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000845532661449 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111606962571 + + Density error is 0.000160071139811 + + Energy Rydberg eV + E_KohnSham -34.2806106775 -466.411636133 + E_Harris -34.2806108607 -466.411638626 + E_Fermi -0.162012622061 -2.20429480795 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000845674430495 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111608399472 + + Density error is 3.20853809035e-05 + + Energy Rydberg eV + E_KohnSham -34.2806019986 -466.411518052 + E_Harris -34.2806018427 -466.411515929 + E_Fermi -0.161941610368 -2.2033286443 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00084564202802 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111604097092 + + Density error is 1.50593835404e-05 + + Energy Rydberg eV + E_KohnSham -34.2806053621 -466.411563814 + E_Harris -34.2806053631 -466.411563827 + E_Fermi -0.161968527016 -2.20369486408 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000845646618151 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0011160263196 + + Density error is 2.78591370591e-06 + + Energy Rydberg eV + E_KohnSham -34.2806041466 -466.411547276 + E_Harris -34.2806041466 -466.411547276 + E_Fermi -0.161954686414 -2.20350655303 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.00084564339282 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111601873097 + + Density error is 4.5497932713e-07 + + Energy Rydberg eV + E_KohnSham -34.2806043583 -466.411550157 + E_Harris -34.2806043583 -466.411550157 + E_Fermi -0.161951885078 -2.20346843891 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000845643936881 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111601917239 + + Density error is 1.64423214061e-07 + + Energy Rydberg eV + E_KohnSham -34.2806043901 -466.41155059 + E_Harris -34.2806043901 -466.41155059 + E_Fermi -0.161951702868 -2.20346595981 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 388 + sender_size = 388 + last sender_buffer = 0.000845644027771 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00111601904355 + + Density error is 1.0812040038e-08 + + Energy Rydberg eV + E_KohnSham -34.2806043933 -466.411550632 + E_Harris -34.2806043933 -466.411550632 + E_band -7.92704423008 -107.852969827 + E_one_elec -68.9997725764 -938.790067744 + E_Hartree +35.8991984444 +488.433652476 + E_xc -8.18700980009 -111.389982863 + E_Ewald +7.13189610175 +97.0344245278 + E_demet -3.55887394659e-69 -4.84209641374e-68 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194309361949 -2.64371449726 + E_Fermi -0.161951547824 -2.20346385032 + + charge density convergence is achieved + final etot is -466.411550632 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1820 2.00000 + 2 -12.8289 2.00000 + 3 -9.19356 2.00000 + 4 -6.72210 2.00000 + 5 1.16377 0.00000 + 6 4.19946 0.00000 + 7 11.1063 0.00000 + 8 11.3659 0.00000 + + EFERMI = -2.203463850319167 eV + OUT.ABACUS/ final etot is -466.4115506320996 eV + correction force for each atom along direction 1 is 1.50827e-05 + correction force for each atom along direction 2 is -0.000176730 + correction force for each atom along direction 3 is 5.77978e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.59360655 -0.68365477 +0.65412126 + H1 -0.30297892 +0.72918922 -0.47228547 + H2 -0.29062763 -0.045534451 -0.18183579 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4115506320996 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6739 11 0.61 1.0e+02% + Run_lcao lcao_line 6.6642 1 6.7 1.e+02% + Potential init_pot 0.28405 2 0.14 4.3% + PW_Basis recip2real 0.27958 17 0.016 4.2% + PW_Basis gathers_scatterp 0.11977 17 0.0070 1.8% + Charge atomic_rho 0.10012 1 0.10 1.5% + Potential v_of_rho 0.92498 14 0.066 14.% + XC_Functional v_xc 0.25857 15 0.017 3.9% + H_Hartree_pw v_hartree 0.62835 14 0.045 9.4% + PW_Basis real2recip 0.61115 41 0.015 9.2% + PW_Basis gatherp_scatters 0.24504 41 0.0060 3.7% + ORB_control set_orb_tables 1.1129 1 1.1 17.% + ORB_gen_tables gen_tables 1.1129 1 1.1 17.% + ORB_table_phi init_Table 0.49055 1 0.49 7.4% + ORB_table_phi cal_ST_Phi12_R 0.48555 126 0.0039 7.3% + ORB_table_beta init_Table_Beta 0.18874 1 0.19 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18723 56 0.0033 2.8% + ORB_table_alpha init_Table_Alpha 0.25400 1 0.25 3.8% + ORB_table_alpha S_PhiAlpha_R 0.25211 66 0.0038 3.8% + LOOP_ions opt_ions 5.0268 1 5.0 75.% + ESolver_KS_LCAO Run 4.4757 1 4.5 67.% + HSolverLCAO solve 2.3462 12 0.20 35.% + HamiltLCAO updateHk 1.2205 12 0.10 18.% + LCAO_Hamilt cal_Hgamma 1.1848 12 0.099 18.% + Gint_interface cal_gint 1.5013 25 0.060 22.% + Gint_Gamma distri_vl_value 0.26681 12 0.022 4.0% + Gint_Gamma distri_vl 2.3267 6 0.39 35.% + LCAO_Deepks cal_projected_DM 4.7926 14 0.34 72.% + LCAO_gen_fixedH add_v_delta 2.1940 6 0.37 33.% + LCAO_DESCRIPTOR add_v_delta 2.1940 6 0.37 33.% + ElecStateLCAO psiToRho 1.1061 12 0.092 17.% + Charge mix_rho 0.71176 11 0.065 11.% + LOOP_ions force_stress 0.55098 1 0.55 8.3% + Force_Stress_LCAO getForceStress 0.55095 1 0.55 8.3% + Force_LCAO_gamma ftable_gamma 0.32887 1 0.33 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.25017 1 0.25 3.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:02:28 2022 + Finish Time : Wed Sep 28 11:02:35 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..5c79a7efb075e5090b95e42dd6eeb0162c5852d8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123761 ima = 3.68878e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 2 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0012312952899 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111913457524 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112566588076 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112789491483 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756963345 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112776946459 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112771168683 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112773587201 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112772925773 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112772832303 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112772815714 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112772807433 + charge after normalized = 8.00000000000002 + charge before normalized = 8.00000000000002 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/STRU new file mode 100644 index 0000000000000000000000000000000000000000..f6927b651ab7569d5dad85b8d3f387423f721d73 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.651774611799 6.871790301925 -1.193543879378 0 0 0 +H +0.0 +2 +-8.844500518008 5.527281658851 -0.151550280974 0 0 0 +-11.116028799829 6.005267817515 -1.878148363328 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/conv new file mode 100644 index 0000000000000000000000000000000000000000..8f1db8709d15893d509c58c321de4652a35122e2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/conv @@ -0,0 +1 @@ +95 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..b072dc9aecc76be42470afa2b693a5034fe2bbe5 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750977861 0.0126086882 1.259636768 1.349500472 1.468827337 0.008712794226 0.01773807275 0.03909273597 +3.852729331e-18 0.0009457911145 0.002576529769 0.012170111 0.04409306456 5.838941286e-19 2.028109061e-06 5.896808464e-06 +0.001610522021 0.005989122499 + +H atom_index 1 n_descriptor 18 +1.208165661 0.03584585752 0.09474808806 0.131466067 0.3063768933 0.02036644331 0.0258430278 0.03916029881 +7.353215125e-18 4.094584635e-05 0.08980575062 0.1124941422 0.1137538083 -2.714538472e-18 5.816280106e-06 0.01397556585 +0.02449249132 0.02869025524 + +H atom_index 2 n_descriptor 18 +1.246692466 0.03455482408 0.1073146664 0.1483562767 0.3198555593 0.0221834512 0.02810237201 0.03772927489 +4.898939458e-17 4.441675149e-05 0.09978588879 0.1151273591 0.1272188509 5.995958627e-18 4.017256141e-06 0.01325238932 +0.02601303995 0.0305917965 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..f5f7b51fdf388c73205308e5662e96ed8418e331 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/log.scf @@ -0,0 +1,104 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:02:28 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874576 SEC) : SETUP UNITCELL + DONE(0.0980918 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.116683 SEC) : INIT PLANEWAVE + DONE(0.164988 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.442709 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652049e+02 0.000000e+00 2.128e-01 4.919e-01 + GE2 -4.664079e+02 -1.202997e+00 9.823e-02 4.141e-01 + GE3 -4.664126e+02 -4.704913e-03 6.320e-02 4.708e-01 + GE4 -4.664119e+02 7.278096e-04 1.947e-03 3.599e-01 + GE5 -4.664113e+02 6.137941e-04 8.901e-04 3.559e-01 + GE6 -4.664116e+02 -3.421938e-04 1.601e-04 3.572e-01 + GE7 -4.664115e+02 1.180812e-04 3.209e-05 3.422e-01 + GE8 -4.664116e+02 -4.576175e-05 1.506e-05 3.363e-01 + GE9 -4.664115e+02 1.653789e-05 2.786e-06 3.374e-01 + GE10 -4.664116e+02 -2.880921e-06 4.550e-07 3.317e-01 + GE11 -4.664116e+02 -4.329567e-07 1.644e-07 3.346e-01 + GE12 -4.664116e+02 -4.254201e-08 1.081e-08 2.811e-01 +E_delta_band = -6.93927991e-02 Ry = -9.44137468e-01 eV +E_delta_NN= -1.94309362e-01 Ry = -2.64371450e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.6739 11 0.61 1e+02 % + Run_lcao lcao_line 6.6642 1 6.7 1e+02 % + Potential init_pot 0.28405 2 0.14 4.3 % + PW_Basis recip2real 0.27958 17 0.016 4.2 % + PW_Basis gathers_scatterp 0.11977 17 0.007 1.8 % + Charge atomic_rho 0.10012 1 0.1 1.5 % + Potential v_of_rho 0.92498 14 0.066 14 % + XC_Functional v_xc 0.25857 15 0.017 3.9 % + H_Hartree_pw v_hartree 0.62835 14 0.045 9.4 % + PW_Basis real2recip 0.61115 41 0.015 9.2 % + PW_Basis gatherp_scatters 0.24504 41 0.006 3.7 % + ORB_control set_orb_tables 1.1129 1 1.1 17 % + ORB_gen_tables gen_tables 1.1129 1 1.1 17 % + ORB_table_phi init_Table 0.49055 1 0.49 7.4 % + ORB_table_phi cal_ST_Phi12_R 0.48555 126 0.0039 7.3 % + ORB_table_beta init_Table_Beta 0.18874 1 0.19 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18723 56 0.0033 2.8 % + ORB_table_alpha init_Table_Alpha 0.254 1 0.25 3.8 % + ORB_table_alpha S_PhiAlpha_R 0.25211 66 0.0038 3.8 % + LOOP_ions opt_ions 5.0268 1 5 75 % + ESolver_KS_LCAO Run 4.4757 1 4.5 67 % + HSolverLCAO solve 2.3462 12 0.2 35 % + HamiltLCAO updateHk 1.2205 12 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1848 12 0.099 18 % + Gint_interface cal_gint 1.5013 25 0.06 22 % + Gint_Gamma distri_vl_value 0.26681 12 0.022 4 % + Gint_Gamma distri_vl 2.3267 6 0.39 35 % + LCAO_Deepks cal_projected_DM 4.7926 14 0.34 72 % + LCAO_gen_fixedH add_v_delta 2.194 6 0.37 33 % + LCAO_DESCRIPTOR add_v_delta 2.194 6 0.37 33 % + ElecStateLCAO psiToRho 1.1061 12 0.092 17 % + Charge mix_rho 0.71176 11 0.065 11 % + LOOP_ions force_stress 0.55098 1 0.55 8.3 % + Force_Stress_LCAO getForceStress 0.55095 1 0.55 8.3 % + Force_LCAO_gamma ftable_gamma 0.32887 1 0.33 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.25017 1 0.25 3.7 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:02:28 2022 + FINISH Time : Wed Sep 28 11:02:35 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/95/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..97030f9151c1f9ea5527061c1dfb7d6dc8fa3071 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.676055 0.254592 0.972041 +H 0.715019 0.201823 0.983268 +H 0.622884 0.227138 0.941761 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..c5f855aa8b51b10267198f141a8541113821d0b0 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.1021 2 + 2 -12.7815 2 + 3 -9.17 2 + 4 -6.70492 2 + 5 1.11138 0 + 6 4.08714 0 + 7 11.1244 0 + 8 11.3834 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..f6055ed403746d1770e5b1b354c563d6bea5c738 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:13:30 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 18.9295317142 7.12856460793 27.2171444266 0 0 0 0 + tauc_H1 20.0205368032 5.65105605796 27.5314922253 0 0 0 0 + tauc_H2 17.4407649799 6.35987292772 26.3693024363 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.087392175412 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877450879767 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105851963833 (SEC) + + DONE : INIT CHARGE Time : 0.148720543678 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.431441 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 0 9 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000665 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00143 + + Density error is 0.212060181231 + + Energy Rydberg eV + E_KohnSham -34.1924764849 -465.212508925 + E_Harris -34.3779916884 -467.736572759 + E_Fermi -0.391851633696 -5.33141498887 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000847277821857 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0012937065416 + + Density error is 0.0984186500655 + + Energy Rydberg eV + E_KohnSham -34.2804395855 -466.409308308 + E_Harris -34.2874325553 -466.504452543 + E_Fermi -0.202972037144 -2.76157623983 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000808480922894 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.001204851983 + + Density error is 0.0633981603498 + + Energy Rydberg eV + E_KohnSham -34.2808057911 -466.41429079 + E_Harris -34.2853123649 -466.475605872 + E_Fermi -0.19487686348 -2.6514357517 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000762401915092 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104290170558 + + Density error is 0.00194812317901 + + Energy Rydberg eV + E_KohnSham -34.2807348793 -466.413325985 + E_Harris -34.2807361415 -466.413343159 + E_Fermi -0.159535705379 -2.1705946276 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000763295999321 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00104133328456 + + Density error is 0.000895920003751 + + Energy Rydberg eV + E_KohnSham -34.2806960554 -466.41279776 + E_Harris -34.2806964587 -466.412803247 + E_Fermi -0.159319814469 -2.16765728108 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000762700043574 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010390766248 + + Density error is 0.000166119641996 + + Energy Rydberg eV + E_KohnSham -34.2807154999 -466.413062316 + E_Harris -34.2807155109 -466.413062466 + E_Fermi -0.158992606976 -2.16320539475 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000762869139504 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103909291961 + + Density error is 2.97459423701e-05 + + Energy Rydberg eV + E_KohnSham -34.2807092537 -466.412977331 + E_Harris -34.280709257 -466.412977377 + E_Fermi -0.158939112902 -2.16247757053 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000762826854398 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103904167701 + + Density error is 1.34855718754e-05 + + Energy Rydberg eV + E_KohnSham -34.2807122025 -466.413017452 + E_Harris -34.2807122033 -466.413017463 + E_Fermi -0.158960629233 -2.16277031523 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000762832211793 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010390261872 + + Density error is 2.04745145123e-06 + + Energy Rydberg eV + E_KohnSham -34.2807110981 -466.413002426 + E_Harris -34.2807110981 -466.413002426 + E_Fermi -0.158947575588 -2.16259271128 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000762831470839 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103902238284 + + Density error is 3.55055427386e-07 + + Energy Rydberg eV + E_KohnSham -34.2807113005 -466.41300518 + E_Harris -34.2807113005 -466.41300518 + E_Fermi -0.158945675241 -2.16256685574 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.00076283201614 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00103902283863 + + Density error is 9.84826145236e-08 + + Energy Rydberg eV + E_KohnSham -34.2807113232 -466.413005489 + E_Harris -34.2807113232 -466.413005489 + E_band -7.90234097569 -107.516864808 + E_one_elec -68.8488863155 -936.737154845 + E_Hartree +35.8285883604 +487.472952997 + E_xc -8.17561012414 -111.234882315 + E_Ewald +7.04042649254 +95.7899166487 + E_demet -1.53118428467e-65 -2.08328309595e-64 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.194029325231 -2.63990440223 + E_Fermi -0.158945510446 -2.16256461358 + + charge density convergence is achieved + final etot is -466.413005489 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.1021 2.00000 + 2 -12.7815 2.00000 + 3 -9.17000 2.00000 + 4 -6.70492 2.00000 + 5 1.11138 0.00000 + 6 4.08714 0.00000 + 7 11.1244 0.00000 + 8 11.3834 0.00000 + + EFERMI = -2.162564613584105 eV + OUT.ABACUS/ final etot is -466.4130054887632 eV + correction force for each atom along direction 1 is -1.47339e-05 + correction force for each atom along direction 2 is -0.000108292 + correction force for each atom along direction 3 is -9.46468e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.38910267 -0.80099559 -0.31535735 + H1 -0.20279416 +0.40181485 -0.037328473 + H2 +0.59189683 +0.39918074 +0.35268582 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4130054887632 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9577 11 0.54 1.0e+02% + Run_lcao lcao_line 5.9481 1 5.9 1.e+02% + Potential init_pot 0.28327 2 0.14 4.8% + PW_Basis recip2real 0.26320 16 0.016 4.4% + PW_Basis gathers_scatterp 0.12130 16 0.0076 2.0% + Potential v_of_rho 0.93887 13 0.072 16.% + XC_Functional v_xc 0.29117 14 0.021 4.9% + H_Hartree_pw v_hartree 0.60481 13 0.047 10.% + PW_Basis real2recip 0.68409 38 0.018 11.% + PW_Basis gatherp_scatters 0.27413 38 0.0072 4.6% + ORB_control set_orb_tables 1.0929 1 1.1 18.% + ORB_gen_tables gen_tables 1.0929 1 1.1 18.% + ORB_table_phi init_Table 0.47457 1 0.47 8.0% + ORB_table_phi cal_ST_Phi12_R 0.46939 126 0.0037 7.9% + ORB_table_beta init_Table_Beta 0.18400 1 0.18 3.1% + ORB_table_beta VNL_PhiBeta_R 0.18243 56 0.0033 3.1% + ORB_table_alpha init_Table_Alpha 0.24704 1 0.25 4.1% + ORB_table_alpha S_PhiAlpha_R 0.24511 66 0.0037 4.1% + LOOP_ions opt_ions 4.3416 1 4.3 73.% + ESolver_KS_LCAO Run 3.9001 1 3.9 65.% + HSolverLCAO solve 1.5049 11 0.14 25.% + HamiltLCAO updateHk 0.87001 11 0.079 15.% + LCAO_Hamilt cal_Hgamma 0.84265 11 0.077 14.% + Gint_interface cal_gint 1.0142 23 0.044 17.% + Gint_Gamma distri_vl 1.8917 6 0.32 32.% + LCAO_Deepks cal_projected_DM 4.1786 13 0.32 70.% + LCAO_gen_fixedH add_v_delta 1.7445 6 0.29 29.% + LCAO_DESCRIPTOR add_v_delta 1.7445 6 0.29 29.% + ElecStateLCAO psiToRho 0.61374 11 0.056 10.% + Charge mix_rho 0.90055 10 0.090 15.% + LOOP_ions force_stress 0.44131 1 0.44 7.4% + Force_Stress_LCAO getForceStress 0.44128 1 0.44 7.4% + Force_LCAO_gamma ftable_gamma 0.23203 1 0.23 3.9% + Force_LCAO_gamma cal_fvl_dphi 0.19405 1 0.19 3.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:13:30 2022 + Finish Time : Wed Sep 28 11:13:36 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..08bfa008a9e4fdb316d496b5630cfe7648bcdfab --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123894 ima = 3.70554e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 1 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123247881601 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111939959921 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112635930891 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112842797987 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011281874898 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112833497284 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112828584941 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112830789222 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112830173779 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112830103159 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112830086264 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/STRU new file mode 100644 index 0000000000000000000000000000000000000000..9bff4dd92c9acdba8661d936bac9e129ca36306b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-9.070468285766 7.128564607954 -0.782855573428 0 0 0 +H +0.0 +2 +-7.979463196760 5.651056057953 -0.468507774681 0 0 0 +-10.559235020128 6.359872927727 -1.630697563676 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/conv new file mode 100644 index 0000000000000000000000000000000000000000..4deba72cc21b55e840bdf563561d8f07d3807edd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/conv @@ -0,0 +1 @@ +96 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..d7f8da3892c6a018fe17706ecf98c9d6ef6c75eb --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.750852724 0.01255115222 1.254757507 1.343604648 1.468490431 0.008629102495 0.01767949925 0.03909585574 +-1.36970102e-18 0.0009191670918 0.002516438949 0.0119455799 0.04316932423 3.87404724e-19 1.905152024e-06 5.62071321e-06 +0.001609555488 0.005963499105 + +H atom_index 1 n_descriptor 18 +1.22342808 0.03532868688 0.09932163404 0.1380329703 0.312134661 0.02099340246 0.02675080149 0.03856029466 +1.558153805e-17 4.090085599e-05 0.09315212368 0.1144123784 0.1182037791 -8.906584528e-19 5.11987287e-06 0.01359372819 +0.02493845017 0.0294698801 + +H atom_index 2 n_descriptor 18 +1.212046579 0.03570448213 0.09572071473 0.1331718114 0.3080422771 0.02045932761 0.02608268418 0.03900693039 +3.120977597e-17 3.990461076e-05 0.09017272295 0.1139479999 0.1140171597 -4.655431653e-18 5.597004072e-06 0.01385627667 +0.0244789581 0.0288908149 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0f7cda72798370a2ae822fc51db81a4311c832c3 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..1aac89566c2470cdd7a1d2274cb58ec07331a9ad Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..722304eddcd2f7788236ff33fd17b6812e584063 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..def02fd71cc2f3886735e1cc43ae86b9eb1b0755 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:13:30 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874155 SEC) : SETUP UNITCELL + DONE(0.0877599 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105873 SEC) : INIT PLANEWAVE + DONE(0.148856 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.431508 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.652125e+02 0.000000e+00 2.121e-01 4.576e-01 + GE2 -4.664093e+02 -1.196799e+00 9.842e-02 4.053e-01 + GE3 -4.664143e+02 -4.982482e-03 6.340e-02 4.788e-01 + GE4 -4.664133e+02 9.648050e-04 1.948e-03 3.376e-01 + GE5 -4.664128e+02 5.282253e-04 8.959e-04 3.337e-01 + GE6 -4.664131e+02 -2.645555e-04 1.661e-04 3.291e-01 + GE7 -4.664130e+02 8.498420e-05 2.975e-05 3.134e-01 + GE8 -4.664130e+02 -4.012099e-05 1.349e-05 3.118e-01 + GE9 -4.664130e+02 1.502614e-05 2.047e-06 3.120e-01 + GE10 -4.664130e+02 -2.753889e-06 3.551e-07 3.144e-01 + GE11 -4.664130e+02 -3.086416e-07 9.848e-08 2.437e-01 +E_delta_band = -6.87995888e-02 Ry = -9.36066427e-01 eV +E_delta_NN= -1.94029325e-01 Ry = -2.63990440e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 5.9577 11 0.54 1e+02 % + Run_lcao lcao_line 5.9481 1 5.9 1e+02 % + Potential init_pot 0.28327 2 0.14 4.8 % + PW_Basis recip2real 0.2632 16 0.016 4.4 % + PW_Basis gathers_scatterp 0.1213 16 0.0076 2 % + Potential v_of_rho 0.93887 13 0.072 16 % + XC_Functional v_xc 0.29117 14 0.021 4.9 % + H_Hartree_pw v_hartree 0.60481 13 0.047 10 % + PW_Basis real2recip 0.68409 38 0.018 11 % + PW_Basis gatherp_scatters 0.27413 38 0.0072 4.6 % + ORB_control set_orb_tables 1.0929 1 1.1 18 % + ORB_gen_tables gen_tables 1.0929 1 1.1 18 % + ORB_table_phi init_Table 0.47457 1 0.47 8 % + ORB_table_phi cal_ST_Phi12_R 0.46939 126 0.0037 7.9 % + ORB_table_beta init_Table_Beta 0.184 1 0.18 3.1 % + ORB_table_beta VNL_PhiBeta_R 0.18243 56 0.0033 3.1 % + ORB_table_alpha init_Table_Alpha 0.24704 1 0.25 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.24511 66 0.0037 4.1 % + LOOP_ions opt_ions 4.3416 1 4.3 73 % + ESolver_KS_LCAO Run 3.9001 1 3.9 65 % + HSolverLCAO solve 1.5049 11 0.14 25 % + HamiltLCAO updateHk 0.87001 11 0.079 15 % + LCAO_Hamilt cal_Hgamma 0.84265 11 0.077 14 % + Gint_interface cal_gint 1.0142 23 0.044 17 % + Gint_Gamma distri_vl 1.8917 6 0.32 32 % + LCAO_Deepks cal_projected_DM 4.1786 13 0.32 70 % + LCAO_gen_fixedH add_v_delta 1.7445 6 0.29 29 % + LCAO_DESCRIPTOR add_v_delta 1.7445 6 0.29 29 % + ElecStateLCAO psiToRho 0.61374 11 0.056 10 % + Charge mix_rho 0.90055 10 0.09 15 % + LOOP_ions force_stress 0.44131 1 0.44 7.4 % + Force_Stress_LCAO getForceStress 0.44128 1 0.44 7.4 % + Force_LCAO_gamma ftable_gamma 0.23203 1 0.23 3.9 % + Force_LCAO_gamma cal_fvl_dphi 0.19405 1 0.19 3.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:13:30 2022 + FINISH Time : Wed Sep 28 11:13:36 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/96/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..370603a79747e1ae9ec535a3e3c364d3b60dfd2d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.698633 0.261492 0.993311 +H 0.742731 0.225625 0.964646 +H 0.642988 0.244162 0.967024 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..1cf0fa5a3e0118996cc9c5d7f1711cfb9266dc28 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5586 2 + 2 -13.3564 2 + 3 -9.10073 2 + 4 -6.80445 2 + 5 1.54846 0 + 6 4.84091 0 + 7 11.0052 0 + 8 11.2463 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..87fb3280c952032cb0d98e16bcf42d1a954f6ea8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/running_scf.log @@ -0,0 +1,779 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:04:19 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.5617291265 7.32178508116 27.8127088035 0 0 0 0 + tauc_H1 20.7964813361 6.31749005215 27.0100803585 0 0 0 0 + tauc_H2 18.0036701106 6.83654181159 27.0766653988 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0732918782041 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0735683755136 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.0899287362279 (SEC) + + DONE : INIT CHARGE Time : 0.132041355423 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.375173 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 313 ; sender_size of each process is: +144 0 25 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000755 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00166 + + Density error is 0.218949119782 + + Energy Rydberg eV + E_KohnSham -34.1853794443 -465.115948734 + E_Harris -34.3857486464 -467.842111587 + E_Fermi -0.423371371775 -5.76026302622 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.00109638222073 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00140090315012 + + Density error is 0.0974322924781 + + Energy Rydberg eV + E_KohnSham -34.2777136149 -466.372219575 + E_Harris -34.2843091648 -466.461956635 + E_Fermi -0.229234859941 -3.11890027543 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.0010525907036 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00128462166364 + + Density error is 0.0622033290398 + + Energy Rydberg eV + E_KohnSham -34.2780321458 -466.376553409 + E_Harris -34.2822443612 -466.43386354 + E_Fermi -0.214717712635 -2.92138435336 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000995009392352 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010845960412 + + Density error is 0.00207786313205 + + Energy Rydberg eV + E_KohnSham -34.2780836168 -466.377253708 + E_Harris -34.2780860032 -466.377286178 + E_Fermi -0.178906690518 -2.43415040137 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000998449095454 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00108140947493 + + Density error is 0.000949882641867 + + Energy Rydberg eV + E_KohnSham -34.2779998394 -466.376113858 + E_Harris -34.2780026763 -466.376152457 + E_Fermi -0.177598400397 -2.41635020109 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000997063532755 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107982457442 + + Density error is 0.00011988597282 + + Energy Rydberg eV + E_KohnSham -34.2780561623 -466.376880171 + E_Harris -34.2780561927 -466.376880584 + E_Fermi -0.177944532048 -2.42105956379 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000997115828527 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010794728127 + + Density error is 5.11319130635e-05 + + Energy Rydberg eV + E_KohnSham -34.278037178 -466.376621877 + E_Harris -34.2780371923 -466.376622071 + E_Fermi -0.177781944188 -2.41884744247 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000997053327029 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107951693536 + + Density error is 1.27641842288e-05 + + Energy Rydberg eV + E_KohnSham -34.2780408335 -466.376671613 + E_Harris -34.2780408342 -466.376671622 + E_Fermi -0.177843726589 -2.41968803517 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.0009970598755 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107949016933 + + Density error is 1.15707168239e-06 + + Energy Rydberg eV + E_KohnSham -34.2780393408 -466.376651302 + E_Harris -34.2780393408 -466.376651302 + E_Fermi -0.177829574618 -2.41949548772 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000997059870393 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107948790222 + + Density error is 1.53391173461e-07 + + Energy Rydberg eV + E_KohnSham -34.2780395413 -466.376654031 + E_Harris -34.2780395413 -466.376654031 + E_Fermi -0.177828426569 -2.41947986771 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 313 + sender_size = 313 + last sender_buffer = 0.000997060115743 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00107948841417 + + Density error is 3.8342105891e-08 + + Energy Rydberg eV + E_KohnSham -34.278039563 -466.376654326 + E_Harris -34.278039563 -466.376654326 + E_band -8.05841622627 -109.640377533 + E_one_elec -69.8822375406 -950.796619541 + E_Hartree +36.3195362639 +494.152641907 + E_xc -8.25489489062 -112.313606903 + E_Ewald +7.66267188398 +104.255999527 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195906000333 -2.66543787691 + E_Fermi -0.177828557756 -2.41948165261 + + charge density convergence is achieved + final etot is -466.376654326 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5586 2.00000 + 2 -13.3564 2.00000 + 3 -9.10073 2.00000 + 4 -6.80445 2.00000 + 5 1.54846 0.00000 + 6 4.84091 0.00000 + 7 11.0052 0.00000 + 8 11.2463 0.00000 + + EFERMI = -2.419481652606313 eV + OUT.ABACUS/ final etot is -466.3766543259404 eV + correction force for each atom along direction 1 is -4.24835e-05 + correction force for each atom along direction 2 is -0.000137175 + correction force for each atom along direction 3 is -0.000138024 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.088698314 +1.3777831 +1.3890872 + H1 +1.2089303 -0.97786341 -0.78023733 + H2 -1.2976287 -0.39991971 -0.60884983 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3766543259404 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5829 11 0.60 1.0e+02% + Run_lcao lcao_line 6.5752 1 6.6 1.e+02% + Potential init_pot 0.24080 2 0.12 3.7% + PW_Basis recip2real 0.23549 16 0.015 3.6% + PW_Basis gathers_scatterp 0.10388 16 0.0065 1.6% + Potential v_of_rho 0.87112 13 0.067 13.% + XC_Functional v_xc 0.26797 14 0.019 4.1% + H_Hartree_pw v_hartree 0.56951 13 0.044 8.7% + PW_Basis real2recip 0.59190 38 0.016 9.0% + PW_Basis gatherp_scatters 0.22428 38 0.0059 3.4% + ORB_control set_orb_tables 0.89131 1 0.89 14.% + ORB_gen_tables gen_tables 0.89130 1 0.89 14.% + ORB_table_phi init_Table 0.37437 1 0.37 5.7% + ORB_table_phi cal_ST_Phi12_R 0.37007 126 0.0029 5.6% + ORB_table_beta init_Table_Beta 0.15373 1 0.15 2.3% + ORB_table_beta VNL_PhiBeta_R 0.15241 56 0.0027 2.3% + ORB_table_alpha init_Table_Alpha 0.20558 1 0.21 3.1% + ORB_table_alpha S_PhiAlpha_R 0.20393 66 0.0031 3.1% + LOOP_ions opt_ions 5.2403 1 5.2 80.% + ESolver_KS_LCAO Run 4.7182 1 4.7 72.% + HSolverLCAO solve 2.5647 11 0.23 39.% + HamiltLCAO updateHk 1.3147 11 0.12 20.% + LCAO_Hamilt cal_Hgamma 1.2913 11 0.12 20.% + Gint_interface cal_gint 1.8752 23 0.082 28.% + Gint_Gamma distri_vl_value 0.22930 11 0.021 3.5% + Gint_Gamma distri_vl 2.2663 6 0.38 34.% + LCAO_Deepks cal_projected_DM 5.0538 13 0.39 77.% + LCAO_gen_fixedH add_v_delta 2.1388 6 0.36 32.% + LCAO_DESCRIPTOR add_v_delta 2.1387 6 0.36 32.% + ElecStateLCAO psiToRho 1.2343 11 0.11 19.% + Charge mix_rho 0.75316 10 0.075 11.% + LOOP_ions force_stress 0.52188 1 0.52 7.9% + Force_Stress_LCAO getForceStress 0.52186 1 0.52 7.9% + Force_LCAO_gamma ftable_gamma 0.32466 1 0.32 4.9% + Force_LCAO_gamma cal_fvl_dphi 0.28079 1 0.28 4.3% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:04:19 2022 + Finish Time : Wed Sep 28 11:04:25 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..d5e50256de416c1d2da39d6948e6317bcac2e72e --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.012421 ima = 3.65995e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 2 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122997651414 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112085323544 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112492786041 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112790726568 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112711823752 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112756244001 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112750399851 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753599226 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753049654 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753003036 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112753004212 + charge after normalized = 7.99999999999999 + charge before normalized = 7.99999999999999 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/STRU new file mode 100644 index 0000000000000000000000000000000000000000..af1979083ac72022d7093bcd86c3a5c52ad4e933 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.438270873450 7.321785081153 -0.187291196512 0 0 0 +H +0.0 +2 +-7.203518663951 6.317490052128 -0.989919641455 0 0 0 +-9.996329889383 6.836541811599 -0.923334601183 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/conv new file mode 100644 index 0000000000000000000000000000000000000000..ec03cfac369bdb2ac1d9fb5c1467fbc0adffc4bc --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/conv @@ -0,0 +1 @@ +97 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..4d59b42dc341426eb04a6c76aa46d2b3fcd11a6f --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.74825759 0.01283015063 1.298445145 1.382606472 1.470670295 0.008562843942 0.01949387193 0.03899912725 +1.402415045e-18 0.00121737495 0.002726823658 0.01319295827 0.04765273666 -1.219727444e-19 2.26335743e-06 6.374564264e-06 +0.001678695326 0.005902235097 + +H atom_index 1 n_descriptor 18 +1.284508233 0.03292049495 0.1215204658 0.1667976518 0.3311888831 0.02396175986 0.0303004254 0.03639689434 +-2.589272779e-17 5.278164037e-05 0.1085030582 0.1202070385 0.1433789656 -1.027451523e-17 2.313570102e-06 0.01331671216 +0.02804435178 0.0322358369 + +H atom_index 2 n_descriptor 18 +1.278458682 0.0331145098 0.1192120026 0.1637323883 0.3294727725 0.02368828283 0.02995558551 0.03648496722 +-3.072117706e-17 5.219776369e-05 0.1082739362 0.1187091445 0.1407782926 -6.565942755e-18 2.651362432e-06 0.01322779528 +0.02784870984 0.03200538072 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..61da5876e0fcd237af16ec246e3998f7556a9161 Binary files /dev/null and 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a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/f_tot.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/f_tot.npy new file mode 100644 index 0000000000000000000000000000000000000000..0455ed7c3012378f913d665da55b7aec6d74031b Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/f_tot.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/grad_vx.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/grad_vx.npy new file mode 100644 index 0000000000000000000000000000000000000000..71d45c770cad2f35188036ab35ea1054a3f73159 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/grad_vx.npy differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/log.scf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/log.scf new file mode 100644 index 0000000000000000000000000000000000000000..eb0faaff8218bdc5782d1b3799d4a918cc164c24 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:04:19 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733068 SEC) : SETUP UNITCELL + DONE(0.0735775 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.089942 SEC) : INIT PLANEWAVE + DONE(0.132147 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.375218 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651159e+02 0.000000e+00 2.189e-01 5.047e-01 + GE2 -4.663722e+02 -1.256271e+00 9.743e-02 4.792e-01 + GE3 -4.663766e+02 -4.333834e-03 6.220e-02 5.385e-01 + GE4 -4.663773e+02 -7.002989e-04 2.078e-03 4.170e-01 + GE5 -4.663761e+02 1.139850e-03 9.499e-04 4.167e-01 + GE6 -4.663769e+02 -7.663128e-04 1.199e-04 4.002e-01 + GE7 -4.663766e+02 2.582944e-04 5.113e-05 4.004e-01 + GE8 -4.663767e+02 -4.973586e-05 1.276e-05 3.911e-01 + GE9 -4.663767e+02 2.031018e-05 1.157e-06 3.936e-01 + GE10 -4.663767e+02 -2.728427e-06 1.534e-07 3.977e-01 + GE11 -4.663767e+02 -2.950501e-07 3.834e-08 3.262e-01 +E_delta_band = -7.27907206e-02 Ry = -9.90368562e-01 eV +E_delta_NN= -1.95906000e-01 Ry = -2.66543788e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.5829 11 0.6 1e+02 % + Run_lcao lcao_line 6.5752 1 6.6 1e+02 % + Potential init_pot 0.2408 2 0.12 3.7 % + PW_Basis recip2real 0.23549 16 0.015 3.6 % + PW_Basis gathers_scatterp 0.10388 16 0.0065 1.6 % + Potential v_of_rho 0.87112 13 0.067 13 % + XC_Functional v_xc 0.26797 14 0.019 4.1 % + H_Hartree_pw v_hartree 0.56951 13 0.044 8.7 % + PW_Basis real2recip 0.5919 38 0.016 9 % + PW_Basis gatherp_scatters 0.22428 38 0.0059 3.4 % + ORB_control set_orb_tables 0.89131 1 0.89 14 % + ORB_gen_tables gen_tables 0.8913 1 0.89 14 % + ORB_table_phi init_Table 0.37437 1 0.37 5.7 % + ORB_table_phi cal_ST_Phi12_R 0.37007 126 0.0029 5.6 % + ORB_table_beta init_Table_Beta 0.15373 1 0.15 2.3 % + ORB_table_beta VNL_PhiBeta_R 0.15241 56 0.0027 2.3 % + ORB_table_alpha init_Table_Alpha 0.20558 1 0.21 3.1 % + ORB_table_alpha S_PhiAlpha_R 0.20393 66 0.0031 3.1 % + LOOP_ions opt_ions 5.2403 1 5.2 80 % + ESolver_KS_LCAO Run 4.7182 1 4.7 72 % + HSolverLCAO solve 2.5647 11 0.23 39 % + HamiltLCAO updateHk 1.3147 11 0.12 20 % + LCAO_Hamilt cal_Hgamma 1.2913 11 0.12 20 % + Gint_interface cal_gint 1.8752 23 0.082 28 % + Gint_Gamma distri_vl_value 0.2293 11 0.021 3.5 % + Gint_Gamma distri_vl 2.2663 6 0.38 34 % + LCAO_Deepks cal_projected_DM 5.0538 13 0.39 77 % + LCAO_gen_fixedH add_v_delta 2.1388 6 0.36 32 % + LCAO_DESCRIPTOR add_v_delta 2.1387 6 0.36 32 % + ElecStateLCAO psiToRho 1.2343 11 0.11 19 % + Charge mix_rho 0.75316 10 0.075 11 % + LOOP_ions force_stress 0.52188 1 0.52 7.9 % + Force_Stress_LCAO getForceStress 0.52186 1 0.52 7.9 % + Force_LCAO_gamma ftable_gamma 0.32466 1 0.32 4.9 % + Force_LCAO_gamma cal_fvl_dphi 0.28079 1 0.28 4.3 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:04:19 2022 + FINISH Time : Wed Sep 28 11:04:25 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/97/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..07fa131195b4daecab7ed48930f21fac12fd26af --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.709671 0.247125 0.994444 +H 0.709758 0.182164 0.970457 +H 0.645789 0.261782 0.00253071 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..0cf8d934719c4f32a55e507aa68401575d6df904 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9375 2 + 2 -12.7671 2 + 3 -9.03905 2 + 4 -6.66463 2 + 5 0.962279 0 + 6 3.92636 0 + 7 11.158 0 + 8 11.3994 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..984ad7e428a51781153c41a30deb4239f3c22ed2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/running_scf.log @@ -0,0 +1,800 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:09:19 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.8707825773 6.91950720826 27.844444436 0 0 0 0 + tauc_H1 19.873210769 5.10058367857 27.1727899476 0 0 0 0 + tauc_H2 18.0820796775 7.32988942674 0.0708599946083 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0879407529748 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0891245359172 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.107151455022 (SEC) + + DONE : INIT CHARGE Time : 0.155740317691 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.436051 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 288 ; sender_size of each process is: +144 0 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000639 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00177 + + Density error is 0.211136669143 + + Energy Rydberg eV + E_KohnSham -34.1897654492 -465.175623392 + E_Harris -34.3733596575 -467.673550745 + E_Fermi -0.384823640159 -5.23579423126 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00088541608355 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00138257599096 + + Density error is 0.0989245238273 + + Energy Rydberg eV + E_KohnSham -34.2770733468 -466.36350828 + E_Harris -34.2842162899 -466.460693007 + E_Fermi -0.195904716413 -2.66542040829 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000847595416293 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00127466724458 + + Density error is 0.063859528237 + + Energy Rydberg eV + E_KohnSham -34.2774324819 -466.368394564 + E_Harris -34.2819930187 -466.43044385 + E_Fermi -0.189292206916 -2.57545260105 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000798194378644 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106914677689 + + Density error is 0.00201870178905 + + Energy Rydberg eV + E_KohnSham -34.2773319633 -466.367026939 + E_Harris -34.277335185 -466.367070772 + E_Fermi -0.154214515766 -2.09819612873 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.00079804719 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106861467572 + + Density error is 0.000875799453144 + + Energy Rydberg eV + E_KohnSham -34.2773095279 -466.366721689 + E_Harris -34.2773099934 -466.366728023 + E_Fermi -0.154151012205 -2.09733211846 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000797576739654 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106567610541 + + Density error is 0.000195708757171 + + Energy Rydberg eV + E_KohnSham -34.2773171013 -466.36682473 + E_Harris -34.2773170866 -466.366824531 + E_Fermi -0.153703240542 -2.09123987244 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000797677862274 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106549709496 + + Density error is 2.65869931113e-05 + + Energy Rydberg eV + E_KohnSham -34.2773160886 -466.366810952 + E_Harris -34.2773160893 -466.366810961 + E_Fermi -0.153676325166 -2.09087366996 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000797661314418 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106548702508 + + Density error is 8.81823278357e-06 + + Energy Rydberg eV + E_KohnSham -34.2773176794 -466.366832596 + E_Harris -34.2773176797 -466.3668326 + E_Fermi -0.153684069529 -2.09097903743 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000797661621027 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106547408998 + + Density error is 2.53784823637e-06 + + Energy Rydberg eV + E_KohnSham -34.2773170369 -466.366823855 + E_Harris -34.2773170369 -466.366823855 + E_Fermi -0.153675584882 -2.09086359788 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000797655796969 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.0010654632424 + + Density error is 5.78180200152e-07 + + Energy Rydberg eV + E_KohnSham -34.2773172325 -466.366826515 + E_Harris -34.2773172325 -466.366826515 + E_Fermi -0.153674693226 -2.09085146627 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000797656506782 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106546294869 + + Density error is 2.2075424088e-07 + + Energy Rydberg eV + E_KohnSham -34.2773172015 -466.366826093 + E_Harris -34.2773172015 -466.366826093 + E_Fermi -0.153674409776 -2.09084760974 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 288 + sender_size = 288 + last sender_buffer = 0.000797656734834 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00106546243867 + + Density error is 1.1063990805e-08 + + Energy Rydberg eV + E_KohnSham -34.2773172045 -466.366826135 + E_Harris -34.2773172045 -466.366826135 + E_band -7.85086111728 -106.816445402 + E_one_elec -68.5664690511 -932.894670835 + E_Hartree +35.6996466103 +485.718610487 + E_xc -8.15517907058 -110.95690357 + E_Ewald +6.87047119361 +93.4775561779 + E_demet -2.39686942064e-57 -3.26110814826e-56 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.193540795527 -2.63325761463 + E_Fermi -0.153674196465 -2.0908447075 + + charge density convergence is achieved + final etot is -466.366826135 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -24.9375 2.00000 + 2 -12.7671 2.00000 + 3 -9.03905 2.00000 + 4 -6.66463 2.00000 + 5 0.962279 0.00000 + 6 3.92636 0.00000 + 7 11.1580 0.00000 + 8 11.3994 0.00000 + + EFERMI = -2.090844707495978 eV + OUT.ABACUS/ final etot is -466.3668261351727 eV + correction force for each atom along direction 1 is -3.37346e-05 + correction force for each atom along direction 2 is -4.34560e-05 + correction force for each atom along direction 3 is -0.000158759 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.031794763 -1.8520364 -0.69238198 + H1 -0.11436118 +1.9842059 +0.74092923 + H2 +0.082566422 -0.13216950 -0.048547252 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3668261351727 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4763 11 0.59 1.0e+02% + Run_lcao lcao_line 6.4663 1 6.5 1.e+02% + Potential init_pot 0.28554 2 0.14 4.4% + PW_Basis recip2real 0.28331 17 0.017 4.4% + PW_Basis gathers_scatterp 0.12185 17 0.0072 1.9% + Potential v_of_rho 0.92719 14 0.066 14.% + XC_Functional v_xc 0.25072 15 0.017 3.9% + H_Hartree_pw v_hartree 0.63498 14 0.045 9.8% + PW_Basis real2recip 0.60015 41 0.015 9.3% + PW_Basis gatherp_scatters 0.23440 41 0.0057 3.6% + ORB_control set_orb_tables 1.0946 1 1.1 17.% + ORB_gen_tables gen_tables 1.0946 1 1.1 17.% + ORB_table_phi init_Table 0.48335 1 0.48 7.5% + ORB_table_phi cal_ST_Phi12_R 0.47841 126 0.0038 7.4% + ORB_table_beta init_Table_Beta 0.18184 1 0.18 2.8% + ORB_table_beta VNL_PhiBeta_R 0.18042 56 0.0032 2.8% + ORB_table_alpha init_Table_Alpha 0.25169 1 0.25 3.9% + ORB_table_alpha S_PhiAlpha_R 0.24981 66 0.0038 3.9% + LOOP_ions opt_ions 4.8589 1 4.9 75.% + ESolver_KS_LCAO Run 4.3366 1 4.3 67.% + HSolverLCAO solve 2.2129 12 0.18 34.% + HamiltLCAO updateHk 1.1629 12 0.097 18.% + LCAO_Hamilt cal_Hgamma 1.1265 12 0.094 17.% + Gint_interface cal_gint 1.8879 25 0.076 29.% + Gint_Gamma distri_vl 2.2555 6 0.38 35.% + LCAO_Deepks cal_projected_DM 4.6904 14 0.34 72.% + LCAO_gen_fixedH add_v_delta 2.1251 6 0.35 33.% + LCAO_DESCRIPTOR add_v_delta 2.1250 6 0.35 33.% + ElecStateLCAO psiToRho 1.0348 12 0.086 16.% + Charge mix_rho 0.71650 11 0.065 11.% + LOOP_ions force_stress 0.52212 1 0.52 8.1% + Force_Stress_LCAO getForceStress 0.52209 1 0.52 8.1% + Force_LCAO_gamma ftable_gamma 0.31068 1 0.31 4.8% + Force_LCAO_gamma cal_fvl_dphi 0.29055 1 0.29 4.5% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:09:19 2022 + Finish Time : Wed Sep 28 11:09:26 2022 + Total Time : 0 h 0 mins 7 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..c2ef03100ed90889d35327bf74f9286d4c934517 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/OUT.ABACUS/warning.log @@ -0,0 +1,78 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123628 ima = 3.65663e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 0 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00123622364732 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112309016202 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113067082242 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113245731059 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113240259173 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113244437653 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113242434452 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113243585661 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.0011324313084 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113243194661 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113243174796 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00113243163335 + charge after normalized = 8.00000000000001 + charge before normalized = 8.00000000000001 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/STRU new file mode 100644 index 0000000000000000000000000000000000000000..7247f9e54a57f3083910e365bc832d88b0a7bd4b --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.129217422687 6.919507208245 -0.155555563999 0 0 0 +H +0.0 +2 +-8.126789231009 5.100583678589 -0.827210052449 0 0 0 +-9.917920322524 7.329889426751 0.070859994584 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/conv new file mode 100644 index 0000000000000000000000000000000000000000..65be9d2ff4ecb9617667d8dc7a837254052b14c8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/conv @@ -0,0 +1 @@ +98 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..e5de7c9043b177182d1d1fd78a6c8a42113ac4a3 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.749477704 0.01236101833 1.24067133 1.340788064 1.467872608 0.008303947402 0.01813006044 0.0390853869 +6.221159213e-18 0.0008966483586 0.002356319974 0.0112907057 0.04105061483 3.349709245e-20 1.505003545e-06 4.783638563e-06 +0.00161695095 0.005786244438 + +H atom_index 1 n_descriptor 18 +1.162359876 0.03699726497 0.08059276212 0.1140395841 0.2900465085 0.01786026017 0.0232604775 0.04090732033 +-4.050855431e-17 3.193893949e-05 0.07627457952 0.09696652996 0.1117228439 -6.42912781e-18 6.715152727e-06 0.01529784489 +0.0219458252 0.02623249846 + +H atom_index 2 n_descriptor 18 +1.233127533 0.03482175843 0.1016085803 0.1427812331 0.3165689501 0.02108509467 0.02739008127 0.03807329748 +-8.963580622e-18 3.758604859e-05 0.09434257592 0.1148636887 0.1222809325 2.747268572e-18 4.676132322e-06 0.01330423131 +0.02487154575 0.02997900056 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..fb07e6d0a658762ba9de4c820e91aab37bd93acb Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/log.scf @@ -0,0 +1,102 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:09:19 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0879659 SEC) : SETUP UNITCELL + DONE(0.0891405 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.107168 SEC) : INIT PLANEWAVE + DONE(0.15587 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.436124 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651756e+02 0.000000e+00 2.111e-01 4.765e-01 + GE2 -4.663635e+02 -1.187885e+00 9.892e-02 4.053e-01 + GE3 -4.663684e+02 -4.886284e-03 6.386e-02 4.571e-01 + GE4 -4.663670e+02 1.367625e-03 2.019e-03 3.516e-01 + GE5 -4.663667e+02 3.052497e-04 8.758e-04 3.514e-01 + GE6 -4.663668e+02 -1.030413e-04 1.957e-04 3.443e-01 + GE7 -4.663668e+02 1.377809e-05 2.659e-05 3.292e-01 + GE8 -4.663668e+02 -2.164328e-05 8.818e-06 3.256e-01 + GE9 -4.663668e+02 8.740756e-06 2.538e-06 3.228e-01 + GE10 -4.663668e+02 -2.660523e-06 5.782e-07 3.231e-01 + GE11 -4.663668e+02 4.222039e-07 2.208e-07 3.221e-01 + GE12 -4.663668e+02 -4.195133e-08 1.106e-08 2.661e-01 +E_delta_band = -6.77539087e-02 Ry = -9.21839220e-01 eV +E_delta_NN= -1.93540796e-01 Ry = -2.63325761e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.4763 11 0.59 1e+02 % + Run_lcao lcao_line 6.4663 1 6.5 1e+02 % + Potential init_pot 0.28554 2 0.14 4.4 % + PW_Basis recip2real 0.28331 17 0.017 4.4 % + PW_Basis gathers_scatterp 0.12185 17 0.0072 1.9 % + Potential v_of_rho 0.92719 14 0.066 14 % + XC_Functional v_xc 0.25072 15 0.017 3.9 % + H_Hartree_pw v_hartree 0.63498 14 0.045 9.8 % + PW_Basis real2recip 0.60015 41 0.015 9.3 % + PW_Basis gatherp_scatters 0.2344 41 0.0057 3.6 % + ORB_control set_orb_tables 1.0946 1 1.1 17 % + ORB_gen_tables gen_tables 1.0946 1 1.1 17 % + ORB_table_phi init_Table 0.48335 1 0.48 7.5 % + ORB_table_phi cal_ST_Phi12_R 0.47841 126 0.0038 7.4 % + ORB_table_beta init_Table_Beta 0.18184 1 0.18 2.8 % + ORB_table_beta VNL_PhiBeta_R 0.18042 56 0.0032 2.8 % + ORB_table_alpha init_Table_Alpha 0.25169 1 0.25 3.9 % + ORB_table_alpha S_PhiAlpha_R 0.24981 66 0.0038 3.9 % + LOOP_ions opt_ions 4.8589 1 4.9 75 % + ESolver_KS_LCAO Run 4.3366 1 4.3 67 % + HSolverLCAO solve 2.2129 12 0.18 34 % + HamiltLCAO updateHk 1.1629 12 0.097 18 % + LCAO_Hamilt cal_Hgamma 1.1265 12 0.094 17 % + Gint_interface cal_gint 1.8879 25 0.076 29 % + Gint_Gamma distri_vl 2.2555 6 0.38 35 % + LCAO_Deepks cal_projected_DM 4.6904 14 0.34 72 % + LCAO_gen_fixedH add_v_delta 2.1251 6 0.35 33 % + LCAO_DESCRIPTOR add_v_delta 2.125 6 0.35 33 % + ElecStateLCAO psiToRho 1.0348 12 0.086 16 % + Charge mix_rho 0.7165 11 0.065 11 % + LOOP_ions force_stress 0.52212 1 0.52 8.1 % + Force_Stress_LCAO getForceStress 0.52209 1 0.52 8.1 % + Force_LCAO_gamma ftable_gamma 0.31068 1 0.31 4.8 % + Force_LCAO_gamma cal_fvl_dphi 0.29055 1 0.29 4.5 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:09:19 2022 + FINISH Time : Wed Sep 28 11:09:26 2022 + TOTAL Time : 7 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/98/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..ac6179dae82b8aedfc7a90689c682df27e3781c2 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional lda +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 1 +deepks_bandgap 0 +deepks_model ../../../model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..41f2b7048660b484e07862cb6eb86361b0dd0e49 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/INPUT @@ -0,0 +1,257 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional lda #exchange correlation functional +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #turn symmetry on or off +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 1000 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 1 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ../../../model.ptg #file dir of traced pytorch model: 'model.ptg +deepks_descriptor_lmax2 #lmax used in generating descriptor +deepks_descriptor_rcut0 #rcut used in generating descriptor +deepks_descriptor_ecut0 #ecut used in generating descriptor + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +dft_functional lda #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.compensating_charge) +comp_chg 0 # add compensating charge +comp_q 0 # total charge of compensating charge +comp_l 1 # total length of compensating charge +comp_center 0 # center of compensating charge on dim +comp_dim 2 # dimension of compensating charge(x, y or z) diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..3d87faf7eee4030f02c17b4e8d288af438c577ba --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.701776 0.233878 0.999332 +H 0.693523 0.173495 0.9835 +H 0.683064 0.238369 0.0609353 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..28e31cf79b767800e36fad6379a54ced8394adaa --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -25.5649 2 + 2 -13.374 2 + 3 -9.09054 2 + 4 -6.80528 2 + 5 1.54895 0 + 6 4.85696 0 + 7 11.0031 0 + 8 11.2408 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..31d3918ba5d86fc5e100b88897566afed01f57de --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/running_scf.log @@ -0,0 +1,778 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Sep 28 11:03:17 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 19.649734758 6.54858151614 27.9812970434 0 0 0 0 + tauc_H1 19.4186489741 4.85784904176 27.5379976423 0 0 0 0 + tauc_H2 19.1257866424 6.67433598766 1.70618941609 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../O_gga_6au_60Ry_2s2p1d.orb + orbital file: ../../../H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ../../../H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3117 262043 + 3 3118 262044 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + number of |g| = 3307 + max |g| = 5.06505102041 + min |g| = 0.00127551020408 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0873866528836 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0877770442243 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + number of plane waves = 131155 + number of sticks = 3125 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 782 32792 + 2 781 32787 + 3 781 32787 + 4 781 32789 + --------------- sum ------------------- + 4 3125 131155 + DONE : INIT PLANEWAVE Time : 0.105818331914 (SEC) + + DONE : INIT CHARGE Time : 0.148726521085 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 0.43256 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 144 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 297 ; sender_size of each process is: +144 9 0 144 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000507 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000982 + + Density error is 0.218107245466 + + Energy Rydberg eV + E_KohnSham -34.1865498267 -465.131872604 + E_Harris -34.3852402505 -467.835194505 + E_Fermi -0.423214118054 -5.75812347958 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000809658475603 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00129003584905 + + Density error is 0.0972297422823 + + Energy Rydberg eV + E_KohnSham -34.2771077893 -466.363976894 + E_Harris -34.2836734996 -466.453307967 + E_Fermi -0.230690269946 -3.13870214442 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000782780702745 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00123844380449 + + Density error is 0.0618929540125 + + Energy Rydberg eV + E_KohnSham -34.2772741548 -466.366240414 + E_Harris -34.2814352867 -466.422855518 + E_Fermi -0.215036661615 -2.92572387686 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000749725497013 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116637254188 + + Density error is 0.00208471752391 + + Energy Rydberg eV + E_KohnSham -34.27734223 -466.367166624 + E_Harris -34.2773447848 -466.367201383 + E_Fermi -0.179409957782 -2.44099770378 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000752151136339 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00117004722118 + + Density error is 0.000908149935981 + + Energy Rydberg eV + E_KohnSham -34.2772627465 -466.366085195 + E_Harris -34.2772659497 -466.366128777 + E_Fermi -0.177924793672 -2.42079100941 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000751106327512 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116844954458 + + Density error is 0.000120553096245 + + Energy Rydberg eV + E_KohnSham -34.2773206813 -466.366873439 + E_Harris -34.2773207104 -466.366873835 + E_Fermi -0.178374898935 -2.42691500568 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000751175763322 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116846051705 + + Density error is 5.05627217464e-05 + + Energy Rydberg eV + E_KohnSham -34.2773011212 -466.36660731 + E_Harris -34.277301135 -466.366607498 + E_Fermi -0.17821003013 -2.42467185052 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000751111950631 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116838254425 + + Density error is 1.14321417378e-05 + + Energy Rydberg eV + E_KohnSham -34.2773047401 -466.366656548 + E_Harris -34.2773047407 -466.366656556 + E_Fermi -0.178269402412 -2.42547965186 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000751119526134 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116838693829 + + Density error is 1.12440957627e-06 + + Energy Rydberg eV + E_KohnSham -34.2773032907 -466.366636828 + E_Harris -34.2773032907 -466.366636828 + E_Fermi -0.178256762668 -2.42530767932 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000751121094821 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116838729438 + + Density error is 1.38267683567e-07 + + Energy Rydberg eV + E_KohnSham -34.2773034703 -466.366639271 + E_Harris -34.2773034703 -466.366639271 + E_Fermi -0.178255689363 -2.42529307625 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 297 + sender_size = 297 + last sender_buffer = 0.000751121159783 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00116838750695 + + Density error is 4.6215323334e-08 + + Energy Rydberg eV + E_KohnSham -34.2773034912 -466.366639555 + E_Harris -34.2773034912 -466.366639555 + E_band -8.06056745095 -109.669646446 + E_one_elec -69.899627842 -951.033226731 + E_Hartree +36.3281258376 +494.269509053 + E_xc -8.25636253978 -112.333575295 + E_Ewald +7.67364905617 +104.405351616 + E_demet -1.24924800815e-88 -1.6996891126e-87 + E_descf +0 +0 + E_efield +0 +0 + E_exx +0 +0 + E_DeePKS -0.195944797456 -2.66596573886 + E_Fermi -0.178255832361 -2.42529502184 + + charge density convergence is achieved + final etot is -466.366639555 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (32792 pws) + 1 -25.5649 2.00000 + 2 -13.3740 2.00000 + 3 -9.09054 2.00000 + 4 -6.80528 2.00000 + 5 1.54895 0.00000 + 6 4.85696 0.00000 + 7 11.0031 0.00000 + 8 11.2408 0.00000 + + EFERMI = -2.425295021844795 eV + OUT.ABACUS/ final etot is -466.3666395550428 eV + correction force for each atom along direction 1 is 0.000115108 + correction force for each atom along direction 2 is -3.07746e-05 + correction force for each atom along direction 3 is 8.24066e-05 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 +0.60545353 +2.2552702 -0.31459297 + H1 -0.32297837 -2.3089118 -0.59378281 + H2 -0.28247516 +0.053641598 +0.90837578 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.3666395550428 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1525 11 0.56 1.0e+02% + Run_lcao lcao_line 6.1435 1 6.1 1.e+02% + Potential init_pot 0.28537 2 0.14 4.6% + PW_Basis recip2real 0.27419 16 0.017 4.5% + PW_Basis gathers_scatterp 0.12632 16 0.0079 2.1% + Potential v_of_rho 0.96571 13 0.074 16.% + XC_Functional v_xc 0.28103 14 0.020 4.6% + H_Hartree_pw v_hartree 0.63935 13 0.049 10.% + PW_Basis real2recip 0.68324 38 0.018 11.% + PW_Basis gatherp_scatters 0.26413 38 0.0070 4.3% + ORB_control set_orb_tables 1.0979 1 1.1 18.% + ORB_gen_tables gen_tables 1.0979 1 1.1 18.% + ORB_table_phi init_Table 0.47677 1 0.48 7.7% + ORB_table_phi cal_ST_Phi12_R 0.47144 126 0.0037 7.7% + ORB_table_beta init_Table_Beta 0.18425 1 0.18 3.0% + ORB_table_beta VNL_PhiBeta_R 0.18267 56 0.0033 3.0% + ORB_table_alpha init_Table_Alpha 0.24983 1 0.25 4.1% + ORB_table_alpha S_PhiAlpha_R 0.24784 66 0.0038 4.0% + LOOP_ions opt_ions 4.5371 1 4.5 74.% + ESolver_KS_LCAO Run 4.0816 1 4.1 66.% + HSolverLCAO solve 1.6676 11 0.15 27.% + HamiltLCAO updateHk 1.0226 11 0.093 17.% + LCAO_Hamilt cal_Hgamma 0.99517 11 0.090 16.% + Gint_interface cal_gint 1.3730 23 0.060 22.% + Gint_Gamma distri_vl 1.9905 6 0.33 32.% + LCAO_Deepks cal_projected_DM 4.3897 13 0.34 71.% + LCAO_gen_fixedH add_v_delta 1.8429 6 0.31 30.% + LCAO_DESCRIPTOR add_v_delta 1.8429 6 0.31 30.% + ElecStateLCAO psiToRho 0.61722 11 0.056 10.% + Charge mix_rho 0.90338 10 0.090 15.% + LOOP_ions force_stress 0.45531 1 0.46 7.4% + Force_Stress_LCAO getForceStress 0.45527 1 0.46 7.4% + Force_LCAO_gamma ftable_gamma 0.24120 1 0.24 3.9% + Force_LCAO_gamma cal_fvl_dphi 0.23301 1 0.23 3.8% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1032. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 32.00 + Charge_Pulay dRrho 28.00 + Charge_Pulay drho 28.00 + PW_Basis struc_fac 7.997 + Charge rho 4.000 + Charge rho_save 4.000 + Charge rho_core 4.000 + Potential vltot 4.000 + Potential vr 4.000 + Potential vr_eff 4.000 + Potential vr_eff1 4.000 + Potential vnew 4.000 + Charge_Pulay rho_save2 4.000 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + Charge rhog 1.999 + Charge rhog_save 1.999 + Charge kin_r 1.999 + Charge kin_r_save 1.999 + Charge rhog_core 1.999 + ---------------------------------------------------------- + + Start Time : Wed Sep 28 11:03:17 2022 + Finish Time : Wed Sep 28 11:03:23 2022 + Total Time : 0 h 0 mins 6 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..6c8b761aed1613f817d6cecad3d9e29961f4f01d --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/OUT.ABACUS/warning.log @@ -0,0 +1,74 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123815 ima = 3.67971e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Grid_Technique::init_atoms_on_grid warning : No atom on this sub-FFT-mesh. + Processor Atom + 1 3 + 2 1 + 3 0 + 4 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00122885522538 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112289735504 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112632312694 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112919755129 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112839554184 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112884838739 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112879114329 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112882219087 + charge after normalized = 8.00000000000001 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112881735345 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112881691578 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112881694385 + charge after normalized = 8 + charge before normalized = 8 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/STRU b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/STRU new file mode 100644 index 0000000000000000000000000000000000000000..584324fe928b2f4f4d7e4ea9da8b0c5cd9936cf7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/STRU @@ -0,0 +1,32 @@ +ATOMIC_SPECIES +O 1.00 ../../../O_ONCV_PBE-1.0.upf +H 1.00 ../../../H_ONCV_PBE-1.0.upf + + +LATTICE_CONSTANT +1 + +LATTICE_VECTORS +28 0 0 +0 28 0 +0 0 28 + +ATOMIC_POSITIONS +Cartesian + +O +0.0 +1 +-8.350265241993 6.548581516153 -0.018702956582 0 0 0 +H +0.0 +2 +-8.581351025879 4.857849041781 -0.462002357726 0 0 0 +-8.874213357631 6.674335987673 1.706189416075 0 0 0 + +NUMERICAL_ORBITAL +../../../O_gga_6au_60Ry_2s2p1d.orb +../../../H_gga_6au_60Ry_2s1p.orb + +NUMERICAL_DESCRIPTOR +../../../jle.orb diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/conv b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/conv new file mode 100644 index 0000000000000000000000000000000000000000..0ef562f788814ea34d6eb1bab63d0977b8a3b868 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/conv @@ -0,0 +1 @@ +99 charge density convergence is achieved diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/descriptor.dat b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/descriptor.dat new file mode 100644 index 0000000000000000000000000000000000000000..56d1563f01da61e4f1d4530fe964ee6cd9a4b4cd --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/descriptor.dat @@ -0,0 +1,15 @@ +O atom_index 1 n_descriptor 18 +1.748108217 0.01282043365 1.298350906 1.384363759 1.470722626 0.008552708453 0.01959154528 0.03899940128 +1.30568497e-19 0.001225386383 0.002723235767 0.01318534832 0.04766030738 -1.900530175e-19 2.237088432e-06 6.332936177e-06 +0.001680056135 0.005879855012 + +H atom_index 1 n_descriptor 18 +1.299646498 0.03243652352 0.1274627492 0.1747422067 0.3353387249 0.02461388928 0.03115880371 0.0362669835 +-1.443869391e-17 5.40716268e-05 0.1084080335 0.12461696 0.1500817086 8.249168769e-19 1.546485548e-06 0.01366317616 +0.02850218411 0.03277371958 + +H atom_index 2 n_descriptor 18 +1.264851872 0.03354183995 0.1141527584 0.1570670081 0.3255265193 0.02304850645 0.02917959076 0.0367388266 +-1.539331993e-17 5.074204235e-05 0.1069435841 0.1161510145 0.1350997928 -5.982889371e-18 3.45505247e-06 0.01311794661 +0.02738367336 0.03145971919 + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/dm_eig.npy b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/dm_eig.npy new file mode 100644 index 0000000000000000000000000000000000000000..0436284979b61dc0e5dbf55fe29936bafadc0ef4 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/dm_eig.npy differ diff --git 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/log.scf @@ -0,0 +1,101 @@ + ********************************************************* + * * + * WELCOME TO ABACUS * + * * + * 'Atomic-orbital Based Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:03:17 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0874095 SEC) : SETUP UNITCELL + DONE(0.0877921 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.105838 SEC) : INIT PLANEWAVE + DONE(0.148863 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.432628 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651319e+02 0.000000e+00 2.181e-01 4.813e-01 + GE2 -4.663640e+02 -1.232104e+00 9.723e-02 4.242e-01 + GE3 -4.663662e+02 -2.263520e-03 6.189e-02 4.956e-01 + GE4 -4.663672e+02 -9.262107e-04 2.085e-03 3.515e-01 + GE5 -4.663661e+02 1.081429e-03 9.081e-04 3.527e-01 + GE6 -4.663669e+02 -7.882436e-04 1.206e-04 3.308e-01 + GE7 -4.663666e+02 2.661283e-04 5.056e-05 3.340e-01 + GE8 -4.663667e+02 -4.923800e-05 1.143e-05 3.312e-01 + GE9 -4.663666e+02 1.972062e-05 1.124e-06 3.305e-01 + GE10 -4.663666e+02 -2.443586e-06 1.383e-07 3.295e-01 + GE11 -4.663666e+02 -2.837282e-07 4.622e-08 2.580e-01 +E_delta_band = -7.28567943e-02 Ry = -9.91267540e-01 eV +E_delta_NN= -1.95944797e-01 Ry = -2.66596574e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.1525 11 0.56 1e+02 % + Run_lcao lcao_line 6.1435 1 6.1 1e+02 % + Potential init_pot 0.28537 2 0.14 4.6 % + PW_Basis recip2real 0.27419 16 0.017 4.5 % + PW_Basis gathers_scatterp 0.12632 16 0.0079 2.1 % + Potential v_of_rho 0.96571 13 0.074 16 % + XC_Functional v_xc 0.28103 14 0.02 4.6 % + H_Hartree_pw v_hartree 0.63935 13 0.049 10 % + PW_Basis real2recip 0.68324 38 0.018 11 % + PW_Basis gatherp_scatters 0.26413 38 0.007 4.3 % + ORB_control set_orb_tables 1.0979 1 1.1 18 % + ORB_gen_tables gen_tables 1.0979 1 1.1 18 % + ORB_table_phi init_Table 0.47677 1 0.48 7.7 % + ORB_table_phi cal_ST_Phi12_R 0.47144 126 0.0037 7.7 % + ORB_table_beta init_Table_Beta 0.18425 1 0.18 3 % + ORB_table_beta VNL_PhiBeta_R 0.18267 56 0.0033 3 % + ORB_table_alpha init_Table_Alpha 0.24983 1 0.25 4.1 % + ORB_table_alpha S_PhiAlpha_R 0.24784 66 0.0038 4 % + LOOP_ions opt_ions 4.5371 1 4.5 74 % + ESolver_KS_LCAO Run 4.0816 1 4.1 66 % + HSolverLCAO solve 1.6676 11 0.15 27 % + HamiltLCAO updateHk 1.0226 11 0.093 17 % + LCAO_Hamilt cal_Hgamma 0.99517 11 0.09 16 % + Gint_interface cal_gint 1.373 23 0.06 22 % + Gint_Gamma distri_vl 1.9905 6 0.33 32 % + LCAO_Deepks cal_projected_DM 4.3897 13 0.34 71 % + LCAO_gen_fixedH add_v_delta 1.8429 6 0.31 30 % + LCAO_DESCRIPTOR add_v_delta 1.8429 6 0.31 30 % + ElecStateLCAO psiToRho 0.61722 11 0.056 10 % + Charge mix_rho 0.90338 10 0.09 15 % + LOOP_ions force_stress 0.45531 1 0.46 7.4 % + Force_Stress_LCAO getForceStress 0.45527 1 0.46 7.4 % + Force_LCAO_gamma ftable_gamma 0.2412 1 0.24 3.9 % + Force_LCAO_gamma cal_fvl_dphi 0.23301 1 0.23 3.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:03:17 2022 + FINISH Time : Wed Sep 28 11:03:23 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/99/tag_0_finished new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/H_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/H_ONCV_PBE-1.0.upf new file mode 100644 index 0000000000000000000000000000000000000000..f8b1ebb63c87d413e9291f7c0b9fd8707f9c8256 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/H_ONCV_PBE-1.0.upf @@ -0,0 +1,897 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + H 1.00 0 1 4 upf +# +# n l f energy (Ha) + 1 0 1.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 0 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.13748 -0.23860 5 8 9.72141 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 0.49352 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 1.27464 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 0.0800 0.0900 0.1000 0.1100 0.1200 0.1300 0.1400 0.1500 + 0.1600 0.1700 0.1800 0.1900 0.2000 0.2100 0.2200 0.2300 + 0.2400 0.2500 0.2600 0.2700 0.2800 0.2900 0.3000 0.3100 + 0.3200 0.3300 0.3400 0.3500 0.3600 0.3700 0.3800 0.3900 + 0.4000 0.4100 0.4200 0.4300 0.4400 0.4500 0.4600 0.4700 + 0.4800 0.4900 0.5000 0.5100 0.5200 0.5300 0.5400 0.5500 + 0.5600 0.5700 0.5800 0.5900 0.6000 0.6100 0.6200 0.6300 + 0.6400 0.6500 0.6600 0.6700 0.6800 0.6900 0.7000 0.7100 + 0.7200 0.7300 0.7400 0.7500 0.7600 0.7700 0.7800 0.7900 + 0.8000 0.8100 0.8200 0.8300 0.8400 0.8500 0.8600 0.8700 + 0.8800 0.8900 0.9000 0.9100 0.9200 0.9300 0.9400 0.9500 + 0.9600 0.9700 0.9800 0.9900 1.0000 1.0100 1.0200 1.0300 + 1.0400 1.0500 1.0600 1.0700 1.0800 1.0900 1.1000 1.1100 + 1.1200 1.1300 1.1400 1.1500 1.1600 1.1700 1.1800 1.1900 + 1.2000 1.2100 1.2200 1.2300 1.2400 1.2500 1.2600 1.2700 + 1.2800 1.2900 1.3000 1.3100 1.3200 1.3300 1.3400 1.3500 + 1.3600 1.3700 1.3800 1.3900 1.4000 1.4100 1.4200 1.4300 + 1.4400 1.4500 1.4600 1.4700 1.4800 1.4900 1.5000 1.5100 + 1.5200 1.5300 1.5400 1.5500 1.5600 1.5700 1.5800 1.5900 + 1.6000 1.6100 1.6200 1.6300 1.6400 1.6500 1.6600 1.6700 + 1.6800 1.6900 1.7000 1.7100 1.7200 1.7300 1.7400 1.7500 + 1.7600 1.7700 1.7800 1.7900 1.8000 1.8100 1.8200 1.8300 + 1.8400 1.8500 1.8600 1.8700 1.8800 1.8900 1.9000 1.9100 + 1.9200 1.9300 1.9400 1.9500 1.9600 1.9700 1.9800 1.9900 + 2.0000 2.0100 2.0200 2.0300 2.0400 2.0500 2.0600 2.0700 + 2.0800 2.0900 2.1000 2.1100 2.1200 2.1300 2.1400 2.1500 + 2.1600 2.1700 2.1800 2.1900 2.2000 2.2100 2.2200 2.2300 + 2.2400 2.2500 2.2600 2.2700 2.2800 2.2900 2.3000 2.3100 + 2.3200 2.3300 2.3400 2.3500 2.3600 2.3700 2.3800 2.3900 + 2.4000 2.4100 2.4200 2.4300 2.4400 2.4500 2.4600 2.4700 + 2.4800 2.4900 2.5000 2.5100 2.5200 2.5300 2.5400 2.5500 + 2.5600 2.5700 2.5800 2.5900 2.6000 2.6100 2.6200 2.6300 + 2.6400 2.6500 2.6600 2.6700 2.6800 2.6900 2.7000 2.7100 + 2.7200 2.7300 2.7400 2.7500 2.7600 2.7700 2.7800 2.7900 + 2.8000 2.8100 2.8200 2.8300 2.8400 2.8500 2.8600 2.8700 + 2.8800 2.8900 2.9000 2.9100 2.9200 2.9300 2.9400 2.9500 + 2.9600 2.9700 2.9800 2.9900 3.0000 3.0100 3.0200 3.0300 + 3.0400 3.0500 3.0600 3.0700 3.0800 3.0900 3.1000 3.1100 + 3.1200 3.1300 3.1400 3.1500 3.1600 3.1700 3.1800 3.1900 + 3.2000 3.2100 3.2200 3.2300 3.2400 3.2500 3.2600 3.2700 + 3.2800 3.2900 3.3000 3.3100 3.3200 3.3300 3.3400 3.3500 + 3.3600 3.3700 3.3800 3.3900 3.4000 3.4100 3.4200 3.4300 + 3.4400 3.4500 3.4600 3.4700 3.4800 3.4900 3.5000 3.5100 + 3.5200 3.5300 3.5400 3.5500 3.5600 3.5700 3.5800 3.5900 + 3.6000 3.6100 3.6200 3.6300 3.6400 3.6500 3.6600 3.6700 + 3.6800 3.6900 3.7000 3.7100 3.7200 3.7300 3.7400 3.7500 + 3.7600 3.7700 3.7800 3.7900 3.8000 3.8100 3.8200 3.8300 + 3.8400 3.8500 3.8600 3.8700 3.8800 3.8900 3.9000 3.9100 + 3.9200 3.9300 3.9400 3.9500 3.9600 3.9700 3.9800 3.9900 + 4.0000 4.0100 4.0200 4.0300 4.0400 4.0500 4.0600 4.0700 + 4.0800 4.0900 4.1000 4.1100 4.1200 4.1300 4.1400 4.1500 + 4.1600 4.1700 4.1800 4.1900 4.2000 4.2100 4.2200 4.2300 + 4.2400 4.2500 4.2600 4.2700 4.2800 4.2900 4.3000 4.3100 + 4.3200 4.3300 4.3400 4.3500 4.3600 4.3700 4.3800 4.3900 + 4.4000 4.4100 4.4200 4.4300 4.4400 4.4500 4.4600 4.4700 + 4.4800 4.4900 4.5000 4.5100 4.5200 4.5300 4.5400 4.5500 + 4.5600 4.5700 4.5800 4.5900 4.6000 4.6100 4.6200 4.6300 + 4.6400 4.6500 4.6600 4.6700 4.6800 4.6900 4.7000 4.7100 + 4.7200 4.7300 4.7400 4.7500 4.7600 4.7700 4.7800 4.7900 + 4.8000 4.8100 4.8200 4.8300 4.8400 4.8500 4.8600 4.8700 + 4.8800 4.8900 4.9000 4.9100 4.9200 4.9300 4.9400 4.9500 + 4.9600 4.9700 4.9800 4.9900 5.0000 5.0100 5.0200 5.0300 + 5.0400 5.0500 5.0600 5.0700 5.0800 5.0900 5.1000 5.1100 + 5.1200 5.1300 5.1400 5.1500 5.1600 5.1700 5.1800 5.1900 + 5.2000 5.2100 5.2200 5.2300 5.2400 5.2500 5.2600 5.2700 + 5.2800 5.2900 5.3000 5.3100 5.3200 5.3300 5.3400 5.3500 + 5.3600 5.3700 5.3800 5.3900 5.4000 5.4100 5.4200 5.4300 + 5.4400 5.4500 5.4600 5.4700 5.4800 5.4900 5.5000 5.5100 + 5.5200 5.5300 5.5400 5.5500 5.5600 5.5700 5.5800 5.5900 + 5.6000 5.6100 5.6200 5.6300 5.6400 5.6500 5.6600 5.6700 + 5.6800 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b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..c1ed9de4b0928ef8f7a5d282d1b178be0d9960f7 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS +calculation scf +ntype 2 +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 50 +basis_type lcao +dft_functional pbe +gamma_only 1 +mixing_type pulay +mixing_beta 0.400000 +nbands 8 +smearing_method gaussian +smearing_sigma 0.020000 +cal_force 1 +cal_stress 0 +deepks_out_labels 1 +deepks_scf 0 +deepks_bandgap 0 +deepks_model ./model.ptg diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/KPT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/KPT new file mode 100644 index 0000000000000000000000000000000000000000..c289c0158aae156b859e94d68a89c8fc3741b1be --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +1 1 1 0 0 0 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/INPUT b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/INPUT new file mode 100644 index 0000000000000000000000000000000000000000..565ac5298ca43d392e6f69e54b71a4873b788f73 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/INPUT @@ -0,0 +1,283 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +stru_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional pbe #exchange correlation functional +xc_temperature 0 #temperature for finite temperature functionals +calculation scf #test; scf; relax; nscf; ienvelope; istate; sto-scf; sto-md +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 0 #the control of symmetry +init_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group +out_freq_elec 0 #the frequency ( >= 0) of electronic iter to output charge density and wavefunction. 0: output only when converged +dft_plus_dmft 0 #true:DFT+DMFT; false: standard DFT calcullation(default) +printe 100 #Print out energy for each band for every printe steps +mem_saver 0 #Only for nscf calculations. if set to 1, then a memory saving technique will be used for many k point calculations. +diago_proc 2 #the number of procs used to do diagonalization +nbspline -1 #the order of B-spline basis +wannier_card #input card for wannier functions +soc_lambda 1 #The fraction of averaged SOC pseudopotential is given by (1-soc_lambda) +cal_force 1 #if calculate the force at the end of the electronic iteration +out_freq_ion 0 #the frequency ( >= 0 ) of ionic step to output charge density and wavefunction. 0: output only when ion steps are finished + +#Parameters (2.PW) +ecutwfc 50 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-07 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg 0 #>0 output charge density for selected electron steps +out_pot 0 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +out_proj_band 0 #output projected band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables +pw_seed 1 #random seed for initializing wave functions + +#Parameters (3.Stochastic DFT) +method_sto 2 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 0 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_wenlarge 10 #control the t interval: dt = PI/wcut/cond_wenlarge +cond_fwhm 0.3 #FWHM for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; hpseps; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +out_force 0 #output the out_force or not +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +relax_method cg #bfgs; sd; cg; cg_bfgs; +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 1 #>0 compute descriptor for deepks +deepks_scf 0 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model ./model.ptg #file dir of traced pytorch model: 'model.ptg +bessel_lmax 2 #lmax used in generating bessel functions +bessel_rcut 6 #rcut used in generating bessel functions +bessel_rcut 6 #tolerence level when generating bessel functions + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +gamma_only 1 #Only for localized orbitals set and gamma point. If set to 1, a fast algorithm is used +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 50 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_element_info 0 #output (projected) wavefunction of each element +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +#Parameters (6.Smearing) +smearing_method gaussian #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.02 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type 1 #choose ensemble +md_nstep 10 #md steps +md_ensolver FP #choose potential +md_dt 1 #time step +md_mnhc 4 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Gate field) +gate_flag 0 #compensating charge or not +zgate 0.5 #position of charged plate +relax 0 #allow relaxation along the specific direction +block 0 #add a block potential or not +block_down 0.45 #low bound of the block +block_up 0.55 #high bound of the block +block_height 0.1 #height of the block + +#Parameters (12.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force +test_skip_ewald 0 #skip ewald energy + +#Parameters (13.vdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_cutoff_type radius #expression model of periodic structure, radius or period +vdw_cutoff_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_cutoff_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold 0 # +exx_cauchy_threshold 0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence 0 # + +#Parameters (16.tddft) +tddft 0 #calculate tddft or not +td_scf_thr 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.dft+u) +dft_plus_u 0 #true:DFT+U correction; false: standard DFT calcullation(default) +dftu_type 2 #1:rotationally invarient formalism; 2:simplified form(default) +double_counting 1 #1:FLL(fully localized limit)(default); 2:AMF(around mean field) +yukawa_lambda -1 #default:0.0 +yukawa_potential 0 #default: false +omc 0 #whether turn on occupation matrix control method or not +hund_j 0 0 #Hund exchange parameter J(ev) +hubbard_u 0 0 #Hubbard Coulomb interaction parameter U(ev) +orbital_corr -1 -1 #which correlated orbitals need corrected ; d:2 ,f:3, do not need correction:-1 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/STRU_READIN_ADJUST.cif b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 0000000000000000000000000000000000000000..8b8f3391d41b64ff6a1c3107f55be9d9f0217091 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,22 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 14.817 +_cell_length_b 14.817 +_cell_length_c 14.817 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +O 0.528821 0.63969 0.372867 +H 0.568517 0.587977 0.36801 +H 0.569422 0.687646 0.35752 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/istate.info b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/istate.info new file mode 100644 index 0000000000000000000000000000000000000000..b1402a8a58913d4b0953a7db5e5fb4c0984b556a --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/istate.info @@ -0,0 +1,11 @@ +BAND Energy(ev) Occupation Kpoint = 1 (0 0 0) + 1 -24.9697 2 + 2 -12.6959 2 + 3 -9.04033 2 + 4 -6.77221 2 + 5 1.47549 0 + 6 4.57749 0 + 7 11.1596 0 + 8 11.4712 0 + + diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/running_scf.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/running_scf.log new file mode 100644 index 0000000000000000000000000000000000000000..7d496a669a0828ce37cd9c109a76e92de46bdf20 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/running_scf.log @@ -0,0 +1,712 @@ + + WELCOME TO ABACUS v3.0 + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 2 + Start Time is Tue Oct 25 16:58:14 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + DRANK = 1 + DSIZE = 2 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + The esolver type has been set to : ksdft_lcao + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = O + atom label for species 2 = H + lattice constant (Bohr) = 1 + lattice constant (Angstrom) = 0.529177 + + READING ATOM TYPE 1 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + atom x y z mag vx vy vz + tauc_O1 14.8069954334 17.9113242282 10.4402890571 0 0 0 0 + tauc_H1 15.9184686019 16.4633684592 10.3042878336 0 0 0 0 + tauc_H2 15.9438195739 19.2540803722 10.0105545672 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ./O_gga_6au_60Ry_2s2p1d.orb + orbital file: ./H_gga_6au_60Ry_2s1p.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 -0 +0 + +0 +0.0357142857143 -0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ./O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ./H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 131072 + nrxx = 1048576 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 6235 524087 + 2 6234 524084 + --------------- sum ------------------- + 2 12469 1048171 + number of |g| = 3312 + max |g| = 5.06505102041 + min |g| = 0 + + SETUP THE ELECTRONS NUMBER + electron number of element O = 6 + total electron number of element O = 6 + electron number of element H = 1 + total electron number of element H = 2 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.125583428056 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.12584207215 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 276 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 1 + Type 2 number_of_atoms 2 + descriptors_per_atom 18 + total_descriptors 54 + DONE : INIT CHARGE Time : 0.861 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 1.56879 (SEC) + + + ------------------------------------------- + SELF-CONSISTENT + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 6 + longest nonlocal projector rcut (Bohr) = 1.5 + searching radius is (Bohr)) = 12 + searching radius unit is (Bohr)) = 1 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + [real space grid] = 128, 128, 128 + [big cell numbers in grid] = 64, 64, 64 + [meshcell numbers in big cell] = 2, 2, 2 + [extended fft grid] = 14, 14, 14 + [dimension of extened grid] = 93, 93, 93 + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 3 + Local orbitals number in sub-FFT-grid = 23 + lgd_last = 0 + lgd_now = 23 + allocate DM , the dimension is 23 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 23 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 23 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +276 253 +sender_size is 552 ; sender_size of each process is: +276 276 + gamma_only_local = 1 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00126 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000573 + + Density error is 0.228780964656 + + Energy Rydberg eV + E_KohnSham -34.2101934337 -465.453560381 + E_Harris -34.4379390025 -468.552197811 + E_Fermi -0.777005774467 -10.5717059117 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00127632722538 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000369686006965 + + Density error is 0.0993660419479 + + Energy Rydberg eV + E_KohnSham -34.2853741178 -466.476446063 + E_Harris -34.2913077423 -466.557177167 + E_Fermi -0.201189313387 -2.73732103877 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00121160649133 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000347064629909 + + Density error is 0.0638826420529 + + Energy Rydberg eV + E_KohnSham -34.2811891725 -466.419506962 + E_Harris -34.285503642 -466.478208332 + E_Fermi -0.187902301759 -2.55654197124 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00109229552292 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000290164689736 + + Density error is 0.0019736360948 + + Energy Rydberg eV + E_KohnSham -34.2812898698 -466.420877019 + E_Harris -34.2812932879 -466.420923525 + E_Fermi -0.151055671008 -2.05521784092 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00109494087707 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00028910825415 + + Density error is 0.00135747081195 + + Energy Rydberg eV + E_KohnSham -34.281291882 -466.420904396 + E_Harris -34.2812958548 -466.420958449 + E_Fermi -0.15258295932 -2.07599766445 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00109226058104 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000288071094009 + + Density error is 0.000181994812812 + + Energy Rydberg eV + E_KohnSham -34.2812907337 -466.420888773 + E_Harris -34.2812908475 -466.420890322 + E_Fermi -0.151416447506 -2.060126457 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00109145400998 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000287912187658 + + Density error is 3.89551665317e-05 + + Energy Rydberg eV + E_KohnSham -34.2812904717 -466.420885208 + E_Harris -34.2812904746 -466.420885248 + E_Fermi -0.151242483561 -2.0577595561 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.0010915034317 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000287895451183 + + Density error is 9.59153931703e-06 + + Energy Rydberg eV + E_KohnSham -34.281290499 -466.42088558 + E_Harris -34.2812904988 -466.420885577 + E_Fermi -0.151257642139 -2.05796579913 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00109150378463 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000287903721349 + + Density error is 1.8661270574e-06 + + Energy Rydberg eV + E_KohnSham -34.2812905124 -466.420885763 + E_Harris -34.281290513 -466.42088577 + E_Fermi -0.151267180314 -2.05809557266 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00109149714167 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000287900809854 + + Density error is 2.85644871662e-07 + + Energy Rydberg eV + E_KohnSham -34.2812905109 -466.420885742 + E_Harris -34.2812905109 -466.420885742 + E_Fermi -0.1512661354 -2.05808135588 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 552 + sender_size = 552 + last sender_buffer = 0.00109149669158 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000287900969865 + + Density error is 6.96555978971e-08 + + Energy Rydberg eV + E_KohnSham -34.2812905112 -466.420885746 + E_Harris -34.2812905112 -466.420885746 + E_band -7.86113825278 -106.956273004 + E_one_elec -69.5860543532 -946.766840541 + E_Hartree +36.3508504018 +494.57869261 + E_xc -8.4643559527 -115.163470857 + E_Ewald +7.41826939284 +100.930733042 + E_demet -6.58741673914e-76 -8.96264027529e-75 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi -0.151266342736 -2.05808417684 + + charge density convergence is achieved + final etot is -466.420885746 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0 0 0 (0 pws) + 1 -24.9697 2.00000 + 2 -12.6959 2.00000 + 3 -9.04033 2.00000 + 4 -6.77221 2.00000 + 5 1.47549 0.00000 + 6 4.57749 0.00000 + 7 11.1596 0.00000 + 8 11.4712 0.00000 + + EFERMI = -2.058084176836640 eV + OUT.ABACUS/ final etot is -466.4208857461284 eV + correction force for each atom along direction 1 is -0.000252454 + correction force for each atom along direction 2 is -0.000147045 + correction force for each atom along direction 3 is -0.000976154 + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + O1 -0.45697774 -0.41927655 +0.10777319 + H1 +0.047387156 -0.53654047 +0.069454325 + H2 +0.40959059 +0.95581702 -0.17722752 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.4208857461284 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 10.697 9 1.2 1.0e+02% + Driver driver_line 10.692 1 11. 1.e+02% + ORB_control set_orb_tables 0.61236 1 0.61 5.7% + ORB_gen_tables gen_tables 0.61236 1 0.61 5.7% + ORB_table_beta init_Table_Beta 0.18356 1 0.18 1.7% + ORB_table_beta VNL_PhiBeta_R 0.18205 56 0.0033 1.7% + ORB_table_alpha init_Table_Alpha 0.19830 1 0.20 1.9% + ORB_table_alpha S_PhiAlpha_R 0.19664 66 0.0030 1.8% + Potential init_pot 1.1225 2 0.56 10.% + PW_Basis recip2real 1.8537 72 0.026 17.% + PW_Basis gathers_scatterp 0.81004 72 0.011 7.6% + Potential v_of_rho 5.8349 13 0.45 55.% + XC_Functional v_xc 5.2282 14 0.37 49.% + PW_Basis real2recip 2.4495 108 0.023 23.% + PW_Basis gatherp_scatters 1.0290 108 0.0095 9.6% + H_Hartree_pw v_hartree 0.89349 13 0.069 8.4% + ESolver_KS_LCAO Run 7.9244 1 7.9 74.% + HSolverLCAO solve 1.2141 11 0.11 11.% + HamiltLCAO updateHk 0.56026 11 0.051 5.2% + LCAO_Hamilt cal_Hgamma 0.49890 11 0.045 4.7% + Gint_interface cal_gint 1.2615 23 0.055 12.% + Gint_Gamma distri_vl 3.6826 6 0.61 34.% + ElecStateLCAO psiToRho 0.63949 11 0.058 6.0% + Charge mix_rho 0.98483 10 0.098 9.2% + Force_Stress_LCAO getForceStress 1.2002 1 1.2 11.% + Force_LCAO_gamma ftable_gamma 0.61645 1 0.62 5.8% + Force_LCAO_gamma cal_fvl_dphi 0.61470 1 0.61 5.7% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + 1175. + ORB_table_phi Jl(x) 97.80 + Charge_Pulay Rrho 64.00 + Charge_Pulay dRrho 56.00 + Charge_Pulay drho 56.00 + PW_Basis struc_fac 15.99 + Charge rho 8.000 + Charge rho_save 8.000 + Charge rho_core 8.000 + Potential vltot 8.000 + Potential vr 8.000 + Potential vr_eff 8.000 + Potential vr_eff1 8.000 + Potential vnew 8.000 + Charge_Pulay rho_save2 8.000 + Charge rhog 3.998 + Charge rhog_save 3.998 + Charge kin_r 3.998 + Charge kin_r_save 3.998 + Charge rhog_core 3.998 + Grid_Meshcell index2normal 3.068 + Grid_Meshcell index2ucell 3.068 + ---------------------------------------------------------- + + Start Time : Tue Oct 25 16:58:14 2022 + Finish Time : Tue Oct 25 16:58:24 2022 + Total Time : 0 h 0 mins 10 secs diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/warning.log b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/warning.log new file mode 100644 index 0000000000000000000000000000000000000000..456ef7b053f1dd55d4ec99f0503e55bdd8e3a610 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/OUT.ABACUS/warning.log @@ -0,0 +1,67 @@ + AUTO_SET ks_solver to genelpa + AUTO_SET lcao_ecut to 50 + In SCAN_BEGIN, can't find: LATTICE_PARAMETERS block. + AUTO_SET NBANDS to 8 + Auto generating k-points file: KPT + startmag_type = 2 + charge from rho_at = 5.99905 + charge should be = 6 + charge from rho_at = 0.997867 + charge should be = 1 + Warning: negative or imaginary starting charge : neg = -0.0123827 ima = 3.05152e-14 SPIN = 0 + + SETUP ATOMIC RHO FOR SPIN 1 + Electron number from rho = 8 + total electron number from rho = 8 + should be = 8 + charge before normalized = 8 + charge after normalized = 8 + Processor Atom + 1 3 + 2 3 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00124378252914 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00111825849528 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112328130828 + charge after normalized = 8.00000000000003 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112537552917 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112556242125 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112536972052 + charge after normalized = 8 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112536548571 + charge after normalized = 7.99999999999998 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112536125812 + charge after normalized = 8.00000000000002 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112536652134 + charge after normalized = 7.99999999999999 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112536672759 + charge after normalized = 7.99999999999997 + + CHECK UPDATE INPUT INFORMATION + charge before normalized = 8.00112536694376 + charge after normalized = 8.00000000000003 + charge before normalized = 8.00000000000003 + charge after normalized = 8 diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/O_ONCV_PBE-1.0.upf b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/O_ONCV_PBE-1.0.upf new file mode 100644 index 0000000000000000000000000000000000000000..7e7db6d66f69ceb7e960ade73fd5d8885fb5ffb8 --- /dev/null +++ b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/O_ONCV_PBE-1.0.upf @@ -0,0 +1,1224 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + O 8.00 1 2 4 upf +# +# n l f energy (Ha) + 1 0 2.00 + 2 0 2.00 + 2 1 4.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 1 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.29195 -0.88057 5 8 8.98916 + 1 1.47310 -0.33187 5 8 9.14990 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 0.90330 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 1.51851 + 1 2 1.53631 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 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Ab-initio * + * Computation at UStc' * + * * + * Website: http://abacus.ustc.edu.cn/ * + * * + ********************************************************* + Wed Sep 28 11:08:55 2022 + MAKE THE DIR : OUT.ABACUS/ + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + dft_functional readin is: lda + dft_functional in pseudopot file is: PBE +In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file +Please make sure this is what you need + UNIFORM GRID DIM : 128 * 128 * 128 + UNIFORM GRID DIM(BIG): 64 * 64 * 64 + DONE(0.0733263 SEC) : SETUP UNITCELL + DONE(0.0877927 SEC) : INIT K-POINTS + --------------------------------------------------------- + Self-consistent calculations for electrons + --------------------------------------------------------- + SPIN KPOINTS PROCESSORS NBASE + 1 Gamma 4 23 + --------------------------------------------------------- + Use Systematically Improvable Atomic bases + --------------------------------------------------------- + ELEMENT ORBITALS NBASE NATOM XC + O 2s2p1d-6au 13 1 + H 2s1p-6au 5 2 + --------------------------------------------------------- + Initial plane wave basis and FFT box + --------------------------------------------------------- + DONE(0.104133 SEC) : INIT PLANEWAVE + DONE(0.146454 SEC) : INIT CHARGE + START POTENTIAL : atomic + DONE(0.389806 SEC) : INIT POTENTIAL + ------------------------------------------- + SELF-CONSISTENT : + ------------------------------------------- + ITER ETOT(eV) EDIFF(eV) DRHO TIME(s) + GE1 -4.651983e+02 0.000000e+00 2.143e-01 4.840e-01 + GE2 -4.664037e+02 -1.205316e+00 9.750e-02 4.451e-01 + GE3 -4.664061e+02 -2.460156e-03 6.238e-02 5.077e-01 + GE4 -4.664062e+02 -1.204132e-04 1.963e-03 3.817e-01 + GE5 -4.664054e+02 8.573619e-04 8.457e-04 3.815e-01 + GE6 -4.664060e+02 -6.164269e-04 9.565e-05 3.579e-01 + GE7 -4.664058e+02 1.938794e-04 3.801e-05 3.733e-01 + GE8 -4.664058e+02 -2.819402e-05 1.038e-05 3.638e-01 + GE9 -4.664058e+02 1.603408e-05 1.571e-06 3.644e-01 + GE10 -4.664058e+02 -2.134258e-06 1.175e-07 3.630e-01 + GE11 -4.664058e+02 -4.408826e-07 3.009e-08 2.993e-01 +E_delta_band = -7.12390160e-02 Ry = -9.69256537e-01 eV +E_delta_NN= -1.95170547e-01 Ry = -2.65543152e+00 eV + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total 6.2686 11 0.57 1e+02 % + Run_lcao lcao_line 6.2619 1 6.3 1e+02 % + Potential init_pot 0.24246 2 0.12 3.9 % + PW_Basis recip2real 0.22684 16 0.014 3.6 % + PW_Basis gathers_scatterp 0.10734 16 0.0067 1.7 % + Potential v_of_rho 0.87626 13 0.067 14 % + XC_Functional v_xc 0.27712 14 0.02 4.4 % + H_Hartree_pw v_hartree 0.56632 13 0.044 9 % + PW_Basis real2recip 0.60447 38 0.016 9.6 % + PW_Basis gatherp_scatters 0.26736 38 0.007 4.3 % + ORB_control set_orb_tables 0.90085 1 0.9 14 % + ORB_gen_tables gen_tables 0.90085 1 0.9 14 % + ORB_table_phi init_Table 0.37756 1 0.38 6 % + ORB_table_phi cal_ST_Phi12_R 0.37337 126 0.003 6 % + ORB_table_beta init_Table_Beta 0.15521 1 0.16 2.5 % + ORB_table_beta VNL_PhiBeta_R 0.15389 56 0.0027 2.5 % + ORB_table_alpha init_Table_Alpha 0.21062 1 0.21 3.4 % + ORB_table_alpha S_PhiAlpha_R 0.20891 66 0.0032 3.3 % + LOOP_ions opt_ions 4.9016 1 4.9 78 % + ESolver_KS_LCAO Run 4.3753 1 4.4 70 % + HSolverLCAO solve 2.1939 11 0.2 35 % + HamiltLCAO updateHk 1.1487 11 0.1 18 % + LCAO_Hamilt cal_Hgamma 1.1194 11 0.1 18 % + Gint_interface cal_gint 0.46261 23 0.02 7.4 % + Gint_Gamma distri_vl_value 0.56982 11 0.052 9.1 % + Gint_Gamma distri_vl 2.1144 6 0.35 34 % + LCAO_Deepks cal_projected_DM 4.5536 13 0.35 73 % + LCAO_gen_fixedH add_v_delta 1.9856 6 0.33 32 % + LCAO_DESCRIPTOR add_v_delta 1.9857 6 0.33 32 % + ElecStateLCAO psiToRho 1.0292 11 0.094 16 % + Charge mix_rho 0.75521 10 0.076 12 % + LOOP_ions force_stress 0.52614 1 0.53 8.4 % + Force_Stress_LCAO getForceStress 0.52612 1 0.53 8.4 % + Force_LCAO_gamma ftable_gamma 0.33136 1 0.33 5.3 % + Force_LCAO_gamma cal_fvl_dphi 0.11589 1 0.12 1.8 % + ---------------------------------------------------------------------------------------- + + START Time : Wed Sep 28 11:08:55 2022 + FINISH Time : Wed Sep 28 11:09:01 2022 + TOTAL Time : 6 + SEE INFORMATION IN : OUT.ABACUS/ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/model.ptg b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/model.ptg new file mode 100644 index 0000000000000000000000000000000000000000..e249ac474f81e03ffd5d88622d28375262fcb541 Binary files /dev/null and b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/model.ptg differ diff --git a/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/tag_0_finished b/ABACUS-DeePKS/water_single_lda2pbe_abacus_ref/systems/group.03/ABACUS/test/tag_0_finished new file mode 100644 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